Citation listings: deposit and third-party usage

GEO third-party usage citations
GEO deposit citations

The following list represents third-party publications that cite GEO data as evidence to support or complement independent studies, or use GEO data as the basis of statistical/analytical hypotheses or tools. Please report omitted publications to geo@ncbi.nlm.nih.gov

Total number of citations: 2,122

Arora M, Zhang J, Heine GF, Ozer G et al. Promoters active in interphase are bookmarked during mitosis by ubiquitination. Nucleic Acids Res 2012 Aug 31. PMID: 22941662
Liu HW, Zhang J, Heine GF, Arora M et al. Chromatin modification by SUMO-1 stimulates the promoters of translation machinery genes. Nucleic Acids Res 2012 Aug 31. PMID: 22941651
Gingold H, Dahan O, Pilpel Y. Dynamic changes in translational efficiency are deduced from codon usage of the transcriptome. Nucleic Acids Res 2012 Aug 31. PMID: 22941644
Huang H, Jeon T, Sedmak G, Pletikos M et al. Coupling Diffusion Imaging with Histological and Gene Expression Analysis to Examine the Dynamics of Cortical Areas across the Fetal Period of Human Brain Development. Cereb Cortex 2012 Aug 28. PMID: 22933464
Foong CS, Sandanaraj E, Brooks HB, Campbell RM et al. Glioma-Propagating Cells as an In Vitro Screening Platform: PLK1 as a Case Study. J Biomol Screen 2012 Aug 27. PMID: 22927677
Lui JC, Nilsson O, Chan Y, Palmer CD et al. Synthesizing genome-wide association studies and expression microarray reveals novel genes that act in the human growth plate to modulate height. Hum Mol Genet 2012 Aug 29. PMID: 22914739
Glubb DM, Dholakia N, Innocenti F. Liver expression quantitative trait loci: a foundation for pharmacogenomic research. Front Genet 2012;3:153. PMID: 22912647
Wuttke D, Connor R, Vora C, Craig T et al. Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes. PLoS Genet 2012 Aug;8(8):e1002834. PMID: 22912585
Dinh HQ, Dubin M, Sedlazeck FJ, Lettner N et al. Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis. PLoS One 2012;7(7):e41528. PMID: 22911809
Haeberle H, Dudley JT, Liu JT, Butte AJ et al. Identification of Cell Surface Targets through Meta-analysis of Microarray Data. Neoplasia 2012 Jul;14(7):666-9. PMID: 22904683
Upton GJ, Harrison AP. Motif effects in Affymetrix GeneChips seriously affect probe intensities. Nucleic Acids Res 2012 Aug 16. PMID: 22904084
Lloret-Llinares M, Pérez-Lluch S, Rossell D, Morán T et al. dKDM5/LID regulates H3K4me3 dynamics at the transcription-start site (TSS) of actively transcribed developmental genes. Nucleic Acids Res 2012 Aug 16. PMID: 22904080
Balaga O, Friedman Y, Linial M. Toward a combinatorial nature of microRNA regulation in human cells. Nucleic Acids Res 2012 Aug 16. PMID: 22904063
Stoecklin-Wasmer C, Guarnieri P, Celenti R, Demmer RT et al. MicroRNAs and Their Target Genes in Gingival Tissues. J Dent Res 2012 Oct;91(10):934-40. PMID: 22879578
Moindrot B, Audit B, Klous P, Baker A et al. 3D chromatin conformation correlates with replication timing and is conserved in resting cells. Nucleic Acids Res 2012 Aug 8. PMID: 22879376
Chen X, Li J, Gray WH, Lehmann BD et al. TNBCtype: A Subtyping Tool for Triple-Negative Breast Cancer. Cancer Inform 2012;11:147-56. PMID: 22872785
Middelbeek J, Kuipers AJ, Henneman L, Visser D et al. TRPM7 Is Required for Breast Tumor Cell Metastasis. Cancer Res 2012 Aug 15;72(16):4250-4261. PMID: 22871386
Vouk K, Hevir N, Ribic-Pucelj M, Haarpaintner G et al. Discovery of phosphatidylcholines and sphingomyelins as biomarkers for ovarian endometriosis. Hum Reprod 2012 Oct;27(10):2955-65. PMID: 22859507
Huang X, Dubuc AM, Hashizume R, Berg J et al. Voltage-gated potassium channel EAG2 controls mitotic entry and tumor growth in medulloblastoma via regulating cell volume dynamics. Genes Dev 2012 Aug 15;26(16):1780-96. PMID: 22855790
Vaquero-Sedas MI, Luo C, Vega-Palas MA. Analysis of the epigenetic status of telomeres by using ChIP-seq data. Nucleic Acids Res 2012 Aug 1. PMID: 22855559
Meredith MM, Liu K, Kamphorst AO, Idoyaga J et al. Zinc finger transcription factor zDC is a negative regulator required to prevent activation of classical dendritic cells in the steady state. J Exp Med 2012 Aug 27;209(9):1583-93. PMID: 22851594
Lazar C, Meganck S, Taminau J, Steenhoff D et al. Batch effect removal methods for microarray gene expression data integration: a survey. Brief Bioinform 2012 Jul 31. PMID: 22851511
Mieczkowski J, Swiatek-Machado K, Kaminska B. Identification of pathway deregulation - gene expression based analysis of consistent signal transduction. PLoS One 2012;7(7):e41541. PMID: 22848524
Nagel S, Ehrentraut S, Tomasch J, Lienenklaus S et al. Transcriptional Activation of Prostate Specific Homeobox Gene NKX3-1 in Subsets of T-Cell Lymphoblastic Leukemia (T-ALL). PLoS One 2012;7(7):e40747. PMID: 22848398
Liu QC, Zha X, Faralli H, Yin H et al. Comparative expression profiling identifies differential roles for Myogenin and p38α MAPK signaling in myogenesis. J Mol Cell Biol 2012 Jul 30. PMID: 22847234
Stocco G, Yang W, Crews KR, Thierfelder WE et al. PACSIN2 polymorphism influences TPMT activity and mercaptopurine-related gastrointestinal toxicity. Hum Mol Genet 2012 Aug 8. PMID: 22846425
Wang B, Lindley LE, Fernandez-Vega V, Rieger ME et al. The T Box Transcription Factor TBX2 Promotes Epithelial-Mesenchymal Transition and Invasion of Normal and Malignant Breast Epithelial Cells. PLoS One 2012;7(7):e41355. PMID: 22844464
García-Alonso L, Alonso R, Vidal E, Amadoz A et al. Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. Nucleic Acids Res 2012 Jul 27. PMID: 22844098
Dümcke S, Seizl M, Etzold S, Pirkl N et al. One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data. Nucleic Acids Res 2012 Jul 25. PMID: 22844089
Acquaah-Mensah GK, Malhotra D, Vulimiri M, McDermott JE et al. Suppressed expression of T-box transcription factors is involved in senescence in chronic obstructive pulmonary disease. PLoS Comput Biol 2012 Jul;8(7):e1002597. PMID: 22829758
Zhuang G, Song W, Amato K, Hwang Y et al. Effects of Cancer-Associated EPHA3 Mutations on Lung Cancer. J Natl Cancer Inst 2012 Aug 8;104(15):1183-98. PMID: 22829656
Medrek C, Pontén F, Jirström K, Leandersson K. The presence of tumor associated macrophages in tumor stroma as a prognostic marker for breast cancer patients. BMC Cancer 2012 Jul 23;12:306. PMID: 22824040
Rodrigo G, Carrera J, Ruiz-Ferrer V, del Toro FJ et al. A meta-analysis reveals the commonalities and differences in Arabidopsis thaliana response to different viral pathogens. PLoS One 2012;7(7):e40526. PMID: 22808182
Singh S, Dev A, Verma R, Pradeep A et al. Defining an EPOR- regulated transcriptome for primary progenitors, including Tnfr-sf13c as a novel mediator of EPO- dependent erythroblast formation. PLoS One 2012;7(7):e38530. PMID: 22808010
Reinhold WC, Sunshine M, Liu H, Varma S et al. CellMiner: a web-based suite of genomic and pharmacologic tools to explore transcript and drug patterns in the NCI-60 cell line set. Cancer Res 2012 Jul 15;72(14):3499-511. PMID: 22802077
Tian S, Simon I, Moreno V, Roepman P et al. A combined oncogenic pathway signature of BRAF, KRAS and PI3KCA mutation improves colorectal cancer classification and cetuximab treatment prediction. Gut 2012 Jul 14. PMID: 22798500
Iskow RC, Gokcumen O, Abyzov A, Malukiewicz J et al. Regulatory element copy number differences shape primate expression profiles. Proc Natl Acad Sci U S A 2012 Jul 31;109(31):12656-61. PMID: 22797897
Amigo I, Traba J, Satrústegui J, del Arco A. SCaMC-1Like a member of the mitochondrial carrier (MC) family preferentially expressed in testis and localized in mitochondria and chromatoid body. PLoS One 2012;7(7):e40470. PMID: 22792342
Schmidt F, van den Eijnden M, Pescini Gobert R, Saborio GP et al. Identification of VHY/Dusp15 as a regulator of oligodendrocyte differentiation through a systematic genomics approach. PLoS One 2012;7(7):e40457. PMID: 22792334
Wenzke KE, Cantemir-Stone C, Zhang J, Marsh CB et al. Identifying common genes and networks in multi-organ fibrosis. AMIA Summits Transl Sci Proc 2012;2012:106-15. PMID: 22779061
Ryan SD, Britigan EM, Zasadil LM, Witte K et al. Up-regulation of the mitotic checkpoint component Mad1 causes chromosomal instability and resistance to microtubule poisons. Proc Natl Acad Sci U S A 2012 Aug 14;109(33):E2205-14. PMID: 22778409
Marina M, Wang L, Conrad SE. The scaffold protein MEK Partner 1 is required for the survival of estrogen receptor positive breast cancer cells. Cell Commun Signal 2012 Jul 9;10(1):18. PMID: 22776333
Muchir A, Wu W, Choi JC, Iwata S et al. Abnormal p38α mitogen-activated protein kinase signaling in dilated cardiomyopathy caused by lamin A/C gene mutation. Hum Mol Genet 2012 Oct 1;21(19):4325-33. PMID: 22773734
Eren K, Deveci M, Küçüktunç O, Catalyürek UV. A comparative analysis of biclustering algorithms for gene expression data. Brief Bioinform 2012 Jul 6. PMID: 22772837
Shih B, Watson S, Bayat A. Whole genome and global expression profiling of Dupuytren's disease: systematic review of current findings and future perspectives. Ann Rheum Dis 2012 Sep;71(9):1440-7. PMID: 22772327
Papadantonakis N, Matsuura S, Ravid K. Megakaryocyte pathology and bone marrow fibrosis: the lysyl oxidase connection. Blood 2012 Aug 30;120(9):1774-81. PMID: 22767499
Gulbahce N, Yan H, Dricot A, Padi M et al. Viral perturbations of host networks reflect disease etiology. PLoS Comput Biol 2012 Jun;8(6):e1002531. PMID: 22761553
Itoh S, Saito T, Hirata M, Ushita M et al. GSK-3α and GSK-3β Proteins Are Involved in Early Stages of Chondrocyte Differentiation with Functional Redundancy through RelA Protein Phosphorylation. J Biol Chem 2012 Aug 24;287(35):29227-36. PMID: 22761446
Kaneda A, Matsusaka K, Aburatani H, Fukayama M. Epstein-Barr virus infection as an epigenetic driver of tumorigenesis. Cancer Res 2012 Jul 15;72(14):3445-50. PMID: 22761333
Eblen JD, Phillips CA, Rogers GL, Langston MA. The maximum clique enumeration problem: algorithms, applications, and implementations. BMC Bioinformatics 2012 Jun 25;13 Suppl 10:S5. PMID: 22759429
Pachynski RK, Zabel BA, Kohrt HE, Tejeda NM et al. The chemoattractant chemerin suppresses melanoma by recruiting natural killer cell antitumor defenses. J Exp Med 2012 Jul 30;209(8):1427-35. PMID: 22753924
Tone AA, Virtanen C, Shaw P, Brown TJ. Prolonged Postovulatory Proinflammatory Signaling in the Fallopian Tube Epithelium May Be Mediated through a BRCA1/DAB2 Axis. Clin Cancer Res 2012 Aug 15;18(16):4334-44. PMID: 22753593
Witwer KW, Clements JE. Evidence for miRNA expression differences of HIV-1-positive, treatment-naive patients and elite suppressors: a re-analysis. Blood 2012 Jun 28;119(26):6395-6. PMID: 22745299
Ho JJ, Metcalf JL, Yan MS, Turgeon PJ et al. Functional importance of dicer protein in the adaptive cellular response to hypoxia. J Biol Chem 2012 Aug 17;287(34):29003-20. PMID: 22745131
Agnelli L, Mereu E, Pellegrino E, Limongi T et al. Identification of a 3-gene model as a powerful diagnostic tool for the recognition of ALK-negative anaplastic large-cell lymphoma. Blood 2012 Aug 9;120(6):1274-1281. PMID: 22740451
Hiraga T, Myoui A, Hashimoto N, Sasaki A et al. Bone-Derived IGF Mediates Crosstalk between Bone and Breast Cancer Cells in Bony Metastases. Cancer Res 2012 Aug 15;72(16):4238-4249. PMID: 22738911
Robinson TJ, Forte E, Salinas RE, Puri S et al. SplicerEX: a tool for the automated detection and classification of mRNA changes from conventional and splice-sensitive microarray expression data. RNA 2012 Aug;18(8):1435-45. PMID: 22736799
Wu Y, Grabsch H, Ivanova T, Tan IB et al. Comprehensive genomic meta-analysis identifies intra-tumoural stroma as a predictor of survival in patients with gastric cancer. Gut 2012 Jun 26. PMID: 22735568
Curry MC, Luk NA, Kenny PA, Roberts-Thomson SJ et al. Distinct Regulation of Cytoplasmic Calcium Signals and Cell Death Pathways by Different Plasma Membrane Calcium ATPase Isoforms in MDA-MB-231 Breast Cancer Cells. J Biol Chem 2012 Aug 17;287(34):28598-608. PMID: 22733819
Wang C, Sandling JK, Hagberg N, Berggren O et al. Genome-wide profiling of target genes for the systemic lupus erythematosus-associated transcription factors IRF5 and STAT4. Ann Rheum Dis 2012 Jun 23. PMID: 22730365
Sérandour AA, Avner S, Oger F, Bizot M et al. Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers. Nucleic Acids Res 2012 Jun 22. PMID: 22730288
Christensen J, El-Gebali S, Natoli M, Sengstag T et al. Defining new criteria for selection of cell-based intestinal models using publicly available databases. BMC Genomics 2012 Jun 22;13:274. PMID: 22726358
Lam KC, Mühlpfordt F, Vaquerizas JM, Raja SJ et al. The NSL complex regulates housekeeping genes in Drosophila. PLoS Genet 2012 Jun;8(6):e1002736. PMID: 22723752
Berthier CC, Bethunaickan R, Gonzalez-Rivera T, Nair V et al. Cross-species transcriptional network analysis defines shared inflammatory responses in murine and human lupus nephritis. J Immunol 2012 Jul 15;189(2):988-1001. PMID: 22723521
Gevaert O, Xu J, Hoang CD, Leung AN et al. Non-small cell lung cancer: identifying prognostic imaging biomarkers by leveraging public gene expression microarray data--methods and preliminary results. Radiology 2012 Aug;264(2):387-96. PMID: 22723499
Chen JL, Li J, Kiriluk KJ, Rosen AM et al. Deregulation of a hox protein regulatory network spanning prostate cancer initiation and progression. Clin Cancer Res 2012 Aug 15;18(16):4291-302. PMID: 22723371
Marotta M, Piontkivska H, Tanaka H. Molecular trajectories leading to the alternative fates of duplicate genes. PLoS One 2012;7(6):e38958. PMID: 22720000
Mefford D, Mefford J. Stromal genes add prognostic information to proliferation and histoclinical markers: a basis for the next generation of breast cancer gene signatures. PLoS One 2012;7(6):e37646. PMID: 22719844
Koestler DC, Marsit CJ, Christensen BC, Accomando W et al. Peripheral blood immune cell methylation profiles are associated with nonhematopoietic cancers. Cancer Epidemiol Biomarkers Prev 2012 Aug;21(8):1293-302. PMID: 22714737
van der Weyden L, Papaspyropoulos A, Poulogiannis G, Rust AG et al. Loss of rassf1a synergizes with deregulated runx2 signaling in tumorigenesis. Cancer Res 2012 Aug 1;72(15):3817-27. PMID: 22710434
Nair VS, Gevaert O, Davidzon G, Napel S et al. Prognostic PET 18F-FDG Uptake Imaging Features Are Associated with Major Oncogenomic Alterations in Patients with Resected Non-Small Cell Lung Cancer. Cancer Res 2012 Aug 1;72(15):3725-34. PMID: 22710433
Xiao Y, Guan J, Ping Y, Xu C et al. Prioritizing cancer-related key miRNA-target interactions by integrative genomics. Nucleic Acids Res 2012 Sep 1;40(16):7653-65. PMID: 22705797
Seckinger A, Meiβner T, Moreaux J, Depeweg D et al. Clinical and prognostic role of annexin A2 in multiple myeloma. Blood 2012 Aug 2;120(5):1087-94. PMID: 22705595
Casellas J, Varona L. Modeling skewness in human transcriptomes. PLoS One 2012;7(6):e38919. PMID: 22701729
Gekonge B, Raymond AD, Yin X, Kostman J et al. Retinoblastoma protein induction by HIV viremia or CCR5 in monocytes exposed to HIV-1 mediates protection from activation-induced apoptosis: ex vivo and in vitro study. J Leukoc Biol 2012 Aug;92(2):397-405. PMID: 22701041
Jeong Y, Xie Y, Lee W, Bookout AL et al. Research resource: diagnostic and therapeutic potential of nuclear receptor expression in lung cancer. Mol Endocrinol 2012 Aug;26(8):1443-54. PMID: 22700587
Wu HJ, Ma YK, Chen T, Wang M et al. PsRobot: a web-based plant small RNA meta-analysis toolbox. Nucleic Acids Res 2012 Jul;40(Web Server issue):W22-8. PMID: 22693224
Wise A, Oltvai ZN, Bar-Joseph Z. Matching experiments across species using expression values and textual information. Bioinformatics 2012 Jun 15;28(12):i258-64. PMID: 22689770
Névéol A, Wilbur WJ, Lu Z. Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE. Database (Oxford) 2012;2012:bas026. PMID: 22685160
Terrados G, Finkernagel F, Stielow B, Sadic D et al. Genome-wide localization and expression profiling establish Sp2 as a sequence-specific transcription factor regulating vitally important genes. Nucleic Acids Res 2012 Sep 1;40(16):7844-57. PMID: 22684502
Feyeux M, Bourgois-Rocha F, Redfern A, Giles P et al. Early transcriptional changes linked to naturally occurring Huntington's disease mutations in neural derivatives of human embryonic stem cells. Hum Mol Genet 2012 Sep 1;21(17):3883-95. PMID: 22678061
Kusko RL, Banerjee C, Long KK, Darcy A et al. Premature expression of a muscle fibrosis axis in chronic HIV infection. Skelet Muscle 2012 Jun 7;2(1):10. PMID: 22676806
Ng FS, Toh TB, Ting EH, Koh GR et al. Progenitor-like Traits Contribute to Patient Survival and Prognosis in Oligodendroglial Tumors. Clin Cancer Res 2012 Aug 1;18(15):4122-4135. PMID: 22675171
Pritchard S, Wick HC, Slonim DK, Johnson KL et al. Comprehensive analysis of genes expressed by rare microchimeric fetal cells in the maternal mouse lung. Biol Reprod 2012;87(2):42. PMID: 22674387
Friese RS, Ye C, Nievergelt CM, Schork AJ et al. Integrated computational and experimental analysis of the neuroendocrine transcriptome in genetic hypertension identifies novel control points for the cardiometabolic syndrome. Circ Cardiovasc Genet 2012 Aug 1;5(4):430-40. PMID: 22670052
Linderman GC, Chance MR, Bebek G. MAGNET: MicroArray Gene expression and Network Evaluation Toolkit. Nucleic Acids Res 2012 Jul;40(Web Server issue):W152-6. PMID: 22669910
Hu B, Nandhu MS, Sim H, Agudelo-Garcia PA et al. Fibulin-3 Promotes Glioma Growth and Resistance through a Novel Paracrine Regulation of Notch Signaling. Cancer Res 2012 Aug 1;72(15):3873-85. PMID: 22665268
Hayashi T, Kato T, Furukawa K. Respiratory Chain Analysis of Zymomonas mobilis Mutants Producing High Levels of Ethanol. Appl Environ Microbiol 2012 Aug;78(16):5622-9. PMID: 22660712
Park C, Ahn J, Yoon Y, Park S. Identification of functional CNV region networks using a CNV-gene mapping algorithm in a genome-wide scale. Bioinformatics 2012 Aug 1;28(15):2045-51. PMID: 22652832
Hattlmann CJ, Kelly JN, Barr SD. TRIM22: A Diverse and Dynamic Antiviral Protein. Mol Biol Int 2012;2012:153415. PMID: 22649727
Voll LM, Horst RJ, Voitsik AM, Zajic D et al. Common Motifs in the Response of Cereal Primary Metabolism to Fungal Pathogens are not Based on Similar Transcriptional Reprogramming. Front Plant Sci 2011;2:39. PMID: 22645534
Yan Z, Shah PK, Amin SB, Samur MK et al. Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancers. Nucleic Acids Res 2012 May 29. PMID: 22645320
Yoshida Y, Tsunoda T, Doi K, Fujimoto T et al. ALPK2 is crucial for luminal apoptosis and DNA repair-related gene expression in a three-dimensional colonic-crypt model. Anticancer Res 2012 Jun;32(6):2301-8. PMID: 22641666
Ota T, Doi K, Fujimoto T, Tanaka Y et al. KRAS up-regulates the expression of miR-181a, miR-200c and miR-210 in a three-dimensional-specific manner in DLD-1 colorectal cancer cells. Anticancer Res 2012 Jun;32(6):2271-5. PMID: 22641662
Wu D, Smyth GK. Camera: a competitive gene set test accounting for inter-gene correlation. Nucleic Acids Res 2012 May 25. PMID: 22638577
Velasco-Velázquez M, Jiao X, De La Fuente M, Pestell TG et al. CCR5 Antagonist Blocks Metastasis of Basal Breast Cancer Cells. Cancer Res 2012 Aug 1;72(15):3839-50. PMID: 22637726
Tong Y, Zheng Y, Zhou J, Oyesiku NM et al. Genomic characterization of human and rat prolactinomas. Endocrinology 2012 Aug;153(8):3679-91. PMID: 22635680
Jahid S, Sun J, Edwards RA, Dizon D et al. miR-23a promotes the transition from indolent to invasive colorectal cancer. Cancer Discov 2012 Jun;2(6):540-53. PMID: 22628407
Fankhauser N, Cima I, Wild P, Krek W. Identification of a gene expression signature common to distinct cancer pathways. Cancer Inform 2012;11:139-46. PMID: 22619501
Mkrtchian S, Kåhlin J, Ebberyd A, Gonzalez C et al. The human carotid body transcriptome with focus on oxygen sensing and inflammation - a comparative analysis. J Physiol 2012 Aug 15;590(Pt 16):3807-19. PMID: 22615433
Meredith MM, Liu K, Darrasse-Jeze G, Kamphorst AO et al. Expression of the zinc finger transcription factor zDC (Zbtb46, Btbd4) defines the classical dendritic cell lineage. J Exp Med 2012 Jun 4;209(6):1153-65. PMID: 22615130
Selamat SA, Chung BS, Girard L, Zhang W et al. Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression. Genome Res 2012 Jul;22(7):1197-211. PMID: 22613842
Dubé E, Dufresne J, Chan PT, Cyr DG. Epidermal growth factor regulates connexin 43 in the human epididymis: role of gap junctions in azoospermia. Hum Reprod 2012 Aug;27(8):2285-96. PMID: 22611165
Tang A, Li N, Li X, Yang H et al. Dynamic activation of the key pathways: linking colitis to colorectal cancer in a mouse model. Carcinogenesis 2012 Jul;33(7):1375-83. PMID: 22610167
Cutts RJ, Dayem Ullah AZ, Sangaralingam A, Gadaleta E et al. O-miner: an integrative platform for automated analysis and mining of -omics data. Nucleic Acids Res 2012 Jul;40(Web Server issue):W560-8. PMID: 22600742
El-Sayed Moustafa JS, Eleftherohorinou H, de Smith AJ, Andersson-Assarsson JC et al. Novel association approach for variable number tandem repeats (VNTRs) identifies DOCK5 as a susceptibility gene for severe obesity. Hum Mol Genet 2012 Aug 15;21(16):3727-38. PMID: 22595969
Bevilacqua V, Pannarale P, Abbrescia M, Cava C et al. Comparison of data-merging methods with SVM attribute selection and classification in breast cancer gene expression. BMC Bioinformatics 2012 May 8;13 Suppl 7:S9. PMID: 22595006
Fang R, Xiao T, Fang Z, Sun Y et al. MicroRNA-143 (miR-143) regulates cancer glycolysis via targeting hexokinase 2 gene. J Biol Chem 2012 Jun 29;287(27):23227-35. PMID: 22593586
Gorlov IP, Byun J, Logothetis CJ. In silico functional profiling of individual prostate cancer tumors: many genes, few functions. Cancer Genomics Proteomics 2012 May-Jun;9(3):109-14. PMID: 22593245
Vendrell JA, Thollet A, Nguyen NT, Ghayad SE et al. ZNF217 is a marker of poor prognosis in breast cancer that drives epithelial-mesenchymal transition and invasion. Cancer Res 2012 Jul 15;72(14):3593-606. PMID: 22593193
Janouskova H, Maglott A, Leger DY, Bossert C et al. Integrin α5β1 plays a critical role in resistance to temozolomide by interfering with the p53 pathway in high-grade glioma. Cancer Res 2012 Jul 15;72(14):3463-70. PMID: 22593187
Fukuhara T, Kambara H, Shiokawa M, Ono C et al. Expression of microRNA miR-122 facilitates an efficient replication in nonhepatic cells upon infection with hepatitis C virus. J Virol 2012 Aug;86(15):7918-33. PMID: 22593164
Liu Y, Sun Y, Broaddus R, Liu J et al. Integrated analysis of gene expression and tumor nuclear image profiles associated with chemotherapy response in serous ovarian carcinoma. PLoS One 2012;7(5):e36383. PMID: 22590536
Dheilly NM, Lelong C, Huvet A, Kellner K et al. Gametogenesis in the Pacific oyster Crassostrea gigas: a microarrays-based analysis identifies sex and stage specific genes. PLoS One 2012;7(5):e36353. PMID: 22590533
Yen CC, Yeh CN, Cheng CT, Jung SM et al. Integrating bioinformatics and clinicopathological research of gastrointestinal stromal tumors: identification of aurora kinase a as a poor risk marker. Ann Surg Oncol 2012 Oct;19(11):3491-9. PMID: 22588468
Smith SC, Baras AS, Owens CR, Dancik G et al. Transcriptional signatures of Ral GTPase are associated with aggressive clinicopathologic characteristics in human cancer. Cancer Res 2012 Jul 15;72(14):3480-91. PMID: 22586063
Benassi B, Flavin R, Marchionni L, Zanata S et al. MYC is activated by USP2a-mediated modulation of microRNAs in prostate cancer. Cancer Discov 2012 Mar;2(3):236-47. PMID: 22585994
Vijaya Satya R, Zavaljevski N, Reifman J. A new strategy to reduce allelic bias in RNA-Seq readmapping. Nucleic Acids Res 2012 Sep 1;40(16):e127. PMID: 22584625
Ros S, Santos CR, Moco S, Baenke F et al. Functional metabolic screen identifies 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 as an important regulator of prostate cancer cell survival. Cancer Discov 2012 Apr;2(4):328-43. PMID: 22576210
Ragunath PK, Reddy BV, Abhinand PA, Ahmed SS. Relevance of systems biological approach in the differential diagnosis of invasive lobular carcinoma & invasive ductal carcinoma. Bioinformation 2012;8(8):359-64. PMID: 22570516
Bao J, Li D, Wang L, Wu J et al. MicroRNA-449 and microRNA-34b/c function redundantly in murine testes by targeting E2F transcription factor-retinoblastoma protein (E2F-pRb) pathway. J Biol Chem 2012 Jun 22;287(26):21686-98. PMID: 22570483
Dreher F, Kreitler T, Hardt C, Kamburov A et al. DIPSBC - data integration platform for systems biology collaborations. BMC Bioinformatics 2012 May 8;13(1):85. PMID: 22568834
Xue W, Kitzing T, Roessler S, Zuber J et al. A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions. Proc Natl Acad Sci U S A 2012 May 22;109(21):8212-7. PMID: 22566646
Goldie SJ, Mulder KW, Tan DW, Lyons SK et al. FRMD4A upregulation in human squamous cell carcinoma promotes tumor growth and metastasis and is associated with poor prognosis. Cancer Res 2012 Jul 1;72(13):3424-36. PMID: 22564525
Zacher B, Abnaof K, Gade S, Younesi E et al. Joint Bayesian inference of condition-specific miRNA and transcription factor activities from combined gene and microRNA expression data. Bioinformatics 2012 Jul 1;28(13):1714-20. PMID: 22563068
Ashida H, Asai K, Hamada M. Shape-based alignment of genomic landscapes in multi-scale resolution. Nucleic Acids Res 2012 Aug 1;40(14):6435-48. PMID: 22561376
Galili N, Tamayo P, Botvinnik OB, Mesirov JP et al. Prediction of response to therapy with ezatiostat in lower risk myelodysplastic syndrome. J Hematol Oncol 2012 May 6;5:20. PMID: 22559819
Ivliev AE, 't Hoen PA, van Roon-Mom WM, Peters DJ et al. Exploring the transcriptome of ciliated cells using in silico dissection of human tissues. PLoS One 2012;7(4):e35618. PMID: 22558177
Iancu OD, Kawane S, Bottomly D, Searles R et al. Utilizing RNA-Seq data for de novo coexpression network inference. Bioinformatics 2012 Jun 15;28(12):1592-7. PMID: 22556371
O'Donnell KA, Keng VW, York B, Reineke EL et al. A Sleeping Beauty mutagenesis screen reveals a tumor suppressor role for Ncoa2/Src-2 in liver cancer. Proc Natl Acad Sci U S A 2012 May 22;109(21):E1377-86. PMID: 22556267
Rombouts K, Mello T, Liotta F, Galli A et al. MARCKS actin-binding capacity mediates actin filament assembly during mitosis in human hepatic stellate cells. Am J Physiol Cell Physiol 2012 Aug;303(4):C357-67. PMID: 22555845
Bindels EM, Havermans M, Lugthart S, Erpelinck C et al. EVI1 is critical for the pathogenesis of a subset of MLL-AF9-rearranged AMLs. Blood 2012 Jun 14;119(24):5838-49. PMID: 22553314
Zeitouni S, Krause U, Clough BH, Halderman H et al. Human mesenchymal stem cell-derived matrices for enhanced osteoregeneration. Sci Transl Med 2012 May 2;4(132):132ra55. PMID: 22553253
Aurelius J, Thorén FB, Akhiani AA, Brune M et al. Monocytic AML cells inactivate antileukemic lymphocytes: role of NADPH oxidase/gp91(phox) expression and the PARP-1/PAR pathway of apoptosis. Blood 2012 Jun 14;119(24):5832-7. PMID: 22550344
Watanabe T, Kobunai T, Yamamoto Y, Matsuda K et al. Chromosomal instability (CIN) phenotype, CIN high or CIN low, predicts survival for colorectal cancer. J Clin Oncol 2012 Jun 20;30(18):2256-64. PMID: 22547595
Schlitzer A, Heiseke AF, Einwächter H, Reindl W et al. Tissue-specific differentiation of a circulating CCR9- pDC-like common dendritic cell precursor. Blood 2012 Jun 21;119(25):6063-71. PMID: 22547585
Tarragona M, Pavlovic M, Arnal-Estapé A, Urosevic J et al. Identification of NOG as a specific breast cancer bone metastasis-supporting gene. J Biol Chem 2012 Jun 15;287(25):21346-55. PMID: 22547073
Chung EY, Psathas JN, Yu D, Li Y et al. CD19 is a major B cell receptor-independent activator of MYC-driven B-lymphomagenesis. J Clin Invest 2012 Jun 1;122(6):2257-66. PMID: 22546857
Patra T, Koley H, Ramamurthy T, Ghose AC et al. The Entner-Doudoroff pathway is obligatory for gluconate utilization and contributes to the pathogenicity of Vibrio cholerae. J Bacteriol 2012 Jul;194(13):3377-85. PMID: 22544275
Lin PP, Bai XJ, Yue ZX, Yan SF et al. [Suppression of NAMPT expression enhances the sensitivity of K562 cells to imatinib and its relative mechanism]. Zhongguo Shi Yan Xue Ye Xue Za Zhi 2012 Apr;20(2):235-41. PMID: 22541073
Zhao G, Ihuegbu N, Lee M, Schriefer L et al. Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans. G3 (Bethesda) 2012 Apr;2(4):469-81. PMID: 22540038
Mérino D, Khaw SL, Glaser SP, Anderson DJ et al. Bcl-2, Bcl-x(L), and Bcl-w are not equivalent targets of ABT-737 and navitoclax (ABT-263) in lymphoid and leukemic cells. Blood 2012 Jun 14;119(24):5807-16. PMID: 22538851
Chen CY, Morris Q, Mitchell JA. Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features. BMC Genomics 2012 Apr 26;13:152. PMID: 22537144
Sanavia T, Aiolli F, Da San Martino G, Bisognin A et al. Improving biomarker list stability by integration of biological knowledge in the learning process. BMC Bioinformatics 2012 Mar 28;13 Suppl 4:S22. PMID: 22536969
Garmire LX, Subramaniam S. Evaluation of normalization methods in mammalian microRNA-Seq data. RNA 2012 Jun;18(6):1279-88. PMID: 22532701
Josset L, Belser JA, Pantin-Jackwood MJ, Chang JH et al. Implication of inflammatory macrophages, nuclear receptors, and interferon regulatory factors in increased virulence of pandemic 2009 H1N1 influenza A virus after host adaptation. J Virol 2012 Jul;86(13):7192-206. PMID: 22532695
Zarychanski R, Schulz VP, Houston BL, Maksimova Y et al. Mutations in the mechanotransduction protein PIEZO1 are associated with hereditary xerocytosis. Blood 2012 Aug 30;120(9):1908-15. PMID: 22529292
Cuperlovic-Culf M, Ferguson D, Culf A, Morin P Jr et al. 1H NMR metabolomics analysis of glioblastoma subtypes: correlation between metabolomics and gene expression characteristics. J Biol Chem 2012 Jun 8;287(24):20164-75. PMID: 22528487
Parizot B, Roberts I, Raes J, Beeckman T et al. In silico analyses of pericycle cell populations reinforce their relation with associated vasculature in Arabidopsis. Philos Trans R Soc Lond B Biol Sci 2012 Jun 5;367(1595):1479-88. PMID: 22527390
Yu J, Valerius MT, Duah M, Staser K et al. Identification of molecular compartments and genetic circuitry in the developing mammalian kidney. Development 2012 May;139(10):1863-73. PMID: 22510988
Cheng Q, Chang JT, Geradts J, Neckers LM et al. Amplification and high-level expression of heat shock protein 90 marks aggressive phenotypes of human epidermal growth factor receptor 2 negative breast cancer. Breast Cancer Res 2012 Apr 17;14(2):R62. PMID: 22510516
Sathyanarayana P, Dev A, Pradeep A, Ufkin M et al. Spry1 as a novel regulator of erythropoiesis, EPO/EPOR target, and suppressor of JAK2. Blood 2012 Jun 7;119(23):5522-31. PMID: 22508938
Ignatiadis M, Singhal SK, Desmedt C, Haibe-Kains B et al. Gene modules and response to neoadjuvant chemotherapy in breast cancer subtypes: a pooled analysis. J Clin Oncol 2012 Jun 1;30(16):1996-2004. PMID: 22508827
He HH, Meyer CA, Chen MW, Jordan VC et al. Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics. Genome Res 2012 Jun;22(6):1015-25. PMID: 22508765
Albino D, Longoni N, Curti L, Mello-Grand M et al. ESE3/EHF controls epithelial cell differentiation and its loss leads to prostate tumors with mesenchymal and stem-like features. Cancer Res 2012 Jun 1;72(11):2889-900. PMID: 22505649
Chen FC, Liao BY, Pan CL, Lin HY et al. Assessing Determinants of Exonic Evolutionary Rates in Mammals. Mol Biol Evol 2012 Aug 7. PMID: 22504521
Kodama K, Horikoshi M, Toda K, Yamada S et al. Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes. Proc Natl Acad Sci U S A 2012 May 1;109(18):7049-54. PMID: 22499789
Leichtmann-Bardoogo Y, Cohen LA, Weiss A, Marohn B et al. Compartmentalization and regulation of iron metabolism proteins protect male germ cells from iron overload. Am J Physiol Endocrinol Metab 2012 Jun 15;302(12):E1519-30. PMID: 22496346
Kemper K, Versloot M, Cameron K, Colak S et al. Mutations in the Ras-Raf Axis underlie the prognostic value of CD133 in colorectal cancer. Clin Cancer Res 2012 Jun 1;18(11):3132-41. PMID: 22496204
Wang C, Tian R, Zhao Q, Xu H et al. Computational inference of mRNA stability from histone modification and transcriptome profiles. Nucleic Acids Res 2012 Aug 1;40(14):6414-23. PMID: 22495509
Ehlén Å, Rosselló CA, von Stedingk K, Höög G et al. Tumors with nonfunctional retinoblastoma protein are killed by reduced γ-tubulin levels. J Biol Chem 2012 May 18;287(21):17241-7. PMID: 22493456
Zhou S, Yi T, Liu R, Bian C et al. Proteomics identification of annexin A2 as a key mediator in the metastasis and proangiogenesis of endometrial cells in human adenomyosis. Mol Cell Proteomics 2012 Jul;11(7):M112.017988. PMID: 22493182
Ribeiro AF, Pratcorona M, Erpelinck-Verschueren C, Rockova V et al. Mutant DNMT3A: a marker of poor prognosis in acute myeloid leukemia. Blood 2012 Jun 14;119(24):5824-31. PMID: 22490330
Suzuki S, Takai-Igarashi T, Fukuoka Y, Wall DP et al. Systems analysis of inflammatory bowel disease based on comprehensive gene information. BMC Med Genet 2012 Apr 5;13:25. PMID: 22480395
Qian W, Yang JR, Pearson NM, Maclean C et al. Balanced codon usage optimizes eukaryotic translational efficiency. PLoS Genet 2012;8(3):e1002603. PMID: 22479199
Pu YS, Huang CY, Chen JY, Kang WY et al. Down-regulation of PKCζ in renal cell carcinoma and its clinicopathological implications. J Biomed Sci 2012 Apr 5;19:39. PMID: 22475628
Wilson TJ, Ge SX. ArraySearch: A Web-Based Genomic Search Engine. Comp Funct Genomics 2012;2012:650842. PMID: 22474412
Xiao Y, Decker PA, Rice T, McCoy LS et al. SSBP2 variants are associated with survival in glioblastoma patients. Clin Cancer Res 2012 Jun 1;18(11):3154-62. PMID: 22472174
Heering J, Weis N, Holeiter M, Neugart F et al. Loss of the ceramide transfer protein augments EGF receptor signaling in breast cancer. Cancer Res 2012 Jun 1;72(11):2855-66. PMID: 22472120
Hu Z, Gu Y, Han B, Zhang J et al. Knockdown of AGR2 induces cellular senescence in prostate cancer cells. Carcinogenesis 2012 Jun;33(6):1178-86. PMID: 22467239
Seo J, Kim SC, Lee HS, Kim JK et al. Genome-wide profiles of H2AX and γ-H2AX differentiate endogenous and exogenous DNA damage hotspots in human cells. Nucleic Acids Res 2012 Jul;40(13):5965-74. PMID: 22467212
Statham AL, Robinson MD, Song JZ, Coolen MW et al. Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA. Genome Res 2012 Jun;22(6):1120-7. PMID: 22466171
Liu JC, Voisin V, Bader GD, Deng T et al. Seventeen-gene signature from enriched Her2/Neu mammary tumor-initiating cells predicts clinical outcome for human HER2+:ERα- breast cancer. Proc Natl Acad Sci U S A 2012 Apr 10;109(15):5832-7. PMID: 22460789
Mao S, Garzon-Muvdi T, Di Fulvio M, Chen Y et al. Molecular and functional expression of cation-chloride cotransporters in dorsal root ganglion neurons during postnatal maturation. J Neurophysiol 2012 Aug;108(3):834-52. PMID: 22457464
Roux J, Gonzàlez-Porta M, Robinson-Rechavi M. Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs. Nucleic Acids Res 2012 Jul;40(13):5890-900. PMID: 22457063
Reed J, Hsueh C, Lam ML, Kjolby R et al. Identifying individual DNA species in a complex mixture by precisely measuring the spacing between nicking restriction enzymes with atomic force microscope. J R Soc Interface 2012 Sep 7;9(74):2341-50. PMID: 22456455
Reddy S, Zhao M, Hu DQ, Fajardo G et al. Dynamic microRNA expression during the transition from right ventricular hypertrophy to failure. Physiol Genomics 2012 May 1;44(10):562-75. PMID: 22454450
Schroder K, Irvine KM, Taylor MS, Bokil NJ et al. Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages. Proc Natl Acad Sci U S A 2012 Apr 17;109(16):E944-53. PMID: 22451944
Willingham SB, Volkmer JP, Gentles AJ, Sahoo D et al. The CD47-signal regulatory protein alpha (SIRPa) interaction is a therapeutic target for human solid tumors. Proc Natl Acad Sci U S A 2012 Apr 24;109(17):6662-7. PMID: 22451913
Schmid PR, Palmer NP, Kohane IS, Berger B. Making sense out of massive data by going beyond differential expression. Proc Natl Acad Sci U S A 2012 Apr 10;109(15):5594-9. PMID: 22447773
Gupta R, Ezashi T, Roberts RM. Squelching of ETS2 transactivation by POU5F1 silences the human chorionic gonadotropin CGA subunit gene in human choriocarcinoma and embryonic stem cells. Mol Endocrinol 2012 May;26(5):859-72. PMID: 22446105
Hewitt SC, Li L, Grimm SA, Chen Y et al. Research resource: whole-genome estrogen receptor α binding in mouse uterine tissue revealed by ChIP-seq. Mol Endocrinol 2012 May;26(5):887-98. PMID: 22446102
Huang CL, Lamb J, Chindelevitch L, Kostrowicki J et al. Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge. BMC Bioinformatics 2012 Mar 23;13:46. PMID: 22443377
Lahti L, Schäfer M, Klein HU, Bicciato S et al. Cancer gene prioritization by integrative analysis of mRNA expression and DNA copy number data: a comparative review. Brief Bioinform 2012 Mar 22. PMID: 22441573
Fernández-Fueyo E, Ruiz-Dueñas FJ, Miki Y, Martínez MJ et al. Lignin-degrading peroxidases from genome of selective ligninolytic fungus Ceriporiopsis subvermispora. J Biol Chem 2012 May 11;287(20):16903-16. PMID: 22437835
Park C, Zhang J. High expression hampers horizontal gene transfer. Genome Biol Evol 2012;4(4):523-32. PMID: 22436996
Fernandez-Fueyo E, Ruiz-Dueñas FJ, Ferreira P, Floudas D et al. Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis. Proc Natl Acad Sci U S A 2012 Apr 3;109(14):5458-63. PMID: 22434909
Kubicek S, Gilbert JC, Fomina-Yadlin D, Gitlin AD et al. Chromatin-targeting small molecules cause class-specific transcriptional changes in pancreatic endocrine cells. Proc Natl Acad Sci U S A 2012 Apr 3;109(14):5364-9. PMID: 22434908
Rajeswaran R, Aregger M, Zvereva AS, Borah BK et al. Sequencing of RDR6-dependent double-stranded RNAs reveals novel features of plant siRNA biogenesis. Nucleic Acids Res 2012 Jul;40(13):6241-54. PMID: 22434877
Yoshida K, Yoshihara K, Adachi S, Haino K et al. Possible involvement of the E-cadherin gene in genetic susceptibility to endometriosis. Hum Reprod 2012 Jun;27(6):1685-9. PMID: 22434855
Smith SB, Dampier W, Tozeren A, Brown JR et al. Identification of common biological pathways and drug targets across multiple respiratory viruses based on human host gene expression analysis. PLoS One 2012;7(3):e33174. PMID: 22432004
Lu J, Zhang C, Baulcombe DC, Chen ZJ. Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds. Proc Natl Acad Sci U S A 2012 Apr 3;109(14):5529-34. PMID: 22431617
Eckel-Mahan KL, Patel VR, Mohney RP, Vignola KS et al. Coordination of the transcriptome and metabolome by the circadian clock. Proc Natl Acad Sci U S A 2012 Apr 3;109(14):5541-6. PMID: 22431615
Zhang H, Li H, Ho N, Li D et al. Scd1 plays a tumor-suppressive role in survival of leukemia stem cells and the development of chronic myeloid leukemia. Mol Cell Biol 2012 May;32(10):1776-87. PMID: 22431519
Yoo SA, You S, Yoon HJ, Kim DH et al. A novel pathogenic role of the ER chaperone GRP78/BiP in rheumatoid arthritis. J Exp Med 2012 Apr 9;209(4):871-86. PMID: 22430489
Luo S, Zhang Y, Hu Q, Chen J et al. Dynamic nucleotide-binding site and leucine-rich repeat-encoding genes in the grass family. Plant Physiol 2012 May;159(1):197-210. PMID: 22422941
Sun H, Guns T, Fierro AC, Thorrez L et al. Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection. Nucleic Acids Res 2012 Jul;40(12):e90. PMID: 22422841
Jung I, Kim SK, Kim M, Han YM et al. H2B monoubiquitylation is a 5'-enriched active transcription mark and correlates with exon-intron structure in human cells. Genome Res 2012 Jun;22(6):1026-35. PMID: 22421545
Mann KM, Ward JM, Yew CC, Kovochich A et al. Sleeping Beauty mutagenesis reveals cooperating mutations and pathways in pancreatic adenocarcinoma. Proc Natl Acad Sci U S A 2012 Apr 17;109(16):5934-41. PMID: 22421440
Pucciariello C, Parlanti S, Banti V, Novi G et al. Reactive oxygen species-driven transcription in Arabidopsis under oxygen deprivation. Plant Physiol 2012 May;159(1):184-96. PMID: 22415514
Reynaud CA, Weill JC. Gene profiling of CD11b⁺ and CD11b⁻ B1 cell subsets reveals potential cell sorting artifacts. J Exp Med 2012 Mar 12;209(3):433-4; author reply 434-6. PMID: 22412175
Wang Y, Roche O, Xu C, Moriyama EH et al. Hypoxia promotes ligand-independent EGF receptor signaling via hypoxia-inducible factor-mediated upregulation of caveolin-1. Proc Natl Acad Sci U S A 2012 Mar 27;109(13):4892-7. PMID: 22411794
Chang JT. Deriving transcriptional programs and functional processes from gene expression databases. Bioinformatics 2012 Apr 15;28(8):1122-9. PMID: 22408194
Ritchie W, Gao D, Rasko JE. Defining and providing robust controls for microRNA prediction. Bioinformatics 2012 Apr 15;28(8):1058-61. PMID: 22408193
Wei C, Salichos L, Wittgrove CM, Rokas A et al. Transcriptome-wide analysis of small RNA expression in early zebrafish development. RNA 2012 May;18(5):915-29. PMID: 22408181
Dong C, Wu Y, Yao J, Wang Y et al. G9a interacts with Snail and is critical for Snail-mediated E-cadherin repression in human breast cancer. J Clin Invest 2012 Apr 2;122(4):1469-86. PMID: 22406531
Schroeder BW, Verhaeghe C, Park SW, Nguyenvu LT et al. AGR2 Is Induced in Asthma and Promotes Allergen-Induced Mucin Overproduction. Am J Respir Cell Mol Biol 2012 Aug;47(2):178-85. PMID: 22403803
Fieuw A, De Wilde B, Speleman F, Vandesompele J et al. Cancer gene prioritization for targeted resequencing using FitSNP scores. PLoS One 2012;7(3):e31333. PMID: 22396732
Ren K, Lu J, Porollo A, Du C. Tumor-suppressing function of caspase-2 requires catalytic site Cys-320 and site Ser-139 in mice. J Biol Chem 2012 Apr 27;287(18):14792-802. PMID: 22396545
Ji Y, Sun S, Xu A, Bhargava P et al. Activation of natural killer T cells promotes M2 Macrophage polarization in adipose tissue and improves systemic glucose tolerance via interleukin-4 (IL-4)/STAT6 protein signaling axis in obesity. J Biol Chem 2012 Apr 20;287(17):13561-71. PMID: 22396530
Azab AK, Hu J, Quang P, Azab F et al. Hypoxia promotes dissemination of multiple myeloma through acquisition of epithelial to mesenchymal transition-like features. Blood 2012 Jun 14;119(24):5782-94. PMID: 22394600
Kapetanovic R, Fairbairn L, Beraldi D, Sester DP et al. Pig bone marrow-derived macrophages resemble human macrophages in their response to bacterial lipopolysaccharide. J Immunol 2012 Apr 1;188(7):3382-94. PMID: 22393154
Easwaran H, Johnstone SE, Van Neste L, Ohm J et al. A DNA hypermethylation module for the stem/progenitor cell signature of cancer. Genome Res 2012 May;22(5):837-49. PMID: 22391556
Vasconcelos EJ, Terrão MC, Ruiz JC, Vêncio RZ et al. In silico identification of conserved intercoding sequences in Leishmania genomes: unraveling putative cis-regulatory elements. Mol Biochem Parasitol 2012 Jun;183(2):140-50. PMID: 22387760
Taşan M, Drabkin HJ, Beaver JE, Chua HN et al. A Resource of Quantitative Functional Annotation for Homo sapiens Genes. G3 (Bethesda) 2012 Feb;2(2):223-33. PMID: 22384401
Orloff MS, Zhang L, Bebek G, Eng C. Integrative genomic analysis reveals extended germline homozygosity with lung cancer risk in the PLCO cohort. PLoS One 2012;7(2):e31975. PMID: 22384118
Buss MC, Read TA, Schniederjan MJ, Gandhi K et al. HDM2 promotes WIP1-mediated medulloblastoma growth. Neuro Oncol 2012 Apr;14(4):440-58. PMID: 22379189
Cieply B, Riley P 4th, Pifer PM, Widmeyer J et al. Suppression of the epithelial-mesenchymal transition by Grainyhead-like-2. Cancer Res 2012 May 1;72(9):2440-53. PMID: 22379025
Worzfeld T, Swiercz JM, Looso M, Straub BK et al. ErbB-2 signals through Plexin-B1 to promote breast cancer metastasis. J Clin Invest 2012 Apr 2;122(4):1296-305. PMID: 22378040
Sin HS, Ichijima Y, Koh E, Namiki M et al. Human postmeiotic sex chromatin and its impact on sex chromosome evolution. Genome Res 2012 May;22(5):827-36. PMID: 22375025
Bien SJ, Park CH, Shim HJ, Yang W et al. Bi-directional semantic similarity for gene ontology to optimize biological and clinical analyses. J Am Med Inform Assoc 2012 Sep 1;19(5):765-74. PMID: 22374934
Deffenbacher KE, Iqbal J, Sanger W, Shen Y et al. Molecular distinctions between pediatric and adult mature B-cell non-Hodgkin lymphomas identified through genomic profiling. Blood 2012 Apr 19;119(16):3757-66. PMID: 22374697
Sy MF, Ranwez S, Montmain J, Regnault A et al. User centered and ontology based information retrieval system for life sciences. BMC Bioinformatics 2012 Jan 25;13 Suppl 1:S4. PMID: 22373375
Chen Z, Liu Q, Nadarajah S. A new statistical approach to detecting differentially methylated loci for case control Illumina array methylation data. Bioinformatics 2012 Apr 15;28(8):1109-13. PMID: 22368244
Warmoes M, Jaspers JE, Pham TV, Piersma SR et al. Proteomics of mouse BRCA1-deficient mammary tumors identifies DNA repair proteins with potential diagnostic and prognostic value in human breast cancer. Mol Cell Proteomics 2012 Jul;11(7):M111.013334. PMID: 22366898
O'Mahony FC, Faratian D, Varley J, Nanda J et al. The use of automated quantitative analysis to evaluate epithelial-to-mesenchymal transition associated proteins in clear cell renal cell carcinoma. PLoS One 2012;7(2):e31557. PMID: 22363672
Sircar K, Huang H, Hu L, Liu Y et al. Mitosis phase enrichment with identification of mitotic centromere-associated kinesin as a therapeutic target in castration-resistant prostate cancer. PLoS One 2012;7(2):e31259. PMID: 22363599
Xue LJ, Zhang JJ, Xue HW. Genome-wide analysis of the complex transcriptional networks of rice developing seeds. PLoS One 2012;7(2):e31081. PMID: 22363552
Gao X, Zhu Y, Li G, Huang H et al. TIM-3 expression characterizes regulatory T cells in tumor tissues and is associated with lung cancer progression. PLoS One 2012;7(2):e30676. PMID: 22363469
Houtman MJ, Takanari H, Kok BG, van Eck M et al. Experimental Mapping of the Canine KCNJ2 and KCNJ12 Gene Structures and Functional Analysis of the Canine K(IR)2.2 ion Channel. Front Physiol 2012;3:9. PMID: 22363290
Rivera-Gonzalez GC, Droop AP, Rippon HJ, Tiemann K et al. Retinoic acid and androgen receptors combine to achieve tissue specific control of human prostatic transglutaminase expression: a novel regulatory network with broader significance. Nucleic Acids Res 2012 Jun;40(11):4825-40. PMID: 22362749
Laczny C, Leidinger P, Haas J, Ludwig N et al. miRTrail--a comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases. BMC Bioinformatics 2012 Feb 22;13:36. PMID: 22356618
Sati S, Tanwar VS, Kumar KA, Patowary A et al. High resolution methylome map of rat indicates role of intragenic DNA methylation in identification of coding region. PLoS One 2012;7(2):e31621. PMID: 22355382
Zhang H, Guo F, Zhu G. Involvement of host cell integrin α2 in Cryptosporidium parvum infection. Infect Immun 2012 May;80(5):1753-8. PMID: 22354032
Fijneman RJ, de Wit M, Pourghiasian M, Piersma SR et al. Proximal fluid proteome profiling of mouse colon tumors reveals biomarkers for early diagnosis of human colorectal cancer. Clin Cancer Res 2012 May 1;18(9):2613-24. PMID: 22351690
Fang Z, Du R, Cui X. Uniform approximation is more appropriate for Wilcoxon Rank-Sum Test in gene set analysis. PLoS One 2012;7(2):e31505. PMID: 22347488
Lembo A, Di Cunto F, Provero P. Shortening of 3'UTRs correlates with poor prognosis in breast and lung cancer. PLoS One 2012;7(2):e31129. PMID: 22347440
Sohur US, Arlotta P, Macklis JD. Developmental Controls are Re-Expressed during Induction of Neurogenesis in the Neocortex of Young Adult Mice. Front Neurosci 2012;6:12. PMID: 22347158
Zhuang J, Jones A, Lee SH, Ng E et al. The dynamics and prognostic potential of DNA methylation changes at stem cell gene loci in women's cancer. PLoS Genet 2012 Feb;8(2):e1002517. PMID: 22346766
Shigemizu D, Hu Z, Hung JH, Huang CL et al. Using functional signatures to identify repositioned drugs for breast, myelogenous leukemia and prostate cancer. PLoS Comput Biol 2012 Feb;8(2):e1002347. PMID: 22346740
Gennarino VA, D'Angelo G, Dharmalingam G, Fernandez S et al. Identification of microRNA-regulated gene networks by expression analysis of target genes. Genome Res 2012 Jun;22(6):1163-72. PMID: 22345618
Wu Q, Wang Y, Cao M, Pantaleo V et al. Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm. Proc Natl Acad Sci U S A 2012 Mar 6;109(10):3938-43. PMID: 22345560
Taslim C, Chen Z, Huang K, Huang TH et al. Integrated analysis identifies a class of androgen-responsive genes regulated by short combinatorial long-range mechanism facilitated by CTCF. Nucleic Acids Res 2012 Jun;40(11):4754-64. PMID: 22344698
Bergholdt R, Brorsson C, Palleja A, Berchtold LA et al. Identification of novel type 1 diabetes candidate genes by integrating genome-wide association data, protein-protein interactions, and human pancreatic islet gene expression. Diabetes 2012 Apr;61(4):954-62. PMID: 22344559
Reid JF, Sokolova V, Zoni E, Lampis A et al. miRNA profiling in colorectal cancer highlights miR-1 involvement in MET-dependent proliferation. Mol Cancer Res 2012 Apr;10(4):504-15. PMID: 22343615
Hodge JC, Kim TM, Dreyfuss JM, Somasundaram P et al. Expression profiling of uterine leiomyomata cytogenetic subgroups reveals distinct signatures in matched myometrium: transcriptional profilingof the t(12;14) and evidence in support of predisposing genetic heterogeneity. Hum Mol Genet 2012 May 15;21(10):2312-29. PMID: 22343407
Ungvári I, Hadadi E, Virág V, Bikov A et al. Implication of BIRC5 in asthma pathogenesis. Int Immunol 2012 May;24(5):293-301. PMID: 22336533
Zhang T, Berrocal JG, Yao J, DuMond ME et al. Regulation of poly(ADP-ribose) polymerase-1-dependent gene expression through promoter-directed recruitment of a nuclear NAD+ synthase. J Biol Chem 2012 Apr 6;287(15):12405-16. PMID: 22334709
Kawaguchi S, Iida K, Harada E, Hanada K et al. Positional correlation analysis improves reconstruction of full-length transcripts and alternative isoforms from noisy array signals or short reads. Bioinformatics 2012 Apr 1;28(7):929-37. PMID: 22332235
Hasegawa N, Sumitomo A, Fujita A, Aritome N et al. Mediator subunits MED1 and MED24 cooperatively contribute to pubertal mammary gland development and growth of breast carcinoma cells. Mol Cell Biol 2012 Apr;32(8):1483-95. PMID: 22331469
Yang D, Zhong F, Li D, Liu Z et al. General trends in the utilization of structural factors contributing to biological complexity. Mol Biol Evol 2012 Aug;29(8):1957-68. PMID: 22328715
Lockwood WW, Thu KL, Lin L, Pikor LA et al. Integrative genomics identified RFC3 as an amplified candidate oncogene in esophageal adenocarcinoma. Clin Cancer Res 2012 Apr 1;18(7):1936-46. PMID: 22328562
Garcia I, Mayol G, Ríos J, Domenech G et al. A three-gene expression signature model for risk stratification of patients with neuroblastoma. Clin Cancer Res 2012 Apr 1;18(7):2012-23. PMID: 22328561
Postel-Vinay S, Véron AS, Tirode F, Pierron G et al. Common variants near TARDBP and EGR2 are associated with susceptibility to Ewing sarcoma. Nat Genet 2012 Feb 12;44(3):323-7. PMID: 22327514
Kotelnikova E, Shkrob MA, Pyatnitskiy MA, Ferlini A et al. Novel approach to meta-analysis of microarray datasets reveals muscle remodeling-related drug targets and biomarkers in Duchenne muscular dystrophy. PLoS Comput Biol 2012 Feb;8(2):e1002365. PMID: 22319435
Morgan AA, Pyrgos VJ, Nadeau KC, Williamson PR et al. Multiplex meta-analysis of RNA expression to identify genes with variants associated with immune dysfunction. J Am Med Inform Assoc 2012 Mar-Apr;19(2):284-8. PMID: 22319178
Volinia S, Galasso M, Sana ME, Wise TF et al. Breast cancer signatures for invasiveness and prognosis defined by deep sequencing of microRNA. Proc Natl Acad Sci U S A 2012 Feb 21;109(8):3024-9. PMID: 22315424
Andersen RS, Thrue CA, Junker N, Lyngaa R et al. Dissection of T-cell antigen specificity in human melanoma. Cancer Res 2012 Apr 1;72(7):1642-50. PMID: 22311675
Schwartz RE, Trehan K, Andrus L, Sheahan TP et al. Modeling hepatitis C virus infection using human induced pluripotent stem cells. Proc Natl Acad Sci U S A 2012 Feb 14;109(7):2544-8. PMID: 22308485
Volkmer JP, Sahoo D, Chin RK, Ho PL et al. Three differentiation states risk-stratify bladder cancer into distinct subtypes. Proc Natl Acad Sci U S A 2012 Feb 7;109(6):2078-83. PMID: 22308455
Bard-Chapeau EA, Jeyakani J, Kok CH, Muller J et al. Ecotopic viral integration site 1 (EVI1) regulates multiple cellular processes important for cancer and is a synergistic partner for FOS protein in invasive tumors. Proc Natl Acad Sci U S A 2012 Feb 7;109(6):2168-73. PMID: 22308434
Martínez MR, Corradin A, Klein U, Álvareza MJ et al. Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis. Proc Natl Acad Sci U S A 2012 Feb 14;109(7):2672-7. PMID: 22308355
Van Hemert JL, Dickerson JA. Discriminating response groups in metabolic and regulatory pathway networks. Bioinformatics 2012 Apr 1;28(7):947-54. PMID: 22308149
Gerson KD, Shearstone JR, Maddula VS, Seligmann BE et al. Integrin β4 regulates SPARC protein to promote invasion. J Biol Chem 2012 Mar 23;287(13):9835-44. PMID: 22308039
Liu BY, Soloviev I, Huang X, Chang P et al. Mammary tumor regression elicited by Wnt signaling inhibitor requires IGFBP5. Cancer Res 2012 Mar 15;72(6):1568-78. PMID: 22307840
Cao X, Voss C, Zhao B, Kaneko T et al. Differential regulation of the activity of deleted in liver cancer 1 (DLC1) by tensins controls cell migration and transformation. Proc Natl Acad Sci U S A 2012 Jan 31;109(5):1455-60. PMID: 22307599
Alisch RS, Barwick BG, Chopra P, Myrick LK et al. Age-associated DNA methylation in pediatric populations. Genome Res 2012 Apr;22(4):623-32. PMID: 22300631
Frost HR, McCray AT. Markov Chain Ontology Analysis (MCOA). BMC Bioinformatics 2012 Feb 3;13:23. PMID: 22300537
Busser BW, Shokri L, Jaeger SA, Gisselbrecht SS et al. Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity. Development 2012 Mar;139(6):1164-74. PMID: 22296846
Yeung KY, Gooley TA, Zhang A, Raftery AE et al. Predicting relapse prior to transplantation in chronic myeloid leukemia by integrating expert knowledge and expression data. Bioinformatics 2012 Mar 15;28(6):823-30. PMID: 22296787
Yamakawa N, Kaneda K, Saito Y, Ichihara E et al. The increased expression of integrin α6 (ITGA6) enhances drug resistance in EVI1(high) leukemia. PLoS One 2012;7(1):e30706. PMID: 22295105
Ulrich DL, Lynch J, Wang Y, Fukuda Y et al. ATP-dependent mitochondrial porphyrin importer ABCB6 protects against phenylhydrazine toxicity. J Biol Chem 2012 Apr 13;287(16):12679-90. PMID: 22294697
Li Y, Zhang Z, Liu F, Vongsangnak W et al. Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis. Nucleic Acids Res 2012 May;40(10):4298-305. PMID: 22287634
McCarthy DJ, Chen Y, Smyth GK. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res 2012 May;40(10):4288-97. PMID: 22287627
Becker MA, Hou X, Harrington SC, Weroha SJ et al. IGFBP ratio confers resistance to IGF targeting and correlates with increased invasion and poor outcome in breast tumors. Clin Cancer Res 2012 Mar 15;18(6):1808-17. PMID: 22287600
Gyorffy B, Lánczky A, Szállási Z. Implementing an online tool for genome-wide validation of survival-associated biomarkers in ovarian-cancer using microarray data from 1287 patients. Endocr Relat Cancer 2012 Apr;19(2):197-208. PMID: 22277193
Bainbridge SA, Minhas A, Whiteley KJ, Qu D et al. Effects of reduced Gcm1 expression on trophoblast morphology, fetoplacental vascularity, and pregnancy outcomes in mice. Hypertension 2012 Mar;59(3):732-9. PMID: 22275534
Ashida S, Orloff MS, Bebek G, Zhang L et al. Integrated analysis reveals critical genomic regions in prostate tumor microenvironment associated with clinicopathologic phenotypes. Clin Cancer Res 2012 Mar 15;18(6):1578-87. PMID: 22275508
Zhang H, Li H, Xi HS, Li S. HIF1α is required for survival maintenance of chronic myeloid leukemia stem cells. Blood 2012 Mar 15;119(11):2595-607. PMID: 22275380
Wei Z, Peterson JM, Lei X, Cebotaru L et al. C1q/TNF-related protein-12 (CTRP12), a novel adipokine that improves insulin sensitivity and glycemic control in mouse models of obesity and diabetes. J Biol Chem 2012 Mar 23;287(13):10301-15. PMID: 22275362
Lynch TP, Ferrer CM, Jackson SR, Shahriari KS et al. Critical role of O-Linked β-N-acetylglucosamine transferase in prostate cancer invasion, angiogenesis, and metastasis. J Biol Chem 2012 Mar 30;287(14):11070-81. PMID: 22275356
Dhahbi JM, Atamna H, Boffelli D, Martin DI et al. mRNA-Seq reveals complex patterns of gene regulation and expression in the mouse skeletal muscle transcriptome associated with calorie restriction. Physiol Genomics 2012 Mar 19;44(6):331-44. PMID: 22274562
Montano-Almendras CP, Essaghir A, Schoemans H, Varis I et al. ETV6-PDGFRB and FIP1L1-PDGFRA stimulate human hematopoietic progenitor cell proliferation and differentiation into eosinophils: the role of nuclear factor-κB. Haematologica 2012 Jul;97(7):1064-72. PMID: 22271894
Li S, Yang X, Wu F, He Y. HYL1 controls the miR156-mediated juvenile phase of vegetative growth. J Exp Bot 2012 Apr;63(7):2787-98. PMID: 22268150
West NR, Murphy LC, Watson PH. Oncostatin M suppresses oestrogen receptor-α expression and is associated with poor outcome in human breast cancer. Endocr Relat Cancer 2012 Apr;19(2):181-95. PMID: 22267707
Jiang Z, Jhunjhunwala S, Liu J, Haverty PM et al. The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients. Genome Res 2012 Apr;22(4):593-601. PMID: 22267523
Gudmundsson J, Sulem P, Gudbjartsson DF, Jonasson JG et al. Discovery of common variants associated with low TSH levels and thyroid cancer risk. Nat Genet 2012 Jan 22;44(3):319-22. PMID: 22267200
Haibe-Kains B, Desmedt C, Loi S, Culhane AC et al. A three-gene model to robustly identify breast cancer molecular subtypes. J Natl Cancer Inst 2012 Feb 22;104(4):311-25. PMID: 22262870
Tseng GC, Ghosh D, Feingold E. Comprehensive literature review and statistical considerations for microarray meta-analysis. Nucleic Acids Res 2012 May;40(9):3785-99. PMID: 22262733
Robinson JF, Verhoef A, Piersma AH. Transcriptomic analysis of neurulation and early organogenesis in rat embryos: an in vivo and ex vivo comparison. Toxicol Sci 2012 Mar;126(1):255-66. PMID: 22262562
Lee JS, Ward WO, Knapp G, Ren H et al. Transcriptional ontogeny of the developing liver. BMC Genomics 2012 Jan 19;13:33. PMID: 22260730
Chang HH, McGeachie M. Phenotype prediction by integrative network analysis of SNP and gene expression microarrays. Conf Proc IEEE Eng Med Biol Soc 2011;2011:6849-52. PMID: 22255912
Lauterbach EC, Fontenelle LF, Teixeira AL. The neuroprotective disease-modifying potential of psychotropics in Parkinson's disease. Parkinsons Dis 2012;2012:753548. PMID: 22254151
Choi W, Shah JB, Tran M, Svatek R et al. p63 expression defines a lethal subset of muscle-invasive bladder cancers. PLoS One 2012;7(1):e30206. PMID: 22253920
Collins CC, Volik SV, Lapuk AV, Wang Y et al. Next generation sequencing of prostate cancer from a patient identifies a deficiency of methylthioadenosine phosphorylase, an exploitable tumor target. Mol Cancer Ther 2012 Mar;11(3):775-83. PMID: 22252602
Lin HH, Li X, Chen JL, Sun X et al. Identification of an AAA ATPase VPS4B-dependent pathway that modulates epidermal growth factor receptor abundance and signaling during hypoxia. Mol Cell Biol 2012 Mar;32(6):1124-38. PMID: 22252323
Li Z, Huang H, Li Y, Jiang X et al. Up-regulation of a HOXA-PBX3 homeobox-gene signature following down-regulation of miR-181 is associated with adverse prognosis in patients with cytogenetically abnormal AML. Blood 2012 Mar 8;119(10):2314-24. PMID: 22251480
Liu W, Xing F, Iiizumi-Gairani M, Okuda H et al. N-myc downstream regulated gene 1 modulates Wnt-β-catenin signalling and pleiotropically suppresses metastasis. EMBO Mol Med 2012 Feb;4(2):93-108. PMID: 22246988
Adrain C, Zettl M, Christova Y, Taylor N et al. Tumor necrosis factor signaling requires iRhom2 to promote trafficking and activation of TACE. Science 2012 Jan 13;335(6065):225-8. PMID: 22246777
Matheu A, Collado M, Wise C, Manterola L et al. Oncogenicity of the developmental transcription factor Sox9. Cancer Res 2012 Mar 1;72(5):1301-15. PMID: 22246670
Yang IV, Tomfohr J, Singh J, Foss CM et al. The clinical and environmental determinants of airway transcriptional profiles in allergic asthma. Am J Respir Crit Care Med 2012 Mar 15;185(6):620-7. PMID: 22246175
Imielinski M, Cha S, Rejtar T, Richardson EA et al. Integrated proteomic, transcriptomic, and biological network analysis of breast carcinoma reveals molecular features of tumorigenesis and clinical relapse. Mol Cell Proteomics 2012 Jun;11(6):M111.014910. PMID: 22240506
Mamtani M, Kulkarni H. Association of HADHA expression with the risk of breast cancer: targeted subset analysis and meta-analysis of microarray data. BMC Res Notes 2012 Jan 12;5:25. PMID: 22240105
Baral A, Kumar P, Halder R, Mani P et al. Quadruplex-single nucleotide polymorphisms (Quad-SNP) influence gene expression difference among individuals. Nucleic Acids Res 2012 May;40(9):3800-11. PMID: 22238381
He C, Li Z, Chen P, Huang H et al. Young intragenic miRNAs are less coexpressed with host genes than old ones: implications of miRNA-host gene coevolution. Nucleic Acids Res 2012 May;40(9):4002-12. PMID: 22238379
Klapper W, Kreuz M, Kohler CW, Burkhardt B et al. Patient age at diagnosis is associated with the molecular characteristics of diffuse large B-cell lymphoma. Blood 2012 Feb 23;119(8):1882-7. PMID: 22238326
Garcia M, Millat-Carus R, Bertucci F, Finetti P et al. Interactome-transcriptome integration for predicting distant metastasis in breast cancer. Bioinformatics 2012 Mar 1;28(5):672-8. PMID: 22238264
Yao C, Li H, Shen X, He Z et al. Reproducibility and concordance of differential DNA methylation and gene expression in cancer. PLoS One 2012;7(1):e29686. PMID: 22235325
Beverly LJ, Lockwood WW, Shah PP, Erdjument-Bromage H et al. Ubiquitination, localization, and stability of an anti-apoptotic BCL2-like protein, BCL2L10/BCLb, are regulated by Ubiquilin1. Proc Natl Acad Sci U S A 2012 Jan 17;109(3):E119-26. PMID: 22233804
Fernando MM, Freudenberg J, Lee A, Morris DL et al. Transancestral mapping of the MHC region in systemic lupus erythematosus identifies new independent and interacting loci at MSH5, HLA-DPB1 and HLA-G. Ann Rheum Dis 2012 May;71(5):777-84. PMID: 22233601
Williams G. A searchable cross-platform gene expression database reveals connections between drug treatments and disease. BMC Genomics 2012 Jan 10;13:12. PMID: 22233519
García-Hoz C, Sánchez-Fernández G, García-Escudero R, Fernández-Velasco M et al. Protein kinase C (PKC)ζ-mediated Gαq stimulation of ERK5 protein pathway in cardiomyocytes and cardiac fibroblasts. J Biol Chem 2012 Mar 2;287(10):7792-802. PMID: 22232556
Joosse SA, Hannemann J, Spötter J, Bauche A et al. Changes in keratin expression during metastatic progression of breast cancer: impact on the detection of circulating tumor cells. Clin Cancer Res 2012 Feb 15;18(4):993-1003. PMID: 22228641
Riester M, Taylor JM, Feifer A, Koppie T et al. Combination of a novel gene expression signature with a clinical nomogram improves the prediction of survival in high-risk bladder cancer. Clin Cancer Res 2012 Mar 1;18(5):1323-33. PMID: 22228636
Hook KE, Garza SJ, Lira ME, Ching KA et al. An integrated genomic approach to identify predictive biomarkers of response to the aurora kinase inhibitor PF-03814735. Mol Cancer Ther 2012 Mar;11(3):710-9. PMID: 22222631
Lattanzi W, Geloso MC, Saulnier N, Giannetti S et al. Neurotrophic features of human adipose tissue-derived stromal cells: in vitro and in vivo studies. J Biomed Biotechnol 2011;2011:468705. PMID: 22219658
Han M, Yang Z, Sayed D, He M et al. GATA4 expression is primarily regulated via a miR-26b-dependent post-transcriptional mechanism during cardiac hypertrophy. Cardiovasc Res 2012 Mar 15;93(4):645-54. PMID: 22219180
Zhao B, Li L, Wang L, Wang CY et al. Cell detachment activates the Hippo pathway via cytoskeleton reorganization to induce anoikis. Genes Dev 2012 Jan 1;26(1):54-68. PMID: 22215811
de Wit E, de Laat W. A decade of 3C technologies: insights into nuclear organization. Genes Dev 2012 Jan 1;26(1):11-24. PMID: 22215806
Brosché M, Kangasjärvi J. Low antioxidant concentrations impact on multiple signalling pathways in Arabidopsis thaliana partly through NPR1. J Exp Bot 2012 Mar;63(5):1849-61. PMID: 22213815
Bauer P, Blondet E. Transcriptome analysis of ein3 eil1 mutants in response to iron deficiency. Plant Signal Behav 2011 Nov;6(11):1669-71. PMID: 22212120
Schneider S, Smith T, Hansen U. SCOREM: statistical consolidation of redundant expression measures. Nucleic Acids Res 2012 Mar;40(6):e46. PMID: 22210887
Backes C, Rurainski A, Klau GW, Müller O et al. An integer linear programming approach for finding deregulated subgraphs in regulatory networks. Nucleic Acids Res 2012 Mar;40(6):e43. PMID: 22210863
McCall MN, Almudevar A. Affymetrix GeneChip microarray preprocessing for multivariate analyses. Brief Bioinform 2012 Sep;13(5):536-46. PMID: 22210854
Lau GJ, Godin N, Maachi H, Lo CS et al. Bcl-2-modifying factor induces renal proximal tubular cell apoptosis in diabetic mice. Diabetes 2012 Feb;61(2):474-84. PMID: 22210314
Schwindinger WF, Mirshahi UL, Baylor KA, Sheridan KM et al. Synergistic roles for G-protein γ3 and γ7 subtypes in seizure susceptibility as revealed in double knock-out mice. J Biol Chem 2012 Mar 2;287(10):7121-33. PMID: 22207761
Feldman DE, Chen C, Punj V, Tsukamoto H et al. Pluripotency factor-mediated expression of the leptin receptor (OB-R) links obesity to oncogenesis through tumor-initiating stem cells. Proc Natl Acad Sci U S A 2012 Jan 17;109(3):829-34. PMID: 22207628
Lasham A, Samuel W, Cao H, Patel R et al. YB-1, the E2F pathway, and regulation of tumor cell growth. J Natl Cancer Inst 2012 Jan 18;104(2):133-46. PMID: 22205655
Simonson MS, Tiktin M, Debanne SM, Rahman M et al. The renal transcriptome of db/db mice identifies putative urinary biomarker proteins in patients with type 2 diabetes: a pilot study. Am J Physiol Renal Physiol 2012 Apr;302(7):F820-9. PMID: 22205226
Giraud M, Yoshida H, Abramson J, Rahl PB et al. Aire unleashes stalled RNA polymerase to induce ectopic gene expression in thymic epithelial cells. Proc Natl Acad Sci U S A 2012 Jan 10;109(2):535-40. PMID: 22203960
Sankaran D, Pakala SB, Nair VS, Sirigiri DN et al. Mechanism of MTA1 protein overexpression-linked invasion: MTA1 regulation of hyaluronan-mediated motility receptor (HMMR) expression and function. J Biol Chem 2012 Feb 17;287(8):5483-91. PMID: 22203674
Planet E, Attolini CS, Reina O, Flores O et al. htSeqTools: high-throughput sequencing quality control, processing and visualization in R. Bioinformatics 2012 Feb 15;28(4):589-90. PMID: 22199381
Kobunai T, Watanabe T, Fukusato T. REG4, NEIL2, and BIRC5 gene expression correlates with gamma-radiation sensitivity in patients with rectal cancer receiving radiotherapy. Anticancer Res 2011 Dec;31(12):4147-53. PMID: 22199273
Shanahan HP, Memon FN, Upton GJ, Harrison AP. Normalized Affymetrix expression data are biased by G-quadruplex formation. Nucleic Acids Res 2012 Apr;40(8):3307-15. PMID: 22199258
Ahmadi A, Behm A, Honnalli N, Li C et al. Hobbes: optimized gram-based methods for efficient read alignment. Nucleic Acids Res 2012 Mar;40(6):e41. PMID: 22199254
Scott MS, Ono M, Yamada K, Endo A et al. Human box C/D snoRNA processing conservation across multiple cell types. Nucleic Acids Res 2012 Apr;40(8):3676-88. PMID: 22199253
Soreq L, Ben-Shaul Y, Israel Z, Bergman H et al. Meta-analysis of genetic and environmental Parkinson's disease models reveals a common role of mitochondrial protection pathways. Neurobiol Dis 2012 Mar;45(3):1018-30. PMID: 22198569
Westholm JO, Ladewig E, Okamura K, Robine N et al. Common and distinct patterns of terminal modifications to mirtrons and canonical microRNAs. RNA 2012 Feb;18(2):177-92. PMID: 22190743
Liu X, Liu ZP, Zhao XM, Chen L. Identifying disease genes and module biomarkers by differential interactions. J Am Med Inform Assoc 2012 Mar-Apr;19(2):241-8. PMID: 22190040
Wang T, Huang C, Lopez-Coral A, Slentz-Kesler KA et al. K12/SECTM1, an interferon-γ regulated molecule, synergizes with CD28 to costimulate human T cell proliferation. J Leukoc Biol 2012 Mar;91(3):449-59. PMID: 22184754
Krassovsky K, Henikoff JG, Henikoff S. Tripartite organization of centromeric chromatin in budding yeast. Proc Natl Acad Sci U S A 2012 Jan 3;109(1):243-8. PMID: 22184235
Marzook H, Li DQ, Nair VS, Mudvari P et al. Metastasis-associated protein 1 drives tumor cell migration and invasion through transcriptional repression of RING finger protein 144A. J Biol Chem 2012 Feb 17;287(8):5615-26. PMID: 22184113
Zhao JC, Yu J, Runkle C, Wu L et al. Cooperation between Polycomb and androgen receptor during oncogenic transformation. Genome Res 2012 Feb;22(2):322-31. PMID: 22179855
Kammers K, Lang M, Hengstler JG, Schmidt M et al. Survival models with preclustered gene groups as covariates. BMC Bioinformatics 2011 Dec 16;12:478. PMID: 22177110
Pascual O, Ben Achour S, Rostaing P, Triller A et al. Microglia activation triggers astrocyte-mediated modulation of excitatory neurotransmission. Proc Natl Acad Sci U S A 2012 Jan 24;109(4):E197-205. PMID: 22167804
Dozmorov MG, Giles CB, Wren JD. Predicting gene ontology from a global meta-analysis of 1-color microarray experiments. BMC Bioinformatics 2011 Oct 18;12 Suppl 10:S14. PMID: 22166114
Dozmorov MG, Wren JD. High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses. BMC Bioinformatics 2011 Oct 18;12 Suppl 10:S2. PMID: 22166002
Zhang F, Chen JY. HOMER: a human organ-specific molecular electronic repository. BMC Bioinformatics 2011 Oct 18;12 Suppl 10:S4. PMID: 22165817
Van Vlierberghe P, Ambesi-Impiombato A, Perez-Garcia A, Haydu JE et al. ETV6 mutations in early immature human T cell leukemias. J Exp Med 2011 Dec 19;208(13):2571-9. PMID: 22162831
He A, Ma Q, Cao J, von Gise A et al. Polycomb repressive complex 2 regulates normal development of the mouse heart. Circ Res 2012 Feb 3;110(3):406-15. PMID: 22158708
Chen DT, Hsu YL, Fulp WJ, Coppola D et al. Prognostic and predictive value of a malignancy-risk gene signature in early-stage non-small cell lung cancer. J Natl Cancer Inst 2011 Dec 21;103(24):1859-70. PMID: 22157961
Zhou A, Chen YI, Zane GM, He Z et al. Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol 2012 Feb;78(4):1168-77. PMID: 22156435
Kidder BL, Palmer S. HDAC1 regulates pluripotency and lineage specific transcriptional networks in embryonic and trophoblast stem cells. Nucleic Acids Res 2012 Apr;40(7):2925-39. PMID: 22156375
Mullican SE, Gaddis CA, Alenghat T, Nair MG et al. Histone deacetylase 3 is an epigenomic brake in macrophage alternative activation. Genes Dev 2011 Dec 1;25(23):2480-8. PMID: 22156208
Mendoza-Parra MA, Sankar M, Walia M, Gronemeyer H. POLYPHEMUS: R package for comparative analysis of RNA polymerase II ChIP-seq profiles by non-linear normalization. Nucleic Acids Res 2012 Feb;40(4):e30. PMID: 22156059
Chimge NO, Baniwal SK, Luo J, Coetzee S et al. Opposing effects of Runx2 and estradiol on breast cancer cell proliferation: in vitro identification of reciprocally regulated gene signature related to clinical letrozole responsiveness. Clin Cancer Res 2012 Feb 1;18(3):901-11. PMID: 22147940
Rajan S, Chu Pham Dang H, Djambazian H, Zuzan H et al. Analysis of early C2C12 myogenesis identifies stably and differentially expressed transcriptional regulators whose knock-down inhibits myoblast differentiation. Physiol Genomics 2012 Feb 1;44(2):183-97. PMID: 22147266
Tiedemann RE, Zhu YX, Schmidt J, Shi CX et al. Identification of molecular vulnerabilities in human multiple myeloma cells by RNA interference lethality screening of the druggable genome. Cancer Res 2012 Feb 1;72(3):757-68. PMID: 22147262
Jurmeister S, Baumann M, Balwierz A, Keklikoglou I et al. MicroRNA-200c represses migration and invasion of breast cancer cells by targeting actin-regulatory proteins FHOD1 and PPM1F. Mol Cell Biol 2012 Feb;32(3):633-51. PMID: 22144583
Li H, Bitler BG, Vathipadiekal V, Maradeo ME et al. ALDH1A1 is a novel EZH2 target gene in epithelial ovarian cancer identified by genome-wide approaches. Cancer Prev Res (Phila) 2012 Mar;5(3):484-91. PMID: 22144423
Mannava S, Zhuang D, Nair JR, Bansal R et al. KLF9 is a novel transcriptional regulator of bortezomib- and LBH589-induced apoptosis in multiple myeloma cells. Blood 2012 Feb 9;119(6):1450-8. PMID: 22144178
Grasso M, Fuso A, Dovere L, de Rooij DG et al. Distribution of GFRA1-expressing spermatogonia in adult mouse testis. Reproduction 2012 Mar;143(3):325-32. PMID: 22143971
Chen G, Yin K, Shi L, Fang Y et al. Comparative analysis of human protein-coding and noncoding RNAs between brain and 10 mixed cell lines by RNA-Seq. PLoS One 2011;6(11):e28318. PMID: 22140575
Ung CY, Lam SH, Zhang X, Li H et al. Existence of inverted profile in chemically responsive molecular pathways in the zebrafish liver. PLoS One 2011;6(11):e27819. PMID: 22140468
Zheng Y, Li YF, Sunkar R, Zhang W. SeqTar: an effective method for identifying microRNA guided cleavage sites from degradome of polyadenylated transcripts in plants. Nucleic Acids Res 2012 Feb;40(4):e28. PMID: 22140118
Kao S, Shiau CK, Gu DL, Ho CM et al. IGDB.NSCLC: integrated genomic database of non-small cell lung cancer. Nucleic Acids Res 2012 Jan;40(Database issue):D972-7. PMID: 22139933
Reed KR, Tunster SJ, Young M, Carrico A et al. Entopic overexpression of Ascl2 does not accelerate tumourigenesis in ApcMin mice. Gut 2012 Oct;61(10):1435-8. PMID: 22138533
Pont C, Murat F, Confolent C, Balzergue S et al. RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.). Genome Biol 2011 Dec 2;12(12):R119. PMID: 22136458
Karnovsky A, Weymouth T, Hull T, Tarcea VG et al. Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data. Bioinformatics 2012 Feb 1;28(3):373-80. PMID: 22135418
Hess KR, Wei C, Qi Y, Iwamoto T et al. Lack of sufficiently strong informative features limits the potential of gene expression analysis as predictive tool for many clinical classification problems. BMC Bioinformatics 2011 Dec 1;12:463. PMID: 22132775
Adamo B, Deal AM, Burrows E, Geradts J et al. Phosphatidylinositol 3-kinase pathway activation in breast cancer brain metastases. Breast Cancer Res 2011;13(6):R125. PMID: 22132754
Wilhite SE, Barrett T. Strategies to explore functional genomics data sets in NCBI's GEO database. Methods Mol Biol 2012;802:41-53. PMID: 22130872
Nadiminty N, Tummala R, Lou W, Zhu Y et al. MicroRNA let-7c suppresses androgen receptor expression and activity via regulation of Myc expression in prostate cancer cells. J Biol Chem 2012 Jan 6;287(2):1527-37. PMID: 22128178
Liu P, Lu Y, Liu H, Wen W et al. Genome-wide association and fine mapping of genetic loci predisposing to colon carcinogenesis in mice. Mol Cancer Res 2012 Jan;10(1):66-74. PMID: 22127497
Markert EK, Mizuno H, Vazquez A, Levine AJ. Molecular classification of prostate cancer using curated expression signatures. Proc Natl Acad Sci U S A 2011 Dec 27;108(52):21276-81. PMID: 22123976
Gellert P, Teranishi M, Jenniches K, De Gaspari P et al. Gene Array Analyzer: alternative usage of gene arrays to study alternative splicing events. Nucleic Acids Res 2012 Mar;40(6):2414-25. PMID: 22123740
Sun S, Dong X, Fu Y, Tian W. An iterative network partition algorithm for accurate identification of dense network modules. Nucleic Acids Res 2012 Feb;40(3):e18. PMID: 22121225
Kharchenko PV, Xi R, Park PJ. Evidence for dosage compensation between the X chromosome and autosomes in mammals. Nat Genet 2011 Nov 28;43(12):1167-9; author reply 1171-2. PMID: 22120048
Berman BP, Weisenberger DJ, Aman JF, Hinoue T et al. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet 2011 Nov 27;44(1):40-6. PMID: 22120008
Buler M, Aatsinki SM, Skoumal R, Komka Z et al. Energy-sensing factors coactivator peroxisome proliferator-activated receptor γ coactivator 1-α (PGC-1α) and AMP-activated protein kinase control expression of inflammatory mediators in liver: induction of interleukin 1 receptor antagonist. J Biol Chem 2012 Jan 13;287(3):1847-60. PMID: 22117073
Kang DD, Sibille E, Kaminski N, Tseng GC. MetaQC: objective quality control and inclusion/exclusion criteria for genomic meta-analysis. Nucleic Acids Res 2012 Jan;40(2):e15. PMID: 22116060
Kiebish MA, Young DM, Lehman JJ, Han X. Chronic caloric restriction attenuates a loss of sulfatide content in PGC-1α-/- mouse cortex: a potential lipidomic role of PGC-1α in neurodegeneration. J Lipid Res 2012 Feb;53(2):273-81. PMID: 22114039
Xiao W, Mindrinos MN, Seok J, Cuschieri J et al. A genomic storm in critically injured humans. J Exp Med 2011 Dec 19;208(13):2581-90. PMID: 22110166
Culhane AC, Schröder MS, Sultana R, Picard SC et al. GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. Nucleic Acids Res 2012 Jan;40(Database issue):D1060-6. PMID: 22110038
Germar K, Dose M, Konstantinou T, Zhang J et al. T-cell factor 1 is a gatekeeper for T-cell specification in response to Notch signaling. Proc Natl Acad Sci U S A 2011 Dec 13;108(50):20060-5. PMID: 22109558
Sun Y, Wang BE, Leong KG, Yue P et al. Androgen deprivation causes epithelial-mesenchymal transition in the prostate: implications for androgen-deprivation therapy. Cancer Res 2012 Jan 15;72(2):527-36. PMID: 22108827
Caldas J, Gehlenborg N, Kettunen E, Faisal A et al. Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma. Bioinformatics 2012 Jan 15;28(2):246-53. PMID: 22106335
Kim SM, Leem SH, Chu IS, Park YY et al. Sixty-five gene-based risk score classifier predicts overall survival in hepatocellular carcinoma. Hepatology 2012 May;55(5):1443-52. PMID: 22105560
Kassambara A, Hose D, Moreaux J, Walker BA et al. Genes with a spike expression are clustered in chromosome (sub)bands and spike (sub)bands have a powerful prognostic value in patients with multiple myeloma. Haematologica 2012 Apr;97(4):622-30. PMID: 22102711
Sharoni AM, Nuruzzaman M, Satoh K, Moumeni A et al. Comparative transcriptome analysis of AP2/EREBP gene family under normal and hormone treatments, and under two drought stresses in NILs setup by Aday Selection and IR64. Mol Genet Genomics 2012 Jan;287(1):1-19. PMID: 22102215
Gagnon-Bartsch JA, Speed TP. Using control genes to correct for unwanted variation in microarray data. Biostatistics 2012 Jul;13(3):539-52. PMID: 22101192
Baron D, Magot A, Ramstein G, Steenman M et al. Immune response and mitochondrial metabolism are commonly deregulated in DMD and aging skeletal muscle. PLoS One 2011;6(11):e26952. PMID: 22096509
Azab AK, Quang P, Azab F, Pitsillides C et al. P-selectin glycoprotein ligand regulates the interaction of multiple myeloma cells with the bone marrow microenvironment. Blood 2012 Feb 9;119(6):1468-78. PMID: 22096244
Dondeti VR, Wubbenhorst B, Lal P, Gordan JD et al. Integrative genomic analyses of sporadic clear cell renal cell carcinoma define disease subtypes and potential new therapeutic targets. Cancer Res 2012 Jan 1;72(1):112-21. PMID: 22094876
Park AK, Lee SJ, Phi JH, Wang KC et al. Prognostic classification of pediatric medulloblastoma based on chromosome 17p loss, expression of MYCC and MYCN, and Wnt pathway activation. Neuro Oncol 2012 Feb;14(2):203-14. PMID: 22090452
Sher N, Bell GW, Li S, Nordman J et al. Developmental control of gene copy number by repression of replication initiation and fork progression. Genome Res 2012 Jan;22(1):64-75. PMID: 22090375
Yuen HF, Chan KK, Grills C, Murray JT et al. Ran is a potential therapeutic target for cancer cells with molecular changes associated with activation of the PI3K/Akt/mTORC1 and Ras/MEK/ERK pathways. Clin Cancer Res 2012 Jan 15;18(2):380-91. PMID: 22090358
Chen Y, Gu J, Li D, Li S. Time-course network analysis reveals TNF-α can promote G1/S transition of cell cycle in vascular endothelial cells. Bioinformatics 2012 Jan 1;28(1):1-4. PMID: 22088844
Zhang X, Zhao XM, He K, Lu L et al. Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information. Bioinformatics 2012 Jan 1;28(1):98-104. PMID: 22088843
Yu T, Bai Y. Improving gene expression data interpretation by finding latent factors that co-regulate gene modules with clinical factors. BMC Genomics 2011 Nov 16;12:563. PMID: 22087761
Punshon T, Hirschi K, Yang J, Lanzirotti A et al. The role of CAX1 and CAX3 in elemental distribution and abundance in Arabidopsis seed. Plant Physiol 2012 Jan;158(1):352-62. PMID: 22086421
Bergsland M, Ramsköld D, Zaouter C, Klum S et al. Sequentially acting Sox transcription factors in neural lineage development. Genes Dev 2011 Dec 1;25(23):2453-64. PMID: 22085726
Chen EY, Xu H, Gordonov S, Lim MP et al. Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. Bioinformatics 2012 Jan 1;28(1):105-11. PMID: 22080467
Tsoi LC, Qin T, Slate EH, Zheng WJ. Consistent Differential Expression Pattern (CDEP) on microarray to identify genes related to metastatic behavior. BMC Bioinformatics 2011 Nov 11;12:438. PMID: 22078224
Marom L, Ulitsky I, Cabilly Y, Shamir R et al. A point mutation in translation initiation factor eIF2B leads to function--and time-specific changes in brain gene expression. PLoS One 2011;6(10):e26992. PMID: 22073122
Bishop CV, Satterwhite S, Xu L, Hennebold JD et al. Microarray analysis of the primate luteal transcriptome during chorionic gonadotrophin administration simulating early pregnancy. Mol Hum Reprod 2012 Apr;18(4):216-27. PMID: 22072816
Morris JH, Apeltsin L, Newman AM, Baumbach J et al. clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinformatics 2011 Nov 9;12:436. PMID: 22070249
Bhattacharya A, Roy R, Snijders AM, Hamilton G et al. Two distinct routes to oral cancer differing in genome instability and risk for cervical node metastasis. Clin Cancer Res 2011 Nov 15;17(22):7024-34. PMID: 22068658
Hulmi JJ, Silvennoinen M, Lehti M, Kivelä R et al. Altered REDD1, myostatin, and Akt/mTOR/FoxO/MAPK signaling in streptozotocin-induced diabetic muscle atrophy. Am J Physiol Endocrinol Metab 2012 Feb 1;302(3):E307-15. PMID: 22068602
Tiana M, Villar D, Pérez-Guijarro E, Gómez-Maldonado L et al. A role for insulator elements in the regulation of gene expression response to hypoxia. Nucleic Acids Res 2012 Mar;40(5):1916-27. PMID: 22067454
Hayward DC, Hetherington S, Behm CA, Grasso LC et al. Differential gene expression at coral settlement and metamorphosis--a subtractive hybridization study. PLoS One 2011;6(10):e26411. PMID: 22065994
Morris LG, Taylor BS, Bivona TG, Gong Y et al. Genomic dissection of the epidermal growth factor receptor (EGFR)/PI3K pathway reveals frequent deletion of the EGFR phosphatase PTPRS in head and neck cancers. Proc Natl Acad Sci U S A 2011 Nov 22;108(47):19024-9. PMID: 22065749
Caskey M, Lefebvre F, Filali-Mouhim A, Cameron MJ et al. Synthetic double-stranded RNA induces innate immune responses similar to a live viral vaccine in humans. J Exp Med 2011 Nov 21;208(12):2357-66. PMID: 22065672
Oh YT, Yue P, Zhou W, Balko JM et al. Oncogenic Ras and B-Raf proteins positively regulate death receptor 5 expression through co-activation of ERK and JNK signaling. J Biol Chem 2012 Jan 2;287(1):257-67. PMID: 22065586
Tonelli R, McIntyre A, Camerin C, Walters ZS et al. Antitumor activity of sustained N-myc reduction in rhabdomyosarcomas and transcriptional block by antigene therapy. Clin Cancer Res 2012 Feb 1;18(3):796-807. PMID: 22065083
Pratcorona M, Abbas S, Sanders MA, Koenders JE et al. Acquired mutations in ASXL1 in acute myeloid leukemia: prevalence and prognostic value. Haematologica 2012 Mar;97(3):388-92. PMID: 22058207
Zhao Y, Huang J. Reconstruction and analysis of human heart-specific metabolic network based on transcriptome and proteome data. Biochem Biophys Res Commun 2011 Nov 25;415(3):450-4. PMID: 22057009
Selth LA, Townley S, Gillis JL, Ochnik AM et al. Discovery of circulating microRNAs associated with human prostate cancer using a mouse model of disease. Int J Cancer 2012 Aug 1;131(3):652-61. PMID: 22052531
Caldeira J, Simões-Correia J, Paredes J, Pinto MT et al. CPEB1, a novel gene silenced in gastric cancer: a Drosophila approach. Gut 2012 Aug;61(8):1115-23. PMID: 22052064
Tuller T, Veksler-Lublinsky I, Gazit N, Kupiec M et al. Composite effects of gene determinants on the translation speed and density of ribosomes. Genome Biol 2011 Nov 3;12(11):R110. PMID: 22050731
Miller TW, Balko JM, Fox EM, Ghazoui Z et al. ERα-dependent E2F transcription can mediate resistance to estrogen deprivation in human breast cancer. Cancer Discov 2011 Sep;1(4):338-51. PMID: 22049316
McCall MN, Kent OA, Yu J, Fox-Talbot K et al. MicroRNA profiling of diverse endothelial cell types. BMC Med Genomics 2011 Nov 2;4:78. PMID: 22047531
Weber CC, Pink CJ, Hurst LD. Late-replicating domains have higher divergence and diversity in Drosophila melanogaster. Mol Biol Evol 2012 Feb;29(2):873-82. PMID: 22046001
Walker CG, Littlejohn MD, Mitchell MD, Roche JR et al. Endometrial gene expression during early pregnancy differs between fertile and subfertile dairy cow strains. Physiol Genomics 2012 Jan 18;44(1):47-58. PMID: 22045914
Kim NH, Kim HS, Kim NG, Lee I et al. p53 and microRNA-34 are suppressors of canonical Wnt signaling. Sci Signal 2011 Nov 1;4(197):ra71. PMID: 22045851
Zhao XW, van Beek EM, Schornagel K, Van der Maaden H et al. CD47-signal regulatory protein-α (SIRPα) interactions form a barrier for antibody-mediated tumor cell destruction. Proc Natl Acad Sci U S A 2011 Nov 8;108(45):18342-7. PMID: 22042861
Atwood A, DeConde R, Wang SS, Mockler TC et al. Cell-autonomous circadian clock of hepatocytes drives rhythms in transcription and polyamine synthesis. Proc Natl Acad Sci U S A 2011 Nov 8;108(45):18560-5. PMID: 22042857
Matsuyama H, Suzuki HI, Nishimori H, Noguchi M et al. miR-135b mediates NPM-ALK-driven oncogenicity and renders IL-17-producing immunophenotype to anaplastic large cell lymphoma. Blood 2011 Dec 22;118(26):6881-92. PMID: 22042699
Rackham O, Shearwood AM, Mercer TR, Davies SM et al. Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins. RNA 2011 Dec;17(12):2085-93. PMID: 22028365
Sundaram P, Hultine S, Smith LM, Dews M et al. p53-responsive miR-194 inhibits thrombospondin-1 and promotes angiogenesis in colon cancers. Cancer Res 2011 Dec 15;71(24):7490-501. PMID: 22028325
Chen JJ, Knudsen S, Mazin W, Dahlgaard J et al. A 71-gene signature of TRAIL sensitivity in cancer cells. Mol Cancer Ther 2012 Jan;11(1):34-44. PMID: 22027696
Toups MA, Pease JB, Hahn MW. No excess gene movement is detected off the avian or lepidopteran Z chromosome. Genome Biol Evol 2011;3:1381-90. PMID: 22024813
Regala RP, Justilien V, Walsh MP, Weems C et al. Matrix metalloproteinase-10 promotes Kras-mediated bronchio-alveolar stem cell expansion and lung cancer formation. PLoS One 2011;6(10):e26439. PMID: 22022614
Vatolina TY, Boldyreva LV, Demakova OV, Demakov SA et al. Identical functional organization of nonpolytene and polytene chromosomes in Drosophila melanogaster. PLoS One 2011;6(10):e25960. PMID: 22022482
Kemppinen AK, Kaprio J, Palotie A, Saarela J. Systematic review of genome-wide expression studies in multiple sclerosis. BMJ Open 2011 Jul 18;1(1):e000053. PMID: 22021740
Wang Y, He X, Ngeow J, Eng C. GATA2 negatively regulates PTEN by preventing nuclear translocation of androgen receptor and by androgen-independent suppression of PTEN transcription in breast cancer. Hum Mol Genet 2012 Feb 1;21(3):569-76. PMID: 22021428
Mathur S, Vyas S, Kapoor S, Tyagi AK. The Mediator complex in plants: structure, phylogeny, and expression profiling of representative genes in a dicot (Arabidopsis) and a monocot (rice) during reproduction and abiotic stress. Plant Physiol 2011 Dec;157(4):1609-27. PMID: 22021418
Raiber EA, Kranaster R, Lam E, Nikan M et al. A non-canonical DNA structure is a binding motif for the transcription factor SP1 in vitro. Nucleic Acids Res 2012 Feb;40(4):1499-508. PMID: 22021377
Nakagawa M, Shimabe M, Watanabe-Okochi N, Arai S et al. AML1/RUNX1 functions as a cytoplasmic attenuator of NF-κB signaling in the repression of myeloid tumors. Blood 2011 Dec 15;118(25):6626-37. PMID: 22021368
Deng X, Hiatt JB, Nguyen DK, Ercan S et al. Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nat Genet 2011 Oct 23;43(12):1179-85. PMID: 22019781
Hu Y, Galkin AV, Wu C, Reddy V et al. CAFET algorithm reveals Wnt/PCP signature in lung squamous cell carcinoma. PLoS One 2011;6(10):e25807. PMID: 22016777
Chang CY, Kazmin D, Jasper JS, Kunder R et al. The metabolic regulator ERRα, a downstream target of HER2/IGF-1R, as a therapeutic target in breast cancer. Cancer Cell 2011 Oct 18;20(4):500-10. PMID: 22014575
Dancik GM, Ru Y, Owens CR, Theodorescu D. A framework to select clinically relevant cancer cell lines for investigation by establishing their molecular similarity with primary human cancers. Cancer Res 2011 Dec 15;71(24):7398-409. PMID: 22012889
Hollenhorst PC, Ferris MW, Hull MA, Chae H et al. Oncogenic ETS proteins mimic activated RAS/MAPK signaling in prostate cells. Genes Dev 2011 Oct 15;25(20):2147-57. PMID: 22012618
Schlage WK, Westra JW, Gebel S, Catlett NL et al. A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue. BMC Syst Biol 2011 Oct 19;5:168. PMID: 22011616
Enroth S, Rada-Iglesisas A, Andersson R, Wallerman O et al. Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa. BMC Cancer 2011 Oct 19;11:450. PMID: 22011431
La Salle S, Palmer K, O'Brien M, Schimenti JC et al. Spata22, a novel vertebrate-specific gene, is required for meiotic progress in mouse germ cells. Biol Reprod 2012 Feb;86(2):45. PMID: 22011390
Elo LL, Kallio A, Laajala TD, Hawkins RD et al. Optimized detection of transcription factor-binding sites in ChIP-seq experiments. Nucleic Acids Res 2012 Jan;40(1):e1. PMID: 22009681
Blomster T, Salojärvi J, Sipari N, Brosché M et al. Apoplastic reactive oxygen species transiently decrease auxin signaling and cause stress-induced morphogenic response in Arabidopsis. Plant Physiol 2011 Dec;157(4):1866-83. PMID: 22007024
Sasaki Y, Negishi H, Idogawa M, Yokota I et al. p53 negatively regulates the hepatoma growth factor HDGF. Cancer Res 2011 Nov 15;71(22):7038-47. PMID: 22006999
Shehadeh LA, Webster KA, Hare JM, Vazquez-Padron RI. Dynamic regulation of vascular myosin light chain (MYL9) with injury and aging. PLoS One 2011;6(10):e25855. PMID: 22003410
Cesana M, Cacchiarelli D, Legnini I, Santini T et al. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 2011 Oct 14;147(2):358-69. PMID: 22000014
Thorsen K, Schepeler T, Øster B, Rasmussen MH et al. Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis. BMC Genomics 2011 Oct 14;12:505. PMID: 21999571
Garcia H, Fleyshman D, Kolesnikova K, Safina A et al. Expression of FACT in mammalian tissues suggests its role in maintaining of undifferentiated state of cells. Oncotarget 2011 Oct;2(10):783-96. PMID: 21998152
Leung JY, Andrechek ER, Cardiff RD, Nevins JR. Heterogeneity in MYC-induced mammary tumors contributes to escape from oncogene dependence. Oncogene 2012 May 17;31(20):2545-54. PMID: 21996730
Boyd KD, Ross FM, Walker BA, Wardell CP et al. Mapping of chromosome 1p deletions in myeloma identifies FAM46C at 1p12 and CDKN2C at 1p32.3 as being genes in regions associated with adverse survival. Clin Cancer Res 2011 Dec 15;17(24):7776-84. PMID: 21994415
Birsoy K, Berry R, Wang T, Ceyhan O et al. Analysis of gene networks in white adipose tissue development reveals a role for ETS2 in adipogenesis. Development 2011 Nov;138(21):4709-19. PMID: 21989915
Beyer SJ, Zhang X, Jimenez RE, Lee ML et al. Microarray analysis of genes associated with cell surface NIS protein levels in breast cancer. BMC Res Notes 2011 Oct 11;4:397. PMID: 21989294
Reis PP, Waldron L, Perez-Ordonez B, Pintilie M et al. A gene signature in histologically normal surgical margins is predictive of oral carcinoma recurrence. BMC Cancer 2011 Oct 11;11:437. PMID: 21989116
Krawetz SA, Kruger A, Lalancette C, Tagett R et al. A survey of small RNAs in human sperm. Hum Reprod 2011 Dec;26(12):3401-12. PMID: 21989093
Poschet G, Hannich B, Raab S, Jungkunz I et al. A novel Arabidopsis vacuolar glucose exporter is involved in cellular sugar homeostasis and affects the composition of seed storage compounds. Plant Physiol 2011 Dec;157(4):1664-76. PMID: 21984725
Tong Y, Zhou J, Mizutani J, Fukuoka H et al. CEBPD suppresses prolactin expression and prolactinoma cell proliferation. Mol Endocrinol 2011 Nov;25(11):1880-91. PMID: 21980073
Leacock SW, Basse AN, Chandler GL, Kirk AM et al. A zebrafish transgenic model of Ewing's sarcoma reveals conserved mediators of EWS-FLI1 tumorigenesis. Dis Model Mech 2012 Jan;5(1):95-106. PMID: 21979944
Ma C, Zhou Y, Huang SH. Inequalities and duality in gene coexpression networks of HIV-1 infection revealed by the combination of the double-connectivity approach and the Gini's method. J Biomed Biotechnol 2011;2011:926407. PMID: 21976970
Li X, Wang Q, Zheng Y, Lv S et al. Prioritizing human cancer microRNAs based on genes' functional consistency between microRNA and cancer. Nucleic Acids Res 2011 Dec;39(22):e153. PMID: 21976726
Sanz-Pamplona R, Cordero D, Berenguer A, Lejbkowicz F et al. Gene expression differences between colon and rectum tumors. Clin Cancer Res 2011 Dec 1;17(23):7303-12. PMID: 21976543
Govin J, Gaucher J, Ferro M, Debernardi A et al. Proteomic strategy for the identification of critical actors in reorganization of the post-meiotic male genome. Mol Hum Reprod 2012 Jan;18(1):1-13. PMID: 21971310
Wexler EM, Rosen E, Lu D, Osborn GE et al. Genome-wide analysis of a Wnt1-regulated transcriptional network implicates neurodegenerative pathways. Sci Signal 2011 Oct 4;4(193):ra65. PMID: 21971039
Emig D, Kacprowski T, Albrecht M. Measuring and analyzing tissue specificity of human genes and protein complexes. EURASIP J Bioinform Syst Biol 2011 Aug 4;2011(1):5. PMID: 21970702
Haughian JM, Pinto MP, Harrell JC, Bliesner BS et al. Maintenance of hormone responsiveness in luminal breast cancers by suppression of Notch. Proc Natl Acad Sci U S A 2012 Feb 21;109(8):2742-7. PMID: 21969591
Hu Y, Chopra V, Chopra R, Locascio JJ et al. Transcriptional modulator H2A histone family, member Y (H2AFY) marks Huntington disease activity in man and mouse. Proc Natl Acad Sci U S A 2011 Oct 11;108(41):17141-6. PMID: 21969577
Magombedze G, Mulder N. A mathematical representation of the development of Mycobacterium tuberculosis active, latent and dormant stages. J Theor Biol 2012 Jan 7;292:44-59. PMID: 21968442
Oh K, Ko E, Kim HS, Park AK et al. Transglutaminase 2 facilitates the distant hematogenous metastasis of breast cancer by modulating interleukin-6 in cancer cells. Breast Cancer Res 2011 Oct 3;13(5):R96. PMID: 21967801
Engreitz JM, Chen R, Morgan AA, Dudley JT et al. ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression. Bioinformatics 2011 Dec 1;27(23):3317-8. PMID: 21967760
Ha DG, Merritt JH, Hampton TH, Hodgkinson JT et al. 2-Heptyl-4-quinolone, a precursor of the Pseudomonas quinolone signal molecule, modulates swarming motility in Pseudomonas aeruginosa. J Bacteriol 2011 Dec;193(23):6770-80. PMID: 21965567
Theis JL, Sharpe KM, Matsumoto ME, Chai HS et al. Homozygosity mapping and exome sequencing reveal GATAD1 mutation in autosomal recessive dilated cardiomyopathy. Circ Cardiovasc Genet 2011 Dec;4(6):585-94. PMID: 21965549
Maravillas-Montero JL, Santos-Argumedo L. The myosin family: unconventional roles of actin-dependent molecular motors in immune cells. J Leukoc Biol 2012 Jan;91(1):35-46. PMID: 21965174
Stott-Miller M, Houck JR, Lohavanichbutr P, Méndez E et al. Tumor and salivary matrix metalloproteinase levels are strong diagnostic markers of oral squamous cell carcinoma. Cancer Epidemiol Biomarkers Prev 2011 Dec;20(12):2628-36. PMID: 21960692
Kodesh E, Nesher N, Simaan A, Hochner B et al. Heat acclimation and exercise training interact when combined in an overriding and trade-off manner: physiologic-genomic linkage. Am J Physiol Regul Integr Comp Physiol 2011 Dec;301(6):R1786-97. PMID: 21957158
Zhang L, Ju X, Cheng Y, Guo X et al. Identifying Tmem59 related gene regulatory network of mouse neural stem cell from a compendium of expression profiles. BMC Syst Biol 2011 Sep 29;5:152. PMID: 21955788
Hench VK, Su L. Regulation of IL-2 gene expression by Siva and FOXP3 in human T cells. BMC Immunol 2011 Sep 28;12:54. PMID: 21955384
Kempster SL, Belteki G, Licence D, Charnock-Jones DS et al. Disruption of paraoxonase 3 impairs proliferation and antioxidant defenses in human A549 cells and causes embryonic lethality in mice. Am J Physiol Endocrinol Metab 2012 Jan 1;302(1):E103-7. PMID: 21952037
Gower AC, Spira A, Lenburg ME. Discovering biological connections between experimental conditions based on common patterns of differential gene expression. BMC Bioinformatics 2011 Sep 27;12:381. PMID: 21951600
Cui H, Hao Y, Kovtun M, Stolc V et al. Genome-wide direct target analysis reveals a role for SHORT-ROOT in root vascular patterning through cytokinin homeostasis. Plant Physiol 2011 Nov;157(3):1221-31. PMID: 21951467
Schmidt A, Wuest SE, Vijverberg K, Baroux C et al. Transcriptome analysis of the Arabidopsis megaspore mother cell uncovers the importance of RNA helicases for plant germline development. PLoS Biol 2011 Sep;9(9):e1001155. PMID: 21949639
Crozat K, Tamoutounour S, Vu Manh TP, Fossum E et al. Cutting edge: expression of XCR1 defines mouse lymphoid-tissue resident and migratory dendritic cells of the CD8α+ type. J Immunol 2011 Nov 1;187(9):4411-5. PMID: 21948982
Wilson BA, Masel J. Putatively noncoding transcripts show extensive association with ribosomes. Genome Biol Evol 2011;3:1245-52. PMID: 21948395
Park J, Xu K, Park T, Yi SV. What are the determinants of gene expression levels and breadths in the human genome? Hum Mol Genet 2012 Jan 1;21(1):46-56. PMID: 21945885
Xiong Q, Ancona N, Hauser ER, Mukherjee S et al. Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets. Genome Res 2012 Feb;22(2):386-97. PMID: 21940837
Nanty L, Carbajosa G, Heap GA, Ratnieks F et al. Comparative methylomics reveals gene-body H3K36me3 in Drosophila predicts DNA methylation and CpG landscapes in other invertebrates. Genome Res 2011 Nov;21(11):1841-50. PMID: 21940836
Hägerstrand D, He X, Bradic Lindh M, Hoefs S et al. Identification of a SOX2-dependent subset of tumor- and sphere-forming glioblastoma cells with a distinct tyrosine kinase inhibitor sensitivity profile. Neuro Oncol 2011 Nov;13(11):1178-91. PMID: 21940738
Keller PJ, Arendt LM, Skibinski A, Logvinenko T et al. Defining the cellular precursors to human breast cancer. Proc Natl Acad Sci U S A 2012 Feb 21;109(8):2772-7. PMID: 21940501
Noordermeer SM, Sanders MA, Gilissen C, Tönnissen E et al. High BRE expression predicts favorable outcome in adult acute myeloid leukemia, in particular among MLL-AF9-positive patients. Blood 2011 Nov 17;118(20):5613-21. PMID: 21937695
Wey S, Luo B, Tseng CC, Ni M et al. Inducible knockout of GRP78/BiP in the hematopoietic system suppresses Pten-null leukemogenesis and AKT oncogenic signaling. Blood 2012 Jan 19;119(3):817-25. PMID: 21937694
Kim SH, Park YY, Kim SW, Lee JS et al. ANGPTL4 induction by prostaglandin E2 under hypoxic conditions promotes colorectal cancer progression. Cancer Res 2011 Nov 15;71(22):7010-20. PMID: 21937683
Mamessier E, Sylvain A, Bertucci F, Castellano R et al. Human breast tumor cells induce self-tolerance mechanisms to avoid NKG2D-mediated and DNAM-mediated NK cell recognition. Cancer Res 2011 Nov 1;71(21):6621-32. PMID: 21937679
Taminau J, Steenhoff D, Coletta A, Meganck S et al. inSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO. Bioinformatics 2011 Nov 15;27(22):3204-5. PMID: 21937664
Lu TP, Lai LC, Tsai MH, Chen PC et al. Integrated analyses of copy number variations and gene expression in lung adenocarcinoma. PLoS One 2011;6(9):e24829. PMID: 21935476
Claerhout S, Lim JY, Choi W, Park YY et al. Gene expression signature analysis identifies vorinostat as a candidate therapy for gastric cancer. PLoS One 2011;6(9):e24662. PMID: 21931799
Gonin J, Larousserie F, Bastard C, Picquenot JM et al. Epstein-Barr virus-induced gene 3 (EBI3): a novel diagnosis marker in Burkitt lymphoma and diffuse large B-cell lymphoma. PLoS One 2011;6(9):e24617. PMID: 21931777
Somwar R, Erdjument-Bromage H, Larsson E, Shum D et al. Superoxide dismutase 1 (SOD1) is a target for a small molecule identified in a screen for inhibitors of the growth of lung adenocarcinoma cell lines. Proc Natl Acad Sci U S A 2011 Sep 27;108(39):16375-80. PMID: 21930909
Liu K, Ling S, Lin WC. TopBP1 mediates mutant p53 gain of function through NF-Y and p63/p73. Mol Cell Biol 2011 Nov;31(22):4464-81. PMID: 21930790
Miura K, Matsuo J, Rahman MA, Kumagai Y et al. Ehrlichia chaffeensis induces monocyte inflammatory responses through MyD88, ERK, and NF-κB but not through TRIF, interleukin-1 receptor 1 (IL-1R1)/IL-18R1, or toll-like receptors. Infect Immun 2011 Dec;79(12):4947-56. PMID: 21930764
Cheng C, Gerstein M. Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells. Nucleic Acids Res 2012 Jan;40(2):553-68. PMID: 21926158
Bai J, Hu S. Transcriptome network analysis reveals potential candidate genes for squamous lung cancer. Int J Mol Med 2012 Jan;29(1):95-101. PMID: 21922129
Engelmann JC, Deeken R, Müller T, Nimtz G et al. Is gene activity in plant cells affected by UMTS-irradiation? A whole genome approach. Adv Appl Bioinform Chem 2008;1:71-83. PMID: 21918607
Knouf EC, Garg K, Arroyo JD, Correa Y et al. An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription. Nucleic Acids Res 2012 Jan;40(2):499-510. PMID: 21917857
Neri P, Ren L, Gratton K, Stebner E et al. Bortezomib-induced "BRCAness" sensitizes multiple myeloma cells to PARP inhibitors. Blood 2011 Dec 8;118(24):6368-79. PMID: 21917757
Tsankov A, Yanagisawa Y, Rhind N, Regev A et al. Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization. Genome Res 2011 Nov;21(11):1851-62. PMID: 21914852
Sima C, Braga-Neto UM, Dougherty ER. High-dimensional bolstered error estimation. Bioinformatics 2011 Nov 1;27(21):3056-64. PMID: 21914630
Zhao J, Yang TH, Huang Y, Holme P. Ranking candidate disease genes from gene expression and protein interaction: a Katz-centrality based approach. PLoS One 2011;6(9):e24306. PMID: 21912686
Martens GA, Jiang L, Hellemans KH, Stangé G et al. Clusters of conserved beta cell marker genes for assessment of beta cell phenotype. PLoS One 2011;6(9):e24134. PMID: 21912665
Hurtz C, Hatzi K, Cerchietti L, Braig M et al. BCL6-mediated repression of p53 is critical for leukemia stem cell survival in chronic myeloid leukemia. J Exp Med 2011 Oct 24;208(11):2163-74. PMID: 21911423
Calvanese V, Fernández AF, Urdinguio RG, Suárez-Alvarez B et al. A promoter DNA demethylation landscape of human hematopoietic differentiation. Nucleic Acids Res 2012 Jan;40(1):116-31. PMID: 21911366
Friedländer MR, Mackowiak SD, Li N, Chen W et al. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res 2012 Jan;40(1):37-52. PMID: 21911355
Turan N, Kalko S, Stincone A, Clarke K et al. A systems biology approach identifies molecular networks defining skeletal muscle abnormalities in chronic obstructive pulmonary disease. PLoS Comput Biol 2011 Sep;7(9):e1002129. PMID: 21909251
Kristensen VN, Vaske CJ, Ursini-Siegel J, Van Loo P et al. Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling. Proc Natl Acad Sci U S A 2012 Feb 21;109(8):2802-7. PMID: 21908711
Li ZH, Liu YF, Li KN, Duanmu HZ et al. Analysis of functional and pathway association of differential co-expressed genes: a case study in drug addiction. J Biomed Inform 2012 Feb;45(1):30-6. PMID: 21907308
Arora H, Qureshi R, Park AK, Park WY. Coordinated regulation of ATF2 by miR-26b in γ-irradiated lung cancer cells. PLoS One 2011;6(8):e23802. PMID: 21901137
Ly-Huynh JD, Lieu KG, Major AT, Whiley PA et al. Importin alpha2-interacting proteins with nuclear roles during mammalian spermatogenesis. Biol Reprod 2011 Dec;85(6):1191-202. PMID: 21900684
Ahn YH, Yang Y, Gibbons DL, Creighton CJ et al. Map2k4 functions as a tumor suppressor in lung adenocarcinoma and inhibits tumor cell invasion by decreasing peroxisome proliferator-activated receptor γ2 expression. Mol Cell Biol 2011 Nov;31(21):4270-85. PMID: 21896780
Spradling AC, Bellen HJ, Hoskins RA. Drosophila P elements preferentially transpose to replication origins. Proc Natl Acad Sci U S A 2011 Sep 20;108(38):15948-53. PMID: 21896744
Soto-Girón MJ, García-Vallejo F. Changes in the topology of gene expression networks by human immunodeficiency virus type 1 (HIV-1) integration in macrophages. Virus Res 2012 Jan;163(1):91-7. PMID: 21896293
Fang Z, Tian W, Ji H. A network-based gene-weighting approach for pathway analysis. Cell Res 2012 Mar;22(3):565-80. PMID: 21894192
Shi M, Zhang B. Semi-supervised learning improves gene expression-based prediction of cancer recurrence. Bioinformatics 2011 Nov 1;27(21):3017-23. PMID: 21893520
Agnelli L, Forcato M, Ferrari F, Tuana G et al. The reconstruction of transcriptional networks reveals critical genes with implications for clinical outcome of multiple myeloma. Clin Cancer Res 2011 Dec 1;17(23):7402-12. PMID: 21890453
Goel M, Sienkiewicz AE, Picciani R, Lee RK et al. Cochlin induced TREK-1 co-expression and annexin A2 secretion: role in trabecular meshwork cell elongation and motility. PLoS One 2011;6(8):e23070. PMID: 21886777
Gulsuner S, Tekinay AB, Doerschner K, Boyaci H et al. Homozygosity mapping and targeted genomic sequencing reveal the gene responsible for cerebellar hypoplasia and quadrupedal locomotion in a consanguineous kindred. Genome Res 2011 Dec;21(12):1995-2003. PMID: 21885617
Hwang PI, Wu HB, Wang CD, Lin BL et al. Tissue-specific gene expression templates for accurate molecular characterization of the normal physiological states of multiple human tissues with implication in development and cancer studies. BMC Genomics 2011 Sep 1;12:439. PMID: 21880155
Aue G, Du Y, Cleveland SM, Smith SB et al. Sox4 cooperates with PU.1 haploinsufficiency in murine myeloid leukemia. Blood 2011 Oct 27;118(17):4674-81. PMID: 21878674
Sommariva M, De Cecco L, De Cesare M, Sfondrini L et al. TLR9 agonists oppositely modulate DNA repair genes in tumor versus immune cells and enhance chemotherapy effects. Cancer Res 2011 Oct 15;71(20):6382-90. PMID: 21878529
Orr KS, Shi Z, Brown WM, O'Hagan KA et al. Potential prognostic marker ubiquitin carboxyl-terminal hydrolase-L1 does not predict patient survival in non-small cell lung carcinoma. J Exp Clin Cancer Res 2011 Aug 30;30:79. PMID: 21878121
Jagannathan V, Robinson-Rechavi M. Meta-analysis of estrogen response in MCF-7 distinguishes early target genes involved in signaling and cell proliferation from later target genes involved in cell cycle and DNA repair. BMC Syst Biol 2011 Aug 30;5:138. PMID: 21878096
Kleger A, Liebau S, Lin Q, von Wichert G et al. The impact of bioactive lipids on cardiovascular development. Stem Cells Int 2011;2011:916180. PMID: 21876704
Zhang ZZ, Liu X, Wang DQ, Teng MK et al. Hepatitis B virus and hepatocellular carcinoma at the miRNA level. World J Gastroenterol 2011 Jul 28;17(28):3353-8. PMID: 21876625
Viatour P, Ehmer U, Saddic LA, Dorrell C et al. Notch signaling inhibits hepatocellular carcinoma following inactivation of the RB pathway. J Exp Med 2011 Sep 26;208(10):1963-76. PMID: 21875955
Ivanov R, Brumbarova T, Bauer P. Fitting into the harsh reality: regulation of iron-deficiency responses in dicotyledonous plants. Mol Plant 2012 Jan;5(1):27-42. PMID: 21873619
Morganella S, Pagnotta SM, Ceccarelli M. Finding recurrent copy number alterations preserving within-sample homogeneity. Bioinformatics 2011 Nov 1;27(21):2949-56. PMID: 21873327
Wang L, Brugge JS, Janes KA. Intersection of FOXO- and RUNX1-mediated gene expression programs in single breast epithelial cells during morphogenesis and tumor progression. Proc Natl Acad Sci U S A 2011 Oct 4;108(40):E803-12. PMID: 21873240
Hicks C, Asfour R, Pannuti A, Miele L. An integrative genomics approach to biomarker discovery in breast cancer. Cancer Inform 2011;10:185-204. PMID: 21869864
Pan D, Kocherginsky M, Conzen SD. Activation of the glucocorticoid receptor is associated with poor prognosis in estrogen receptor-negative breast cancer. Cancer Res 2011 Oct 15;71(20):6360-70. PMID: 21868756
Ellegren H. Emergence of male-biased genes on the chicken Z-chromosome: sex-chromosome contrasts between male and female heterogametic systems. Genome Res 2011 Dec;21(12):2082-6. PMID: 21868722
Lee YS, Chao A, Chen CH, Chou T et al. Analysis of human meiotic recombination events with a parent-sibling tracing approach. BMC Genomics 2011 Aug 26;12:434. PMID: 21867557
Marshall E, Lowrey J, MacPherson S, Maybin JA et al. In silico analysis identifies a novel role for androgens in the regulation of human endometrial apoptosis. J Clin Endocrinol Metab 2011 Nov;96(11):E1746-55. PMID: 21865353
Lamers F, van der Ploeg I, Schild L, Ebus ME et al. Knockdown of survivin (BIRC5) causes apoptosis in neuroblastoma via mitotic catastrophe. Endocr Relat Cancer 2011 Oct;18(6):657-68. PMID: 21859926
Mareschal S, Lanic H, Ruminy P, Bastard C et al. The proportion of activated B-cell like subtype among de novo diffuse large B-cell lymphoma increases with age. Haematologica 2011 Dec;96(12):1888-90. PMID: 21859735
Bourgo RJ, Thangavel C, Ertel A, Bergseid J et al. RB restricts DNA damage-initiated tumorigenesis through an LXCXE-dependent mechanism of transcriptional control. Mol Cell 2011 Aug 19;43(4):663-72. PMID: 21855804
Koth LL, Solberg OD, Peng JC, Bhakta NR et al. Sarcoidosis blood transcriptome reflects lung inflammation and overlaps with tuberculosis. Am J Respir Crit Care Med 2011 Nov 15;184(10):1153-63. PMID: 21852540
Sirota M, Dudley JT, Kim J, Chiang AP et al. Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med 2011 Aug 17;3(96):96ra77. PMID: 21849665
Dudley JT, Sirota M, Shenoy M, Pai RK et al. Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Sci Transl Med 2011 Aug 17;3(96):96ra76. PMID: 21849664
Hao H, Tummala P, Guzman E, Mali RS et al. The transcription factor neural retina leucine zipper (NRL) controls photoreceptor-specific expression of myocyte enhancer factor Mef2c from an alternative promoter. J Biol Chem 2011 Oct 7;286(40):34893-902. PMID: 21849497
Nozaki T, Yachie N, Ogawa R, Kratz A et al. Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification. BMC Genomics 2011 Aug 17;12:416. PMID: 21846408
Chowdhury N. Histopathological and genomic grading provide complementary prognostic information in breast cancer: a study on publicly available datasets. Patholog Res Int 2011;2011:890938. PMID: 21845210
Tomikawa J, Shimokawa H, Uesaka M, Yamamoto N et al. Single-stranded noncoding RNAs mediate local epigenetic alterations at gene promoters in rat cell lines. J Biol Chem 2011 Oct 7;286(40):34788-99. PMID: 21844201
Young JC, Major AT, Miyamoto Y, Loveland KL et al. Distinct effects of importin α2 and α4 on Oct3/4 localization and expression in mouse embryonic stem cells. FASEB J 2011 Nov;25(11):3958-65. PMID: 21840941
Mahmoudi M, Laurent S, Shokrgozar MA, Hosseinkhani M. Toxicity evaluations of superparamagnetic iron oxide nanoparticles: cell "vision" versus physicochemical properties of nanoparticles. ACS Nano 2011 Sep 27;5(9):7263-76. PMID: 21838310
Mestdagh P, Lefever S, Pattyn F, Ridzon D et al. The microRNA body map: dissecting microRNA function through integrative genomics. Nucleic Acids Res 2011 Nov 1;39(20):e136. PMID: 21835775
Sin S, Bonin F, Petit V, Meseure D et al. Role of the focal adhesion protein kindlin-1 in breast cancer growth and lung metastasis. J Natl Cancer Inst 2011 Sep 7;103(17):1323-37. PMID: 21832234
Barth AS, Kumordzie A, Frangakis C, Margulies KB et al. Reciprocal transcriptional regulation of metabolic and signaling pathways correlates with disease severity in heart failure. Circ Cardiovasc Genet 2011 Oct;4(5):475-83. PMID: 21828333
Woo AJ, Kim J, Xu J, Huang H et al. Role of ZBP-89 in human globin gene regulation and erythroid differentiation. Blood 2011 Sep 29;118(13):3684-93. PMID: 21828133
Andersson ER, Sandberg R, Lendahl U. Notch signaling: simplicity in design, versatility in function. Development 2011 Sep;138(17):3593-612. PMID: 21828089
Cruchaga C, Nowotny P, Kauwe JS, Ridge PG et al. Association and expression analyses with single-nucleotide polymorphisms in TOMM40 in Alzheimer disease. Arch Neurol 2011 Aug;68(8):1013-9. PMID: 21825236
Hwang T, Zhang W, Xie M, Liu J et al. Inferring disease and gene set associations with rank coherence in networks. Bioinformatics 2011 Oct 1;27(19):2692-9. PMID: 21824970
Park D, Jeong HO, Kim BC, Ha YM et al. Computational approach to identify enzymes that are potential therapeutic candidates for psoriasis. Enzyme Res 2011;2011:826784. PMID: 21822480
Chang AY, Liao BY. DNA methylation rebalances gene dosage after mammalian gene duplications. Mol Biol Evol 2012 Jan;29(1):133-44. PMID: 21821837
Esposito N, Colavita I, Quintarelli C, Sica AR et al. SHP-1 expression accounts for resistance to imatinib treatment in Philadelphia chromosome-positive cells derived from patients with chronic myeloid leukemia. Blood 2011 Sep 29;118(13):3634-44. PMID: 21821701
Krig SR, Frietze S, Simion C, Miller JK et al. Lrig1 is an estrogen-regulated growth suppressor and correlates with longer relapse-free survival in ERα-positive breast cancer. Mol Cancer Res 2011 Oct;9(10):1406-17. PMID: 21821674
Noh M, Smith JL, Huh YH, Sherley JL. A resource for discovering specific and universal biomarkers for distributed stem cells. PLoS One 2011;6(7):e22077. PMID: 21818293
Sanford T, Chung PH, Reinish A, Valera V et al. Molecular sub-classification of renal epithelial tumors using meta-analysis of gene expression microarrays. PLoS One 2011;6(7):e21260. PMID: 21818257
Jiang L, Schlesinger F, Davis CA, Zhang Y et al. Synthetic spike-in standards for RNA-seq experiments. Genome Res 2011 Sep;21(9):1543-51. PMID: 21816910
Huff CD, Witherspoon DJ, Zhang Y, Gatenbee C et al. Crohn's disease and genetic hitchhiking at IBD5. Mol Biol Evol 2012 Jan;29(1):101-11. PMID: 21816865
Martin MM, Ryan M, Kim R, Zakas AL et al. Genome-wide depletion of replication initiation events in highly transcribed regions. Genome Res 2011 Nov;21(11):1822-32. PMID: 21813623
Hollink IH, van den Heuvel-Eibrink MM, Arentsen-Peters ST, Pratcorona M et al. NUP98/NSD1 characterizes a novel poor prognostic group in acute myeloid leukemia with a distinct HOX gene expression pattern. Blood 2011 Sep 29;118(13):3645-56. PMID: 21813447
Taft RJ, Hawkins PG, Mattick JS, Morris KV. The relationship between transcription initiation RNAs and CCCTC-binding factor (CTCF) localization. Epigenetics Chromatin 2011 Aug 3;4:13. PMID: 21813016
Geertz M, Travers A, Mehandziska S, Sobetzko P et al. Structural coupling between RNA polymerase composition and DNA supercoiling in coordinating transcription: a global role for the omega subunit? MBio 2011;2(4). PMID: 21810966
Kato M, Chen X, Inukai S, Zhao H et al. Age-associated changes in expression of small, noncoding RNAs, including microRNAs, in C. elegans. RNA 2011 Oct;17(10):1804-20. PMID: 21810936
Kossenkov AV, Vachani A, Chang C, Nichols C et al. Resection of non-small cell lung cancers reverses tumor-induced gene expression changes in the peripheral immune system. Clin Cancer Res 2011 Sep 15;17(18):5867-77. PMID: 21807633
Chern SR, Li SH, Chiu CL, Chang HH et al. Spatiotemporal expression of SERPINE2 in the human placenta and its role in extravillous trophoblast migration and invasion. Reprod Biol Endocrinol 2011 Aug 2;9:106. PMID: 21806836
Coyne MJ, Fletcher CM, Reinap B, Comstock LE. UDP-glucuronic acid decarboxylases of Bacteroides fragilis and their prevalence in bacteria. J Bacteriol 2011 Oct;193(19):5252-9. PMID: 21804000
Huang W, Umbach DM, Vincent Jordan N, Abell AN et al. Efficiently identifying genome-wide changes with next-generation sequencing data. Nucleic Acids Res 2011 Oct;39(19):e130. PMID: 21803788
Trinh XB, Tjalma WA, Dirix LY, Vermeulen PB et al. Microarray-based oncogenic pathway profiling in advanced serous papillary ovarian carcinoma. PLoS One 2011;6(7):e22469. PMID: 21799864
Childs KL, Davidson RM, Buell CR. Gene coexpression network analysis as a source of functional annotation for rice genes. PLoS One 2011;6(7):e22196. PMID: 21799793
Miller S, Rogers HA, Lyon P, Rand V et al. Genome-wide molecular characterization of central nervous system primitive neuroectodermal tumor and pineoblastoma. Neuro Oncol 2011 Aug;13(8):866-79. PMID: 21798848
Al-Mayhani MT, Grenfell R, Narita M, Piccirillo S et al. NG2 expression in glioblastoma identifies an actively proliferating population with an aggressive molecular signature. Neuro Oncol 2011 Aug;13(8):830-45. PMID: 21798846
Zarrabi K, Dufour A, Li J, Kuscu C et al. Inhibition of matrix metalloproteinase 14 (MMP-14)-mediated cancer cell migration. J Biol Chem 2011 Sep 23;286(38):33167-77. PMID: 21795678
Coward J, Kulbe H, Chakravarty P, Leader D et al. Interleukin-6 as a therapeutic target in human ovarian cancer. Clin Cancer Res 2011 Sep 15;17(18):6083-96. PMID: 21795409
Xia K, Liu T, Ouyang J, Wang R et al. Genome-wide identification, classification, and expression analysis of autophagy-associated gene homologues in rice (Oryza sativa L.). DNA Res 2011 Oct;18(5):363-77. PMID: 21795261
Scheubert L, Schmidt R, Repsilber D, Lustrek M et al. Learning biomarkers of pluripotent stem cells in mouse. DNA Res 2011 Aug;18(4):233-51. PMID: 21791477
Harten SK, Esteban MA, Shukla D, Ashcroft M et al. Inactivation of the von Hippel-Lindau tumour suppressor gene induces Neuromedin U expression in renal cancer cells. Mol Cancer 2011 Jul 26;10:89. PMID: 21791076
Liang Y, Zhang F, Wang J, Joshi T et al. Prediction of drought-resistant genes in Arabidopsis thaliana using SVM-RFE. PLoS One 2011;6(7):e21750. PMID: 21789178
Pham L, Christadore L, Schaus S, Kolaczyk ED. Network-based prediction for sources of transcriptional dysregulation using latent pathway identification analysis. Proc Natl Acad Sci U S A 2011 Aug 9;108(32):13347-52. PMID: 21788508
Höög G, Zarrizi R, von Stedingk K, Jonsson K et al. Nuclear localization of γ-tubulin affects E2F transcriptional activity and S-phase progression. FASEB J 2011 Nov;25(11):3815-27. PMID: 21788450
Steininger A, Möbs M, Ullmann R, Köchert K et al. Genomic loss of the putative tumor suppressor gene E2A in human lymphoma. J Exp Med 2011 Aug 1;208(8):1585-93. PMID: 21788410
Kranz AL, Eils R, König R. Enhancers regulate progression of development in mammalian cells. Nucleic Acids Res 2011 Nov 1;39(20):8689-702. PMID: 21785139
Roylance R, Endesfelder D, Gorman P, Burrell RA et al. Relationship of extreme chromosomal instability with long-term survival in a retrospective analysis of primary breast cancer. Cancer Epidemiol Biomarkers Prev 2011 Oct;20(10):2183-94. PMID: 21784954
Pritchard JR, Gilbert LA, Meacham CE, Ricks JL et al. Bcl-2 family genetic profiling reveals microenvironment-specific determinants of chemotherapeutic response. Cancer Res 2011 Sep 1;71(17):5850-8. PMID: 21784872
LaBreche HG, Nevins JR, Huang E. Integrating factor analysis and a transgenic mouse model to reveal a peripheral blood predictor of breast tumors. BMC Med Genomics 2011 Jul 22;4:61. PMID: 21781289
Strong ER, Schimenti JC. Evidence Implicating CCNB1IP1, a RING Domain-Containing Protein Required for Meiotic Crossing Over in Mice, as an E3 SUMO Ligase. Genes (Basel) 2010 Dec 2;1(3):440-451. PMID: 21779533
Ukena SN, Velaga S, Geffers R, Grosse J et al. Human regulatory T cells in allogeneic stem cell transplantation. Blood 2011 Sep 29;118(13):e82-92. PMID: 21778340
Zhang Y, Chertov O, Zhang J, Hassan R et al. Cytotoxic activity of immunotoxin SS1P is modulated by TACE-dependent mesothelin shedding. Cancer Res 2011 Sep 1;71(17):5915-22. PMID: 21775520
Fini MA, Monks J, Farabaugh SM, Wright RM. Contribution of xanthine oxidoreductase to mammary epithelial and breast cancer cell differentiation in part modulates inhibitor of differentiation-1. Mol Cancer Res 2011 Sep;9(9):1242-54. PMID: 21775420
Sadanandam A, Futakuchi M, Lyssiotis CA, Gibb WJ et al. A cross-species analysis of a mouse model of breast cancer-specific osteolysis and human bone metastases using gene expression profiling. BMC Cancer 2011 Jul 20;11:304. PMID: 21774828
Niu Z, Goodyear SM, Rao S, Wu X et al. MicroRNA-21 regulates the self-renewal of mouse spermatogonial stem cells. Proc Natl Acad Sci U S A 2011 Aug 2;108(31):12740-5. PMID: 21768389
Piwowar HA. Who shares? Who doesn't? Factors associated with openly archiving raw research data. PLoS One 2011;6(7):e18657. PMID: 21765886
Kim K, Chadalapaka G, Lee SO, Yamada D et al. Identification of oncogenic microRNA-17-92/ZBTB4/specificity protein axis in breast cancer. Oncogene 2012 Feb 23;31(8):1034-44. PMID: 21765466
Weissglas-Volkov D, Calkin AC, Tusie-Luna T, Sinsheimer JS et al. The N342S MYLIP polymorphism is associated with high total cholesterol and increased LDL receptor degradation in humans. J Clin Invest 2011 Aug;121(8):3062-71. PMID: 21765216
Gao LL, Xue HW. Global analysis of expression profiles of rice receptor-like kinase genes. Mol Plant 2012 Jan;5(1):143-53. PMID: 21765177
Zagar L, Mulas F, Garagna S, Zuccotti M et al. Stage prediction of embryonic stem cell differentiation from genome-wide expression data. Bioinformatics 2011 Sep 15;27(18):2546-53. PMID: 21765096
Sontrop HM, Verhaegh WF, Reinders MJ, Moerland PD. An evaluation protocol for subtype-specific breast cancer event prediction. PLoS One 2011;6(7):e21681. PMID: 21760900
de Jonge HJ, Woolthuis CM, Vos AZ, Mulder A et al. Gene expression profiling in the leukemic stem cell-enriched CD34+ fraction identifies target genes that predict prognosis in normal karyotype AML. Leukemia 2011 Dec;25(12):1825-33. PMID: 21760593
Waardenberg AJ, Bernardo BC, Ng DC, Shepherd PR et al. Phosphoinositide 3-kinase (PI3K(p110alpha)) directly regulates key components of the Z-disc and cardiac structure. J Biol Chem 2011 Sep 2;286(35):30837-46. PMID: 21757757
Tzatsos A, Paskaleva P, Lymperi S, Contino G et al. Lysine-specific demethylase 2B (KDM2B)-let-7-enhancer of zester homolog 2 (EZH2) pathway regulates cell cycle progression and senescence in primary cells. J Biol Chem 2011 Sep 23;286(38):33061-9. PMID: 21757686
Stany MP, Vathipadiekal V, Ozbun L, Stone RL et al. Identification of novel therapeutic targets in microdissected clear cell ovarian cancers. PLoS One 2011;6(7):e21121. PMID: 21754983
Wu H, Zhang Y. Tet1 and 5-hydroxymethylation: a genome-wide view in mouse embryonic stem cells. Cell Cycle 2011 Aug 1;10(15):2428-36. PMID: 21750410
Song L, Zhang Z, Grasfeder LL, Boyle AP et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res 2011 Oct;21(10):1757-67. PMID: 21750106
Hansen KD, Wu Z, Irizarry RA, Leek JT. Sequencing technology does not eliminate biological variability. Nat Biotechnol 2011 Jul 11;29(7):572-3. PMID: 21747377
Shtutman M, Baig M, Levina E, Hurteau G et al. Tumor-specific silencing of COPZ2 gene encoding coatomer protein complex subunit ζ 2 renders tumor cells dependent on its paralogous gene COPZ1. Proc Natl Acad Sci U S A 2011 Jul 26;108(30):12449-54. PMID: 21746916
Silk JD, Lakhal S, Laynes R, Vallius L et al. IDO induces expression of a novel tryptophan transporter in mouse and human tumor cells. J Immunol 2011 Aug 15;187(4):1617-25. PMID: 21742973
Desai SS, Rajpurohit YS, Misra HS, Deobagkar DN. Characterization of the role of the RadS/RadR two-component system in the radiation resistance of Deinococcus radiodurans. Microbiology 2011 Oct;157(Pt 10):2974-82. PMID: 21737498
Buffa FM, Camps C, Winchester L, Snell CE et al. microRNA-associated progression pathways and potential therapeutic targets identified by integrated mRNA and microRNA expression profiling in breast cancer. Cancer Res 2011 Sep 1;71(17):5635-45. PMID: 21737487
Luk JM, Burchard J, Zhang C, Liu AM et al. DLK1-DIO3 genomic imprinted microRNA cluster at 14q32.2 defines a stemlike subtype of hepatocellular carcinoma associated with poor survival. J Biol Chem 2011 Sep 2;286(35):30706-13. PMID: 21737452
Ezashi T, Matsuyama H, Telugu BP, Roberts RM. Generation of colonies of induced trophoblast cells during standard reprogramming of porcine fibroblasts to induced pluripotent stem cells. Biol Reprod 2011 Oct;85(4):779-87. PMID: 21734265
Pukkila-Worley R, Ausubel FM, Mylonakis E. Candida albicans infection of Caenorhabditis elegans induces antifungal immune defenses. PLoS Pathog 2011 Jun;7(6):e1002074. PMID: 21731485
Wang D, Zavadil J, Martin L, Parisi F et al. Inhibition of nonsense-mediated RNA decay by the tumor microenvironment promotes tumorigenesis. Mol Cell Biol 2011 Sep;31(17):3670-80. PMID: 21730287
Nguyen AT, Emelyanov A, Koh CH, Spitsbergen JM et al. A high level of liver-specific expression of oncogenic Kras(V12) drives robust liver tumorigenesis in transgenic zebrafish. Dis Model Mech 2011 Nov;4(6):801-13. PMID: 21729876
Fulton DL, Denarier E, Friedman HC, Wasserman WW et al. Towards resolving the transcription factor network controlling myelin gene expression. Nucleic Acids Res 2011 Oct;39(18):7974-91. PMID: 21729871
Yang B, Cai LL, Chi XH, Lu XC et al. [Prediction and bioinformatics analysis of human gene expression profiling regulated by amifostine]. Zhongguo Shi Yan Xue Ye Xue Za Zhi 2011 Jun;19(3):711-6. PMID: 21729556
Libregts SF, Gutiérrez L, de Bruin AM, Wensveen FM et al. Chronic IFN-γ production in mice induces anemia by reducing erythrocyte life span and inhibiting erythropoiesis through an IRF-1/PU.1 axis. Blood 2011 Sep 1;118(9):2578-88. PMID: 21725055
Peng YM, van de Garde MD, Cheng KF, Baars PA et al. Specific expression of GPR56 by human cytotoxic lymphocytes. J Leukoc Biol 2011 Oct;90(4):735-40. PMID: 21724806
Kang K, Kim J, Chung JH, Lee D. Decoding the genome with an integrative analysis tool: combinatorial CRM Decoder. Nucleic Acids Res 2011 Sep 1;39(17):e116. PMID: 21724599
Westra JW, Schlage WK, Frushour BP, Gebel S et al. Construction of a computable cell proliferation network focused on non-diseased lung cells. BMC Syst Biol 2011 Jul 2;5:105. PMID: 21722388
Xie Z, Bi C, Cheong LL, Liu SC et al. Determinants of sensitivity to DZNep induced apoptosis in multiple myeloma cells. PLoS One 2011;6(6):e21583. PMID: 21720561
Morrissy AS, Griffith M, Marra MA. Extensive relationship between antisense transcription and alternative splicing in the human genome. Genome Res 2011 Aug;21(8):1203-12. PMID: 21719572
Nair JR, Carlson LM, Koorella C, Rozanski CH et al. CD28 expressed on malignant plasma cells induces a prosurvival and immunosuppressive microenvironment. J Immunol 2011 Aug 1;187(3):1243-53. PMID: 21715687
Liao Q, Xiao H, Bu D, Xie C et al. ncFANs: a web server for functional annotation of long non-coding RNAs. Nucleic Acids Res 2011 Jul;39(Web Server issue):W118-24. PMID: 21715382
Wu YH, Hu TF, Chen YC, Tsai YN et al. The manipulation of miRNA-gene regulatory networks by KSHV induces endothelial cell motility. Blood 2011 Sep 8;118(10):2896-905. PMID: 21715310
Mitra AK, Crews KR, Pounds S, Cao X et al. Genetic variants in cytosolic 5'-nucleotidase II are associated with its expression and cytarabine sensitivity in HapMap cell lines and in patients with acute myeloid leukemia. J Pharmacol Exp Ther 2011 Oct;339(1):9-23. PMID: 21712425
Babiarz JE, Hsu R, Melton C, Thomas M et al. A role for noncanonical microRNAs in the mammalian brain revealed by phenotypic differences in Dgcr8 versus Dicer1 knockouts and small RNA sequencing. RNA 2011 Aug;17(8):1489-501. PMID: 21712401
Ohno Y, Narangajavana J, Yamamoto A, Hattori T et al. Ectopic gene expression and organogenesis in Arabidopsis mutants missing BRU1 required for genome maintenance. Genetics 2011 Sep;189(1):83-95. PMID: 21705754
Wang D, Cheng L, Wang M, Wu R et al. Extensive increase of microarray signals in cancers calls for novel normalization assumptions. Comput Biol Chem 2011 Jun;35(3):126-30. PMID: 21704257
Tseng CW, Lin CC, Chen CN, Huang HC et al. Integrative network analysis reveals active microRNAs and their functions in gastric cancer. BMC Syst Biol 2011 Jun 26;5:99. PMID: 21703006
Bolen CR, Uduman M, Kleinstein SH. Cell subset prediction for blood genomic studies. BMC Bioinformatics 2011 Jun 24;12:258. PMID: 21702940
Shiraishi Y, Okada-Hatakeyama M, Miyano S. A rank-based statistical test for measuring synergistic effects between two gene sets. Bioinformatics 2011 Sep 1;27(17):2399-405. PMID: 21700673
Li W, Liu CC, Zhang T, Li H et al. Integrative analysis of many weighted co-expression networks using tensor computation. PLoS Comput Biol 2011 Jun;7(6):e1001106. PMID: 21698123
Radfar MH, Wong W, Morris Q. Computational prediction of intronic microRNA targets using host gene expression reveals novel regulatory mechanisms. PLoS One 2011;6(6):e19312. PMID: 21694770
Porro A, Iraci N, Soverini S, Diolaiti D et al. c-MYC oncoprotein dictates transcriptional profiles of ATP-binding cassette transporter genes in chronic myelogenous leukemia CD34+ hematopoietic progenitor cells. Mol Cancer Res 2011 Aug;9(8):1054-66. PMID: 21693596
Doehlemann G, Reissmann S, Assmann D, Fleckenstein M et al. Two linked genes encoding a secreted effector and a membrane protein are essential for Ustilago maydis-induced tumour formation. Mol Microbiol 2011 Aug;81(3):751-66. PMID: 21692877
Splinter E, de Wit E, Nora EP, Klous P et al. The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. Genes Dev 2011 Jul 1;25(13):1371-83. PMID: 21690198
Bauer T, Eils R, König R. RIP: the regulatory interaction predictor--a machine learning-based approach for predicting target genes of transcription factors. Bioinformatics 2011 Aug 15;27(16):2239-47. PMID: 21690103
Dudley JT, Deshpande T, Butte AJ. Exploiting drug-disease relationships for computational drug repositioning. Brief Bioinform 2011 Jul;12(4):303-11. PMID: 21690101
Bushati N, Smith J, Briscoe J, Watkins C. An intuitive graphical visualization technique for the interrogation of transcriptome data. Nucleic Acids Res 2011 Sep 1;39(17):7380-9. PMID: 21690098
Shu W, Chen H, Bo X, Wang S. Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains. Nucleic Acids Res 2011 Sep 1;39(17):7428-43. PMID: 21685456
Furlotte NA, Kang HM, Ye C, Eskin E. Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity. Bioinformatics 2011 Jul 1;27(13):i288-94. PMID: 21685083
Dao P, Wang K, Collins C, Ester M et al. Optimally discriminative subnetwork markers predict response to chemotherapy. Bioinformatics 2011 Jul 1;27(13):i205-13. PMID: 21685072
Maneck M, Schrader A, Kube D, Spang R. Genomic data integration using guided clustering. Bioinformatics 2011 Aug 15;27(16):2231-8. PMID: 21685050
Ben-David E, Granot-Hershkovitz E, Monderer-Rothkoff G, Lerer E et al. Identification of a functional rare variant in autism using genome-wide screen for monoallelic expression. Hum Mol Genet 2011 Sep 15;20(18):3632-41. PMID: 21680558
Faro A, Giordano D, Spampinato C. Combining literature text mining with microarray data: advances for system biology modeling. Brief Bioinform 2012 Jan;13(1):61-82. PMID: 21677032
Kais Z, Barsky SH, Mathsyaraja H, Zha A et al. KIAA0101 interacts with BRCA1 and regulates centrosome number. Mol Cancer Res 2011 Aug;9(8):1091-9. PMID: 21673012
Chen JL, Li J, Stadler WM, Lussier YA. Protein-network modeling of prostate cancer gene signatures reveals essential pathways in disease recurrence. J Am Med Inform Assoc 2011 Jul-Aug;18(4):392-402. PMID: 21672909
Alizadeh AA, Gentles AJ, Alencar AJ, Liu CL et al. Prediction of survival in diffuse large B-cell lymphoma based on the expression of 2 genes reflecting tumor and microenvironment. Blood 2011 Aug 4;118(5):1350-8. PMID: 21670469
Hu Q, Guo C, Li Y, Aronow BJ et al. LMO7 mediates cell-specific activation of the Rho-myocardin-related transcription factor-serum response factor pathway and plays an important role in breast cancer cell migration. Mol Cell Biol 2011 Aug;31(16):3223-40. PMID: 21670154
Symons S, Nieselt K. MGV: a generic graph viewer for comparative omics data. Bioinformatics 2011 Aug 15;27(16):2248-55. PMID: 21666268
Graeber K, Linkies A, Wood AT, Leubner-Metzger G. A guideline to family-wide comparative state-of-the-art quantitative RT-PCR analysis exemplified with a Brassicaceae cross-species seed germination case study. Plant Cell 2011 Jun;23(6):2045-63. PMID: 21666000
Wang H, Huang M, Zhang DY, Zhang F. Global profiling of signaling networks: study of breast cancer stem cells and potential regulation. Oncologist 2011;16(7):966-79. PMID: 21665913
Ke S, Shang S, Kalachikov SM, Morozova I et al. Quantitative evaluation of all hexamers as exonic splicing elements. Genome Res 2011 Aug;21(8):1360-74. PMID: 21659425
Briggs J, Paoloni M, Chen QR, Wen X et al. A compendium of canine normal tissue gene expression. PLoS One 2011;6(5):e17107. PMID: 21655323
Zhang X, Gamble MJ, Stadler S, Cherrington BD et al. Genome-wide analysis reveals PADI4 cooperates with Elk-1 to activate c-Fos expression in breast cancer cells. PLoS Genet 2011 Jun;7(6):e1002112. PMID: 21655091
Hebenstreit D, Fang M, Gu M, Charoensawan V et al. RNA sequencing reveals two major classes of gene expression levels in metazoan cells. Mol Syst Biol 2011 Jun 7;7:497. PMID: 21654674
Greene CS, Troyanskaya OG. PILGRM: an interactive data-driven discovery platform for expert biologists. Nucleic Acids Res 2011 Jul;39(Web Server issue):W368-74. PMID: 21653547
Young MD, Willson TA, Wakefield MJ, Trounson E et al. ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity. Nucleic Acids Res 2011 Sep 1;39(17):7415-27. PMID: 21652639
Chang TY, Wu YH, Cheng CC, Wang HW. Differentially regulated splice variants and systems biology analysis of Kaposi's sarcoma-associated herpesvirus-infected lymphatic endothelial cells. Nucleic Acids Res 2011 Sep 1;39(16):6970-85. PMID: 21646333
Innocenti F, Cooper GM, Stanaway IB, Gamazon ER et al. Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue. PLoS Genet 2011 May;7(5):e1002078. PMID: 21637794
Beane J, Vick J, Schembri F, Anderlind C et al. Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq. Cancer Prev Res (Phila) 2011 Jun;4(6):803-17. PMID: 21636547
Lehmann BD, Bauer JA, Chen X, Sanders ME et al. Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies. J Clin Invest 2011 Jul;121(7):2750-67. PMID: 21633166
Zentner GE, Tesar PJ, Scacheri PC. Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res 2011 Aug;21(8):1273-83. PMID: 21632746
Li Y, Wu B, Yu Y, Yang G et al. Genome-wide analysis of the RING finger gene family in apple. Mol Genet Genomics 2011 Jul;286(1):81-94. PMID: 21630098
Taher L, McGaughey DM, Maragh S, Aneas I et al. Genome-wide identification of conserved regulatory function in diverged sequences. Genome Res 2011 Jul;21(7):1139-49. PMID: 21628450
Chu JH, Lazarus R, Carey VJ, Raby BA. Quantifying differential gene connectivity between disease states for objective identification of disease-relevant genes. BMC Syst Biol 2011 May 31;5:89. PMID: 21627793
Luciani MG, Seok J, Sayeed A, Champion S et al. Distinctive responsiveness to stromal signaling accompanies histologic grade programming of cancer cells. PLoS One 2011;6(5):e20016. PMID: 21625507
Chi SM, Kim J, Kim SY, Nam D. ADGO 2.0: interpreting microarray data and list of genes using composite annotations. Nucleic Acids Res 2011 Jul;39(Web Server issue):W302-6. PMID: 21624890
Suvorova IA, Tutukina MN, Ravcheev DA, Rodionov DA et al. Comparative genomic analysis of the hexuronate metabolism genes and their regulation in gammaproteobacteria. J Bacteriol 2011 Aug;193(15):3956-63. PMID: 21622752
Taniue K, Oda T, Hayashi T, Okuno M et al. A member of the ETS family, EHF, and the ATPase RUVBL1 inhibit p53-mediated apoptosis. EMBO Rep 2011 Jul 1;12(7):682-9. PMID: 21617703
Theunissen PT, Pennings JL, Robinson JF, Claessen SM et al. Time-response evaluation by transcriptomics of methylmercury effects on neural differentiation of murine embryonic stem cells. Toxicol Sci 2011 Aug;122(2):437-47. PMID: 21613230
Xu Y, Duanmu H, Chang Z, Zhang S et al. The application of gene co-expression network reconstruction based on CNVs and gene expression microarray data in breast cancer. Mol Biol Rep 2012 Feb;39(2):1627-37. PMID: 21611746
Heluane H, Evans MR, Dagher SF, Bruno-Bárcena JM. Meta-analysis and functional validation of nutritional requirements of solventogenic Clostridia growing under butanol stress conditions and coutilization of D-glucose and D-xylose. Appl Environ Microbiol 2011 Jul;77(13):4473-85. PMID: 21602379
Gan H, Lin X, Zhang Z, Zhang W et al. piRNA profiling during specific stages of mouse spermatogenesis. RNA 2011 Jul;17(7):1191-203. PMID: 21602304
Tang H, Lee M, Budak MT, Pietras N et al. Intrinsic apoptosis in mechanically ventilated human diaphragm: linkage to a novel Fos/FoxO1/Stat3-Bim axis. FASEB J 2011 Sep;25(9):2921-36. PMID: 21597002
Maver A, Peterlin B. Positional integratomic approach in identification of genomic candidate regions for Parkinson's disease. Bioinformatics 2011 Jul 15;27(14):1971-8. PMID: 21596793
Liang Z, Zhou H, He Z, Zheng H et al. mirAct: a web tool for evaluating microRNA activity based on gene expression data. Nucleic Acids Res 2011 Jul;39(Web Server issue):W139-44. PMID: 21596785
Duy C, Hurtz C, Shojaee S, Cerchietti L et al. BCL6 enables Ph+ acute lymphoblastic leukaemia cells to survive BCR-ABL1 kinase inhibition. Nature 2011 May 19;473(7347):384-8. PMID: 21593872
Ahmed I, Sarazin A, Bowler C, Colot V et al. Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis. Nucleic Acids Res 2011 Sep 1;39(16):6919-31. PMID: 21586580
Hicks C, Pannuti A, Miele L. Associating GWAS Information with the Notch Signaling Pathway Using Transcription Profiling. Cancer Inform 2011 Apr 6;10:93-108. PMID: 21584266
Biswas S, Manikandan J, Pushparaj PN. Decoding the differential biomarkers of Rheumatoid arthritis and Osteoarthritis: A functional genomics paradigm to design disease specific therapeutics. Bioinformation 2011 May 7;6(4):153-7. PMID: 21572882
Hackett NR, Shaykhiev R, Walters MS, Wang R et al. The human airway epithelial basal cell transcriptome. PLoS One 2011 May 4;6(5):e18378. PMID: 21572528
Feurtado JA, Huang D, Wicki-Stordeur L, Hemstock LE et al. The Arabidopsis C2H2 zinc finger INDETERMINATE DOMAIN1/ENHYDROUS promotes the transition to germination by regulating light and hormonal signaling during seed maturation. Plant Cell 2011 May;23(5):1772-94. PMID: 21571950
Hoenerhoff MJ, Pandiri AR, Lahousse SA, Hong HH et al. Global gene profiling of spontaneous hepatocellular carcinoma in B6C3F1 mice: similarities in the molecular landscape with human liver cancer. Toxicol Pathol 2011 Jun;39(4):678-99. PMID: 21571946
Kim YJ, Yoon HY, Kim SK, Kim YW et al. EFEMP1 as a novel DNA methylation marker for prostate cancer: array-based DNA methylation and expression profiling. Clin Cancer Res 2011 Jul 1;17(13):4523-30. PMID: 21571867
Movahedi S, Van de Peer Y, Vandepoele K. Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice. Plant Physiol 2011 Jul;156(3):1316-30. PMID: 21571672
Li Y, Li C, Ding G, Jin Y. Evolution of MIR159/319 microRNA genes and their post-transcriptional regulatory link to siRNA pathways. BMC Evol Biol 2011 May 12;11(1):122. PMID: 21569383
Dinavahi R, George A, Tretin A, Akalin E et al. Antibodies reactive to non-HLA antigens in transplant glomerulopathy. J Am Soc Nephrol 2011 Jun;22(6):1168-78. PMID: 21566057
Didon L, Barton JL, Roos AB, Gaschler GJ et al. Lung epithelial CCAAT/enhancer-binding protein-β is necessary for the integrity of inflammatory responses to cigarette smoke. Am J Respir Crit Care Med 2011 Jul 15;184(2):233-42. PMID: 21562127
Boegsted M, Holst JM, Fogd K, Falgreen S et al. Generation of a predictive melphalan resistance index by drug screen of B-cell cancer cell lines. PLoS One 2011 Apr 29;6(4):e19322. PMID: 21559449
Guerrero-Preston R, Soudry E, Acero J, Orera M et al. NID2 and HOXA9 promoter hypermethylation as biomarkers for prevention and early detection in oral cavity squamous cell carcinoma tissues and saliva. Cancer Prev Res (Phila) 2011 Jul;4(7):1061-72. PMID: 21558411
Wei Z, Biswas N, Wang L, Courel M et al. A common genetic variant in the 3'-UTR of vacuolar H+-ATPase ATP6V0A1 creates a micro-RNA motif to alter chromogranin A processing and hypertension risk. Circ Cardiovasc Genet 2011 Aug 1;4(4):381-9. PMID: 21558123
Giangreco A, Lu L, Mazzatti DJ, Spencer-Dene B et al. Myd88 deficiency influences murine tracheal epithelial metaplasia and submucosal gland abundance. J Pathol 2011 Jun;224(2):190-202. PMID: 21557220
Holweg CT, Potena L, Luikart H, Yu T et al. Identification and classification of acute cardiac rejection by intragraft transcriptional profiling. Circulation 2011 May 24;123(20):2236-43. PMID: 21555702
Becker N, Toedt G, Lichter P, Benner A. Elastic SCAD as a novel penalization method for SVM classification tasks in high-dimensional data. BMC Bioinformatics 2011 May 9;12:138. PMID: 21554689
Muiño JM, Kaufmann K, van Ham RC, Angenent GC et al. ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions. Plant Methods 2011 May 9;7:11. PMID: 21554688
Deveshwar P, Bovill WD, Sharma R, Able JA et al. Analysis of anther transcriptomes to identify genes contributing to meiosis and male gametophyte development in rice. BMC Plant Biol 2011 May 9;11:78. PMID: 21554676
Isci S, Ozturk C, Jones J, Otu HH. Pathway analysis of high-throughput biological data within a Bayesian network framework. Bioinformatics 2011 Jun 15;27(12):1667-74. PMID: 21551144
Norddahl GL, Pronk CJ, Wahlestedt M, Sten G et al. Accumulating mitochondrial DNA mutations drive premature hematopoietic aging phenotypes distinct from physiological stem cell aging. Cell Stem Cell 2011 May 6;8(5):499-510. PMID: 21549326
McCall MN, Murakami PN, Lukk M, Huber W et al. Assessing affymetrix GeneChip microarray quality. BMC Bioinformatics 2011 May 7;12:137. PMID: 21548974
Warth A, Muley T, Meister M, Herpel E et al. Loss of aquaporin-4 expression and putative function in non-small cell lung cancer. BMC Cancer 2011 May 6;11:161. PMID: 21548930
Tommasi S, Mangia A, Iannelli G, Chiarappa P et al. Gene copy number variation in male breast cancer by aCGH. Cell Oncol (Dordr) 2011 Oct;34(5):467-73. PMID: 21547577
Yan Z, Hu HY, Jiang X, Maierhofer V et al. Widespread expression of piRNA-like molecules in somatic tissues. Nucleic Acids Res 2011 Aug;39(15):6596-607. PMID: 21546553
Yang X, Yang YN, Xue LJ, Zou MJ et al. Rice ABI5-Like1 regulates abscisic acid and auxin responses by affecting the expression of ABRE-containing genes. Plant Physiol 2011 Jul;156(3):1397-409. PMID: 21546455
Liberzon A, Subramanian A, Pinchback R, Thorvaldsdóttir H et al. Molecular signatures database (MSigDB) 3.0. Bioinformatics 2011 Jun 15;27(12):1739-40. PMID: 21546393
Chen ZX, Zhang YE, Vibranovski M, Luo J et al. Deficiency of X-linked inverted duplicates with male-biased expression and the underlying evolutionary mechanisms in the Drosophila genome. Mol Biol Evol 2011 Oct;28(10):2823-32. PMID: 21546357
Gower AC, Steiling K, Brothers JF 2nd, Lenburg ME et al. Transcriptomic studies of the airway field of injury associated with smoking-related lung disease. Proc Am Thorac Soc 2011 May;8(2):173-9. PMID: 21543797
Wang A, Huang K, Shen Y, Xue Z et al. Functional modules distinguish human induced pluripotent stem cells from embryonic stem cells. Stem Cells Dev 2011 Nov;20(11):1937-50. PMID: 21542696
Ponz-Sarvisé M, Nguewa PA, Pajares MJ, Agorreta J et al. Inhibitor of differentiation-1 as a novel prognostic factor in NSCLC patients with adenocarcinoma histology and its potential contribution to therapy resistance. Clin Cancer Res 2011 Jun 15;17(12):4155-66. PMID: 21540238
Todoric J, Strobl B, Jais A, Boucheron N et al. Cross-talk between interferon-γ and hedgehog signaling regulates adipogenesis. Diabetes 2011 Jun;60(6):1668-76. PMID: 21536945
Lamonica JM, Deng W, Kadauke S, Campbell AE et al. Bromodomain protein Brd3 associates with acetylated GATA1 to promote its chromatin occupancy at erythroid target genes. Proc Natl Acad Sci U S A 2011 May 31;108(22):E159-68. PMID: 21536911
Wang L, Sun L, Huang J, Jiang M. Cyclin-dependent kinase inhibitor 3 (CDKN3) novel cell cycle computational network between human non-malignancy associated hepatitis/cirrhosis and hepatocellular carcinoma (HCC) transformation. Cell Prolif 2011 Jun;44(3):291-9. PMID: 21535270
Zhou L, Opalinska J, Sohal D, Yu Y et al. Aberrant epigenetic and genetic marks are seen in myelodysplastic leukocytes and reveal Dock4 as a candidate pathogenic gene on chromosome 7q. J Biol Chem 2011 Jul 15;286(28):25211-23. PMID: 21532034
Redmond LC, Dumur CI, Archer KJ, Grayson DR et al. Krüppel-like factor 2 regulated gene expression in mouse embryonic yolk sac erythroid cells. Blood Cells Mol Dis 2011 Jun 15;47(1):1-11. PMID: 21530336
Duval E, Bigot N, Hervieu M, Kou I et al. Asporin expression is highly regulated in human chondrocytes. Mol Med 2011;17(7-8):816-23. PMID: 21528154
Lu J, Kerns RT, Peddada SD, Bushel PR. Principal component analysis-based filtering improves detection for Affymetrix gene expression arrays. Nucleic Acids Res 2011 Jul;39(13):e86. PMID: 21525126
Gallo CA, Carballido JA, Ponzoni I. Discovering time-lagged rules from microarray data using gene profile classifiers. BMC Bioinformatics 2011 Apr 27;12:123. PMID: 21524308
Hu Z, Gu X, Baraoidan K, Ibanez V et al. RUNX1 regulates corepressor interactions of PU.1. Blood 2011 Jun 16;117(24):6498-508. PMID: 21518930
Kim T, Veronese A, Pichiorri F, Lee TJ et al. p53 regulates epithelial-mesenchymal transition through microRNAs targeting ZEB1 and ZEB2. J Exp Med 2011 May 9;208(5):875-83. PMID: 21518799
Hartman ZC, Yang XY, Glass O, Lei G et al. HER2 overexpression elicits a proinflammatory IL-6 autocrine signaling loop that is critical for tumorigenesis. Cancer Res 2011 Jul 1;71(13):4380-91. PMID: 21518778
Wu LC, Pfeiffer DR, Calhoon EA, Madiai F et al. Purification, identification, and cloning of lysoplasmalogenase, the enzyme that catalyzes hydrolysis of the vinyl ether bond of lysoplasmalogen. J Biol Chem 2011 Jul 15;286(28):24916-30. PMID: 21515882
Moyroud E, Minguet EG, Ott F, Yant L et al. Prediction of regulatory interactions from genome sequences using a biophysical model for the Arabidopsis LEAFY transcription factor. Plant Cell 2011 Apr;23(4):1293-306. PMID: 21515819
Hackenberg M, Rodríguez-Ezpeleta N, Aransay AM. miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. Nucleic Acids Res 2011 Jul;39(Web Server issue):W132-8. PMID: 21515631
Wei AY, Luo XG, Yang Y, He SH et al. [Microarray data analysis of genes related with erectile dysfunction in diabetic rats]. Nan Fang Yi Ke Da Xue Xue Bao 2011 Apr;31(4):694-7. PMID: 21515472
Rhind N, Chen Z, Yassour M, Thompson DA et al. Comparative functional genomics of the fission yeasts. Science 2011 May 20;332(6032):930-6. PMID: 21511999
Wang M, Wang Q, Zhang X, Yang Y et al. Uncovering the transcriptional circuitry in skeletal muscle regeneration. Mamm Genome 2011 Jun;22(5-6):272-81. PMID: 21509518
Ogawa D, Abe K, Miyao A, Kojima M et al. RSS1 regulates the cell cycle and maintains meristematic activity under stress conditions in rice. Nat Commun 2011;2:278. PMID: 21505434
Popovici V, Budinská E, Delorenzi M. Rgtsp: a generalized top scoring pairs package for class prediction. Bioinformatics 2011 Jun 15;27(12):1729-30. PMID: 21505033
Ohi Y, Qin H, Hong C, Blouin L et al. Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nat Cell Biol 2011 May;13(5):541-9. PMID: 21499256
Lockstone HE. Exon array data analysis using Affymetrix power tools and R statistical software. Brief Bioinform 2011 Nov;12(6):634-44. PMID: 21498550
Ahmady E, Deeke SA, Rabaa S, Kouri L et al. Identification of a novel muscle A-type lamin-interacting protein (MLIP). J Biol Chem 2011 Jun 3;286(22):19702-13. PMID: 21498514
Galante PA, Parmigiani RB, Zhao Q, Caballero OL et al. Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual. Nucleic Acids Res 2011 Aug;39(14):6056-68. PMID: 21493686
Nasser S, Cunliffe HE, Black MA, Kim S. Context-specific gene regulatory networks subdivide intrinsic subtypes of breast cancer. BMC Bioinformatics 2011 Mar 29;12 Suppl 2:S3. PMID: 21489222
Zaravinos A, Lambrou GI, Boulalas I, Delakas D et al. Identification of common differentially expressed genes in urinary bladder cancer. PLoS One 2011 Apr 4;6(4):e18135. PMID: 21483740
Mendes-Pereira AM, Sims D, Dexter T, Fenwick K et al. Genome-wide functional screen identifies a compendium of genes affecting sensitivity to tamoxifen. Proc Natl Acad Sci U S A 2012 Feb 21;109(8):2730-5. PMID: 21482774
Wu N, Castel D, Debily MA, Vigano MA et al. Large scale RNAi screen reveals that the inhibitor of DNA binding 2 (ID2) protein is repressed by p53 family member p63 and functions in human keratinocyte differentiation. J Biol Chem 2011 Jun 10;286(23):20870-9. PMID: 21478550
Kossler N, Stricker S, Rödelsperger C, Robinson PN et al. Neurofibromin (Nf1) is required for skeletal muscle development. Hum Mol Genet 2011 Jul 15;20(14):2697-709. PMID: 21478499
Neri P, Ren L, Azab AK, Brentnall M et al. Integrin β7-mediated regulation of multiple myeloma cell adhesion, migration, and invasion. Blood 2011 Jun 9;117(23):6202-13. PMID: 21474670
Parker MA, Jiang K, Kempfle JS, Mizutari K et al. TAK1 expression in the cochlea: a specific marker for adult supporting cells. J Assoc Res Otolaryngol 2011 Aug;12(4):471-83. PMID: 21472480
Luk F, Yu Y, Dong HT, Walsh WR et al. New gene groups associated with dissimilar osteoblastic differentiation are linked to osteosarcomagenesis. Cancer Genomics Proteomics 2011 Mar-Apr;8(2):65-75. PMID: 21471516
Everett LJ, Jensen ST, Hannenhalli S. Transcriptional regulation via TF-modifying enzymes: an integrative model-based analysis. Nucleic Acids Res 2011 Jul;39(12):e78. PMID: 21470963
Gawriluk TR, Hale AN, Flaws JA, Dillon CP et al. Autophagy is a cell survival program for female germ cells in the murine ovary. Reproduction 2011 Jun;141(6):759-65. PMID: 21464117
Namiki T, Tanemura A, Valencia JC, Coelho SG et al. AMP kinase-related kinase NUAK2 affects tumor growth, migration, and clinical outcome of human melanoma. Proc Natl Acad Sci U S A 2011 Apr 19;108(16):6597-602. PMID: 21460252
Kayano M, Takigawa I, Shiga M, Tsuda K et al. ROS-DET: robust detector of switching mechanisms in gene expression. Nucleic Acids Res 2011 Jun;39(11):e74. PMID: 21459849
Xue GP, Way HM, Richardson T, Drenth J et al. Overexpression of TaNAC69 leads to enhanced transcript levels of stress up-regulated genes and dehydration tolerance in bread wheat. Mol Plant 2011 Jul;4(4):697-712. PMID: 21459832
Kwee I, Rancoita PM, Rinaldi A, Ferreri AJ et al. Genomic profiles of MALT lymphomas: variability across anatomical sites. Haematologica 2011 Jul;96(7):1064-6. PMID: 21459788
MacDonald MJ, Longacre MJ, Stoker SW, Kendrick M et al. Differences between human and rodent pancreatic islets: low pyruvate carboxylase, atp citrate lyase, and pyruvate carboxylation and high glucose-stimulated acetoacetate in human pancreatic islets. J Biol Chem 2011 May 27;286(21):18383-96. PMID: 21454710
Hao F, Pysz MA, Curry KJ, Haas KN et al. Protein kinase Cα signaling regulates inhibitor of DNA binding 1 in the intestinal epithelium. J Biol Chem 2011 May 20;286(20):18104-17. PMID: 21454537
Kilpinen SK, Ojala KA, Kallioniemi OP. Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data. BioData Min 2011 Mar 31;4:5. PMID: 21453538
Knop E, Knop N, Millar T, Obata H et al. The international workshop on meibomian gland dysfunction: report of the subcommittee on anatomy, physiology, and pathophysiology of the meibomian gland. Invest Ophthalmol Vis Sci 2011 Mar;52(4):1938-78. PMID: 21450915
Wang Q, Sun J, Zhou M, Yang H et al. A novel network-based method for measuring the functional relationship between gene sets. Bioinformatics 2011 Jun 1;27(11):1521-8. PMID: 21450716
Chen L, Wu G, Ji H. hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. Bioinformatics 2011 May 15;27(10):1447-8. PMID: 21450710
Schödel J, Oikonomopoulos S, Ragoussis J, Pugh CW et al. High-resolution genome-wide mapping of HIF-binding sites by ChIP-seq. Blood 2011 Jun 9;117(23):e207-17. PMID: 21447827
Barone I, Brusco L, Gu G, Selever J et al. Loss of Rho GDIα and resistance to tamoxifen via effects on estrogen receptor α. J Natl Cancer Inst 2011 Apr 6;103(7):538-52. PMID: 21447808
Oosterhof R, Ith M, Trepp R, Christ E et al. Regulation of whole body energy homeostasis with growth hormone replacement therapy and endurance exercise. Physiol Genomics 2011 Jun 28;43(12):739-48. PMID: 21447747
Ter Elst A, Ma B, Scherpen FJ, de Jonge HJ et al. Repression of vascular endothelial growth factor expression by the runt-related transcription factor 1 in acute myeloid leukemia. Cancer Res 2011 Apr 1;71(7):2761-71. PMID: 21447743
Ringnér M, Fredlund E, Häkkinen J, Borg Å et al. GOBO: gene expression-based outcome for breast cancer online. PLoS One 2011 Mar 21;6(3):e17911. PMID: 21445301
Rantala JK, Mäkelä R, Aaltola AR, Laasola P et al. A cell spot microarray method for production of high density siRNA transfection microarrays. BMC Genomics 2011 Mar 28;12:162. PMID: 21443765
Yeh SH, Yang WB, Gean PW, Hsu CY et al. Translational and transcriptional control of Sp1 against ischaemia through a hydrogen peroxide-activated internal ribosomal entry site pathway. Nucleic Acids Res 2011 Jul;39(13):5412-23. PMID: 21441538
Mochida K, Uehara-Yamaguchi Y, Yoshida T, Sakurai T et al. Global landscape of a co-expressed gene network in barley and its application to gene discovery in Triticeae crops. Plant Cell Physiol 2011 May;52(5):785-803. PMID: 21441235
Cserháti M, Turóczy Z, Zombori Z, Cserzo M et al. Prediction of new abiotic stress genes in Arabidopsis thaliana and Oryza sativa according to enumeration-based statistical analysis. Mol Genet Genomics 2011 May;285(5):375-91. PMID: 21437642
Jeffries MA, Dozmorov M, Tang Y, Merrill JT et al. Genome-wide DNA methylation patterns in CD4+ T cells from patients with systemic lupus erythematosus. Epigenetics 2011 May;6(5):593-601. PMID: 21436623
Shi F, Abraham G, Leckie C, Haviv I et al. Meta-analysis of gene expression microarrays with missing replicates. BMC Bioinformatics 2011 Mar 24;12:84. PMID: 21435268
Shah MA, Khanin R, Tang L, Janjigian YY et al. Molecular classification of gastric cancer: a new paradigm. Clin Cancer Res 2011 May 1;17(9):2693-701. PMID: 21430069
Chao SY, Chiang JH, Huang AM, Chang WS. An integrative approach to identifying cancer chemoresistance-associated pathways. BMC Med Genomics 2011 Mar 24;4:23. PMID: 21429228
Li GH, Cheung CL, Xiao SM, Lau KS et al. Identification of QTL genes for BMD variation using both linkage and gene-based association approaches. Hum Genet 2011 Oct;130(4):539-46. PMID: 21424381
Aporntewan C, Phokaew C, Piriyapongsa J, Ngamphiw C et al. Hypomethylation of intragenic LINE-1 represses transcription in cancer cells through AGO2. PLoS One 2011 Mar 15;6(3):e17934. PMID: 21423624
Koschmieder A, Zimmermann K, Trissl S, Stoltmann T et al. Tools for managing and analyzing microarray data. Brief Bioinform 2012 Jan;13(1):46-60. PMID: 21422065
Mackay A, Weigelt B, Grigoriadis A, Kreike B et al. Microarray-based class discovery for molecular classification of breast cancer: analysis of interobserver agreement. J Natl Cancer Inst 2011 Apr 20;103(8):662-73. PMID: 21421860
Merlos-Suárez A, Barriga FM, Jung P, Iglesias M et al. The intestinal stem cell signature identifies colorectal cancer stem cells and predicts disease relapse. Cell Stem Cell 2011 May 6;8(5):511-24. PMID: 21419747
He A, Kong SW, Ma Q, Pu WT. Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart. Proc Natl Acad Sci U S A 2011 Apr 5;108(14):5632-7. PMID: 21415370
Pettersson F, Yau C, Dobocan MC, Culjkovic-Kraljacic B et al. Ribavirin treatment effects on breast cancers overexpressing eIF4E, a biomarker with prognostic specificity for luminal B-type breast cancer. Clin Cancer Res 2011 May 1;17(9):2874-84. PMID: 21415224
Momin AA, Park H, Portz BJ, Haynes CA et al. A method for visualization of "omic" datasets for sphingolipid metabolism to predict potentially interesting differences. J Lipid Res 2011 Jun;52(6):1073-83. PMID: 21415121
Ma H, Schadt EE, Kaplan LM, Zhao H. COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method. Bioinformatics 2011 May 1;27(9):1290-8. PMID: 21414987
Vrzalikova K, Vockerodt M, Leonard S, Bell A et al. Down-regulation of BLIMP1α by the EBV oncogene, LMP-1, disrupts the plasma cell differentiation program and prevents viral replication in B cells: implications for the pathogenesis of EBV-associated B-cell lymphomas. Blood 2011 Jun 2;117(22):5907-17. PMID: 21411757
Bermejo-Alvarez P, Rizos D, Lonergan P, Gutierrez-Adan A. Transcriptional sexual dimorphism in elongating bovine embryos: implications for XCI and sex determination genes. Reproduction 2011 Jun;141(6):801-8. PMID: 21411694
Lee SH, Jia S, Zhu Y, Utermark T et al. Transgenic expression of polyomavirus middle T antigen in the mouse prostate gives rise to carcinoma. J Virol 2011 Jun;85(11):5581-92. PMID: 21411524
Kim J, Patel K, Jung H, Kuo WP et al. AnyExpress: integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm. BMC Bioinformatics 2011 Mar 17;12:75. PMID: 21410990
Welle S, Mehta S, Burgess K. Effect of postdevelopmental myostatin depletion on myofibrillar protein metabolism. Am J Physiol Endocrinol Metab 2011 Jun;300(6):E993-E1001. PMID: 21406613
Chin L, Hahn WC, Getz G, Meyerson M. Making sense of cancer genomic data. Genes Dev 2011 Mar 15;25(6):534-55. PMID: 21406553
Pietras A, von Stedingk K, Lindgren D, Påhlman S et al. JAG2 induction in hypoxic tumor cells alters Notch signaling and enhances endothelial cell tube formation. Mol Cancer Res 2011 May;9(5):626-36. PMID: 21402725
Seitz V, Thomas PE, Zimmermann K, Paul U et al. Classical Hodgkin's lymphoma shows epigenetic features of abortive plasma cell differentiation. Haematologica 2011 Jun;96(6):863-70. PMID: 21393330
Creekmore AL, Silkworth WT, Cimini D, Jensen RV et al. Changes in gene expression and cellular architecture in an ovarian cancer progression model. PLoS One 2011 Mar 3;6(3):e17676. PMID: 21390237
Wen J, Parker BJ, Jacobsen A, Krogh A. MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action. RNA 2011 May;17(5):820-34. PMID: 21389147
Alajez NM, Lenarduzzi M, Ito E, Hui AB et al. MiR-218 suppresses nasopharyngeal cancer progression through downregulation of survivin and the SLIT2-ROBO1 pathway. Cancer Res 2011 Mar 15;71(6):2381-91. PMID: 21385904
Kim TM, Huang W, Park R, Park PJ et al. A developmental taxonomy of glioblastoma defined and maintained by MicroRNAs. Cancer Res 2011 May 1;71(9):3387-99. PMID: 21385897
Torres Acosta JA, Fowke LC, Wang H. Analyses of phylogeny, evolution, conserved sequences and genome-wide expression of the ICK/KRP family of plant CDK inhibitors. Ann Bot 2011 May;107(7):1141-57. PMID: 21385782
Newnham GM, Conron M, McLachlan S, Dobrovic A et al. Integrated mutation, copy number and expression profiling in resectable non-small cell lung cancer. BMC Cancer 2011 Mar 7;11:93. PMID: 21385341
Yoneya T, Miyazawa T. Integration of pre-normalized microarray data using quantile correction. Bioinformation 2011 Feb 7;5(9):382-5. PMID: 21383905
Jan M, Chao MP, Cha AC, Alizadeh AA et al. Prospective separation of normal and leukemic stem cells based on differential expression of TIM3, a human acute myeloid leukemia stem cell marker. Proc Natl Acad Sci U S A 2011 Mar 22;108(12):5009-14. PMID: 21383193
Wang L, Rubinstein R, Lines JL, Wasiuk A et al. VISTA, a novel mouse Ig superfamily ligand that negatively regulates T cell responses. J Exp Med 2011 Mar 14;208(3):577-92. PMID: 21383057
Jin SG, Wu X, Li AX, Pfeifer GP. Genomic mapping of 5-hydroxymethylcytosine in the human brain. Nucleic Acids Res 2011 Jul;39(12):5015-24. PMID: 21378125
Rosenwasser S, Rot I, Sollner E, Meyer AJ et al. Organelles contribute differentially to reactive oxygen species-related events during extended darkness. Plant Physiol 2011 May;156(1):185-201. PMID: 21372201
Liu S, Richards SM, Lo K, Hatton M et al. Changes in gene expression in human meibomian gland dysfunction. Invest Ophthalmol Vis Sci 2011 Apr;52(5):2727-40. PMID: 21372006
Fox AD, Hescott BJ, Blumer AC, Slonim DK. Connectedness of PPI network neighborhoods identifies regulatory hub proteins. Bioinformatics 2011 Apr 15;27(8):1135-42. PMID: 21367871
Thangavel C, Dean JL, Ertel A, Knudsen KE et al. Therapeutically activating RB: reestablishing cell cycle control in endocrine therapy-resistant breast cancer. Endocr Relat Cancer 2011 Jun;18(3):333-45. PMID: 21367843
Mpindi JP, Sara H, Haapa-Paananen S, Kilpinen S et al. GTI: a novel algorithm for identifying outlier gene expression profiles from integrated microarray datasets. PLoS One 2011 Feb 18;6(2):e17259. PMID: 21365010
Fassbender JM, Whittemore SR, Hagg T. Targeting microvasculature for neuroprotection after SCI. Neurotherapeutics 2011 Apr;8(2):240-51. PMID: 21360237
Ricci G, Astolfi A, Remondini D, Cipriani F et al. Pooled genome-wide analysis to identify novel risk loci for pediatric allergic asthma. PLoS One 2011 Feb 16;6(2):e16912. PMID: 21359210
Polymenidou M, Lagier-Tourenne C, Hutt KR, Huelga SC et al. Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43. Nat Neurosci 2011 Apr;14(4):459-68. PMID: 21358643
Tamayo P, Cho YJ, Tsherniak A, Greulich H et al. Predicting relapse in patients with medulloblastoma by integrating evidence from clinical and genomic features. J Clin Oncol 2011 Apr 10;29(11):1415-23. PMID: 21357789
Santisteban MS, Hang M, Smith MM. Histone variant H2A.Z and RNA polymerase II transcription elongation. Mol Cell Biol 2011 May;31(9):1848-60. PMID: 21357739
Onaitis M, D'Amico TA, Clark CP, Guinney J et al. A 10-gene progenitor cell signature predicts poor prognosis in lung adenocarcinoma. Ann Thorac Surg 2011 Apr;91(4):1046-50; discussion 1050. PMID: 21353202
Kasturi SP, Skountzou I, Albrecht RA, Koutsonanos D et al. Programming the magnitude and persistence of antibody responses with innate immunity. Nature 2011 Feb 24;470(7335):543-7. PMID: 21350488
Marques F, Sousa JC, Coppola G, Gao F et al. Transcriptome signature of the adult mouse choroid plexus. Fluids Barriers CNS 2011 Jan 18;8(1):10. PMID: 21349147
Coco S, Valdora F, Bonassi S, Scaruffi P et al. Chromosome 9q and 16q loss identified by genome-wide pooled-analysis are associated with tumor aggressiveness in patients with classic medulloblastoma. OMICS 2011 May;15(5):273-80. PMID: 21348762
Miller TW, Balko JM, Ghazoui Z, Dunbier A et al. A gene expression signature from human breast cancer cells with acquired hormone independence identifies MYC as a mediator of antiestrogen resistance. Clin Cancer Res 2011 Apr 1;17(7):2024-34. PMID: 21346144
Scherbak N, Ala-Häivälä A, Brosché M, Böwer N et al. The pea SAD short-chain dehydrogenase/reductase: quinone reduction, tissue distribution, and heterologous expression. Plant Physiol 2011 Apr;155(4):1839-50. PMID: 21343423
Anglesio MS, George J, Kulbe H, Friedlander M et al. IL6-STAT3-HIF signaling and therapeutic response to the angiogenesis inhibitor sunitinib in ovarian clear cell cancer. Clin Cancer Res 2011 Apr 15;17(8):2538-48. PMID: 21343371
Molineris I, Grassi E, Ala U, Di Cunto F et al. Evolution of promoter affinity for transcription factors in the human lineage. Mol Biol Evol 2011 Aug;28(8):2173-83. PMID: 21335606
Mar JC, Wells CA, Quackenbush J. Defining an informativeness metric for clustering gene expression data. Bioinformatics 2011 Apr 15;27(8):1094-100. PMID: 21330289
Knappskog S, Myklebust LM, Busch C, Aloysius T et al. RINF (CXXC5) is overexpressed in solid tumors and is an unfavorable prognostic factor in breast cancer. Ann Oncol 2011 Oct;22(10):2208-15. PMID: 21325450
Butler MW, Fukui T, Salit J, Shaykhiev R et al. Modulation of cystatin A expression in human airway epithelium related to genotype, smoking, COPD, and lung cancer. Cancer Res 2011 Apr 1;71(7):2572-81. PMID: 21325429
Ghazoui Z, Buffa FM, Dunbier AK, Anderson H et al. Close and stable relationship between proliferation and a hypoxia metagene in aromatase inhibitor-treated ER-positive breast cancer. Clin Cancer Res 2011 May 1;17(9):3005-12. PMID: 21325071
Román AC, González-Rico FJ, Moltó E, Hernando H et al. Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch. Genome Res 2011 Mar;21(3):422-32. PMID: 21324874
Baron D, Dubois E, Bihouée A, Teusan R et al. Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns. BMC Genomics 2011 Feb 16;12:113. PMID: 21324190
Tsuzuki S, Taguchi O, Seto M. Promotion and maintenance of leukemia by ERG. Blood 2011 Apr 7;117(14):3858-68. PMID: 21321361
Kwak YT, Radaideh SM, Ding L, Li R et al. Cells lacking IKKα show nuclear cyclin D1 overexpression and a neoplastic phenotype: role of IKKα as a tumor suppressor. Mol Cancer Res 2011 Mar;9(3):341-9. PMID: 21317297
Vicoso B, Bachtrog D. Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite. Genome Biol Evol 2011;3:230-5. PMID: 21317157
Zhang B, Chen B, Wu T, Xuan Z et al. Estimating developmental states of tumors and normal tissues using a linear time-ordered model. BMC Bioinformatics 2011 Feb 11;12:53. PMID: 21310084
Zhang Y, Liu H, Lv J, Xiao X et al. QDMR: a quantitative method for identification of differentially methylated regions by entropy. Nucleic Acids Res 2011 May;39(9):e58. PMID: 21306990
Sugawara H, Iwamoto K, Bundo M, Ueda J et al. Comprehensive DNA methylation analysis of human peripheral blood leukocytes and lymphoblastoid cell lines. Epigenetics 2011 Apr;6(4):508-15. PMID: 21304276
Ouyang J, Juszczynski P, Rodig SJ, Green MR et al. Viral induction and targeted inhibition of galectin-1 in EBV+ posttransplant lymphoproliferative disorders. Blood 2011 Apr 21;117(16):4315-22. PMID: 21300977
Cole SW, Hawkley LC, Arevalo JM, Cacioppo JT. Transcript origin analysis identifies antigen-presenting cells as primary targets of socially regulated gene expression in leukocytes. Proc Natl Acad Sci U S A 2011 Feb 15;108(7):3080-5. PMID: 21300872
Grills C, Jithesh PV, Blayney J, Zhang SD et al. Gene expression meta-analysis identifies VDAC1 as a predictor of poor outcome in early stage non-small cell lung cancer. PLoS One 2011 Jan 31;6(1):e14635. PMID: 21297950
Schulte A, Günther HS, Phillips HS, Kemming D et al. A distinct subset of glioma cell lines with stem cell-like properties reflects the transcriptional phenotype of glioblastomas and overexpresses CXCR4 as therapeutic target. Glia 2011 Apr;59(4):590-602. PMID: 21294158
Saintigny P, Zhang L, Fan YH, El-Naggar AK et al. Gene expression profiling predicts the development of oral cancer. Cancer Prev Res (Phila) 2011 Feb;4(2):218-29. PMID: 21292635
Chen Y, Meyer CA, Liu T, Li W et al. MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data. Genome Biol 2011;12(2):R11. PMID: 21284836
Wang G, Ye Y, Yang X, Liao H et al. Expression-based in silico screening of candidate therapeutic compounds for lung adenocarcinoma. PLoS One 2011 Jan 21;6(1):e14573. PMID: 21283735
Zhang B, Chen B, Wu T, Tan Y et al. Estimating the quality of reprogrammed cells using ES cell differentiation expression patterns. PLoS One 2011 Jan 11;6(1):e15336. PMID: 21283513
Kang HS, Baba T, Mandai M, Matsumura N et al. GPR54 is a target for suppression of metastasis in endometrial cancer. Mol Cancer Ther 2011 Apr;10(4):580-90. PMID: 21282360
Scott MS, Boisvert FM, Lamond AI, Barton GJ. PNAC: a protein nucleolar association classifier. BMC Genomics 2011 Jan 27;12:74. PMID: 21272300
Han J, Qureshi AA, Nan H, Zhang J et al. A germline variant in the interferon regulatory factor 4 gene as a novel skin cancer risk locus. Cancer Res 2011 Mar 1;71(5):1533-9. PMID: 21270109
Birkbak NJ, Eklund AC, Li Q, McClelland SE et al. Paradoxical relationship between chromosomal instability and survival outcome in cancer. Cancer Res 2011 May 15;71(10):3447-52. PMID: 21270108
Zhou Y, Shi R, Bao Y, Li CZ et al. [Bioinformatic analysis of genes related to temporal epilepsy]. Nan Fang Yi Ke Da Xue Xue Bao 2011 Jan;31(1):180-3. PMID: 21269987
Diez-Roux G, Banfi S, Sultan M, Geffers L et al. A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol 2011 Jan 18;9(1):e1000582. PMID: 21267068
Ivanov IP, Firth AE, Michel AM, Atkins JF et al. Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences. Nucleic Acids Res 2011 May;39(10):4220-34. PMID: 21266472
Niemi NM, Lanning NJ, Klomp JA, Tait SW et al. MK-STYX, a catalytically inactive phosphatase regulating mitochondrially dependent apoptosis. Mol Cell Biol 2011 Apr;31(7):1357-68. PMID: 21262771
Prat Y, Fromer M, Linial N, Linial M. Recovering key biological constituents through sparse representation of gene expression. Bioinformatics 2011 Mar 1;27(5):655-61. PMID: 21258061
Smith SC, Havaleshko DM, Moon K, Baras AS et al. Use of yeast chemigenomics and COXEN informatics in preclinical evaluation of anticancer agents. Neoplasia 2011 Jan;13(1):72-80. PMID: 21253455
Gamazon ER, Im HK, O'Donnell PH, Ziliak D et al. Comprehensive evaluation of the contribution of X chromosome genes to platinum sensitivity. Mol Cancer Ther 2011 Mar;10(3):472-80. PMID: 21252287
Søkilde R, Kaczkowski B, Podolska A, Cirera S et al. Global microRNA analysis of the NCI-60 cancer cell panel. Mol Cancer Ther 2011 Mar;10(3):375-84. PMID: 21252286
Posekany A, Felsenstein K, Sykacek P. Biological assessment of robust noise models in microarray data analysis. Bioinformatics 2011 Mar 15;27(6):807-14. PMID: 21252077
Gao L, Fang Z, Zhang K, Zhi D et al. Length bias correction for RNA-seq data in gene set analyses. Bioinformatics 2011 Mar 1;27(5):662-9. PMID: 21252076
Coutant C, Rouzier R, Qi Y, Lehmann-Che J et al. Distinct p53 gene signatures are needed to predict prognosis and response to chemotherapy in ER-positive and ER-negative breast cancers. Clin Cancer Res 2011 Apr 15;17(8):2591-601. PMID: 21248301
Liao Q, Liu C, Yuan X, Kang S et al. Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. Nucleic Acids Res 2011 May;39(9):3864-78. PMID: 21247874
Steffen B, Knop M, Bergholz U, Vakhrusheva O et al. AML1/ETO induces self-renewal in hematopoietic progenitor cells via the Groucho-related amino-terminal AES protein. Blood 2011 Apr 21;117(16):4328-37. PMID: 21245488
Fujiwara K, Yuwanita I, Hollern DP, Andrechek ER. Prediction and genetic demonstration of a role for activator E2Fs in Myc-induced tumors. Cancer Res 2011 Mar 1;71(5):1924-32. PMID: 21245101
Mitra R, Lee J, Jo J, Milani M et al. Prediction of postoperative recurrence-free survival in non-small cell lung cancer by using an internationally validated gene expression model. Clin Cancer Res 2011 May 1;17(9):2934-46. PMID: 21242119
Fukao T, Yeung E, Bailey-Serres J. The submergence tolerance regulator SUB1A mediates crosstalk between submergence and drought tolerance in rice. Plant Cell 2011 Jan;23(1):412-27. PMID: 21239643
Sasaki D, Imaizumi Y, Hasegawa H, Osaka A et al. Overexpression of Enhancer of zeste homolog 2 with trimethylation of lysine 27 on histone H3 in adult T-cell leukemia/lymphoma as a target for epigenetic therapy. Haematologica 2011 May;96(5):712-9. PMID: 21228036
Lu ZX, Jiang P, Cai JJ, Xing Y. Context-dependent robustness to 5' splice site polymorphisms in human populations. Hum Mol Genet 2011 Mar 15;20(6):1084-96. PMID: 21224255
Cruchaga C, Graff C, Chiang HH, Wang J et al. Association of TMEM106B gene polymorphism with age at onset in granulin mutation carriers and plasma granulin protein levels. Arch Neurol 2011 May;68(5):581-6. PMID: 21220649
Baron D, Bihouée A, Teusan R, Dubois E et al. MADGene: retrieval and processing of gene identifier lists for the analysis of heterogeneous microarray datasets. Bioinformatics 2011 Mar 1;27(5):725-6. PMID: 21216776
Mustafiz A, Singh AK, Pareek A, Sopory SK et al. Genome-wide analysis of rice and Arabidopsis identifies two glyoxalase genes that are highly expressed in abiotic stresses. Funct Integr Genomics 2011 Jun;11(2):293-305. PMID: 21213008
Gonzalez-Roca E, Garcia-Albéniz X, Rodriguez-Mulero S, Gomis RR et al. Accurate expression profiling of very small cell populations. PLoS One 2010 Dec 28;5(12):e14418. PMID: 21203435
Haddrill PR, Zeng K, Charlesworth B. Determinants of synonymous and nonsynonymous variability in three species of Drosophila. Mol Biol Evol 2011 May;28(5):1731-43. PMID: 21191087
Pedicini M, Barrenäs F, Clancy T, Castiglione F et al. Combining network modeling and gene expression microarray analysis to explore the dynamics of Th1 and Th2 cell regulation. PLoS Comput Biol 2010 Dec 16;6(12):e1001032. PMID: 21187905
Chen X, Xu J, Huang B, Li J et al. A sub-pathway-based approach for identifying drug response principal network. Bioinformatics 2011 Mar 1;27(5):649-54. PMID: 21186246
Yang CH, Chuang LY, Shih TM, Chang HW. hSAGEing: an improved SAGE-based software for identification of human tissue-specific or common tumor markers and suppressors. PLoS One 2010 Dec 17;5(12):e14369. PMID: 21179408
Kaya KD, Karakülah G, Yakicier CM, Acar AC et al. mESAdb: microRNA expression and sequence analysis database. Nucleic Acids Res 2011 Jan;39(Database issue):D170-80. PMID: 21177657
Ye T, Krebs AR, Choukrallah MA, Keime C et al. seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res 2011 Mar;39(6):e35. PMID: 21177645
Gentles AJ, Plevritis SK, Majeti R, Alizadeh AA. Association of a leukemic stem cell gene expression signature with clinical outcomes in acute myeloid leukemia. JAMA 2010 Dec 22;304(24):2706-15. PMID: 21177505
Xu H, Lemischka IR, Ma'ayan A. SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells. BMC Syst Biol 2010 Dec 21;4:173. PMID: 21176149
Klemm F, Bleckmann A, Siam L, Chuang HN et al. β-catenin-independent WNT signaling in basal-like breast cancer and brain metastasis. Carcinogenesis 2011 Mar;32(3):434-42. PMID: 21173432
Moreaux J, Klein B, Bataille R, Descamps G et al. A high-risk signature for patients with multiple myeloma established from the molecular classification of human myeloma cell lines. Haematologica 2011 Apr;96(4):574-82. PMID: 21173094
Liu W, Li D, Liu Q, Zhu Y et al. A novel parametric approach to mine gene regulatory relationship from microarray datasets. BMC Bioinformatics 2010 Dec 14;11 Suppl 11:S15. PMID: 21172050
Xu T, Ping J, Yu Y, Yu F et al. Revealing parasite influence in metabolic pathways in Apicomplexa infected patients. BMC Bioinformatics 2010 Dec 14;11 Suppl 11:S13. PMID: 21172048
Yu Y, Xu T, Yu Y, Hao P et al. Association of tissue lineage and gene expression: conservatively and differentially expressed genes define common and special functions of tissues. BMC Bioinformatics 2010 Dec 14;11 Suppl 11:S1. PMID: 21172044
Engreitz JM, Morgan AA, Dudley JT, Chen R et al. Content-based microarray search using differential expression profiles. BMC Bioinformatics 2010 Dec 21;11:603. PMID: 21172034
Shats I, Gatza ML, Chang JT, Mori S et al. Using a stem cell-based signature to guide therapeutic selection in cancer. Cancer Res 2011 Mar 1;71(5):1772-80. PMID: 21169407
Rybarczyk-Filho JL, Castro MA, Dalmolin RJ, Moreira JC et al. Towards a genome-wide transcriptogram: the Saccharomyces cerevisiae case. Nucleic Acids Res 2011 Apr;39(8):3005-16. PMID: 21169199
Wang L, Guo K, Li Y, Tu Y et al. Expression profiling and integrative analysis of the CESA/CSL superfamily in rice. BMC Plant Biol 2010 Dec 20;10:282. PMID: 21167079
McCole RB, Loughran NB, Chahal M, Fernandes LP et al. A case-by-case evolutionary analysis of four imprinted retrogenes. Evolution 2011 May;65(5):1413-27. PMID: 21166792
Klomp JA, Petillo D, Niemi NM, Dykema KJ et al. Birt-Hogg-Dubé renal tumors are genetically distinct from other renal neoplasias and are associated with up-regulation of mitochondrial gene expression. BMC Med Genomics 2010 Dec 16;3:59. PMID: 21162720
Richter W, Xie M, Scheitrum C, Krall J et al. Conserved expression and functions of PDE4 in rodent and human heart. Basic Res Cardiol 2011 Mar;106(2):249-62. PMID: 21161247
Sarasquete ME, Gutiérrez NC, Misiewicz-Krzeminska I, Paiva B et al. Upregulation of Dicer is more frequent in monoclonal gammopathies of undetermined significance than in multiple myeloma patients and is associated with longer survival in symptomatic myeloma patients. Haematologica 2011 Mar;96(3):468-71. PMID: 21160068
Tuna M, Smid M, Zhu D, Martens JW et al. Association between acquired uniparental disomy and homozygous mutations and HER2/ER/PR status in breast cancer. PLoS One 2010 Nov 30;5(11):e15094. PMID: 21152100
Kilpinen S, Ojala K, Kallioniemi O. Analysis of kinase gene expression patterns across 5681 human tissue samples reveals functional genomic taxonomy of the kinome. PLoS One 2010 Dec 3;5(12):e15068. PMID: 21151926
Tominaga D. Periodicity detection method for small-sample time series datasets. Bioinform Biol Insights 2010 Nov 22;4:127-36. PMID: 21151841
Rolland AD, Lehmann KP, Johnson KJ, Gaido KW et al. Uncovering gene regulatory networks during mouse fetal germ cell development. Biol Reprod 2011 Apr;84(4):790-800. PMID: 21148109
Ghosh HS, Cisse B, Bunin A, Lewis KL et al. Continuous expression of the transcription factor e2-2 maintains the cell fate of mature plasmacytoid dendritic cells. Immunity 2010 Dec 14;33(6):905-16. PMID: 21145760
Maresh EL, Mah V, Alavi M, Horvath S et al. Differential expression of anterior gradient gene AGR2 in prostate cancer. BMC Cancer 2010 Dec 13;10:680. PMID: 21144054
Kim J, Ji M, DiDonato JA, Rackley RR et al. An hTERT-immortalized human urothelial cell line that responds to anti-proliferative factor. In Vitro Cell Dev Biol Anim 2011 Jan;47(1):2-9. PMID: 21136194
Wang L, Huang J, Jiang M. CREB5 computational regulation network construction and analysis between frontal cortex of HIV encephalitis (HIVE) and HIVE-control patients. Cell Biochem Biophys 2011 Jul;60(3):199-207. PMID: 21132541
Saito M, Kumamoto K, Robles AI, Horikawa I et al. Targeted disruption of Ing2 results in defective spermatogenesis and development of soft-tissue sarcomas. PLoS One 2010 Nov 19;5(11):e15541. PMID: 21124965
Kerkel K, Schupf N, Hatta K, Pang D et al. Altered DNA methylation in leukocytes with trisomy 21. PLoS Genet 2010 Nov 18;6(11):e1001212. PMID: 21124956
Wang X, Björklund S, Wasik AM, Grandien A et al. Gene expression profiling and chromatin immunoprecipitation identify DBN1, SETMAR and HIG2 as direct targets of SOX11 in mantle cell lymphoma. PLoS One 2010 Nov 22;5(11):e14085. PMID: 21124928
Ye ZQ, Niu S, Yu Y, Yu H et al. Analyses of copy number variation of GK rat reveal new putative type 2 diabetes susceptibility loci. PLoS One 2010 Nov 23;5(11):e14077. PMID: 21124896
Nodine MD, Bartel DP. MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis. Genes Dev 2010 Dec 1;24(23):2678-92. PMID: 21123653
Maess MB, Sendelbach S, Lorkowski S. Selection of reliable reference genes during THP-1 monocyte differentiation into macrophages. BMC Mol Biol 2010 Dec 1;11:90. PMID: 21122122
Daniels JP, Gull K, Wickstead B. Cell biology of the trypanosome genome. Microbiol Mol Biol Rev 2010 Dec;74(4):552-69. PMID: 21119017
Warsow G, Greber B, Falk SS, Harder C et al. ExprEssence--revealing the essence of differential experimental data in the context of an interaction/regulation net-work. BMC Syst Biol 2010 Nov 30;4:164. PMID: 21118483
Wu FL, Jin WB, Li JH, Guo AG. Targets for human encoded microRNAs in HBV genes. Virus Genes 2011 Apr;42(2):157-61. PMID: 21113793
Neveu P, Kye MJ, Qi S, Buchholz DE et al. MicroRNA profiling reveals two distinct p53-related human pluripotent stem cell states. Cell Stem Cell 2010 Dec 3;7(6):671-81. PMID: 21112562
Anton MA, Aramburu A, Rubio A. Improvements to previous algorithms to predict gene structure and isoform concentrations using Affymetrix Exon arrays. BMC Bioinformatics 2010 Nov 26;11:578. PMID: 21110835
Rödelsperger C, Guo G, Kolanczyk M, Pletschacher A et al. Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactions. Nucleic Acids Res 2011 Apr;39(7):2492-502. PMID: 21109530
Narsai R, Castleden I, Whelan J. Common and distinct organ and stress responsive transcriptomic patterns in Oryza sativa and Arabidopsis thaliana. BMC Plant Biol 2010 Nov 24;10:262. PMID: 21106056
Xiong Y, Chen X, Chen Z, Wang X et al. RNA sequencing shows no dosage compensation of the active X-chromosome. Nat Genet 2010 Dec;42(12):1043-7. PMID: 21102464
Cho YJ, Tsherniak A, Tamayo P, Santagata S et al. Integrative genomic analysis of medulloblastoma identifies a molecular subgroup that drives poor clinical outcome. J Clin Oncol 2011 Apr 10;29(11):1424-30. PMID: 21098324
Gupta R, Bhattacharyya A, Agosto-Perez FJ, Wickramasinghe P et al. MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data. Nucleic Acids Res 2011 Jan;39(Database issue):D92-7. PMID: 21097880
Thomas R, de la Torre L, Chang X, Mehrotra S. Validation and characterization of DNA microarray gene expression data distribution and associated moments. BMC Bioinformatics 2010 Nov 24;11:576. PMID: 21092329
Dubey S, Misra P, Dwivedi S, Chatterjee S et al. Transcriptomic and metabolomic shifts in rice roots in response to Cr (VI) stress. BMC Genomics 2010 Nov 20;11:648. PMID: 21092124
Thorrez L, Laudadio I, Van Deun K, Quintens R et al. Tissue-specific disallowance of housekeeping genes: the other face of cell differentiation. Genome Res 2011 Jan;21(1):95-105. PMID: 21088282
Merico D, Isserlin R, Stueker O, Emili A et al. Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One 2010 Nov 15;5(11):e13984. PMID: 21085593
Folsom JP, Richards L, Pitts B, Roe F et al. Physiology of Pseudomonas aeruginosa in biofilms as revealed by transcriptome analysis. BMC Microbiol 2010 Nov 17;10:294. PMID: 21083928
Cahan P, Graubert TA. Integrated genomics of susceptibility to alkylator-induced leukemia in mice. BMC Genomics 2010 Nov 17;11:638. PMID: 21080971
Verzi MP, Shin H, He HH, Sulahian R et al. Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2. Dev Cell 2010 Nov 16;19(5):713-26. PMID: 21074721
Komurov K, Ram PT. Patterns of human gene expression variance show strong associations with signaling network hierarchy. BMC Syst Biol 2010 Nov 12;4:154. PMID: 21073694
Peng S, Rao VS, Adelman RA, Rizzolo LJ. Claudin-19 and the barrier properties of the human retinal pigment epithelium. Invest Ophthalmol Vis Sci 2011 Mar;52(3):1392-403. PMID: 21071746
Pastuszak AW, Joachimiak MP, Blanchette M, Rio DC et al. An SF1 affinity model to identify branch point sequences in human introns. Nucleic Acids Res 2011 Mar;39(6):2344-56. PMID: 21071404
Uckun FM, Pitt J, Qazi S. JAK3 pathway is constitutively active in B-lineage acute lymphoblastic leukemia. Expert Rev Anticancer Ther 2011 Jan;11(1):37-48. PMID: 21070101
Gonçalves A, Finetti P, Sabatier R, Gilabert M et al. Poly(ADP-ribose) polymerase-1 mRNA expression in human breast cancer: a meta-analysis. Breast Cancer Res Treat 2011 May;127(1):273-81. PMID: 21069454
Cho S, Jun Y, Lee S, Choi HS et al. miRGator v2.0: an integrated system for functional investigation of microRNAs. Nucleic Acids Res 2011 Jan;39(Database issue):D158-62. PMID: 21062822
Murthy SR, Pacak K, Loh YP. Carboxypeptidase E: elevated expression correlated with tumor growth and metastasis in pheochromocytomas and other cancers. Cell Mol Neurobiol 2010 Nov;30(8):1377-81. PMID: 21061162
Wang L, Huang J, Jiang M, Sun L. MYBPC1 computational phosphoprotein network construction and analysis between frontal cortex of HIV encephalitis (HIVE) and HIVE-control patients. Cell Mol Neurobiol 2011 Mar;31(2):233-41. PMID: 21061152
Censi F, Calcagnini G, Bartolini P, Giuliani A. A systems biology strategy on differential gene expression data discloses some biological features of atrial fibrillation. PLoS One 2010 Oct 29;5(10):e13668. PMID: 21060823
Jones L, Wei G, Sevcikova S, Phan V et al. Gain of MYC underlies recurrent trisomy of the MYC chromosome in acute promyelocytic leukemia. J Exp Med 2010 Nov 22;207(12):2581-94. PMID: 21059853
Wang L, Srivastava AK, Schwartz CE. Microarray data integration for genome-wide analysis of human tissue-selective gene expression. BMC Genomics 2010 Nov 2;11 Suppl 2:S15. PMID: 21047382
Mercer TR, Dinger ME, Bracken CP, Kolle G et al. Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome. Genome Res 2010 Dec;20(12):1639-50. PMID: 21045082
Garg R, Jhanwar S, Tyagi AK, Jain M. Genome-wide survey and expression analysis suggest diverse roles of glutaredoxin gene family members during development and response to various stimuli in rice. DNA Res 2010 Dec;17(6):353-67. PMID: 21044985
Lacson R, Mbagwu M, Yousif H, Ohno-Machado L. Assessing the quality of annotations in asthma gene expression experiments. BMC Bioinformatics 2010 Oct 28;11 Suppl 9:S8. PMID: 21044366
Morgan AA, Khatri P, Jones RH, Sarwal MM et al. Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants. BMC Bioinformatics 2010 Oct 28;11 Suppl 9:S6. PMID: 21044364
Zhang J, Xiang Y, Ding L, Keen-Circle K et al. Using gene co-expression network analysis to predict biomarkers for chronic lymphocytic leukemia. BMC Bioinformatics 2010 Oct 28;11 Suppl 9:S5. PMID: 21044363
Payne PR, Huang K, Keen-Circle K, Kundu A et al. Multi-dimensional discovery of biomarker and phenotype complexes. BMC Bioinformatics 2010 Oct 28;11 Suppl 9:S3. PMID: 21044361
Chang HH, McGeachie M, Alterovitz G, Ramoni MF. Mapping transcription mechanisms from multimodal genomic data. BMC Bioinformatics 2010 Oct 28;11 Suppl 9:S2. PMID: 21044360
Yang X, Lee Y, Huang Y, Chen JL et al. Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models. BMC Bioinformatics 2010 Oct 28;11 Suppl 9:S11. PMID: 21044358
Gorlov IP, Sircar K, Zhao H, Maity SN et al. Prioritizing genes associated with prostate cancer development. BMC Cancer 2010 Nov 2;10:599. PMID: 21044312
Pottelberge GR, Mestdagh P, Bracke KR, Thas O et al. MicroRNA expression in induced sputum of smokers and patients with chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2011 Apr 1;183(7):898-906. PMID: 21037022
Langdon WB, Upton GJ, da Silva Camargo R, Harrison AP. A survey of spatial defects in Homo Sapiens Affymetrix GeneChips. IEEE/ACM Trans Comput Biol Bioinform 2010 Oct-Dec;7(4):647-53. PMID: 21030732
Suo C, Salim A, Chia KS, Pawitan Y et al. Modified least-variant set normalization for miRNA microarray. RNA 2010 Dec;16(12):2293-303. PMID: 20980676
Li J, Lenferink AE, Deng Y, Collins C et al. Identification of high-quality cancer prognostic markers and metastasis network modules. Nat Commun 2010 Jul 13;1:34. PMID: 20975711
Cushing L, Kuang PP, Qian J, Shao F et al. miR-29 is a major regulator of genes associated with pulmonary fibrosis. Am J Respir Cell Mol Biol 2011 Aug;45(2):287-94. PMID: 20971881
Bareke E, Pierre M, Gaigneaux A, De Meulder B et al. PathEx: a novel multi factors based datasets selector web tool. BMC Bioinformatics 2010 Oct 22;11:528. PMID: 20969778
Miecznikowski JC, Wang D, Liu S, Sucheston L et al. Comparative survival analysis of breast cancer microarray studies identifies important prognostic genetic pathways. BMC Cancer 2010 Oct 21;10:573. PMID: 20964848
Kleger A, Seufferlein T, Malan D, Tischendorf M et al. Modulation of calcium-activated potassium channels induces cardiogenesis of pluripotent stem cells and enrichment of pacemaker-like cells. Circulation 2010 Nov 2;122(18):1823-36. PMID: 20956206
Gatti DM, Barry WT, Nobel AB, Rusyn I et al. Heading down the wrong pathway: on the influence of correlation within gene sets. BMC Genomics 2010 Oct 18;11:574. PMID: 20955544
Liu Y, Han D, Han Y, Yan Z et al. Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq. Nucleic Acids Res 2011 Mar;39(4):1408-18. PMID: 20952408
Thorner AR, Parker JS, Hoadley KA, Perou CM. Potential tumor suppressor role for the c-Myb oncogene in luminal breast cancer. PLoS One 2010 Oct 7;5(10):e13073. PMID: 20949095
Wang Y, Robbins KR, Rekaya R. Comparison of computational models for assessing conservation of gene expression across species. PLoS One 2010 Oct 8;5(10):e13239. PMID: 20949029
Gunaratne GH, Gunaratne PH, Seemann L, Török A. Using effective subnetworks to predict selected properties of gene networks. PLoS One 2010 Oct 8;5(10):e13080. PMID: 20949025
Nguyen TT, Almon RR, Dubois DC, Jusko WJ et al. Comparative analysis of acute and chronic corticosteroid pharmacogenomic effects in rat liver: transcriptional dynamics and regulatory structures. BMC Bioinformatics 2010 Oct 14;11:515. PMID: 20946642
Kelly VR, Xu B, Kuick R, Koenig RJ et al. Dax1 up-regulates Oct4 expression in mouse embryonic stem cells via LRH-1 and SRA. Mol Endocrinol 2010 Dec;24(12):2281-91. PMID: 20943815
Xu Y, Hu W, Chang Z, Duanmu H et al. Prediction of human protein-protein interaction by a mixed Bayesian model and its application to exploring underlying cancer-related pathway crosstalk. J R Soc Interface 2011 Apr 6;8(57):555-67. PMID: 20943681
Berger F, De Meulder B, Gaigneaux A, Depiereux S et al. Functional analysis: evaluation of response intensities--tailoring ANOVA for lists of expression subsets. BMC Bioinformatics 2010 Oct 13;11:510. PMID: 20942918
Lai Y. Differential expression analysis of Digital Gene Expression data: RNA-tag filtering, comparison of t-type tests and their genome-wide co-expression based adjustments. Int J Bioinform Res Appl 2010;6(4):353-65. PMID: 20940123
Gurtowski J, Cancio A, Shah H, Levovitz C et al. Geoseq: a tool for dissecting deep-sequencing datasets. BMC Bioinformatics 2010 Oct 12;11:506. PMID: 20939882
Weber CC, Hurst LD. Intronic AT skew is a defendable proxy for germline transcription but does not predict crossing-over or protein evolution rates in Drosophila melanogaster. J Mol Evol 2010 Dec;71(5-6):415-26. PMID: 20938653
Thorsen K, Mansilla F, Schepeler T, Øster B et al. Alternative splicing of SLC39A14 in colorectal cancer is regulated by the Wnt pathway. Mol Cell Proteomics 2011 Jan;10(1):M110.002998. PMID: 20938052
Freyhult E, Landfors M, Önskog J, Hvidsten TR et al. Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering. BMC Bioinformatics 2010 Oct 11;11:503. PMID: 20937082
Gaspar N, Marshall L, Perryman L, Bax DA et al. MGMT-independent temozolomide resistance in pediatric glioblastoma cells associated with a PI3-kinase-mediated HOX/stem cell gene signature. Cancer Res 2010 Nov 15;70(22):9243-52. PMID: 20935218
Swindell WR. Metallothionein and the biology of aging. Ageing Res Rev 2011 Jan;10(1):132-45. PMID: 20933613
Ciraci C, Tuggle CK, Wannemuehler MJ, Nettleton D et al. Unique genome-wide transcriptome profiles of chicken macrophages exposed to Salmonella-derived endotoxin. BMC Genomics 2010 Oct 8;11:545. PMID: 20929591
Kupershmidt I, Su QJ, Grewal A, Sundaresh S et al. Ontology-based meta-analysis of global collections of high-throughput public data. PLoS One 2010 Sep 29;5(9). PMID: 20927376
Cao K, Chen-Plotkin AS, Plotkin JB, Wang LS. Age-correlated gene expression in normal and neurodegenerative human brain tissues. PLoS One 2010 Sep 29;5(9). PMID: 20927326
Mangelsen E, Kilian J, Harter K, Jansson C et al. Transcriptome analysis of high-temperature stress in developing barley caryopses: early stress responses and effects on storage compound biosynthesis. Mol Plant 2011 Jan;4(1):97-115. PMID: 20924027
Huang JX, Wang L, Jiang MH. TNFRSF11B computational development network construction and analysis between frontal cortex of HIV encephalitis (HIVE) and HIVE-control patients. J Inflamm (Lond) 2010 Sep 30;7:50. PMID: 20920282
Chen R, Sigdel TK, Li L, Kambham N et al. Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions. PLoS Comput Biol 2010 Sep 23;6(9). PMID: 20885780
Lin CC, Chen LC, Tseng VS, Yan JJ et al. Malignant pleural effusion cells show aberrant glucose metabolism gene expression. Eur Respir J 2011 Jun;37(6):1453-65. PMID: 20884743
Marvi M, Rose JB, Bang A, Moon BC et al. Nucleoside transporter expression profiles in human cardiac tissue show striking individual variability with overall predominance of hENT1. Eur J Pharm Sci 2010 Dec 23;41(5):685-91. PMID: 20883780
Agam A, Yalcin B, Bhomra A, Cubin M et al. Elusive copy number variation in the mouse genome. PLoS One 2010 Sep 21;5(9):e12839. PMID: 20877625
Dawany NB, Tozeren A. Asymmetric microarray data produces gene lists highly predictive of research literature on multiple cancer types. BMC Bioinformatics 2010 Sep 27;11:483. PMID: 20875095
Toedling J, Ciaudo C, Voinnet O, Heard E et al. Girafe--an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads. Bioinformatics 2010 Nov 15;26(22):2902-3. PMID: 20861030
Aryee MJ, Wu Z, Ladd-Acosta C, Herb B et al. Accurate genome-scale percentage DNA methylation estimates from microarray data. Biostatistics 2011 Apr;12(2):197-210. PMID: 20858772
Yau C, Mouradov D, Jorissen RN, Colella S et al. A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data. Genome Biol 2010;11(9):R92. PMID: 20858232
Cai YD, Huang T, Feng KY, Hu L et al. A unified 35-gene signature for both subtype classification and survival prediction in diffuse large B-cell lymphomas. PLoS One 2010 Sep 13;5(9):e12726. PMID: 20856936
Spade DJ, Griffitt RJ, Liu L, Brown-Peterson NJ et al. Queen conch (Strombus gigas) testis regresses during the reproductive season at nearshore sites in the Florida Keys. PLoS One 2010 Sep 15;5(9):e12737. PMID: 20856805
Bishop CV, Bogan RL, Hennebold JD, Stouffer RL. Analysis of microarray data from the macaque corpus luteum; the search for common themes in primate luteal regression. Mol Hum Reprod 2011 Mar;17(3):143-51. PMID: 20855453
Zheng M, Liu GX, Zhou CG, Liang YC et al. Gravitation field algorithm and its application in gene cluster. Algorithms Mol Biol 2010 Sep 20;5:32. PMID: 20854683
Zaravinos A, Chatziioannou M, Lambrou GI, Boulalas I et al. Implication of RAF and RKIP genes in urinary bladder cancer. Pathol Oncol Res 2011 Jun;17(2):181-90. PMID: 20853079
Park YY, Choi HS, Lee JS. Systems-level analysis of gene expression data revealed NR0B2/SHP as potential tumor suppressor in human liver cancer. Mol Cells 2010 Nov;30(5):485-91. PMID: 20853064
Teider N, Scott DK, Neiss A, Weeraratne SD et al. Neuralized1 causes apoptosis and downregulates Notch target genes in medulloblastoma. Neuro Oncol 2010 Dec;12(12):1244-56. PMID: 20847082
Sun H, Wu J, Wickramasinghe P, Pal S et al. Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq. Nucleic Acids Res 2011 Jan;39(1):190-201. PMID: 20843783
Nitsch D, Gonçalves JP, Ojeda F, de Moor B et al. Candidate gene prioritization by network analysis of differential expression using machine learning approaches. BMC Bioinformatics 2010 Sep 14;11:460. PMID: 20840752
Rao S, Zhen S, Roumiantsev S, McDonald LT et al. Differential roles of Sall4 isoforms in embryonic stem cell pluripotency. Mol Cell Biol 2010 Nov;30(22):5364-80. PMID: 20837710
Gelly JC, Orgeur M, Jacq C, Lelandais G. MitoGenesisDB: an expression data mining tool to explore spatio-temporal dynamics of mitochondrial biogenesis. Nucleic Acids Res 2011 Jan;39(Database issue):D1079-84. PMID: 20833631
Dexter TJ, Sims D, Mitsopoulos C, Mackay A et al. Genomic distance entrained clustering and regression modelling highlights interacting genomic regions contributing to proliferation in breast cancer. BMC Syst Biol 2010 Sep 8;4:127. PMID: 20825665
Patel VN, Bebek G, Mariadason JM, Wang D et al. Prediction and testing of biological networks underlying intestinal cancer. PLoS One 2010 Sep 1;5(9). PMID: 20824133
Serb JM, Orr MC, West Greenlee MH. Using evolutionary conserved modules in gene networks as a strategy to leverage high throughput gene expression queries. PLoS One 2010 Sep 2;5(9). PMID: 20824082
Gille C, Bölling C, Hoppe A, Bulik S et al. HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. Mol Syst Biol 2010 Sep 7;6:411. PMID: 20823849
Dao P, Colak R, Salari R, Moser F et al. Inferring cancer subnetwork markers using density-constrained biclustering. Bioinformatics 2010 Sep 15;26(18):i625-31. PMID: 20823331
Zavadil J, Ye H, Liu Z, Wu J et al. Profiling and functional analyses of microRNAs and their target gene products in human uterine leiomyomas. PLoS One 2010 Aug 24;5(8):e12362. PMID: 20808773
Fernandez-Valverde SL, Taft RJ, Mattick JS. Dynamic isomiR regulation in Drosophila development. RNA 2010 Oct;16(10):1881-8. PMID: 20805289
Lu TP, Tsai MH, Lee JM, Hsu CP et al. Identification of a novel biomarker, SEMA5A, for non-small cell lung carcinoma in nonsmoking women. Cancer Epidemiol Biomarkers Prev 2010 Oct;19(10):2590-7. PMID: 20802022
Yu Y, Ping J, Chen H, Jiao L et al. A comparative analysis of liver transcriptome suggests divergent liver function among human, mouse and rat. Genomics 2010 Nov;96(5):281-9. PMID: 20800674
Zhang XY, Shi L, Liu Y, Tian F et al. ICPS: an integrative cancer profiler system. Bioinformatics 2010 Oct 15;26(20):2649-50. PMID: 20736342
Blow MJ, McCulley DJ, Li Z, Zhang T et al. ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet 2010 Sep;42(9):806-10. PMID: 20729851
Zhang M, Zhang Y, Liu L, Yu L et al. Gene Expression Browser: large-scale and cross-experiment microarray data integration, management, search & visualization. BMC Bioinformatics 2010 Aug 20;11:433. PMID: 20727159
Takasugi M, Yagi S, Hirabayashi K, Shiota K. DNA methylation status of nuclear-encoded mitochondrial genes underlies the tissue-dependent mitochondrial functions. BMC Genomics 2010 Aug 19;11:481. PMID: 20723256
Wong EH, Smith DK, Rabadan R, Peiris M et al. Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus. BMC Evol Biol 2010 Aug 19;10:253. PMID: 20723216
Assou S, Boumela I, Haouzi D, Anahory T et al. Dynamic changes in gene expression during human early embryo development: from fundamental aspects to clinical applications. Hum Reprod Update 2011 Mar-Apr;17(2):272-90. PMID: 20716614
Jennen DG, Gaj S, Giesbertz PJ, van Delft JH et al. Biotransformation pathway maps in WikiPathways enable direct visualization of drug metabolism related expression changes. Drug Discov Today 2010 Oct;15(19-20):851-8. PMID: 20708095
Le HS, Oltvai ZN, Bar-Joseph Z. Cross-species queries of large gene expression databases. Bioinformatics 2010 Oct 1;26(19):2416-23. PMID: 20702396
Sa Q, Hart E, Nadeau JH, Hoover-Plow JL. Mouse chromosome 17 candidate modifier genes for thrombosis. Mamm Genome 2010 Aug;21(7-8):337-49. PMID: 20700597
Cheng WC, Tsai ML, Chang CW, Huang CL et al. Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database. BMC Bioinformatics 2010 Aug 10;11:421. PMID: 20698961
Verzi MP, Hatzis P, Sulahian R, Philips J et al. TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions. Proc Natl Acad Sci U S A 2010 Aug 24;107(34):15157-62. PMID: 20696899
Zhang W, Gao S, Zhou X, Xia J et al. Multiple distinct small RNAs originate from the same microRNA precursors. Genome Biol 2010;11(8):R81. PMID: 20696037
Finka A, Mattoo RU, Goloubinoff P. Meta-analysis of heat- and chemically upregulated chaperone genes in plant and human cells. Cell Stress Chaperones 2011 Jan;16(1):15-31. PMID: 20694844
Ling KH, Hewitt CA, Beissbarth T, Hyde L et al. Spatiotemporal regulation of multiple overlapping sense and novel natural antisense transcripts at the Nrgn and Camk2n1 gene loci during mouse cerebral corticogenesis. Cereb Cortex 2011 Mar;21(3):683-97. PMID: 20693275
Park SG, Choi SS. Expression breadth and expression abundance behave differently in correlations with evolutionary rates. BMC Evol Biol 2010 Aug 7;10:241. PMID: 20691101
Salmon-Divon M, Dvinge H, Tammoja K, Bertone P. PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci. BMC Bioinformatics 2010 Aug 6;11:415. PMID: 20691053
Swindell WR, Johnston A, Gudjonsson JE. Transcriptional profiles of leukocyte populations provide a tool for interpreting gene expression patterns associated with high fat diet in mice. PLoS One 2010 Jul 29;5(7):e11861. PMID: 20686622
Ochsner SA, Watkins CM, LaGrone BS, Steffen DL et al. Research resource: Tissue-specific transcriptomics and cistromics of nuclear receptor signaling: a web research resource. Mol Endocrinol 2010 Oct;24(10):2065-9. PMID: 20685849
De S, Zhang Y, Garner JR, Wang SA et al. Disease and phenotype gene set analysis of disease-based gene expression in mouse and human. Physiol Genomics 2010 Oct;42A(2):162-7. PMID: 20682848
Newman AM, Cooper JB. Lab-specific gene expression signatures in pluripotent stem cells. Cell Stem Cell 2010 Aug 6;7(2):258-62. PMID: 20682451
Weng YI, Hsu PY, Liyanarachchi S, Liu J et al. Epigenetic influences of low-dose bisphenol A in primary human breast epithelial cells. Toxicol Appl Pharmacol 2010 Oct 15;248(2):111-21. PMID: 20678512
Wang G, Ye Y, Zheng W, Ma W. [Identification of candidate genes for lung adenocarcinoma using Toppgene]. Zhongguo Fei Ai Za Zhi 2010 Apr;13(4):282-6. PMID: 20677550
Tsai CC, Chen CL, Liu HC, Lee YT et al. Overexpression of hTERT increases stem-like properties and decreases spontaneous differentiation in human mesenchymal stem cell lines. J Biomed Sci 2010 Jul 29;17:64. PMID: 20670406
Cappallo-Obermann H, von Kopylow K, Schulze W, Spiess AN. A biopsy sample reduction approach to identify significant alterations of the testicular transcriptome in the presence of Y-chromosomal microdeletions that are independent of germ cell composition. Hum Genet 2010 Oct;128(4):421-31. PMID: 20668881
Irie HY, Shrestha Y, Selfors LM, Frye F et al. PTK6 regulates IGF-1-induced anchorage-independent survival. PLoS One 2010 Jul 23;5(7):e11729. PMID: 20668531
Joseph EW, Pratilas CA, Poulikakos PI, Tadi M et al. The RAF inhibitor PLX4032 inhibits ERK signaling and tumor cell proliferation in a V600E BRAF-selective manner. Proc Natl Acad Sci U S A 2010 Aug 17;107(33):14903-8. PMID: 20668238
Junk AK, Goel M, Mundorf T, Rockwood EJ et al. Decreased carbohydrate metabolism enzyme activities in the glaucomatous trabecular meshwork. Mol Vis 2010 Jul 10;16:1286-91. PMID: 20664702
Nakagawa M, Takizawa N, Narita M, Ichisaka T et al. Promotion of direct reprogramming by transformation-deficient Myc. Proc Natl Acad Sci U S A 2010 Aug 10;107(32):14152-7. PMID: 20660764
Plaisier SB, Taschereau R, Wong JA, Graeber TG. Rank-rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures. Nucleic Acids Res 2010 Sep;38(17):e169. PMID: 20660011
Benner MJ, Drew RE, Hardy RW, Robison BD. Zebrafish (Danio rerio) vary by strain and sex in their behavioral and transcriptional responses to selenium supplementation. Comp Biochem Physiol A Mol Integr Physiol 2010 Dec;157(4):310-8. PMID: 20659579
Schnetz MP, Handoko L, Akhtar-Zaidi B, Bartels CF et al. CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. PLoS Genet 2010 Jul 15;6(7):e1001023. PMID: 20657823
Luo Y, Yang C, Lu W, Xie R et al. Metabolic regulator betaKlotho interacts with fibroblast growth factor receptor 4 (FGFR4) to induce apoptosis and inhibit tumor cell proliferation. J Biol Chem 2010 Sep 24;285(39):30069-78. PMID: 20657013
Jiang SS, Fang WT, Hou YH, Huang SF et al. Upregulation of SOX9 in lung adenocarcinoma and its involvement in the regulation of cell growth and tumorigenicity. Clin Cancer Res 2010 Sep 1;16(17):4363-73. PMID: 20651055
Li D, Zhang Y, Xu L, Zhou L et al. Regulation of gene expression by FSP27 in white and brown adipose tissue. BMC Genomics 2010 Jul 22;11:446. PMID: 20649970
McMullen PD, Morimoto RI, Amaral LA. Physically grounded approach for estimating gene expression from microarray data. Proc Natl Acad Sci U S A 2010 Aug 3;107(31):13690-5. PMID: 20643961
Yu H, Huang J, Qiao N, Green CD et al. Evaluating diabetes and hypertension disease causality using mouse phenotypes. BMC Syst Biol 2010 Jul 20;4:97. PMID: 20642857
Kalushkova A, Fryknäs M, Lemaire M, Fristedt C et al. Polycomb target genes are silenced in multiple myeloma. PLoS One 2010 Jul 9;5(7):e11483. PMID: 20634887
Pantzartzi C, Drosopoulou E, Yiangou M, Drozdov I et al. Promoter complexity and tissue-specific expression of stress response components in Mytilus galloprovincialis, a sessile marine invertebrate species. PLoS Comput Biol 2010 Jul 8;6(7):e1000847. PMID: 20628614
Laganà A, Forte S, Russo F, Giugno R et al. Prediction of human targets for viral-encoded microRNAs by thermodynamics and empirical constraints. J RNAi Gene Silencing 2010 May 24;6(1):379-85. PMID: 20628498
Plager DA, Kahl JC, Asmann YW, Nilson AE et al. Gene transcription changes in asthmatic chronic rhinosinusitis with nasal polyps and comparison to those in atopic dermatitis. PLoS One 2010 Jul 6;5(7):e11450. PMID: 20625511
Zhang Z, Maurer K, Perin JC, Song L et al. Cytokine-induced monocyte characteristics in SLE. J Biomed Biotechnol 2010;2010:507475. PMID: 20625490
Kavak E, Unlü M, Nistér M, Koman A. Meta-analysis of cancer gene expression signatures reveals new cancer genes, SAGE tags and tumor associated regions of co-regulation. Nucleic Acids Res 2010 Nov;38(20):7008-21. PMID: 20621981
Chellappan P, Xia J, Zhou X, Gao S et al. siRNAs from miRNA sites mediate DNA methylation of target genes. Nucleic Acids Res 2010 Nov;38(20):6883-94. PMID: 20621980
Engreitz JM, Daigle BJ Jr, Marshall JJ, Altman RB. Independent component analysis: mining microarray data for fundamental human gene expression modules. J Biomed Inform 2010 Dec;43(6):932-44. PMID: 20619355
Riz I, Hawley TS, Luu TV, Lee NH et al. TLX1 and NOTCH coregulate transcription in T cell acute lymphoblastic leukemia cells. Mol Cancer 2010 Jul 9;9:181. PMID: 20618946
Miller JA, Horvath S, Geschwind DH. Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways. Proc Natl Acad Sci U S A 2010 Jul 13;107(28):12698-703. PMID: 20616000
Appaiah H, Bhat-Nakshatri P, Mehta R, Thorat M et al. ITF2 is a target of CXCR4 in MDA-MB-231 breast cancer cells and is associated with reduced survival in estrogen receptor-negative breast cancer. Cancer Biol Ther 2010 Sep;10(6):600-14. PMID: 20603605
Choi JK. Contrasting chromatin organization of CpG islands and exons in the human genome. Genome Biol 2010;11(7):R70. PMID: 20602769
Fong CY, Chak LL, Biswas A, Tan JH et al. Human Wharton's jelly stem cells have unique transcriptome profiles compared to human embryonic stem cells and other mesenchymal stem cells. Stem Cell Rev 2011 Mar;7(1):1-16. PMID: 20602182
Berkofsky-Fessler W, Buzzai M, Kim MK, Fruchtman S et al. Transcriptional profiling of polycythemia vera identifies gene expression patterns both dependent and independent from the action of JAK2V617F. Clin Cancer Res 2010 Sep 1;16(17):4339-52. PMID: 20601445
Liu Y, Chu A, Chakroun I, Islam U et al. Cooperation between myogenic regulatory factors and SIX family transcription factors is important for myoblast differentiation. Nucleic Acids Res 2010 Nov;38(20):6857-71. PMID: 20601407
Nuruzzaman M, Manimekalai R, Sharoni AM, Satoh K et al. Genome-wide analysis of NAC transcription factor family in rice. Gene 2010 Oct 1;465(1-2):30-44. PMID: 20600702
Qin ZS, Yu J, Shen J, Maher CA et al. HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. BMC Bioinformatics 2010 Jul 2;11:369. PMID: 20598134
Zhang C, Zhu C, Chen H, Li L et al. Kif18A is involved in human breast carcinogenesis. Carcinogenesis 2010 Sep;31(9):1676-84. PMID: 20595236
Loboda A, Nebozhyn M, Klinghoffer R, Frazier J et al. A gene expression signature of RAS pathway dependence predicts response to PI3K and RAS pathway inhibitors and expands the population of RAS pathway activated tumors. BMC Med Genomics 2010 Jun 30;3:26. PMID: 20591134
Puig O, Wang IM, Cheng P, Zhou P et al. Transcriptome profiling and network analysis of genetically hypertensive mice identifies potential pharmacological targets of hypertension. Physiol Genomics 2010 Sep;42A(1):24-32. PMID: 20587620
Sánchez-Navarro I, Gámez-Pozo A, Pinto A, Hardisson D et al. An 8-gene qRT-PCR-based gene expression score that has prognostic value in early breast cancer. BMC Cancer 2010 Jun 28;10:336. PMID: 20584321
Caron C, Lestrat C, Marsal S, Escoffier E et al. Functional characterization of ATAD2 as a new cancer/testis factor and a predictor of poor prognosis in breast and lung cancers. Oncogene 2010 Sep 16;29(37):5171-81. PMID: 20581866
Ko K, Araúzo-Bravo MJ, Tapia N, Kim J et al. Human adult germline stem cells in question. Nature 2010 Jun 24;465(7301):E1; discussion E3. PMID: 20577160
Riggins RB, Mazzotta MM, Maniya OZ, Clarke R. Orphan nuclear receptors in breast cancer pathogenesis and therapeutic response. Endocr Relat Cancer 2010 Sep;17(3):R213-31. PMID: 20576803
Hinze CH, Fall N, Thornton S, Mo JQ et al. Immature cell populations and an erythropoiesis gene-expression signature in systemic juvenile idiopathic arthritis: implications for pathogenesis. Arthritis Res Ther 2010;12(3):R123. PMID: 20576155
Broyl A, Hose D, Lokhorst H, de Knegt Y et al. Gene expression profiling for molecular classification of multiple myeloma in newly diagnosed patients. Blood 2010 Oct 7;116(14):2543-53. PMID: 20574050
Irgon J, Huang CC, Zhang Y, Talantov D et al. Robust multi-tissue gene panel for cancer detection. BMC Cancer 2010 Jun 22;10:319. PMID: 20569444
Wang Z, Du J, Lam SH, Mathavan S et al. Morphological and molecular evidence for functional organization along the rostrocaudal axis of the adult zebrafish intestine. BMC Genomics 2010 Jun 22;11:392. PMID: 20565988
Yano K. Gene expression correlation analysis predicts involvement of high- and low-confidence risk genes in different stages of prostate carcinogenesis. Prostate 2010 Dec 1;70(16):1746-59. PMID: 20564324
Cai J, Kandagatla P, Singareddy R, Kropinski A et al. Androgens Induce Functional CXCR4 through ERG Factor Expression in TMPRSS2-ERG Fusion-Positive Prostate Cancer Cells. Transl Oncol 2010 Jun 1;3(3):195-203. PMID: 20563261
Jiang X, Zhu T, Yang J, Li S et al. Identification of novel epithelial ovarian cancer biomarkers by cross-laboratory microarray analysis. J Huazhong Univ Sci Technolog Med Sci 2010 Jun;30(3):354-9. PMID: 20556581
Summers KM, Raza S, van Nimwegen E, Freeman TC et al. Co-expression of FBN1 with mesenchyme-specific genes in mouse cell lines: implications for phenotypic variability in Marfan syndrome. Eur J Hum Genet 2010 Nov;18(11):1209-15. PMID: 20551991
Weidle UH, Scheuer W, Eggle D, Klostermann S et al. Cancer-related issues of CD147. Cancer Genomics Proteomics 2010 May-Jun;7(3):157-69. PMID: 20551248
Wu H, Ji H. JAMIE: joint analysis of multiple ChIP-chip experiments. Bioinformatics 2010 Aug 1;26(15):1864-70. PMID: 20551135
Hsu YH, Zillikens MC, Wilson SG, Farber CR et al. An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility Loci for osteoporosis-related traits. PLoS Genet 2010 Jun 10;6(6):e1000977. PMID: 20548944
Niida A, Imoto S, Yamaguchi R, Nagasaki M et al. Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues. PLoS One 2010 Jun 9;5(6):e10910. PMID: 20544005
Irvin DK, Jouanneau E, Duvall G, Zhang XX et al. T cells enhance stem-like properties and conditional malignancy in gliomas. PLoS One 2010 Jun 7;5(6):e10974. PMID: 20539758
Kavak E, Najafov A, Ozturk N, Seker T et al. Analysis of the Wnt/B-catenin/TCF4 pathway using SAGE, genome-wide microarray and promoter analysis: Identification of BRI3 and HSF2 as novel targets. Cell Signal 2010 Oct;22(10):1523-35. PMID: 20538055
Lee SH, Poulogiannis G, Pyne S, Jia S et al. A constitutively activated form of the p110beta isoform of PI3-kinase induces prostatic intraepithelial neoplasia in mice. Proc Natl Acad Sci U S A 2010 Jun 15;107(24):11002-7. PMID: 20534477
Bapat SA, Krishnan A, Ghanate AD, Kusumbe AP et al. Gene expression: protein interaction systems network modeling identifies transformation-associated molecules and pathways in ovarian cancer. Cancer Res 2010 Jun 15;70(12):4809-19. PMID: 20530682
Vaske CJ, Benz SC, Sanborn JZ, Earl D et al. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics 2010 Jun 15;26(12):i237-45. PMID: 20529912
Ortiz-Estevez M, Bengtsson H, Rubio A. ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays. Bioinformatics 2010 Aug 1;26(15):1827-33. PMID: 20529889
Yun T, Hwang T, Cha K, Yi GS. CLIC: clustering analysis of large microarray datasets with individual dimension-based clustering. Nucleic Acids Res 2010 Jul;38(Web Server issue):W246-53. PMID: 20529873
Altman MK, Gopal V, Jia W, Yu S et al. Targeting melanoma growth and viability reveals dualistic functionality of the phosphonothionate analogue of carba cyclic phosphatidic acid. Mol Cancer 2010 Jun 9;9:140. PMID: 20529378
Gottlieb A, Varshavsky R, Linial M, Horn D. UFFizi: a generic platform for ranking informative features. BMC Bioinformatics 2010 Jun 3;11:300. PMID: 20525252
Hutchison EA, Glass NL. Meiotic regulators Ndt80 and ime2 have different roles in Saccharomyces and Neurospora. Genetics 2010 Aug;185(4):1271-82. PMID: 20519745
Guan H, Xie L, Leithäuser F, Flossbach L et al. KLF4 is a tumor suppressor in B-cell non-Hodgkin lymphoma and in classic Hodgkin lymphoma. Blood 2010 Sep 2;116(9):1469-78. PMID: 20519630
Vazquez M, Nogales-Cadenas R, Arroyo J, Botías P et al. MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures. Nucleic Acids Res 2010 Jul;38(Web Server issue):W228-32. PMID: 20513648
Kim JY, Kim JH, Park TJ, Bae JS et al. Positive association between aspirin-intolerant asthma and genetic polymorphisms of FSIP1: a case-case study. BMC Pulm Med 2010 Jun 1;10:34. PMID: 20513247
Kim C, Choi J, Park H, Park Y et al. Global analysis of microarray data reveals intrinsic properties in gene expression and tissue selectivity. Bioinformatics 2010 Jul 15;26(14):1723-30. PMID: 20511364
Morse DL, Balagurunathan Y, Hostetter G, Trissal M et al. Identification of novel pancreatic adenocarcinoma cell-surface targets by gene expression profiling and tissue microarray. Biochem Pharmacol 2010 Sep 1;80(5):748-54. PMID: 20510208
Carro A, Rico D, Rueda OM, Díaz-Uriarte R et al. waviCGH: a web application for the analysis and visualization of genomic copy number alterations. Nucleic Acids Res 2010 Jul;38(Web Server issue):W182-7. PMID: 20507915
Shi Z, Derow CK, Zhang B. Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression. BMC Syst Biol 2010 May 27;4:74. PMID: 20507583
Ren X, Zhou X, Wu LY, Zhang XS. An information-flow-based model with dissipation, saturation and direction for active pathway inference. BMC Syst Biol 2010 May 27;4:72. PMID: 20504374
Tun HW, Marlow LA, von Roemeling CA, Cooper SJ et al. Pathway signature and cellular differentiation in clear cell renal cell carcinoma. PLoS One 2010 May 18;5(5):e10696. PMID: 20502531
Wrzaczek M, Brosché M, Salojärvi J, Kangasjärvi S et al. Transcriptional regulation of the CRK/DUF26 group of receptor-like protein kinases by ozone and plant hormones in Arabidopsis. BMC Plant Biol 2010 May 25;10:95. PMID: 20500828
Abraham G, Kowalczyk A, Loi S, Haviv I et al. Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context. BMC Bioinformatics 2010 May 25;11:277. PMID: 20500821
Farber CR. Identification of a gene module associated with BMD through the integration of network analysis and genome-wide association data. J Bone Miner Res 2010 Nov;25(11):2359-67. PMID: 20499364
Liao JY, Ma LM, Guo YH, Zhang YC et al. Deep sequencing of human nuclear and cytoplasmic small RNAs reveals an unexpectedly complex subcellular distribution of miRNAs and tRNA 3' trailers. PLoS One 2010 May 14;5(5):e10563. PMID: 20498841
Rodríguez-Prados JC, Través PG, Cuenca J, Rico D et al. Substrate fate in activated macrophages: a comparison between innate, classic, and alternative activation. J Immunol 2010 Jul 1;185(1):605-14. PMID: 20498354
Pantazatos SP, Li J, Pavlidis P, Lussier YA. Integration of Neuroimaging and Microarray Datasets through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes. Cancer Inform 2009 Jun 8;8:75-94. PMID: 20495688
Parikh JR, Klinger B, Xia Y, Marto JA et al. Discovering causal signaling pathways through gene-expression patterns. Nucleic Acids Res 2010 Jul;38(Web Server issue):W109-17. PMID: 20494976
Yu G, Zhao Y, He J, Lonard DM et al. Comparative analysis of REG{gamma} expression in mouse and human tissues. J Mol Cell Biol 2010 Aug;2(4):192-8. PMID: 20494959
Thienpont B, Zhang L, Postma AV, Breckpot J et al. Haploinsufficiency of TAB2 causes congenital heart defects in humans. Am J Hum Genet 2010 Jun 11;86(6):839-49. PMID: 20493459
Tai SK, Wu G, Yuan S, Li KC. Genome-wide expression links the electron transfer pathway of Shewanella oneidensis to chemotaxis. BMC Genomics 2010 May 21;11:319. PMID: 20492688
Blangiardo M, Cassese A, Richardson S. sdef: an R package to synthesize lists of significant features in related experiments. BMC Bioinformatics 2010 May 20;11:270. PMID: 20487547
Kim MS, Kim JR, Cho KH. Dynamic network rewiring determines temporal regulatory functions in Drosophila melanogaster development processes. Bioessays 2010 Jun;32(6):505-13. PMID: 20486137
Gout JF, Kahn D, Duret L, Paramecium Post-Genomics Consortium. The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution. PLoS Genet 2010 May 13;6(5):e1000944. PMID: 20485561
Sales G, Coppe A, Bisognin A, Biasiolo M et al. MAGIA, a web-based tool for miRNA and Genes Integrated Analysis. Nucleic Acids Res 2010 Jul;38(Web Server issue):W352-9. PMID: 20484379
De Rijck J, Bartholomeeusen K, Ceulemans H, Debyser Z et al. High-resolution profiling of the LEDGF/p75 chromatin interaction in the ENCODE region. Nucleic Acids Res 2010 Oct;38(18):6135-47. PMID: 20484370
Alonso A, Julià A, Tortosa R, Canaleta C et al. CNstream: a method for the identification and genotyping of copy number polymorphisms using Illumina microarrays. BMC Bioinformatics 2010 May 19;11:264. PMID: 20482829
Madden SF, Carpenter SB, Jeffery IB, Björkbacka H et al. Detecting microRNA activity from gene expression data. BMC Bioinformatics 2010 May 18;11:257. PMID: 20482775
Crozat K, Guiton R, Contreras V, Feuillet V et al. The XC chemokine receptor 1 is a conserved selective marker of mammalian cells homologous to mouse CD8alpha+ dendritic cells. J Exp Med 2010 Jun 7;207(6):1283-92. PMID: 20479118
Huang PJ, Liu YC, Lee CC, Lin WC et al. DSAP: deep-sequencing small RNA analysis pipeline. Nucleic Acids Res 2010 Jul;38(Web Server issue):W385-91. PMID: 20478825
Winn ME, Zapala MA, Hovatta I, Risbrough VB et al. The effects of globin on microarray-based gene expression analysis of mouse blood. Mamm Genome 2010 Jun;21(5-6):268-75. PMID: 20473674
Riester M, Stephan-Otto Attolini C, Downey RJ, Singer S et al. A differentiation-based phylogeny of cancer subtypes. PLoS Comput Biol 2010 May 6;6(5):e1000777. PMID: 20463876
Hughes T, Webb R, Fei Y, Wren JD et al. DNA methylome in human CD4+ T cells identifies transcriptionally repressive and non-repressive methylation peaks. Genes Immun 2010 Oct;11(7):554-60. PMID: 20463746
Fan J, Traore K, Li W, Amri H et al. Molecular mechanisms mediating the effect of mono-(2-ethylhexyl) phthalate on hormone-stimulated steroidogenesis in MA-10 mouse tumor Leydig cells. Endocrinology 2010 Jul;151(7):3348-62. PMID: 20463053
Makareeva E, Han S, Vera JC, Sackett DL et al. Carcinomas contain a matrix metalloproteinase-resistant isoform of type I collagen exerting selective support to invasion. Cancer Res 2010 Jun 1;70(11):4366-74. PMID: 20460529
Dey JH, Bianchi F, Voshol J, Bonenfant D et al. Targeting fibroblast growth factor receptors blocks PI3K/AKT signaling, induces apoptosis, and impairs mammary tumor outgrowth and metastasis. Cancer Res 2010 May 15;70(10):4151-62. PMID: 20460524
Jönsson G, Busch C, Knappskog S, Geisler J et al. Gene expression profiling-based identification of molecular subtypes in stage IV melanomas with different clinical outcome. Clin Cancer Res 2010 Jul 1;16(13):3356-67. PMID: 20460471
Sun CH, Hwang T, Oh K, Yi GS. DynaMod: dynamic functional modularity analysis. Nucleic Acids Res 2010 Jul;38(Web Server issue):W103-8. PMID: 20460468
Patel CJ, Butte AJ. Predicting environmental chemical factors associated with disease-related gene expression data. BMC Med Genomics 2010 May 6;3:17. PMID: 20459635
Scheff JD, Almon RR, DuBois DC, Jusko WJ et al. A new symbolic representation for the identification of informative genes in replicated microarray experiments. OMICS 2010 Jun;14(3):239-48. PMID: 20455749
Martínez O, Reyes-Valdés MH, Herrera-Estrella L. Cancer reduces transcriptome specialization. PLoS One 2010 May 3;5(5):e10398. PMID: 20454660
Uddin M, Aiello AE, Wildman DE, Koenen KC et al. Epigenetic and immune function profiles associated with posttraumatic stress disorder. Proc Natl Acad Sci U S A 2010 May 18;107(20):9470-5. PMID: 20439746
Towfic F, VanderPlas S, Oliver CA, Couture O et al. Detection of gene orthology from gene co-expression and protein interaction networks. BMC Bioinformatics 2010 Apr 29;11 Suppl 3:S7. PMID: 20438654
Xiang H, Zhu J, Chen Q, Dai F et al. Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nat Biotechnol 2010 May;28(5):516-20. PMID: 20436463
Lacson R, Pitzer E, Kim J, Galante P et al. DSGeo: software tools for cross-platform analysis of gene expression data in GEO. J Biomed Inform 2010 Oct;43(5):709-15. PMID: 20435161
Pierre M, DeHertogh B, Gaigneaux A, DeMeulder B et al. Meta-analysis of archived DNA microarrays identifies genes regulated by hypoxia and involved in a metastatic phenotype in cancer cells. BMC Cancer 2010 Apr 30;10:176. PMID: 20433688
Risueño A, Fontanillo C, Dinger ME, De Las Rivas J. GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC Bioinformatics 2010 Apr 29;11:221. PMID: 20429936
Moulder S, Yan K, Huang F, Hess KR et al. Development of candidate genomic markers to select breast cancer patients for dasatinib therapy. Mol Cancer Ther 2010 May;9(5):1120-7. PMID: 20423993
Ma H, Zhao J. Genome-wide identification, classification, and expression analysis of the arabinogalactan protein gene family in rice (Oryza sativa L.). J Exp Bot 2010 Jun;61(10):2647-68. PMID: 20423940
Fasold M, Stadler PF, Binder H. G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration. BMC Bioinformatics 2010 Apr 27;11:207. PMID: 20423484
Hou J, Aerts J, den Hamer B, van Ijcken W et al. Gene expression-based classification of non-small cell lung carcinomas and survival prediction. PLoS One 2010 Apr 22;5(4):e10312. PMID: 20421987
Nagarajan M, Veyrieras JB, de Dieuleveult M, Bottin H et al. Natural single-nucleosome epi-polymorphisms in yeast. PLoS Genet 2010 Apr 22;6(4):e1000913. PMID: 20421933
Wu AH, Drees JC, Wang H, VandenBerg SR et al. Gene expression profiles help identify the tissue of origin for metastatic brain cancers. Diagn Pathol 2010 Apr 26;5:26. PMID: 20420692
Lin B, Madan A, Yoon JG, Fang X et al. Massively parallel signature sequencing and bioinformatics analysis identifies up-regulation of TGFBI and SOX4 in human glioblastoma. PLoS One 2010 Apr 19;5(4):e10210. PMID: 20419098
Blackledge NP, Zhou JC, Tolstorukov MY, Farcas AM et al. CpG islands recruit a histone H3 lysine 36 demethylase. Mol Cell 2010 Apr 23;38(2):179-90. PMID: 20417597
Lu XC, Chi XH, Yang B, Zhu HL et al. [Gene expression profile analysis of T lymphocytes involved in pathogenesis of severe aplastic anemia by using bioinformatics method as a novel way of drug screening]. Zhongguo Shi Yan Xue Ye Xue Za Zhi 2010 Apr;18(2):416-20. PMID: 20416179
Borsics T, Lundberg E, Geerts D, Koomoa DL et al. Subcellular distribution and expression of prenylated Rab acceptor 1 domain family, member 2 (PRAF2) in malignant glioma: Influence on cell survival and migration. Cancer Sci 2010 Jul;101(7):1624-31. PMID: 20412121
Benita Y, Cao Z, Giallourakis C, Li C et al. Gene enrichment profiles reveal T-cell development, differentiation, and lineage-specific transcription factors including ZBTB25 as a novel NF-AT repressor. Blood 2010 Jul 1;115(26):5376-84. PMID: 20410506
Sørensen AL, Jacobsen BM, Reiner AH, Andersen IS et al. Promoter DNA methylation patterns of differentiated cells are largely programmed at the progenitor stage. Mol Biol Cell 2010 Jun 15;21(12):2066-77. PMID: 20410135
Docquier A, Harmand PO, Fritsch S, Chanrion M et al. The transcriptional coregulator RIP140 represses E2F1 activity and discriminates breast cancer subtypes. Clin Cancer Res 2010 Jun 1;16(11):2959-70. PMID: 20410059
Olaussen KA, Soria JC. Validation of ERCC1-XPF immunodetection--letter. Cancer Res 2010 May 1;70(9):3851-2; author reply 3852. PMID: 20406965
Gu J, Chen Y, Li S, Li Y. Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis. BMC Syst Biol 2010 Apr 21;4:47. PMID: 20406493
Gómez Ravetti M, Rosso OA, Berretta R, Moscato P. Uncovering molecular biomarkers that correlate cognitive decline with the changes of hippocampus' gene expression profiles in Alzheimer's disease. PLoS One 2010 Apr 13;5(4):e10153. PMID: 20405009
Mondal T, Rasmussen M, Pandey GK, Isaksson A et al. Characterization of the RNA content of chromatin. Genome Res 2010 Jul;20(7):899-907. PMID: 20404130
Sharma A, Zhao J, Podolsky R, McIndoe RA. ParaSAM: a parallelized version of the significance analysis of microarrays algorithm. Bioinformatics 2010 Jun 1;26(11):1465-7. PMID: 20400455
Le BH, Cheng C, Bui AQ, Wagmaister JA et al. Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors. Proc Natl Acad Sci U S A 2010 May 4;107(18):8063-70. PMID: 20385809
Mollet IG, Ben-Dov C, Felício-Silva D, Grosso AR et al. Unconstrained mining of transcript data reveals increased alternative splicing complexity in the human transcriptome. Nucleic Acids Res 2010 Aug;38(14):4740-54. PMID: 20385588
Ohnishi Y, Totoki Y, Toyoda A, Watanabe T et al. Small RNA class transition from siRNA/piRNA to miRNA during pre-implantation mouse development. Nucleic Acids Res 2010 Aug;38(15):5141-51. PMID: 20385573
Surendran K, Selassie M, Liapis H, Krigman H et al. Reduced Notch signaling leads to renal cysts and papillary microadenomas. J Am Soc Nephrol 2010 May;21(5):819-32. PMID: 20378824
Rowsell J, da Silva Camargo R, Langdon WB, Stalteri MA et al. Uncovering the expression patterns of chimeric transcripts using surveys of affymetrix GeneChips. J Integr Bioinform 2010 Mar 25;7(3). PMID: 20375459
Gustafson AM, Soldi R, Anderlind C, Scholand MB et al. Airway PI3K pathway activation is an early and reversible event in lung cancer development. Sci Transl Med 2010 Apr 7;2(26):26ra25. PMID: 20375364
Brase JC, Schmidt M, Fischbach T, Sültmann H et al. ERBB2 and TOP2A in breast cancer: a comprehensive analysis of gene amplification, RNA levels, and protein expression and their influence on prognosis and prediction. Clin Cancer Res 2010 Apr 15;16(8):2391-401. PMID: 20371687
Vohradsky J, Panek J, Vomastek T. Numerical modelling of microRNA-mediated mRNA decay identifies novel mechanism of microRNA controlled mRNA downregulation. Nucleic Acids Res 2010 Aug;38(14):4579-85. PMID: 20371515
Barry WT, Kernagis DN, Dressman HK, Griffis RJ et al. Intratumor heterogeneity and precision of microarray-based predictors of breast cancer biology and clinical outcome. J Clin Oncol 2010 May 1;28(13):2198-206. PMID: 20368555
Huang H, Liu CC, Zhou XJ. Bayesian approach to transforming public gene expression repositories into disease diagnosis databases. Proc Natl Acad Sci U S A 2010 Apr 13;107(15):6823-8. PMID: 20360561
Narsai R, Ivanova A, Ng S, Whelan J. Defining reference genes in Oryza sativa using organ, development, biotic and abiotic transcriptome datasets. BMC Plant Biol 2010 Mar 31;10:56. PMID: 20353606
Voelckel C, Borevitz JO, Kramer EM, Hodges SA. Within and between whorls: comparative transcriptional profiling of Aquilegia and Arabidopsis. PLoS One 2010 Mar 23;5(3):e9735. PMID: 20352114
Piwowar H, Chapman W. Recall and bias of retrieving gene expression microarray datasets through PubMed identifiers. J Biomed Discov Collab 2010 Mar 28;5:7-20. PMID: 20349403
Thorrez L, Tranchevent LC, Chang HJ, Moreau Y et al. Detection of novel 3' untranslated region extensions with 3' expression microarrays. BMC Genomics 2010 Mar 26;11:205. PMID: 20346121
Kang UB, Ahn Y, Lee JW, Kim YH et al. Differential profiling of breast cancer plasma proteome by isotope-coded affinity tagging method reveals biotinidase as a breast cancer biomarker. BMC Cancer 2010 Mar 26;10:114. PMID: 20346108
Watanabe M, Hubberten HM, Saito K, Hoefgen R. General regulatory patterns of plant mineral nutrient depletion as revealed by serat quadruple mutants disturbed in cysteine synthesis. Mol Plant 2010 Mar;3(2):438-66. PMID: 20339158
Gatza ML, Lucas JE, Barry WT, Kim JW et al. A pathway-based classification of human breast cancer. Proc Natl Acad Sci U S A 2010 Apr 13;107(15):6994-9. PMID: 20335537
Barth AS, Kumordzie A, Colantuoni C, Margulies KB et al. Reciprocal regulation of metabolic and signaling pathways. BMC Genomics 2010 Mar 24;11:197. PMID: 20334672
Rouam S, Moreau T, Broët P. Identifying common prognostic factors in genomic cancer studies: a novel index for censored outcomes. BMC Bioinformatics 2010 Mar 24;11:150. PMID: 20334636
Williams RD, Al-Saadi R, Chagtai T, Popov S et al. Subtype-specific FBXW7 mutation and MYCN copy number gain in Wilms' tumor. Clin Cancer Res 2010 Apr 1;16(7):2036-45. PMID: 20332316
Palmer RD, Murray MJ, Saini HK, van Dongen S et al. Malignant germ cell tumors display common microRNA profiles resulting in global changes in expression of messenger RNA targets. Cancer Res 2010 Apr 1;70(7):2911-23. PMID: 20332240
Zou F, Huang H, Ibrahim JG. A semiparametric Bayesian approach for estimating the gene expression distribution. J Biopharm Stat 2010 Mar;20(2):267-80. PMID: 20309758
Lu Z, Xu X, Hu X, Lee S et al. Oxidative stress regulates left ventricular PDE5 expression in the failing heart. Circulation 2010 Apr 6;121(13):1474-83. PMID: 20308615
Vivanco I, Rohle D, Versele M, Iwanami A et al. The phosphatase and tensin homolog regulates epidermal growth factor receptor (EGFR) inhibitor response by targeting EGFR for degradation. Proc Natl Acad Sci U S A 2010 Apr 6;107(14):6459-64. PMID: 20308550
Lunardi A, Di Minin G, Provero P, Dal Ferro M et al. A genome-scale protein interaction profile of Drosophila p53 uncovers additional nodes of the human p53 network. Proc Natl Acad Sci U S A 2010 Apr 6;107(14):6322-7. PMID: 20308539
Innocenti P, Morrow EH. The sexually antagonistic genes of Drosophila melanogaster. PLoS Biol 2010 Mar 16;8(3):e1000335. PMID: 20305719
Ogata Y, Suzuki H, Sakurai N, Shibata D. CoP: a database for characterizing co-expressed gene modules with biological information in plants. Bioinformatics 2010 May 1;26(9):1267-8. PMID: 20305269
Waluk DP, Schultz N, Hunt MC. Identification of glycine N-acyltransferase-like 2 (GLYATL2) as a transferase that produces N-acyl glycines in humans. FASEB J 2010 Aug;24(8):2795-803. PMID: 20305126
Chen XD. Extracellular matrix provides an optimal niche for the maintenance and propagation of mesenchymal stem cells. Birth Defects Res C Embryo Today 2010 Mar;90(1):45-54. PMID: 20301219
Romanowska M, Reilly L, Palmer CN, Gustafsson MC et al. Activation of PPARbeta/delta causes a psoriasis-like skin disease in vivo. PLoS One 2010 Mar 16;5(3):e9701. PMID: 20300524
Backes C, Meese E, Lenhof HP, Keller A. A dictionary on microRNAs and their putative target pathways. Nucleic Acids Res 2010 Jul;38(13):4476-86. PMID: 20299343
Ameur A, Wetterbom A, Feuk L, Gyllensten U. Global and unbiased detection of splice junctions from RNA-seq data. Genome Biol 2010;11(3):R34. PMID: 20236510
Staaf J, Ringnér M, Vallon-Christersson J, Jönsson G et al. Identification of subtypes in human epidermal growth factor receptor 2--positive breast cancer reveals a gene signature prognostic of outcome. J Clin Oncol 2010 Apr 10;28(11):1813-20. PMID: 20231686
Sahoo D, Seita J, Bhattacharya D, Inlay MA et al. MiDReG: a method of mining developmentally regulated genes using Boolean implications. Proc Natl Acad Sci U S A 2010 Mar 30;107(13):5732-7. PMID: 20231483
Holman TJ, Wilson MH, Kenobi K, Dryden IL et al. Statistical evaluation of transcriptomic data generated using the Affymetrix one-cycle, two-cycle and IVT-Express RNA labelling protocols with the Arabidopsis ATH1 microarray. Plant Methods 2010 Mar 15;6:9. PMID: 20230623
Weinberg Z, Wang JX, Bogue J, Yang J et al. Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol 2010;11(3):R31. PMID: 20230605
Verissimo CS, Molenaar JJ, Meerman J, Puigvert JC et al. Silencing of the microtubule-associated proteins doublecortin-like and doublecortin-like kinase-long induces apoptosis in neuroblastoma cells. Endocr Relat Cancer 2010 Jun;17(2):399-414. PMID: 20228126
Jaspers P, Overmyer K, Wrzaczek M, Vainonen JP et al. The RST and PARP-like domain containing SRO protein family: analysis of protein structure, function and conservation in land plants. BMC Genomics 2010 Mar 12;11:170. PMID: 20226034
Mourier T, Willerslev E. Large-scale transcriptome data reveals transcriptional activity of fission yeast LTR retrotransposons. BMC Genomics 2010 Mar 12;11:167. PMID: 20226011
Tanaka Y, Yoshimura I, Nakai K. Positional variations among heterogeneous nucleosome maps give dynamical information on chromatin. Chromosoma 2010 Aug;119(4):391-404. PMID: 20224866
Shiraishi Y, Kimura S, Okada M. Inferring cluster-based networks from differently stimulated multiple time-course gene expression data. Bioinformatics 2010 Apr 15;26(8):1073-81. PMID: 20223837
De Biase LM, Nishiyama A, Bergles DE. Excitability and synaptic communication within the oligodendrocyte lineage. J Neurosci 2010 Mar 10;30(10):3600-11. PMID: 20219994
Xie D, Chen CC, Ptaszek LM, Xiao S et al. Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species. Genome Res 2010 Jun;20(6):804-15. PMID: 20219939
Dry JR, Pavey S, Pratilas CA, Harbron C et al. Transcriptional pathway signatures predict MEK addiction and response to selumetinib (AZD6244). Cancer Res 2010 Mar 15;70(6):2264-73. PMID: 20215513
Ng WL, Wei Y, Perez LJ, Cong J et al. Probing bacterial transmembrane histidine kinase receptor-ligand interactions with natural and synthetic molecules. Proc Natl Acad Sci U S A 2010 Mar 23;107(12):5575-80. PMID: 20212168
Fowler JH, Christakis NA. Cooperative behavior cascades in human social networks. Proc Natl Acad Sci U S A 2010 Mar 23;107(12):5334-8. PMID: 20212120
Tuna S, Niranjan M. Reducing the algorithmic variability in transcriptome-based inference. Bioinformatics 2010 May 1;26(9):1185-91. PMID: 20212019
Hu Z, Huang G, Sadanandam A, Gu S et al. The expression level of HJURP has an independent prognostic impact and predicts the sensitivity to radiotherapy in breast cancer. Breast Cancer Res 2010;12(2):R18. PMID: 20211017
Mejhert N, Laurencikiene J, Pettersson AT, Kaaman M et al. Role of Receptor-Interacting Protein 140 in human fat cells. BMC Endocr Disord 2010 Jan 29;10:1. PMID: 20205832
Rodríguez-Flores JL, Zhang K, Kang SW, Wen G et al. Conserved regulatory motifs at phenylethanolamine N-methyltransferase (PNMT) are disrupted by common functional genetic variation: an integrated computational/experimental approach. Mamm Genome 2010 Apr;21(3-4):195-204. PMID: 20204374
Clarke J, Seo P, Clarke B. Statistical expression deconvolution from mixed tissue samples. Bioinformatics 2010 Apr 15;26(8):1043-9. PMID: 20202973
Newman AM, Cooper JB. AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number. BMC Bioinformatics 2010 Mar 4;11:117. PMID: 20202218
Shimamura T, Imoto S, Yamaguchi R, Nagasaki M et al. Inferring dynamic gene networks under varying conditions for transcriptomic network comparison. Bioinformatics 2010 Apr 15;26(8):1064-72. PMID: 20197286
Nielsen TO, West RB. Translating gene expression into clinical care: sarcomas as a paradigm. J Clin Oncol 2010 Apr 1;28(10):1796-805. PMID: 20194847
Thompson RF, Fazzari MJ, Niu H, Barzilai N et al. Experimental intrauterine growth restriction induces alterations in DNA methylation and gene expression in pancreatic islets of rats. J Biol Chem 2010 May 14;285(20):15111-8. PMID: 20194508
Dubois PC, Trynka G, Franke L, Hunt KA et al. Multiple common variants for celiac disease influencing immune gene expression. Nat Genet 2010 Apr;42(4):295-302. PMID: 20190752
Juul N, Szallasi Z, Eklund AC, Li Q et al. Assessment of an RNA interference screen-derived mitotic and ceramide pathway metagene as a predictor of response to neoadjuvant paclitaxel for primary triple-negative breast cancer: a retrospective analysis of five clinical trials. Lancet Oncol 2010 Apr;11(4):358-65. PMID: 20189874
Hung JH, Whitfield TW, Yang TH, Hu Z et al. Identification of functional modules that correlate with phenotypic difference: the influence of network topology. Genome Biol 2010;11(2):R23. PMID: 20187943
Doss MX, Wagh V, Schulz H, Kull M et al. Global transcriptomic analysis of murine embryonic stem cell-derived brachyury (T) cells. Genes Cells 2010 Feb 24. PMID: 20184659
Garge N, Pan H, Rowland MD, Cargile BJ et al. Identification of quantitative trait loci underlying proteome variation in human lymphoblastoid cells. Mol Cell Proteomics 2010 Jul;9(7):1383-99. PMID: 20179311
De Preter K, Vermeulen J, Brors B, Delattre O et al. Accurate outcome prediction in neuroblastoma across independent data sets using a multigene signature. Clin Cancer Res 2010 Mar 1;16(5):1532-41. PMID: 20179214
Creighton CJ, Fountain MD, Yu Z, Nagaraja AK et al. Molecular profiling uncovers a p53-associated role for microRNA-31 in inhibiting the proliferation of serous ovarian carcinomas and other cancers. Cancer Res 2010 Mar 1;70(5):1906-15. PMID: 20179198
Wang HW, Wu YH, Hsieh JY, Liang ML et al. Pediatric primary central nervous system germ cell tumors of different prognosis groups show characteristic miRNome traits and chromosome copy number variations. BMC Genomics 2010 Feb 24;11:132. PMID: 20178649
Dada JO, Spasić I, Paton NW, Mendes P. SBRML: a markup language for associating systems biology data with models. Bioinformatics 2010 Apr 1;26(7):932-8. PMID: 20176582
Zhang S, Cao J, Kong YM, Scheuermann RH. GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach. Bioinformatics 2010 Apr 1;26(7):905-11. PMID: 20176581
Gustafsson M, Hörnquist M. Gene expression prediction by soft integration and the elastic net-best performance of the DREAM3 gene expression challenge. PLoS One 2010 Feb 16;5(2):e9134. PMID: 20169069
Raleigh DR, Marchiando AM, Zhang Y, Shen L et al. Tight junction-associated MARVEL proteins marveld3, tricellulin, and occludin have distinct but overlapping functions. Mol Biol Cell 2010 Apr 1;21(7):1200-13. PMID: 20164257
Lonergan KM, Chari R, Coe BP, Wilson IM et al. Transcriptome profiles of carcinoma-in-situ and invasive non-small cell lung cancer as revealed by SAGE. PLoS One 2010 Feb 11;5(2):e9162. PMID: 20161782
Shehadeh LA, Yu K, Wang L, Guevara A et al. SRRM2, a potential blood biomarker revealing high alternative splicing in Parkinson's disease. PLoS One 2010 Feb 8;5(2):e9104. PMID: 20161708
Barrios F, Filipponi D, Pellegrini M, Paronetto MP et al. Opposing effects of retinoic acid and FGF9 on Nanos2 expression and meiotic entry of mouse germ cells. J Cell Sci 2010 Mar 15;123(Pt 6):871-80. PMID: 20159962
Yu H, Yu FD, Zhang GQ, Shen X et al. DBH2H: vertebrate head-to-head gene pairs annotated at genomic and post-genomic levels. Database (Oxford) 2009;2009:bap006. PMID: 20157479
Sun W, Ibrahim JG, Zou F. Genomewide multiple-loci mapping in experimental crosses by iterative adaptive penalized regression. Genetics 2010 May;185(1):349-59. PMID: 20157003
Oldridge DA, Banerjee S, Setlur SR, Sboner A et al. Optimizing copy number variation analysis using genome-wide short sequence oligonucleotide arrays. Nucleic Acids Res 2010 Jun;38(10):3275-86. PMID: 20156996
Richard H, Schulz MH, Sultan M, Nürnberger A et al. Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Res 2010 Jun;38(10):e112. PMID: 20150413
Qu HQ, Jacob K, Fatet S, Ge B et al. Genome-wide profiling using single-nucleotide polymorphism arrays identifies novel chromosomal imbalances in pediatric glioblastomas. Neuro Oncol 2010 Feb;12(2):153-63. PMID: 20150382
Faulk C, Kim J. Position-based clustering of microarray expression data. Cold Spring Harb Protoc 2009 Sep;2009(9):pdb.prot5280. PMID: 20147265
Lottaz C, Beier D, Meyer K, Kumar P et al. Transcriptional profiles of CD133+ and CD133- glioblastoma-derived cancer stem cell lines suggest different cells of origin. Cancer Res 2010 Mar 1;70(5):2030-40. PMID: 20145155
Zabuawala T, Taffany DA, Sharma SM, Merchant A et al. An ets2-driven transcriptional program in tumor-associated macrophages promotes tumor metastasis. Cancer Res 2010 Feb 15;70(4):1323-33. PMID: 20145133
Hong Y, Downey T, Eu KW, Koh PK et al. A 'metastasis-prone' signature for early-stage mismatch-repair proficient sporadic colorectal cancer patients and its implications for possible therapeutics. Clin Exp Metastasis 2010 Feb;27(2):83-90. PMID: 20143136
Dellinger AE, Saw SM, Goh LK, Seielstad M et al. Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays. Nucleic Acids Res 2010 May;38(9):e105. PMID: 20142258
Suthram S, Dudley JT, Chiang AP, Chen R et al. Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets. PLoS Comput Biol 2010 Feb 5;6(2):e1000662. PMID: 20140234
Huang HC, Jupiter D, VanBuren V. Classification of genes and putative biomarker identification using distribution metrics on expression profiles. PLoS One 2010 Feb 4;5(2):e9056. PMID: 20140228
Turcan S, Slonim DK, Vetter DE. Lack of nAChR activity depresses cochlear maturation and up-regulates GABA system components: temporal profiling of gene expression in alpha9 null mice. PLoS One 2010 Feb 4;5(2):e9058. PMID: 20140217
Duggan SP, Behan FM, Kirca M, Smith S et al. An integrative genomic approach in oesophageal cells identifies TRB3 as a bile acid responsive gene, downregulated in Barrett's oesophagus, which regulates NF-kappaB activation and cytokine levels. Carcinogenesis 2010 May;31(5):936-45. PMID: 20139130
Gao P, Bai X, Yang L, Lv D et al. Over-expression of osa-MIR396c decreases salt and alkali stress tolerance. Planta 2010 Apr;231(5):991-1001. PMID: 20135324
Lima WR, Parreira KS, Devuyst O, Caplanusi A et al. ZONAB promotes proliferation and represses differentiation of proximal tubule epithelial cells. J Am Soc Nephrol 2010 Mar;21(3):478-88. PMID: 20133480
Mithraprabhu S, Mendis S, Meachem SJ, Tubino L et al. Activin bioactivity affects germ cell differentiation in the postnatal mouse testis in vivo. Biol Reprod 2010 May;82(5):980-90. PMID: 20130270
Yao L, Barontini M, Niederle B, Jech M et al. Mutations of the metabolic genes IDH1, IDH2, and SDHAF2 are not major determinants of the pseudohypoxic phenotype of sporadic pheochromocytomas and paragangliomas. J Clin Endocrinol Metab 2010 Mar;95(3):1469-72. PMID: 20130071
Chen W, Hilton IB, Staudt MR, Burd CE et al. Distinct p53, p53:LANA, and LANA complexes in Kaposi's Sarcoma--associated Herpesvirus Lymphomas. J Virol 2010 Apr;84(8):3898-908. PMID: 20130056
Meier S, Ruzvidzo O, Morse M, Donaldson L et al. The Arabidopsis wall associated kinase-like 10 gene encodes a functional guanylyl cyclase and is co-expressed with pathogen defense related genes. PLoS One 2010 Jan 26;5(1):e8904. PMID: 20126659
Hussenet T, Dali S, Exinger J, Monga B et al. SOX2 is an oncogene activated by recurrent 3q26.3 amplifications in human lung squamous cell carcinomas. PLoS One 2010 Jan 29;5(1):e8960. PMID: 20126410
Notani D, Gottimukkala KP, Jayani RS, Limaye AS et al. Global regulator SATB1 recruits beta-catenin and regulates T(H)2 differentiation in Wnt-dependent manner. PLoS Biol 2010 Jan 26;8(1):e1000296. PMID: 20126258
Kong SW, Hu YW, Ho JW, Ikeda S et al. Heart failure-associated changes in RNA splicing of sarcomere genes. Circ Cardiovasc Genet 2010 Apr;3(2):138-46. PMID: 20124440
Shen Y, Chen CS, Ichikawa H, Goldberg GS. SRC induces podoplanin expression to promote cell migration. J Biol Chem 2010 Mar 26;285(13):9649-56. PMID: 20123990
Gupta R, Wikramasinghe P, Bhattacharyya A, Perez FA et al. Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data. BMC Bioinformatics 2010 Jan 18;11 Suppl 1:S65. PMID: 20122241
Yang P, Zhou BB, Zhang Z, Zomaya AY. A multi-filter enhanced genetic ensemble system for gene selection and sample classification of microarray data. BMC Bioinformatics 2010 Jan 18;11 Suppl 1:S5. PMID: 20122224
Sone H, Okura M, Zaha H, Fujibuchi W et al. Profiles of Chemical Effects on Cells (pCEC): a toxicogenomics database with a toxicoinformatics system for risk evaluation and toxicity prediction of environmental chemicals. J Toxicol Sci 2010 Feb;35(1):115-23. PMID: 20118632
Jung CH, Hansen MA, Makunin IV, Korbie DJ et al. Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data. BMC Genomics 2010 Feb 1;11:77. PMID: 20113528
Tsai HK, Huang PY, Kao CY, Wang D. Co-Expression of neighboring genes in the zebrafish (Danio rerio) genome. Int J Mol Sci 2009 Aug 21;10(8):3658-70. PMID: 20111688
Jain M, Ghanashyam C, Bhattacharjee A. Comprehensive expression analysis suggests overlapping and specific roles of rice glutathione S-transferase genes during development and stress responses. BMC Genomics 2010 Jan 29;11:73. PMID: 20109239
Jung KH, Seo YS, Walia H, Cao P et al. The submergence tolerance regulator Sub1A mediates stress-responsive expression of AP2/ERF transcription factors. Plant Physiol 2010 Mar;152(3):1674-92. PMID: 20107022
Jennen DG, Magkoufopoulou C, Ketelslegers HB, van Herwijnen MH et al. Comparison of HepG2 and HepaRG by whole-genome gene expression analysis for the purpose of chemical hazard identification. Toxicol Sci 2010 May;115(1):66-79. PMID: 20106945
McKeen HD, Byrne C, Jithesh PV, Donley C et al. FKBPL regulates estrogen receptor signaling and determines response to endocrine therapy. Cancer Res 2010 Feb 1;70(3):1090-100. PMID: 20103631
Lawrence MG, Lai J, Clements JA. Kallikreins on steroids: structure, function, and hormonal regulation of prostate-specific antigen and the extended kallikrein locus. Endocr Rev 2010 Aug;31(4):407-46. PMID: 20103546
Auman JT, McLeod HL. Colorectal cancer cell lines lack the molecular heterogeneity of clinical colorectal tumors. Clin Colorectal Cancer 2010 Jan;9(1):40-7. PMID: 20100687
Wooten EC, Iyer LK, Montefusco MC, Hedgepeth AK et al. Application of gene network analysis techniques identifies AXIN1/PDIA2 and endoglin haplotypes associated with bicuspid aortic valve. PLoS One 2010 Jan 21;5(1):e8830. PMID: 20098615
McCall MN, Bolstad BM, Irizarry RA. Frozen robust multiarray analysis (fRMA). Biostatistics 2010 Apr;11(2):242-53. PMID: 20097884
Mustroph A, Lee SC, Oosumi T, Zanetti ME et al. Cross-kingdom comparison of transcriptomic adjustments to low-oxygen stress highlights conserved and plant-specific responses. Plant Physiol 2010 Mar;152(3):1484-500. PMID: 20097791
Waldman YY, Tuller T, Shlomi T, Sharan R et al. Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages. Nucleic Acids Res 2010 May;38(9):2964-74. PMID: 20097653
Haugen AC, Di Prospero NA, Parker JS, Fannin RD et al. Altered gene expression and DNA damage in peripheral blood cells from Friedreich's ataxia patients: cellular model of pathology. PLoS Genet 2010 Jan 15;6(1):e1000812. PMID: 20090835
Nibbe RK, Koyutürk M, Chance MR. An integrative -omics approach to identify functional sub-networks in human colorectal cancer. PLoS Comput Biol 2010 Jan 15;6(1):e1000639. PMID: 20090827
Christen B, Robles V, Raya M, Paramonov I et al. Regeneration and reprogramming compared. BMC Biol 2010 Jan 20;8:5. PMID: 20089153
Chia CY, Lim CW, Leong WT, Ling MH. High expression stability of microtubule affinity regulating kinase 3 (MARK3) makes it a reliable reference gene. IUBMB Life 2010 Mar;62(3):200-3. PMID: 20087965
Ariazi EA, Brailoiu E, Yerrum S, Shupp HA et al. The G protein-coupled receptor GPR30 inhibits proliferation of estrogen receptor-positive breast cancer cells. Cancer Res 2010 Feb 1;70(3):1184-94. PMID: 20086172
Zaravinos A, Spandidos DA. Yin yang 1 expression in human tumors. Cell Cycle 2010 Feb 1;9(3):512-22. PMID: 20081375
Ralston A, Cox BJ, Nishioka N, Sasaki H et al. Gata3 regulates trophoblast development downstream of Tead4 and in parallel to Cdx2. Development 2010 Feb;137(3):395-403. PMID: 20081188
Markitsis A, Lai Y. A censored beta mixture model for the estimation of the proportion of non-differentially expressed genes. Bioinformatics 2010 Mar 1;26(5):640-6. PMID: 20080506
Anvar SY, 't Hoen PA, Tucker A. The identification of informative genes from multiple datasets with increasing complexity. BMC Bioinformatics 2010 Jan 15;11:32. PMID: 20078860
Sales G, Coppe A, Bicciato S, Bortoluzzi S et al. Impact of probe annotation on the integration of miRNA-mRNA expression profiles for miRNA target detection. Nucleic Acids Res 2010 Apr;38(7):e97. PMID: 20071740
Shinde K, Phatak M, Johannes FM, Chen J et al. Genomics Portals: integrative web-platform for mining genomics data. BMC Genomics 2010 Jan 13;11:27. PMID: 20070909
Barwick BG, Abramovitz M, Kodani M, Moreno CS et al. Prostate cancer genes associated with TMPRSS2-ERG gene fusion and prognostic of biochemical recurrence in multiple cohorts. Br J Cancer 2010 Feb 2;102(3):570-6. PMID: 20068566
Freidlin B, Jiang W, Simon R. The cross-validated adaptive signature design. Clin Cancer Res 2010 Jan 15;16(2):691-8. PMID: 20068112
Petry IB, Fieber E, Schmidt M, Gehrmann M et al. ERBB2 induces an antiapoptotic expression pattern of Bcl-2 family members in node-negative breast cancer. Clin Cancer Res 2010 Jan 15;16(2):451-60. PMID: 20068093
Kandasamy K, Mohan SS, Raju R, Keerthikumar S et al. NetPath: a public resource of curated signal transduction pathways. Genome Biol 2010 Jan 12;11(1):R3. PMID: 20067622
De Hertogh B, De Meulder B, Berger F, Pierre M et al. A benchmark for statistical microarray data analysis that preserves actual biological and technical variance. BMC Bioinformatics 2010 Jan 11;11:17. PMID: 20064233
Yamaguchi K, Mandai M, Oura T, Matsumura N et al. Identification of an ovarian clear cell carcinoma gene signature that reflects inherent disease biology and the carcinogenic processes. Oncogene 2010 Mar 25;29(12):1741-52. PMID: 20062075
Ortiz-Barahona A, Villar D, Pescador N, Amigo J et al. Genome-wide identification of hypoxia-inducible factor binding sites and target genes by a probabilistic model integrating transcription-profiling data and in silico binding site prediction. Nucleic Acids Res 2010 Apr;38(7):2332-45. PMID: 20061373
Boles NC, Peddibhotla S, Chen AJ, Goodell MA et al. Chk1 haploinsufficiency results in anemia and defective erythropoiesis. PLoS One 2010 Jan 5;5(1):e8581. PMID: 20052416
Hampton TH, Stanton BA. A novel approach to analyze gene expression data demonstrates that the DeltaF508 mutation in CFTR downregulates the antigen presentation pathway. Am J Physiol Lung Cell Mol Physiol 2010 Apr;298(4):L473-82. PMID: 20044437
Parikh H, Lyssenko V, Groop LC. Prioritizing genes for follow-up from genome wide association studies using information on gene expression in tissues relevant for type 2 diabetes mellitus. BMC Med Genomics 2009 Dec 31;2:72. PMID: 20043853
Ma J, Meng Y, Kwiatkowski DJ, Chen X et al. Mammalian target of rapamycin regulates murine and human cell differentiation through STAT3/p63/Jagged/Notch cascade. J Clin Invest 2010 Jan;120(1):103-14. PMID: 20038814
Mořkovský L, Storchová R, Plachý J, Ivánek R et al. The chicken z chromosome is enriched for genes with preferential expression in ovarian somatic cells. J Mol Evol 2010 Feb;70(2):129-36. PMID: 20037757
Ji Z, Tian B. Reprogramming of 3' untranslated regions of mRNAs by alternative polyadenylation in generation of pluripotent stem cells from different cell types. PLoS One 2009 Dec 23;4(12):e8419. PMID: 20037631
Main H, Lee KL, Yang H, Haapa-Paananen S et al. Interactions between Notch- and hypoxia-induced transcriptomes in embryonic stem cells. Exp Cell Res 2010 May 15;316(9):1610-24. PMID: 20034489
Wallace HA, Plata MP, Kang HJ, Ross M et al. Chromatin insulators specifically associate with different levels of higher-order chromatin organization in Drosophila. Chromosoma 2010 Apr;119(2):177-94. PMID: 20033198
Pfeifle C, Reinhardt K, Heins S, Burdach S et al. Development and characterization of HAT-sensitive Ewing tumour cells for immunotherapy. Anticancer Res 2009 Nov;29(11):4489-96. PMID: 20032396
Barth AS, Aiba T, Halperin V, DiSilvestre D et al. Cardiac resynchronization therapy corrects dyssynchrony-induced regional gene expression changes on a genomic level. Circ Cardiovasc Genet 2009 Aug;2(4):371-8. PMID: 20031609
Putt ME, Hannenhalli S, Lu Y, Haines P et al. Evidence for coregulation of myocardial gene expression by MEF2 and NFAT in human heart failure. Circ Cardiovasc Genet 2009 Jun;2(3):212-9. PMID: 20031589
Sheehy SP, Huang S, Parker KK. Time-warped comparison of gene expression in adaptive and maladaptive cardiac hypertrophy. Circ Cardiovasc Genet 2009 Apr;2(2):116-24. PMID: 20031575
He M, Mangiameli DP, Kachala S, Hunter K et al. Expression signature developed from a complex series of mouse models accurately predicts human breast cancer survival. Clin Cancer Res 2010 Jan 1;16(1):249-59. PMID: 20028755
Shi W, Bugrim A, Nikolsky Y, Nikolskya T et al. Characteristics of genomic signatures derived using univariate methods and mechanistically anchored functional descriptors for predicting drug- and xenobiotic-induced nephrotoxicity. Toxicol Mech Methods 2008;18(2-3):267-76. PMID: 20020920
Southworth LK, Owen AB, Kim SK. Aging mice show a decreasing correlation of gene expression within genetic modules. PLoS Genet 2009 Dec;5(12):e1000776. PMID: 20019809
Dressaire C, Gitton C, Loubière P, Monnet V et al. Transcriptome and proteome exploration to model translation efficiency and protein stability in Lactococcus lactis. PLoS Comput Biol 2009 Dec;5(12):e1000606. PMID: 20019804
Yoda A, Yoda Y, Chiaretti S, Bar-Natan M et al. Functional screening identifies CRLF2 in precursor B-cell acute lymphoblastic leukemia. Proc Natl Acad Sci U S A 2010 Jan 5;107(1):252-7. PMID: 20018760
Makarevitch I, Harris C. Aneuploidy causes tissue-specific qualitative changes in global gene expression patterns in maize. Plant Physiol 2010 Feb;152(2):927-38. PMID: 20018594
Gevaert O, Daemen A, De Moor B, Libbrecht L. A taxonomy of epithelial human cancer and their metastases. BMC Med Genomics 2009 Dec 17;2:69. PMID: 20017941
Mans JJ, Hendrickson EL, Hackett M, Lamont RJ. Cellular and bacterial profiles associated with oral epithelium-microbiota interactions. Periodontol 2000 2010 Feb;52(1):207-17. PMID: 20017802
Kim M, Cho SB, Kim JH. Mixture-model based estimation of gene expression variance from public database improves identification of differentially expressed genes in small sized microarray data. Bioinformatics 2010 Feb 15;26(4):486-92. PMID: 20015947
Chang SJ, Wang TY, Tsai CY, Hu TF et al. Increased epithelial stem cell traits in advanced endometrial endometrioid carcinoma. BMC Genomics 2009 Dec 16;10:613. PMID: 20015385
Buisine N, Sachs L. Impact of genome assembly status on ChIP-Seq and ChIP-PET data mapping. BMC Res Notes 2009 Dec 16;2:257. PMID: 20015379
Haag M, Van Linthout S, Schröder SE, Freymann U et al. Endomyocardial biopsy derived adherent proliferating cells - a potential cell source for cardiac tissue engineering. J Cell Biochem 2010 Feb 15;109(3):564-75. PMID: 20013794
Camateros P, Marino R, Fortin A, Martin JG et al. Identification of novel chromosomal regions associated with airway hyperresponsiveness in recombinant congenic strains of mice. Mamm Genome 2010 Feb;21(1-2):28-38. PMID: 20012967
Sartor MA, Mahavisno V, Keshamouni VG, Cavalcoli J et al. ConceptGen: a gene set enrichment and gene set relation mapping tool. Bioinformatics 2010 Feb 15;26(4):456-63. PMID: 20007254
Wu J, Qiu Q, Xie L, Fullerton J et al. Web-based interrogation of gene expression signatures using EXALT. BMC Bioinformatics 2009 Dec 14;10:420. PMID: 20003458
Cavalieri D, Calura E, Romualdi C, Marchi E et al. Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis. BMC Genomics 2009 Dec 11;10:596. PMID: 20003344
Galindo CL, Skinner MA, Errami M, Olson LD et al. Transcriptional profile of isoproterenol-induced cardiomyopathy and comparison to exercise-induced cardiac hypertrophy and human cardiac failure. BMC Physiol 2009 Dec 9;9:23. PMID: 20003209
Glazer CA, Smith IM, Ochs MF, Begum S et al. Integrative discovery of epigenetically derepressed cancer testis antigens in NSCLC. PLoS One 2009 Dec 4;4(12):e8189. PMID: 19997593
Jorissen RN, Gibbs P, Christie M, Prakash S et al. Metastasis-Associated Gene Expression Changes Predict Poor Outcomes in Patients with Dukes Stage B and C Colorectal Cancer. Clin Cancer Res 2009 Dec 15;15(24):7642-7651. PMID: 19996206
Fu Y, Chen Z, Blakemore AI, Orwoll E et al. Absence of AVPR2 copy number variation in eunatremic and dysnatremic subjects in non-Hispanic Caucasian populations. Physiol Genomics 2010 Feb 4;40(3):121-7. PMID: 19996159
Chen L. A global comparison between nuclear and cytosolic transcriptomes reveals differential compartmentalization of alternative transcript isoforms. Nucleic Acids Res 2010 Mar;38(4):1086-97. PMID: 19969546
Johnson JE, Cao K, Ryvkin P, Wang LS et al. Altered gene expression in the Werner and Bloom syndromes is associated with sequences having G-quadruplex forming potential. Nucleic Acids Res 2010 Mar;38(4):1114-22. PMID: 19966276
Yang JH, Shao P, Zhou H, Chen YQ et al. deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res 2010 Jan;38(Database issue):D123-30. PMID: 19966272
Huang Y, de Reyniès A, de Leval L, Ghazi B et al. Gene expression profiling identifies emerging oncogenic pathways operating in extranodal NK/T-cell lymphoma, nasal type. Blood 2010 Feb 11;115(6):1226-37. PMID: 19965620
Keller MA, Watschinger K, Golderer G, Maglione M et al. Monitoring of fatty aldehyde dehydrogenase by formation of pyrenedecanoic acid from pyrenedecanal. J Lipid Res 2010 Jun;51(6):1554-9. PMID: 19965611
Edelman LB, Toia G, Geman D, Zhang W et al. Two-transcript gene expression classifiers in the diagnosis and prognosis of human diseases. BMC Genomics 2009 Dec 5;10:583. PMID: 19961616
Geerts D, Koster J, Albert D, Koomoa DL et al. The polyamine metabolism genes ornithine decarboxylase and antizyme 2 predict aggressive behavior in neuroblastomas with and without MYCN amplification. Int J Cancer 2010 May 1;126(9):2012-24. PMID: 19960435
Ho JW, Stefani M, dos Remedios CG, Charleston MA. A model selection approach to discover age-dependent gene expression patterns using quantile regression models. BMC Genomics 2009 Dec 3;10 Suppl 3:S16. PMID: 19958479
Keum C, Woo JH, Oh WS, Park SN et al. Improving gene expression similarity measurement using pathway-based analytic dimension. BMC Genomics 2009 Dec 3;10 Suppl 3:S15. PMID: 19958478
Jiang P, Rushing SN, Kong CW, Fu J et al. Electrophysiological properties of human induced pluripotent stem cells. Am J Physiol Cell Physiol 2010 Mar;298(3):C486-95. PMID: 19955484
Maver A, Medica I, Peterlin B. Search for sarcoidosis candidate genes by integration of data from genomic, transcriptomic and proteomic studies. Med Sci Monit 2009 Dec;15(12):SR22-8. PMID: 19946248
Noma H, Matsui S, Omori T, Sato T. Bayesian ranking and selection methods using hierarchical mixture models in microarray studies. Biostatistics 2010 Apr;11(2):281-9. PMID: 19946026
Sontrop HM, Moerland PD, van den Ham R, Reinders MJ et al. A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability. BMC Bioinformatics 2009 Nov 26;10:389. PMID: 19941644
Nakamura K, Salomonis N, Tomoda K, Yamanaka S et al. G(i)-coupled GPCR signaling controls the formation and organization of human pluripotent colonies. PLoS One 2009 Nov 10;4(11):e7780. PMID: 19936228
Tategu M, Arauchi T, Tanaka R, Nakagawa H et al. Systems biology-based identification of crosstalk between E2F transcription factors and the Fanconi anemia pathway. Gene Regul Syst Bio 2007 May 1;1:1-8. PMID: 19936073
Hong BS, Cho JH, Kim H, Choi EJ et al. Colorectal cancer cell-derived microvesicles are enriched in cell cycle-related mRNAs that promote proliferation of endothelial cells. BMC Genomics 2009 Nov 25;10:556. PMID: 19930720
Wan R, Kiseleva L, Harada H, Mamitsuka H et al. HAMSTER: visualizing microarray experiments as a set of minimum spanning trees. Source Code Biol Med 2009 Nov 20;4:8. PMID: 19925686
Rolland AD, Lareyre JJ, Goupil AS, Montfort J et al. Expression profiling of rainbow trout testis development identifies evolutionary conserved genes involved in spermatogenesis. BMC Genomics 2009 Nov 20;10:546. PMID: 19925684
Zhang W, Dolan ME. Use of cell lines in the investigation of pharmacogenetic loci. Curr Pharm Des 2009;15(32):3782-95. PMID: 19925429
Huang S, Taylor NL, Narsai R, Eubel H et al. Functional and composition differences between mitochondrial complex II in Arabidopsis and rice are correlated with the complex genetic history of the enzyme. Plant Mol Biol 2010 Feb;72(3):331-42. PMID: 19924544
Barbosa-Morais NL, Dunning MJ, Samarajiwa SA, Darot JF et al. A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nucleic Acids Res 2010 Jan;38(3):e17. PMID: 19923232
Morgan AA, Dudley JT, Deshpande T, Butte AJ. Dynamism in gene expression across multiple studies. Physiol Genomics 2010 Feb 4;40(3):128-40. PMID: 19920211
Wu C, Orozco C, Boyer J, Leglise M et al. BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol 2009;10(11):R130. PMID: 19919682
Motallebipour M, Ameur A, Reddy Bysani MS, Patra K et al. Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq. Genome Biol 2009;10(11):R129. PMID: 19919681
Okamura K, Liu N, Lai EC. Distinct mechanisms for microRNA strand selection by Drosophila Argonautes. Mol Cell 2009 Nov 13;36(3):431-44. PMID: 19917251
Asmann YW, Klee EW, Thompson EA, Perez EA et al. 3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer. BMC Genomics 2009 Nov 16;10:531. PMID: 19917133
Kroll KM, Barkema GT, Carlon E. Linear model for fast background subtraction in oligonucleotide microarrays. Algorithms Mol Biol 2009 Nov 16;4:15. PMID: 19917117
Imielinski M, Baldassano RN, Griffiths A, Russell RK et al. Common variants at five new loci associated with early-onset inflammatory bowel disease. Nat Genet 2009 Dec;41(12):1335-40. PMID: 19915574
Yamada M, Hamatani T, Akutsu H, Chikazawa N et al. Involvement of a novel preimplantation-specific gene encoding the high mobility group box protein Hmgpi in early embryonic development. Hum Mol Genet 2010 Feb 1;19(3):480-93. PMID: 19915186
Grinchuk OV, Jenjaroenpun P, Orlov YL, Zhou J et al. Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns. Nucleic Acids Res 2010 Jan;38(2):534-47. PMID: 19906709
Serre D, Lee BH, Ting AH. MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res 2010 Jan;38(2):391-9. PMID: 19906696
Ruckhäberle E, Holtrich U, Engels K, Hanker L et al. Acid ceramidase 1 expression correlates with a better prognosis in ER-positive breast cancer. Climacteric 2009 Dec;12(6):502-13. PMID: 19905902
Yang G, Thieu K, Tsai KY, Piris A et al. Dynamic gene expression analysis links melanocyte growth arrest with nevogenesis. Cancer Res 2009 Dec 1;69(23):9029-37. PMID: 19903842
Hillion J, Wood LJ, Mukherjee M, Bhattacharya R et al. Upregulation of MMP-2 by HMGA1 promotes transformation in undifferentiated, large-cell lung cancer. Mol Cancer Res 2009 Nov;7(11):1803-12. PMID: 19903768
Pai VP, Marshall AM, Hernandez LL, Buckley AR et al. Altered serotonin physiology in human breast cancers favors paradoxical growth and cell survival. Breast Cancer Res 2009;11(6):R81. PMID: 19903352
Beck AH, Lee CH, Witten DM, Gleason BC et al. Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling. Oncogene 2010 Feb 11;29(6):845-54. PMID: 19901961
DuSell CD, Nelson ER, Wittmann BM, Fretz JA et al. Regulation of aryl hydrocarbon receptor function by selective estrogen receptor modulators. Mol Endocrinol 2010 Jan;24(1):33-46. PMID: 19901195
Volinia S, Visone R, Galasso M, Rossi E et al. Identification of microRNA activity by Targets' Reverse EXpression. Bioinformatics 2010 Jan 1;26(1):91-7. PMID: 19897564
Yang J, Cogdell D, Yang D, Hu L et al. Deletion of the WWOX gene and frequent loss of its protein expression in human osteosarcoma. Cancer Lett 2010 May 1;291(1):31-8. PMID: 19896763
Kobayashi I, Ono H, Moritomo T, Kano K et al. Comparative gene expression analysis of zebrafish and mammals identifies common regulators in hematopoietic stem cells. Blood 2010 Jan 14;115(2):e1-9. PMID: 19890097
Cohen NM, Dighe V, Landan G, Reynisdóttir S et al. DNA methylation programming and reprogramming in primate embryonic stem cells. Genome Res 2009 Dec;19(12):2193-201. PMID: 19887575
Edson MA, Lin YN, Matzuk MM. Deletion of the novel oocyte-enriched gene, Gpr149, leads to increased fertility in mice. Endocrinology 2010 Jan;151(1):358-68. PMID: 19887567
Lendahl U, Lee KL, Yang H, Poellinger L. Generating specificity and diversity in the transcriptional response to hypoxia. Nat Rev Genet 2009 Dec;10(12):821-32. PMID: 19884889
Heydemann A, Ceco E, Lim JE, Hadhazy M et al. Latent TGF-beta-binding protein 4 modifies muscular dystrophy in mice. J Clin Invest 2009 Dec;119(12):3703-12. PMID: 19884661
Martina E, Degen M, Rüegg C, Merlo A et al. Tenascin-W is a specific marker of glioma-associated blood vessels and stimulates angiogenesis in vitro. FASEB J 2010 Mar;24(3):778-87. PMID: 19884327
Yang X, Sun X. Meta-analysis of cancer gene-profiling data. Methods Mol Biol 2010;576:409-26. PMID: 19882274
Fortin SP, Ennis MJ, Savitch BA, Carpentieri D et al. Tumor necrosis factor-like weak inducer of apoptosis stimulation of glioma cell survival is dependent on Akt2 function. Mol Cancer Res 2009 Nov;7(11):1871-81. PMID: 19861406
Liu M, Casimiro MC, Wang C, Shirley LA et al. p21CIP1 attenuates Ras- and c-Myc-dependent breast tumor epithelial mesenchymal transition and cancer stem cell-like gene expression in vivo. Proc Natl Acad Sci U S A 2009 Nov 10;106(45):19035-9. PMID: 19858489
Unger K, Wienberg J, Riches A, Hieber L et al. Novel gene rearrangements in transformed breast cells identified by high-resolution breakpoint analysis of chromosomal aberrations. Endocr Relat Cancer 2010 Mar;17(1):87-98. PMID: 19858224
Rullo OJ, Woo JM, Wu H, Hoftman AD et al. Association of IRF5 polymorphisms with activation of the interferon alpha pathway. Ann Rheum Dis 2010 Mar;69(3):611-7. PMID: 19854706
Ivanova AV, Ivanov SV, Prudkin L, Nonaka D et al. Mechanisms of FUS1/TUSC2 deficiency in mesothelioma and its tumorigenic transcriptional effects. Mol Cancer 2009 Oct 24;8:91. PMID: 19852844
Day RC, Müller S, Macknight RC. Identification of cytoskeleton-associated genes expressed during Arabidopsis syncytial endosperm development. Plant Signal Behav 2009 Sep;4(9):883-6. PMID: 19847098
Qian CN, Furge KA, Knol J, Huang D et al. Activation of the PI3K/AKT pathway induces urothelial carcinoma of the renal pelvis: identification in human tumors and confirmation in animal models. Cancer Res 2009 Nov 1;69(21):8256-64. PMID: 19843858
Agrawal A, Sinha A, Ahmad T, Aich J et al. Maladaptation of critical cellular functions in asthma: bioinformatic analysis. Physiol Genomics 2009 Dec 30;40(1):1-7. PMID: 19843653
Ying H, Epps J, Williams R, Huttley G. Evidence that localized variation in primate sequence divergence arises from an influence of nucleosome placement on DNA repair. Mol Biol Evol 2010 Mar;27(3):637-49. PMID: 19843619
Bommer GT, Feng Y, Iura A, Giordano TJ et al. IRS1 regulation by Wnt/beta-catenin signaling and varied contribution of IRS1 to the neoplastic phenotype. J Biol Chem 2010 Jan 15;285(3):1928-38. PMID: 19843521
Platts AE, Lalancette C, Emery BR, Carrell DT et al. Disease progression and solid tumor survival: a transcriptome decoherence model. Mol Cell Probes 2010 Feb;24(1):53-60. PMID: 19835949
Knoop KA, Kumar N, Butler BR, Sakthivel SK et al. RANKL is necessary and sufficient to initiate development of antigen-sampling M cells in the intestinal epithelium. J Immunol 2009 Nov 1;183(9):5738-47. PMID: 19828638
Balestrieri C, Alberghina L, Vanoni M, Chiaradonna F. Data recovery and integration from public databases uncovers transformation-specific transcriptional downregulation of cAMP-PKA pathway-encoding genes. BMC Bioinformatics 2009 Oct 15;10 Suppl 12:S1. PMID: 19828069
Jupiter D, Chen H, VanBuren V. STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data. BMC Bioinformatics 2009 Oct 14;10:332. PMID: 19828039
Nevo J, Mattila E, Pellinen T, Yamamoto DL et al. Mammary-derived growth inhibitor alters traffic of EGFR and induces a novel form of cetuximab resistance. Clin Cancer Res 2009 Nov 1;15(21):6570-81. PMID: 19825952
Wallerman O, Motallebipour M, Enroth S, Patra K et al. Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing. Nucleic Acids Res 2009 Dec;37(22):7498-508. PMID: 19822575
Kusakabe M, Kutomi T, Watanabe K, Emoto N et al. Identification of G0S2 as a gene frequently methylated in squamous lung cancer by combination of in silico and experimental approaches. Int J Cancer 2010 Apr 15;126(8):1895-902. PMID: 19816938
Hecker LA, Alcon TC, Honavar VG, Greenlee MH. Using a seed-network to query multiple large-scale gene expression datasets from the developing retina in order to identify and prioritize experimental targets. Bioinform Biol Insights 2008 Feb 1;2:401-12. PMID: 19812791
Engelmann JC, Schwarz R, Blenk S, Friedrich T et al. Unsupervised meta-analysis on diverse gene expression datasets allows insight into gene function and regulation. Bioinform Biol Insights 2008 May 26;2:265-80. PMID: 19812781
Hirakawa A, Sato Y, Hamada C, Yoshimura I. A new test statistic based on shrunken sample variance for identifying differentially expressed genes in small microarray experiments. Bioinform Biol Insights 2008 Feb 29;2:145-56. PMID: 19812772
Gao C, Dang X, Chen Y, Wilkins D. Graph ranking for exploratory gene data analysis. BMC Bioinformatics 2009 Oct 8;10 Suppl 11:S19. PMID: 19811684
Reina-Pinto JJ, Voisin D, Teodor R, Yephremov A. Probing differentially expressed genes against a microarray database for in silico suppressor/enhancer and inhibitor/activator screens. Plant J 2010 Jan;61(1):166-75. PMID: 19811619
Zhang Z, Yu J, Li D, Zhang Z et al. PMRD: plant microRNA database. Nucleic Acids Res 2010 Jan;38(Database issue):D806-13. PMID: 19808935
Lim PS, Hardy K, Bunting KL, Ma L et al. Defining the chromatin signature of inducible genes in T cells. Genome Biol 2009;10(10):R107. PMID: 19807913
Nobuta K, McCormick K, Nakano M, Meyers BC. Bioinformatics analysis of small RNAs in plants using next generation sequencing technologies. Methods Mol Biol 2010;592:89-106. PMID: 19802591
Chase A, Ernst T, Fiebig A, Collins A et al. TFG, a target of chromosome translocations in lymphoma and soft tissue tumors, fuses to GPR128 in healthy individuals. Haematologica 2010 Jan;95(1):20-6. PMID: 19797732
McCusker JP, Phillips JA, González Beltrán A, Finkelstein A et al. Semantic web data warehousing for caGrid. BMC Bioinformatics 2009 Oct 1;10 Suppl 10:S2. PMID: 19796399
Park PJ, Kong SW, Tebaldi T, Lai WR et al. Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance. Bioinformatics 2009 Dec 1;25(23):3121-7. PMID: 19786482
Moreira JM, Ohlsson G, Gromov P, Simon R et al. Bladder cancer-associated protein, a potential prognostic biomarker in human bladder cancer. Mol Cell Proteomics 2010 Jan;9(1):161-77. PMID: 19783793
Ritchie W, Rajasekhar M, Flamant S, Rasko JE. Conserved expression patterns predict microRNA targets. PLoS Comput Biol 2009 Sep;5(9):e1000513. PMID: 19779543
Bogan RL, Hennebold JD. The reverse cholesterol transport system as a potential mediator of luteolysis in the primate corpus luteum. Reproduction 2010 Jan;139(1):163-76. PMID: 19776099
Pitzer E, Lacson R, Hinske C, Kim J et al. Towards large-scale sample annotation in gene expression repositories. BMC Bioinformatics 2009 Sep 17;10 Suppl 9:S9. PMID: 19761579
Shivakumar P, Krauthammer M. Structural similarity assessment for drug sensitivity prediction in cancer. BMC Bioinformatics 2009 Sep 17;10 Suppl 9:S17. PMID: 19761571
Lacson R, Pitzer E, Hinske C, Galante P et al. Evaluation of a large-scale biomedical data annotation initiative. BMC Bioinformatics 2009 Sep 17;10 Suppl 9:S10. PMID: 19761564
Chang HH, Ramoni MF. Transcriptional network classifiers. BMC Bioinformatics 2009 Sep 17;10 Suppl 9:S1. PMID: 19761563
Davey MW, Graham NS, Vanholme B, Swennen R et al. Heterologous oligonucleotide microarrays for transcriptomics in a non-model species; a proof-of-concept study of drought stress in Musa. BMC Genomics 2009 Sep 16;10:436. PMID: 19758430
Dudley JT, Tibshirani R, Deshpande T, Butte AJ. Disease signatures are robust across tissues and experiments. Mol Syst Biol 2009;5:307. PMID: 19756046
Scharl T, Voglhuber I, Leisch F. Exploratory and inferential analysis of gene cluster neighborhood graphs. BMC Bioinformatics 2009 Sep 14;10:288. PMID: 19751523
Aid-Pavlidis T, Pavlidis P, Timmusk T. Meta-coexpression conservation analysis of microarray data: a "subset" approach provides insight into brain-derived neurotrophic factor regulation. BMC Genomics 2009 Sep 8;10:420. PMID: 19737418
Wu Y, Yan L, Liu H, Sun H et al. A new outlier removal approach for cDNA microarray normalization. Biotechniques 2009 Aug;47(2):691-2, 694-700. PMID: 19737130
Lai Y, Sun Y, Skinner CM, Son EL et al. Reconstitution of marrow-derived extracellular matrix ex vivo: a robust culture system for expanding large-scale highly functional human mesenchymal stem cells. Stem Cells Dev 2010 Jul;19(7):1095-107. PMID: 19737070
Kayano M, Takigawa I, Shiga M, Tsuda K et al. Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data. Bioinformatics 2009 Nov 1;25(21):2735-43. PMID: 19736252
Zhao H, Wang Q, Bai C, He K et al. A cross-study gene set enrichment analysis identifies critical pathways in endometriosis. Reprod Biol Endocrinol 2009 Sep 8;7:94. PMID: 19735579
Upton GJ, Sanchez-Graillet O, Rowsell J, Arteaga-Salas JM et al. On the causes of outliers in Affymetrix GeneChip data. Brief Funct Genomic Proteomic 2009 May;8(3):199-212. PMID: 19734302
Hu HY, Yan Z, Xu Y, Hu H et al. Sequence features associated with microRNA strand selection in humans and flies. BMC Genomics 2009 Sep 4;10:413. PMID: 19732433
Arbour M, Epp E, Hogues H, Sellam A et al. Widespread occurrence of chromosomal aneuploidy following the routine production of Candida albicans mutants. FEMS Yeast Res 2009 Oct;9(7):1070-7. PMID: 19732157
Freishtat RJ, Benton AS, Watson AM, Wang Z et al. Delineation of a gene network underlying the pulmonary response to oxidative stress in asthma. J Investig Med 2009 Oct;57(7):756-64. PMID: 19730131
Wang W, Nunez-Iglesias J, Luan Y, Sun F. Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach. BMC Bioinformatics 2009 Sep 3;10:277. PMID: 19728875
Feng C, Araki M, Kunimoto R, Tamon A et al. GEM-TREND: a web tool for gene expression data mining toward relevant network discovery. BMC Genomics 2009 Sep 3;10:411. PMID: 19728865
Shiryaev SA, Remacle AG, Savinov AY, Chernov AV et al. Inflammatory proprotein convertase-matrix metalloproteinase proteolytic pathway in antigen-presenting cells as a step to autoimmune multiple sclerosis. J Biol Chem 2009 Oct 30;284(44):30615-26. PMID: 19726693
Culhane AC, Quackenbush J. Confounding effects in "A six-gene signature predicting breast cancer lung metastasis". Cancer Res 2009 Sep 15;69(18):7480-5. PMID: 19723662
Francis SM, Larsen JE, Pavey SJ, Bowman RV et al. Expression profiling identifies genes involved in emphysema severity. Respir Res 2009 Sep 2;10:81. PMID: 19723343
Choi JK, Bae JB, Lyu J, Kim TY et al. Nucleosome deposition and DNA methylation at coding region boundaries. Genome Biol 2009;10(9):R89. PMID: 19723310
Le Martelot G, Claudel T, Gatfield D, Schaad O et al. REV-ERBalpha participates in circadian SREBP signaling and bile acid homeostasis. PLoS Biol 2009 Sep;7(9):e1000181. PMID: 19721697
Yuan Z, Pei H, Roberts DJ, Zhang Z et al. Quantitative trait locus analysis of neointimal formation in an intercross between C57BL/6 and C3H/HeJ apolipoprotein E-deficient mice. Circ Cardiovasc Genet 2009 Jun;2(3):220-8. PMID: 19718279
Shin J, Li B, Davis ME, Suh Y et al. Comparative analysis of fatty acid-binding protein 4 promoters: conservation of peroxisome proliferator-activated receptor binding sites. J Anim Sci 2009 Dec;87(12):3923-34. PMID: 19717768
Keller A, Backes C, Gerasch A, Kaufmann M et al. A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis. Bioinformatics 2009 Nov 1;25(21):2787-94. PMID: 19713416
Mertsch S, Schurgers LJ, Weber K, Paulus W et al. Matrix gla protein (MGP): an overexpressed and migration-promoting mesenchymal component in glioblastoma. BMC Cancer 2009 Aug 27;9:302. PMID: 19712474
Lively GD, Jiang B, Hedberg-Buenz A, Chang B et al. Genetic dependence of central corneal thickness among inbred strains of mice. Invest Ophthalmol Vis Sci 2010 Jan;51(1):160-71. PMID: 19710407
Li C, Li X, Miao Y, Wang Q et al. SubpathwayMiner: a software package for flexible identification of pathways. Nucleic Acids Res 2009 Oct;37(19):e131. PMID: 19706733
Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N et al. Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A 2009 Sep 1;106(35):14926-31. PMID: 19706456
Hsu SC, Patel R, Bédard J, Jarvis P et al. Two distinct Omp85 paralogs in the chloroplast outer envelope membrane are essential for embryogenesis in Arabidopsis thaliana. Plant Signal Behav 2008 Dec;3(12):1134-5. PMID: 19704458
Yu Y, Tu K, Zheng S, Li Y et al. GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction. BMC Bioinformatics 2009 Aug 25;10:264. PMID: 19703314
Kim EY, Kim SY, Ashlock D, Nam D. MULTI-K: accurate classification of microarray subtypes using ensemble k-means clustering. BMC Bioinformatics 2009 Aug 22;10:260. PMID: 19698124
Bandyopadhyay S, Mitra R. TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples. Bioinformatics 2009 Oct 15;25(20):2625-31. PMID: 19692556
Li J, Zimmerman LJ, Park BH, Tabb DL et al. Network-assisted protein identification and data interpretation in shotgun proteomics. Mol Syst Biol 2009;5:303. PMID: 19690572
Choi Y, Kendziorski C. Statistical methods for gene set co-expression analysis. Bioinformatics 2009 Nov 1;25(21):2780-6. PMID: 19689953
Lafferty-Whyte K, Cairney CJ, Will MB, Serakinci N et al. A gene expression signature classifying telomerase and ALT immortalization reveals an hTERT regulatory network and suggests a mesenchymal stem cell origin for ALT. Oncogene 2009 Oct 29;28(43):3765-74. PMID: 19684619
Tu K, Yu H, Hua YJ, Li YY et al. Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms. Nucleic Acids Res 2009 Oct;37(18):5969-80. PMID: 19671526
Li X, Cai H, Xu J, Ying S et al. A mouse protein interactome through combined literature mining with multiple sources of interaction evidence. Amino Acids 2010 Apr;38(4):1237-52. PMID: 19669079
Kim WY, Perera S, Zhou B, Carretero J et al. HIF2alpha cooperates with RAS to promote lung tumorigenesis in mice. J Clin Invest 2009 Aug;119(8):2160-70. PMID: 19662677
Hu G, Agarwal P. Human disease-drug network based on genomic expression profiles. PLoS One 2009 Aug 6;4(8):e6536. PMID: 19657382
Nilsson R, Schultz IJ, Pierce EL, Soltis KA et al. Discovery of genes essential for heme biosynthesis through large-scale gene expression analysis. Cell Metab 2009 Aug;10(2):119-30. PMID: 19656490
Houot R, Goldstein MJ, Kohrt HE, Myklebust JH et al. Therapeutic effect of CD137 immunomodulation in lymphoma and its enhancement by Treg depletion. Blood 2009 Oct 15;114(16):3431-8. PMID: 19641184
Freudenberg JM, Joshi VK, Hu Z, Medvedovic M. CLEAN: CLustering Enrichment ANalysis. BMC Bioinformatics 2009 Jul 29;10:234. PMID: 19640299
Galvez-Valdivieso G, Fryer MJ, Lawson T, Slattery K et al. The high light response in Arabidopsis involves ABA signaling between vascular and bundle sheath cells. Plant Cell 2009 Jul;21(7):2143-62. PMID: 19638476
Mehan MR, Nunez-Iglesias J, Kalakrishnan M, Waterman MS et al. An integrative network approach to map the transcriptome to the phenome. J Comput Biol 2009 Aug;16(8):1023-34. PMID: 19630539
Zhu W, Yang L, Du Z. Layered functional network analysis of gene expression in human heart failure. PLoS One 2009 Jul 24;4(7):e6288. PMID: 19629191
Kutlu B, Kayali AG, Jung S, Parnaud G et al. Meta-analysis of gene expression in human pancreatic islets after in vitro expansion. Physiol Genomics 2009 Sep 9;39(1):72-81. PMID: 19622797
Wessells H, Sullivan CJ, Tsubota Y, Engel KL et al. Transcriptional profiling of human cavernosal endothelial cells reveals distinctive cell adhesion phenotype and role for claudin 11 in vascular barrier function. Physiol Genomics 2009 Oct 7;39(2):100-8. PMID: 19622796
Buechler S. Low expression of a few genes indicates good prognosis in estrogen receptor positive breast cancer. BMC Cancer 2009 Jul 20;9:243. PMID: 19619298
Zhang J, Liu B, Jiang X, Zhao H et al. A systems biology-based gene expression classifier of glioblastoma predicts survival with solid tumors. PLoS One 2009 Jul 17;4(7):e6274. PMID: 19609451
Saiki A, Olsson M, Jernås M, Gummesson A et al. Tenomodulin is highly expressed in adipose tissue, increased in obesity, and down-regulated during diet-induced weight loss. J Clin Endocrinol Metab 2009 Oct;94(10):3987-94. PMID: 19602561
Smith LR, Pontén E, Hedström Y, Ward SR et al. Novel transcriptional profile in wrist muscles from cerebral palsy patients. BMC Med Genomics 2009 Jul 14;2:44. PMID: 19602279
Kuznetsov VA. Relative avidity, specificity, and sensitivity of transcription factor-DNA binding in genome-scale experiments. Methods Mol Biol 2009;563:15-50. PMID: 19597778
Seike M, Goto A, Okano T, Bowman ED et al. MiR-21 is an EGFR-regulated anti-apoptotic factor in lung cancer in never-smokers. Proc Natl Acad Sci U S A 2009 Jul 21;106(29):12085-90. PMID: 19597153
Ahmed SS, Santosh W, Kumar S, Christlet HT. Metabolic profiling of Parkinson's disease: evidence of biomarker from gene expression analysis and rapid neural network detection. J Biomed Sci 2009 Jul 13;16:63. PMID: 19594911
Hennetin J, Pehkonen P, Bellis M. Construction and use of gene expression covariation matrix. BMC Bioinformatics 2009 Jul 13;10:214. PMID: 19594909
Guda P, Chittur SV, Guda C. Comparative analysis of protein-protein interactions in cancer-associated genes. Genomics Proteomics Bioinformatics 2009 Jun;7(1-2):25-36. PMID: 19591789
Arpanahi A, Brinkworth M, Iles D, Krawetz SA et al. Endonuclease-sensitive regions of human spermatozoal chromatin are highly enriched in promoter and CTCF binding sequences. Genome Res 2009 Aug;19(8):1338-49. PMID: 19584098
Kennedy L, Vass JK, Haggart DR, Moore S et al. Hematopoietic Lineage Transcriptome Stability and Representation in PAXgene Collected Peripheral Blood Utilising SPIA Single-Stranded cDNA Probes for Microarray. Biomark Insights 2008 Aug 25;3:403-417. PMID: 19578521
Lee BT, Liew L, Lim J, Tan JK et al. Candidate List of yoUr Biomarker (CLUB): A Web-based Platform to Aid Cancer Biomarker Research. Biomark Insights 2008 Feb 9;3:65-71. PMID: 19578495
Witten DM, Tibshirani RJ. Extensions of sparse canonical correlation analysis with applications to genomic data. Stat Appl Genet Mol Biol 2009;8(1):Article28. PMID: 19572827
Narsai R, Howell KA, Carroll A, Ivanova A et al. Defining core metabolic and transcriptomic responses to oxygen availability in rice embryos and young seedlings. Plant Physiol 2009 Sep;151(1):306-22. PMID: 19571305
Chin MH, Mason MJ, Xie W, Volinia S et al. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell 2009 Jul 2;5(1):111-23. PMID: 19570518
Bisognin A, Coppe A, Ferrari F, Risso D et al. A-MADMAN: annotation-based microarray data meta-analysis tool. BMC Bioinformatics 2009 Jun 29;10:201. PMID: 19563634
Israel A, Sharan R, Ruppin E, Galun E. Increased microRNA activity in human cancers. PLoS One 2009 Jun 25;4(6):e6045. PMID: 19557174
Alves BN, Marshall K, Tamang DL, Leong J et al. Lipid-dependent cytotoxicity by the lipase PLRP2 and by PLRP2-positive cytotoxic T lymphocytes (CTLs). Cell Biochem Funct 2009 Jul;27(5):296-308. PMID: 19548271
Melamud E, Moult J. Stochastic noise in splicing machinery. Nucleic Acids Res 2009 Aug;37(14):4873-86. PMID: 19546110
Howard BE, Sick B, Heber S. Unsupervised assessment of microarray data quality using a Gaussian mixture model. BMC Bioinformatics 2009 Jun 22;10:191. PMID: 19545436
Rao MR, Halfhill MD, Abercrombie LG, Ranjan P et al. Phytoremediation and phytosensing of chemical contaminants, RDX and TNT: identification of the required target genes. Funct Integr Genomics 2009 Nov;9(4):537-47. PMID: 19543758
Makeyev AV, Bayarsaihan D. New TFII-I family target genes involved in embryonic development. Biochem Biophys Res Commun 2009 Sep 4;386(4):554-8. PMID: 19527686
Mayburd AL. Expression variation: its relevance to emergence of chronic disease and to therapy. PLoS One 2009 Jun 15;4(6):e5921. PMID: 19526064
Xu D, Holko M, Sadler AJ, Scott B et al. Promyelocytic leukemia zinc finger protein regulates interferon-mediated innate immunity. Immunity 2009 Jun 19;30(6):802-16. PMID: 19523849
Packham IM, Gray C, Heath PR, Hellewell PG et al. Microarray profiling reveals CXCR4a is downregulated by blood flow in vivo and mediates collateral formation in zebrafish embryos. Physiol Genomics 2009 Aug 7;38(3):319-27. PMID: 19509081
Godmann M, Gashaw I, Eildermann K, Schweyer S et al. The pluripotency transcription factor Krüppel-like factor 4 is strongly expressed in intratubular germ cell neoplasia unclassified and seminoma. Mol Hum Reprod 2009 Aug;15(8):479-88. PMID: 19505997
Yin Y, Yan Y, Jiang X, Mai J et al. Inflammasomes are differentially expressed in cardiovascular and other tissues. Int J Immunopathol Pharmacol 2009 Apr-Jun;22(2):311-22. PMID: 19505385
Viswanathan SR, Powers JT, Einhorn W, Hoshida Y et al. Lin28 promotes transformation and is associated with advanced human malignancies. Nat Genet 2009 Jul;41(7):843-8. PMID: 19483683
Danko CG, Pertsov AM. Identification of gene co-regulatory modules and associated cis-elements involved in degenerative heart disease. BMC Med Genomics 2009 May 28;2:31. PMID: 19476647
Glover CN, Zheng D, Jayashankar S, Sales GD et al. Methylmercury speciation influences brain gene expression and behavior in gestationally-exposed mice pups. Toxicol Sci 2009 Aug;110(2):389-400. PMID: 19465457
Swanton C, Nicke B, Schuett M, Eklund AC et al. Chromosomal instability determines taxane response. Proc Natl Acad Sci U S A 2009 May 26;106(21):8671-6. PMID: 19458043
Karn T, Metzler D, Ruckhäberle E, Hanker L et al. Data-driven derivation of cutoffs from a pool of 3,030 Affymetrix arrays to stratify distinct clinical types of breast cancer. Breast Cancer Res Treat 2010 Apr;120(3):567-79. PMID: 19455418
Ko Y, Zhai C, Rodriguez-Zas S. Inference of gene pathways using mixture Bayesian networks. BMC Syst Biol 2009 May 19;3:54. PMID: 19454027
Bierie B, Chung CH, Parker JS, Stover DG et al. Abrogation of TGF-beta signaling enhances chemokine production and correlates with prognosis in human breast cancer. J Clin Invest 2009 Jun;119(6):1571-82. PMID: 19451693
Choi H, Nesvizhskii AI, Ghosh D, Qin ZS. Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data. Bioinformatics 2009 Jul 15;25(14):1715-21. PMID: 19447789
Wan J, Lin J, Zack DJ, Qian J. Relating periodicity of nucleosome organization and gene regulation. Bioinformatics 2009 Jul 15;25(14):1782-8. PMID: 19447785
Du Z, Zhou X, Li L, Su Z. plantsUPS: a database of plants' Ubiquitin Proteasome System. BMC Genomics 2009 May 16;10:227. PMID: 19445698
Kim SY. Effects of sample size on robustness and prediction accuracy of a prognostic gene signature. BMC Bioinformatics 2009 May 16;10:147. PMID: 19445687
Murph MM, Liu W, Yu S, Lu Y et al. Lysophosphatidic acid-induced transcriptional profile represents serous epithelial ovarian carcinoma and worsened prognosis. PLoS One 2009;4(5):e5583. PMID: 19440550
Nitsch D, Tranchevent LC, Thienpont B, Thorrez L et al. Network analysis of differential expression for the identification of disease-causing genes. PLoS One 2009;4(5):e5526. PMID: 19436755
Hackenberg M, Sturm M, Langenberger D, Falcón-Pérez JM et al. miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res 2009 Jul;37(Web Server issue):W68-76. PMID: 19433510
Edwards YJ, Lobley AE, Pentony MM, Jones DT. Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data. Genome Biol 2009;10(5):R50. PMID: 19432952
Lin X, Liu M, Chen XW. Assessing reliability of protein-protein interactions by integrative analysis of data in model organisms. BMC Bioinformatics 2009 Apr 29;10 Suppl 4:S5. PMID: 19426453
Haverty PM, Hon LS, Kaminker JS, Chant J et al. High-resolution analysis of copy number alterations and associated expression changes in ovarian tumors. BMC Med Genomics 2009 May 6;2:21. PMID: 19419571
Lahusen T, Henke RT, Kagan BL, Wellstein A et al. The role and regulation of the nuclear receptor co-activator AIB1 in breast cancer. Breast Cancer Res Treat 2009 Jul;116(2):225-37. PMID: 19418218
Gohlke JM, Thomas R, Zhang Y, Rosenstein MC et al. Genetic and environmental pathways to complex diseases. BMC Syst Biol 2009 May 5;3:46. PMID: 19416532
Kauer M, Ban J, Kofler R, Walker B et al. A molecular function map of Ewing's sarcoma. PLoS One 2009;4(4):e5415. PMID: 19404404
Foat BC, Stormo GD. Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs. Mol Syst Biol 2009;5:268. PMID: 19401680
Staub E, Groene J, Heinze M, Mennerich D et al. An expression module of WIPF1-coexpressed genes identifies patients with favorable prognosis in three tumor types. J Mol Med (Berl) 2009 Jun;87(6):633-44. PMID: 19399471
Folkersen L, Diez D, Wheelock CE, Haeggström JZ et al. GeneRegionScan: a Bioconductor package for probe-level analysis of specific, small regions of the genome. Bioinformatics 2009 Aug 1;25(15):1978-9. PMID: 19398447
Mizuno H, Kitada K, Nakai K, Sarai A. PrognoScan: a new database for meta-analysis of the prognostic value of genes. BMC Med Genomics 2009 Apr 24;2:18. PMID: 19393097
Shimamura T, Imoto S, Yamaguchi R, Fujita A et al. Recursive regularization for inferring gene networks from time-course gene expression profiles. BMC Syst Biol 2009 Apr 22;3:41. PMID: 19386091
Holt JE, Ly-Huynh JD, Efthymiadis A, Hime GR et al. Regulation of Nuclear Import During Differentiation; The IMP alpha Gene Family and Spermatogenesis. Curr Genomics 2007 Aug;8(5):323-34. PMID: 19384428
Guess CM, Lafleur BJ, Weidow BL, Quaranta V. A decreased ratio of laminin-332 beta3 to gamma2 subunit mRNA is associated with poor prognosis in colon cancer. Cancer Epidemiol Biomarkers Prev 2009 May;18(5):1584-90. PMID: 19383890
Li H, Sun Y, Zhan M. Exploring pathways from gene co-expression to network dynamics. Methods Mol Biol 2009;541:249-67. PMID: 19381544
French L, Lane S, Law T, Xu L et al. Application and evaluation of automated semantic annotation of gene expression experiments. Bioinformatics 2009 Jun 15;25(12):1543-9. PMID: 19376825
Cho SB, Kim J, Kim JH. Identifying set-wise differential co-expression in gene expression microarray data. BMC Bioinformatics 2009 Apr 16;10:109. PMID: 19371436
Shay T, Lambiv WL, Reiner-Benaim A, Hegi ME et al. Combining chromosomal arm status and significantly aberrant genomic locations reveals new cancer subtypes. Cancer Inform 2009;7:91-104. PMID: 19352461
Wang G, Haile S, Comuzzi B, Tien AH et al. Osteoblast-derived factors induce an expression signature that identifies prostate cancer metastasis and hormonal progression. Cancer Res 2009 Apr 15;69(8):3433-42. PMID: 19351846
Haldar M, Hedberg ML, Hockin MF, Capecchi MR. A CreER-based random induction strategy for modeling translocation-associated sarcomas in mice. Cancer Res 2009 Apr 15;69(8):3657-64. PMID: 19351831
Daniel VC, Marchionni L, Hierman JS, Rhodes JT et al. A primary xenograft model of small-cell lung cancer reveals irreversible changes in gene expression imposed by culture in vitro. Cancer Res 2009 Apr 15;69(8):3364-73. PMID: 19351829
Wendland JR, Moya PR, Timpano KR, Anavitarte AP et al. A haplotype containing quantitative trait loci for SLC1A1 gene expression and its association with obsessive-compulsive disorder. Arch Gen Psychiatry 2009 Apr;66(4):408-16. PMID: 19349310
Taylor RC, Singhal M, Weller J, Khoshnevis S et al. A network inference workflow applied to virulence-related processes in Salmonella typhimurium. Ann N Y Acad Sci 2009 Mar;1158:143-58. PMID: 19348639
Kim S, Lee D. Mining metastasis related genes by primary-secondary tumor comparisons from large-scale databases. BMC Bioinformatics 2009 Mar 19;10 Suppl 3:S2. PMID: 19344478
Chandramohanadas R, Davis PH, Beiting DP, Harbut MB et al. Apicomplexan parasites co-opt host calpains to facilitate their escape from infected cells. Science 2009 May 8;324(5928):794-7. PMID: 19342550
Williams-Devane CR, Wolf MA, Richard AM. Toward a public toxicogenomics capability for supporting predictive toxicology: survey of current resources and chemical indexing of experiments in GEO and ArrayExpress. Toxicol Sci 2009 Jun;109(2):358-71. PMID: 19332651
Hennah W, Porteous D. The DISC1 pathway modulates expression of neurodevelopmental, synaptogenic and sensory perception genes. PLoS One 2009;4(3):e4906. PMID: 19300510
Akerman M, David-Eden H, Pinter RY, Mandel-Gutfreund Y. A computational approach for genome-wide mapping of splicing factor binding sites. Genome Biol 2009;10(3):R30. PMID: 19296853
Siddique ZL, Drozdov I, Floch J, Gustafsson BI et al. KRJ-I and BON cell lines: defining an appropriate enterochromaffin cell neuroendocrine tumor model. Neuroendocrinology 2009;89(4):458-70. PMID: 19295186
Lee YS, Chen CH, Tsai CN, Tsai CL et al. Microarray labeling extension values: laboratory signatures for Affymetrix GeneChips. Nucleic Acids Res 2009 May;37(8):e61. PMID: 19295132
Motallebipour M, Enroth S, Punga T, Ameur A et al. Novel genes in cell cycle control and lipid metabolism with dynamically regulated binding sites for sterol regulatory element-binding protein 1 and RNA polymerase II in HepG2 cells detected by chromatin immunoprecipitation with microarray detection. FEBS J 2009 Apr;276(7):1878-90. PMID: 19292868
Sunagawa S, DeSalvo MK, Voolstra CR, Reyes-Bermudez A et al. Identification and gene expression analysis of a taxonomically restricted cysteine-rich protein family in reef-building corals. PLoS One 2009;4(3):e4865. PMID: 19283069
Carlsson LM, Jacobson P, Walley A, Froguel P et al. ALK7 expression is specific for adipose tissue, reduced in obesity and correlates to factors implicated in metabolic disease. Biochem Biophys Res Commun 2009 May 1;382(2):309-14. PMID: 19275893
Rody A, Holtrich U, Pusztai L, Liedtke C et al. T-cell metagene predicts a favorable prognosis in estrogen receptor-negative and HER2-positive breast cancers. Breast Cancer Res 2009;11(2):R15. PMID: 19272155
Alles MC, Gardiner-Garden M, Nott DJ, Wang Y et al. Meta-analysis and gene set enrichment relative to er status reveal elevated activity of MYC and E2F in the "basal" breast cancer subgroup. PLoS One 2009;4(3):e4710. PMID: 19270750
Menssen A, Edinger G, Grün JR, Haase U et al. SiPaGene: A new repository for instant online retrieval, sharing and meta-analyses of GeneChip expression data. BMC Genomics 2009 Mar 5;10:98. PMID: 19265543
Leimgruber E, Seguín-Estévez Q, Dunand-Sauthier I, Rybtsova N et al. Nucleosome eviction from MHC class II promoters controls positioning of the transcription start site. Nucleic Acids Res 2009 May;37(8):2514-28. PMID: 19264803
Zhao Y, Simon R. BRB-ArrayTools Data Archive for human cancer gene expression: a unique and efficient data sharing resource. Cancer Inform 2008;6:9-15. PMID: 19259398
Guillén N, Navarro MA, Arnal C, Noone E et al. Microarray analysis of hepatic gene expression identifies new genes involved in steatotic liver. Physiol Genomics 2009 May 13;37(3):187-98. PMID: 19258494
Cho IJ, Ki SH, Brooks C 3rd, Kim SG. Role of hepatitis B virus X repression of C/EBPbeta activity in the down-regulation of glutathione S-transferase A2 gene: implications in other phase II detoxifying enzyme expression. Xenobiotica 2009 Feb;39(2):182-92. PMID: 19255944
Ebhardt HA, Tsang HH, Dai DC, Liu Y et al. Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications. Nucleic Acids Res 2009 May;37(8):2461-70. PMID: 19255090
Rybaczyk L, Rozmiarek A, Circle K, Grants I et al. New bioinformatics approach to analyze gene expressions and signaling pathways reveals unique purine gene dysregulation profiles that distinguish between CD and UC. Inflamm Bowel Dis 2009 Jul;15(7):971-84. PMID: 19253308
Xiong DH, Liu XG, Guo YF, Tan LJ et al. Genome-wide association and follow-up replication studies identified ADAMTS18 and TGFBR3 as bone mass candidate genes in different ethnic groups. Am J Hum Genet 2009 Mar;84(3):388-98. PMID: 19249006
Miyagawa Y, Okita H, Itagaki M, Toyoda M et al. EWS/ETS regulates the expression of the Dickkopf family in Ewing family tumor cells. PLoS One 2009;4(2):e4634. PMID: 19247449
Huttenhower C, Haley EM, Hibbs MA, Dumeaux V et al. Exploring the human genome with functional maps. Genome Res 2009 Jun;19(6):1093-106. PMID: 19246570
Tang B, Chang WL, Lanigan CM, Dean B et al. Normal human aging and early-stage schizophrenia share common molecular profiles. Aging Cell 2009 Jun;8(3):339-42. PMID: 19245676
Li A, Walling J, Ahn S, Kotliarov Y et al. Unsupervised analysis of transcriptomic profiles reveals six glioma subtypes. Cancer Res 2009 Mar 1;69(5):2091-9. PMID: 19244127
James MA, Lu Y, Liu Y, Vikis HG et al. RGS17, an overexpressed gene in human lung and prostate cancer, induces tumor cell proliferation through the cyclic AMP-PKA-CREB pathway. Cancer Res 2009 Mar 1;69(5):2108-16. PMID: 19244110
Eiseler T, Döppler H, Yan IK, Goodison S et al. Protein kinase D1 regulates matrix metalloproteinase expression and inhibits breast cancer cell invasion. Breast Cancer Res 2009;11(1):R13. PMID: 19243594
Cardoso CM, Groth-Pedersen L, Høyer-Hansen M, Kirkegaard T et al. Depletion of kinesin 5B affects lysosomal distribution and stability and induces peri-nuclear accumulation of autophagosomes in cancer cells. PLoS One 2009;4(2):e4424. PMID: 19242560
Tsuchihara K, Suzuki Y, Wakaguri H, Irie T et al. Massive transcriptional start site analysis of human genes in hypoxia cells. Nucleic Acids Res 2009 Apr;37(7):2249-63. PMID: 19237398
Missiaglia E, Selfe J, Hamdi M, Williamson D et al. Genomic imbalances in rhabdomyosarcoma cell lines affect expression of genes frequently altered in primary tumors: an approach to identify candidate genes involved in tumor development. Genes Chromosomes Cancer 2009 Jun;48(6):455-67. PMID: 19235922
Yoon H, McDermott JE, Porwollik S, McClelland M et al. Coordinated regulation of virulence during systemic infection of Salmonella enterica serovar Typhimurium. PLoS Pathog 2009 Feb;5(2):e1000306. PMID: 19229334
Erdogan E, Klee EW, Thompson EA, Fields AP. Meta-analysis of oncogenic protein kinase Ciota signaling in lung adenocarcinoma. Clin Cancer Res 2009 Mar 1;15(5):1527-33. PMID: 19223491
Liu Q, Feng Y, Zhu Z. Dicer-like (DCL) proteins in plants. Funct Integr Genomics 2009 Aug;9(3):277-86. PMID: 19221817
Birks DK, Kleinschmidt-DeMasters BK, Donson AM, Barton VN et al. Claudin 6 is a positive marker for atypical teratoid/rhabdoid tumors. Brain Pathol 2010 Jan;20(1):140-50. PMID: 19220299
Winklmeier A, Poser I, Hoek KS, Bosserhoff AK. Loss of full length CtBP1 expression enhances the invasive potential of human melanoma. BMC Cancer 2009 Feb 12;9:52. PMID: 19216735
Yang S, Wang K, Gregory B, Berrettini W et al. Genomic landscape of a three-generation pedigree segregating affective disorder. PLoS One 2009;4(2):e4474. PMID: 19214233
Dudley JT, Butte AJ. Identification of discriminating biomarkers for human disease using integrative network biology. Pac Symp Biocomput 2009;:27-38. PMID: 19209693
Yang E, Androulakis IP. Assessing and selecting gene expression signals based upon the quality of the measured dynamics. BMC Bioinformatics 2009 Feb 10;10:55. PMID: 19208252
Parker BJ, Wen J. Predicting microRNA targets in time-series microarray experiments via functional data analysis. BMC Bioinformatics 2009 Jan 30;10 Suppl 1:S32. PMID: 19208133
Beck AH, Espinosa I, Edris B, Li R et al. The macrophage colony-stimulating factor 1 response signature in breast carcinoma. Clin Cancer Res 2009 Feb 1;15(3):778-87. PMID: 19188147
Jourdan M, Reme T, Goldschmidt H, Fiol G et al. Gene expression of anti- and pro-apoptotic proteins in malignant and normal plasma cells. Br J Haematol 2009 Apr;145(1):45-58. PMID: 19183193
Pendino F, Nguyen E, Jonassen I, Dysvik B et al. Functional involvement of RINF, retinoid-inducible nuclear factor (CXXC5), in normal and tumoral human myelopoiesis. Blood 2009 Apr 2;113(14):3172-81. PMID: 19182210
Sun Z, Luo J, Zhou Y, Luo J et al. Exploring phenotype-associated modules in an oral cavity tumor using an integrated framework. Bioinformatics 2009 Mar 15;25(6):795-800. PMID: 19181684
Watanabe S, Ueda Y, Akaboshi S, Hino Y et al. HMGA2 maintains oncogenic RAS-induced epithelial-mesenchymal transition in human pancreatic cancer cells. Am J Pathol 2009 Mar;174(3):854-68. PMID: 19179606
Nilsson R, Björkegren J, Tegnér J. On reliable discovery of molecular signatures. BMC Bioinformatics 2009 Jan 29;10:38. PMID: 19178740
McDermott JE, Taylor RC, Yoon H, Heffron F. Bottlenecks and hubs in inferred networks are important for virulence in Salmonella typhimurium. J Comput Biol 2009 Feb;16(2):169-80. PMID: 19178137
Murphy TM, Belmonte M, Shu S, Britt AB et al. Requirement for abasic endonuclease gene homologues in Arabidopsis seed development. PLoS One 2009;4(1):e4297. PMID: 19172180
van Staveren WC, Solís DY, Hébrant A, Detours V et al. Human cancer cell lines: Experimental models for cancer cells in situ? For cancer stem cells? Biochim Biophys Acta 2009 Apr;1795(2):92-103. PMID: 19167460
Fukuoka Y, Inaoka H, Noshiro M. Adaptive threshold to detect biologically meaningful changes in microarray data. Conf Proc IEEE Eng Med Biol Soc 2008;2008:5708-11. PMID: 19164013
Williams-DeVane CR, Wolf MA, Richard AM. DSSTox chemical-index files for exposure-related experiments in ArrayExpress and Gene Expression Omnibus: enabling toxico-chemogenomics data linkages. Bioinformatics 2009 Mar 1;25(5):692-4. PMID: 19158160
de Tayrac M, Lê S, Aubry M, Mosser J et al. Simultaneous analysis of distinct Omics data sets with integration of biological knowledge: Multiple Factor Analysis approach. BMC Genomics 2009 Jan 20;10:32. PMID: 19154582
Halperin Y, Linhart C, Ulitsky I, Shamir R. Allegro: analyzing expression and sequence in concert to discover regulatory programs. Nucleic Acids Res 2009 Apr;37(5):1566-79. PMID: 19151090
Tung CY, Jen CH, Hsu MT, Wang HW et al. A novel regulatory event-based gene set analysis method for exploring global functional changes in heterogeneous genomic data sets. BMC Genomics 2009 Jan 16;10:26. PMID: 19146704
Zhang X, Lian Z, Padden C, Gerstein MB et al. A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood 2009 Mar 12;113(11):2526-34. PMID: 19144990
Chien AJ, Moore EC, Lonsdorf AS, Kulikauskas RM et al. Activated Wnt/beta-catenin signaling in melanoma is associated with decreased proliferation in patient tumors and a murine melanoma model. Proc Natl Acad Sci U S A 2009 Jan 27;106(4):1193-8. PMID: 19144919
Rauch TA, Wu X, Zhong X, Riggs AD et al. A human B cell methylome at 100-base pair resolution. Proc Natl Acad Sci U S A 2009 Jan 20;106(3):671-8. PMID: 19139413
Malhas AN, Lee CF, Vaux DJ. Lamin B1 controls oxidative stress responses via Oct-1. J Cell Biol 2009 Jan 12;184(1):45-55. PMID: 19139261
O'Neal J, Gao F, Hassan A, Monahan R et al. Neurobeachin (NBEA) is a target of recurrent interstitial deletions at 13q13 in patients with MGUS and multiple myeloma. Exp Hematol 2009 Feb;37(2):234-44. PMID: 19135901
Pei Y, Zhang T, Renault V, Zhang X. An overview of hepatocellular carcinoma study by omics-based methods. Acta Biochim Biophys Sin (Shanghai) 2009 Jan;41(1):1-15. PMID: 19129945
Beltrame L, Rizzetto L, Paola R, Rocca-Serra P et al. Using pathway signatures as means of identifying similarities among microarray experiments. PLoS One 2009;4(1):e4128. PMID: 19125200
Balasubramanian S, Zheng D, Liu YJ, Fang G et al. Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes. Genome Biol 2009;10(1):R2. PMID: 19123937
Ochsner SA, Steffen DL, Hilsenbeck SG, Chen ES et al. GEMS (Gene Expression MetaSignatures), a Web resource for querying meta-analysis of expression microarray datasets: 17beta-estradiol in MCF-7 cells. Cancer Res 2009 Jan 1;69(1):23-6. PMID: 19117983
Kim WK, Hwang HR, Kim do H, Lee PY et al. Glycoproteomic analysis of plasma from patients with atopic dermatitis: CD5L and ApoE as potential biomarkers. Exp Mol Med 2008 Dec 31;40(6):677-85. PMID: 19116453
Gur-Dedeoglu B, Konu O, Kir S, Ozturk AR et al. A resampling-based meta-analysis for detection of differential gene expression in breast cancer. BMC Cancer 2008 Dec 30;8:396. PMID: 19116033
Morris KE, St Laurent CD, Hoeve RS, Forsythe P et al. Autonomic nervous system regulates secretion of anti-inflammatory prohormone SMR1 from rat salivary glands. Am J Physiol Cell Physiol 2009 Mar;296(3):C514-24. PMID: 19109528
Kolesnikova TV, Kazarov AR, Lemieux ME, Lafleur MA et al. Glioblastoma inhibition by cell surface immunoglobulin protein EWI-2, in vitro and in vivo. Neoplasia 2009 Jan;11(1):77-86, 4p following 86. PMID: 19107234
Ertel A, Tozeren A. Human and mouse switch-like genes share common transcriptional regulatory mechanisms for bimodality. BMC Genomics 2008 Dec 23;9:628. PMID: 19105848
Lopez F, Textoris J, Bergon A, Didier G et al. TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database. PLoS One 2008;3(12):e4001. PMID: 19104654
Bailey MJ, Coon SL, Carter DA, Humphries A et al. Night/day changes in pineal expression of >600 genes: central role of adrenergic/cAMP signaling. J Biol Chem 2009 Mar 20;284(12):7606-22. PMID: 19103603
Schnackenberg LK, Chen M, Sun J, Holland RD et al. Evaluations of the trans-sulfuration pathway in multiple liver toxicity studies. Toxicol Appl Pharmacol 2009 Feb 15;235(1):25-32. PMID: 19103213
Keller A, Backes C, Al-Awadhi M, Gerasch A et al. GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments. BMC Bioinformatics 2008 Dec 22;9:552. PMID: 19099609
Vazin T, Chen J, Spivak CE, Amable R et al. Dopaminergic neurons derived from BG01V2, a variant of human embryonic stem cell line BG01. Restor Neurol Neurosci 2008;26(6):447-58. PMID: 19096132
Chen R, Mallelwar R, Thosar A, Venkatasubrahmanyam S et al. GeneChaser: identifying all biological and clinical conditions in which genes of interest are differentially expressed. BMC Bioinformatics 2008 Dec 18;9:548. PMID: 19094235
Upton GJ, Langdon WB, Harrison AP. G-spots cause incorrect expression measurement in Affymetrix microarrays. BMC Genomics 2008 Dec 18;9:613. PMID: 19094220
Sharabi AB, Aldrich M, Sosic D, Olson EN et al. Twist-2 controls myeloid lineage development and function. PLoS Biol 2008 Dec 16;6(12):e316. PMID: 19090621
Guo NL, Wan YW, Tosun K, Lin H et al. Confirmation of gene expression-based prediction of survival in non-small cell lung cancer. Clin Cancer Res 2008 Dec 15;14(24):8213-20. PMID: 19088038
Liang Y. An expression meta-analysis of predicted microRNA targets identifies a diagnostic signature for lung cancer. BMC Med Genomics 2008 Dec 16;1:61. PMID: 19087325
McPartland JM. Expression of the endocannabinoid system in fibroblasts and myofascial tissues. J Bodyw Mov Ther 2008 Apr;12(2):169-82. PMID: 19083670
Straub T, Grimaud C, Gilfillan GD, Mitterweger A et al. The chromosomal high-affinity binding sites for the Drosophila dosage compensation complex. PLoS Genet 2008 Dec;4(12):e1000302. PMID: 19079572
Sakai Y, Honda M, Fujinaga H, Tatsumi I et al. Common transcriptional signature of tumor-infiltrating mononuclear inflammatory cells and peripheral blood mononuclear cells in hepatocellular carcinoma patients. Cancer Res 2008 Dec 15;68(24):10267-79. PMID: 19074895
Howell KA, Narsai R, Carroll A, Ivanova A et al. Mapping metabolic and transcript temporal switches during germination in rice highlights specific transcription factors and the role of RNA instability in the germination process. Plant Physiol 2009 Feb;149(2):961-80. PMID: 19074628
Praz V, Bucher P. CleanEx: new data extraction and merging tools based on MeSH term annotation. Nucleic Acids Res 2009 Jan;37(Database issue):D880-4. PMID: 19073704
Blizard DA, Lionikas A, Vandenbergh DJ, Vasilopoulos T et al. Blood pressure and heart rate QTL in mice of the B6/D2 lineage: sex differences and environmental influences. Physiol Genomics 2009 Feb 2;36(3):158-66. PMID: 19066325
Street NR, Sjödin A, Bylesjö M, Gustafsson P et al. A cross-species transcriptomics approach to identify genes involved in leaf development. BMC Genomics 2008 Dec 5;9:589. PMID: 19061504
Chen R, Morgan AA, Dudley J, Deshpande T et al. FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease. Genome Biol 2008;9(12):R170. PMID: 19061490
Wang-Sattler R, Yu Y, Mittelstrass K, Lattka E et al. Metabolic profiling reveals distinct variations linked to nicotine consumption in humans--first results from the KORA study. PLoS One 2008;3(12):e3863. PMID: 19057651
Preker P, Nielsen J, Kammler S, Lykke-Andersen S et al. RNA exosome depletion reveals transcription upstream of active human promoters. Science 2008 Dec 19;322(5909):1851-4. PMID: 19056938
Pi M, Chen L, Huang MZ, Zhu W et al. GPRC6A null mice exhibit osteopenia, feminization and metabolic syndrome. PLoS One 2008;3(12):e3858. PMID: 19050760
Garman KS, Acharya CR, Edelman E, Grade M et al. A genomic approach to colon cancer risk stratification yields biologic insights into therapeutic opportunities. Proc Natl Acad Sci U S A 2008 Dec 9;105(49):19432-7. PMID: 19050079
Le DT, Lee BC, Marino SM, Zhang Y et al. Functional analysis of free methionine-R-sulfoxide reductase from Saccharomyces cerevisiae. J Biol Chem 2009 Feb 13;284(7):4354-64. PMID: 19049972
Wang G, Wang J, Sadar MD. Crosstalk between the androgen receptor and beta-catenin in castrate-resistant prostate cancer. Cancer Res 2008 Dec 1;68(23):9918-27. PMID: 19047173
Richards AL, Holmans P, O'Donovan MC, Owen MJ et al. A comparison of four clustering methods for brain expression microarray data. BMC Bioinformatics 2008 Nov 25;9:490. PMID: 19032745
Anas MK, Lee MB, Zhou C, Hammer MA et al. SIT1 is a betaine/proline transporter that is activated in mouse eggs after fertilization and functions until the 2-cell stage. Development 2008 Dec;135(24):4123-30. PMID: 19029042
Reid RW, Fodor AA. Determining gene expression on a single pair of microarrays. BMC Bioinformatics 2008 Nov 21;9:489. PMID: 19025600
Gormley M, Tozeren A. Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification. BMC Bioinformatics 2008 Nov 17;9:486. PMID: 19014681
Pichler K, Schneider G, Grassmann R. MicroRNA miR-146a and further oncogenesis-related cellular microRNAs are dysregulated in HTLV-1-transformed T lymphocytes. Retrovirology 2008 Nov 12;5:100. PMID: 19014482
Huang S, Taylor NL, Narsai R, Eubel H et al. Experimental analysis of the rice mitochondrial proteome, its biogenesis, and heterogeneity. Plant Physiol 2009 Feb;149(2):719-34. PMID: 19010998
Lito P, Mets BD, Appledorn DM, Maher VM et al. Sprouty 2 regulates DNA damage-induced apoptosis in Ras-transformed human fibroblasts. J Biol Chem 2009 Jan 9;284(2):848-54. PMID: 19008219
Kienhuis AS, van de Poll MC, Wortelboer H, van Herwijnen M et al. Parallelogram approach using rat-human in vitro and rat in vivo toxicogenomics predicts acetaminophen-induced hepatotoxicity in humans. Toxicol Sci 2009 Feb;107(2):544-52. PMID: 19008212
Liu H, Li X, Yoon V, Clarke R. Annotating breast cancer microarray samples using ontologies. AMIA Annu Symp Proc 2008 Nov 6;:414-8. PMID: 18999108
Hishiki T, Tamada I, Okubo K. Gene-L'EXPO: a tool to extract knowledge From transcriptomes and find 'Literature-Sparse' relationships between genes and tissues. AMIA Annu Symp Proc 2008 Nov 6;:313-7. PMID: 18999036
Miranda-Saavedra D, De S, Trotter MW, Teichmann SA et al. BloodExpress: a database of gene expression in mouse haematopoiesis. Nucleic Acids Res 2009 Jan;37(Database issue):D873-9. PMID: 18987008
van Dongen S, Abreu-Goodger C, Enright AJ. Detecting microRNA binding and siRNA off-target effects from expression data. Nat Methods 2008 Dec;5(12):1023-5. PMID: 18978784
He F, Zhang Y, Chen H, Zhang Z et al. The prediction of protein-protein interaction networks in rice blast fungus. BMC Genomics 2008 Nov 2;9:519. PMID: 18976500
Arteaga-Salas JM, Harrison AP, Upton GJ. Reducing spatial flaws in oligonucleotide arrays by using neighborhood information. Stat Appl Genet Mol Biol 2008;7(1):Article29. PMID: 18976225
Konishi T, Konishi F, Takasaki S, Inoue K et al. Coincidence between transcriptome analyses on different microarray platforms using a parametric framework. PLoS One 2008;3(10):e3555. PMID: 18958174
Malaspina A, Jokic N, Huang WL, Priestley JV. Comparative analysis of the time-dependent functional and molecular changes in spinal cord degeneration induced by the G93A SOD1 gene mutation and by mechanical compression. BMC Genomics 2008 Oct 23;9:500. PMID: 18947433
Taccioli C, Fabbri E, Visone R, Volinia S et al. UCbase & miRfunc: a database of ultraconserved sequences and microRNA function. Nucleic Acids Res 2009 Jan;37(Database issue):D41-8. PMID: 18945703
Waardenberg AJ, Reverter A, Wells CA, Dalrymple BP. Using a 3D virtual muscle model to link gene expression changes during myogenesis to protein spatial location in muscle. BMC Syst Biol 2008 Oct 22;2:88. PMID: 18945372
Maurer J, Nelson B, Ceceña G, Bajpai R et al. Contrasting expression of keratins in mouse and human embryonic stem cells. PLoS One 2008;3(10):e3451. PMID: 18941637
Camargo A, Azuaje F, Wang H, Zheng H. Permutation - based statistical tests for multiple hypotheses. Source Code Biol Med 2008 Oct 21;3:15. PMID: 18939983
Tenenbaum JD, Walker MG, Utz PJ, Butte AJ. Expression-based Pathway Signature Analysis (EPSA): mining publicly available microarray data for insight into human disease. BMC Med Genomics 2008 Oct 20;1:51. PMID: 18937865
Wang S, Yang S, Yin Y, Guo X et al. An in silico strategy identified the target gene candidates regulated by dehydration responsive element binding proteins (DREBs) in Arabidopsis genome. Plant Mol Biol 2009 Jan;69(1-2):167-78. PMID: 18931920
Fukushima A, Wada M, Kanaya S, Arita M. SVD-based anatomy of gene expressions for correlation analysis in Arabidopsis thaliana. DNA Res 2008 Dec;15(6):367-74. PMID: 18931094
Bréhélin L, Dufayard JF, Gascuel O. PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data. BMC Bioinformatics 2008 Oct 16;9:440. PMID: 18925948
Sun Y, Li H, Liu Y, Mattson MP et al. Evolutionarily conserved transcriptional co-expression guiding embryonic stem cell differentiation. PLoS One 2008;3(10):e3406. PMID: 18923680
Janoueix-Lerosey I, Lequin D, Brugières L, Ribeiro A et al. Somatic and germline activating mutations of the ALK kinase receptor in neuroblastoma. Nature 2008 Oct 16;455(7215):967-70. PMID: 18923523
Gaetje R, Holtrich U, Engels K, Kissler S et al. Differential expression of claudins in human endometrium and endometriosis. Gynecol Endocrinol 2008 Aug;24(8):442-9. PMID: 18850381
Ouyang C, Smith DD, Krontiris TG. Evolutionary signatures of common human cis-regulatory haplotypes. PLoS One 2008;3(10):e3362. PMID: 18846218
Li Y, Hao P, Zheng S, Tu K et al. Gene expression module-based chemical function similarity search. Nucleic Acids Res 2008 Nov;36(20):e137. PMID: 18842630
Vazquez F, Blevins T, Ailhas J, Boller T et al. Evolution of Arabidopsis MIR genes generates novel microRNA classes. Nucleic Acids Res 2008 Nov;36(20):6429-38. PMID: 18842626
Zhu Y, Davis S, Stephens R, Meltzer PS et al. GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. Bioinformatics 2008 Dec 1;24(23):2798-800. PMID: 18842599
Yellaboina S, Dudekula DB, Ko MSh. Prediction of evolutionarily conserved interologs in Mus musculus. BMC Genomics 2008 Oct 8;9:465. PMID: 18842131
Venanzi ES, Melamed R, Mathis D, Benoist C. The variable immunological self: genetic variation and nongenetic noise in Aire-regulated transcription. Proc Natl Acad Sci U S A 2008 Oct 14;105(41):15860-5. PMID: 18838677
Alter MD, Rubin DB, Ramsey K, Halpern R et al. Variation in the large-scale organization of gene expression levels in the hippocampus relates to stable epigenetic variability in behavior. PLoS One 2008 Oct 6;3(10):e3344. PMID: 18836535
Elkon R, Agami R. Removal of AU bias from microarray mRNA expression data enhances computational identification of active microRNAs. PLoS Comput Biol 2008 Oct 3;4(10):e1000189. PMID: 18833292
Kamimura D, Bevan MJ. Endoplasmic reticulum stress regulator XBP-1 contributes to effector CD8+ T cell differentiation during acute infection. J Immunol 2008 Oct 15;181(8):5433-41. PMID: 18832700
Shema E, Tirosh I, Aylon Y, Huang J et al. The histone H2B-specific ubiquitin ligase RNF20/hBRE1 acts as a putative tumor suppressor through selective regulation of gene expression. Genes Dev 2008 Oct 1;22(19):2664-76. PMID: 18832071
Soong TT, Wrzeszczynski KO, Rost B. Physical protein-protein interactions predicted from microarrays. Bioinformatics 2008 Nov 15;24(22):2608-14. PMID: 18829707
Kapoor M, Arora R, Lama T, Nijhawan A et al. Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA Polymerase gene families and their expression analysis during reproductive development and stress in rice. BMC Genomics 2008 Oct 1;9:451. PMID: 18826656
Chain FJ, Ilieva D, Evans BJ. Single-species microarrays and comparative transcriptomics. PLoS One 2008 Sep 25;3(9):e3279. PMID: 18815615
Pi M, Chen L, Huang M, Luo Q et al. Parathyroid-specific interaction of the calcium-sensing receptor and G alpha q. Kidney Int 2008 Dec;74(12):1548-56. PMID: 18813283
Schnütgen F, Hansen J, De-Zolt S, Horn C et al. Enhanced gene trapping in mouse embryonic stem cells. Nucleic Acids Res 2008 Nov;36(20):e133. PMID: 18812397
Tuller T, Kupiec M, Ruppin E. Evolutionary rate and gene expression across different brain regions. Genome Biol 2008;9(9):R142. PMID: 18811952
Sims AH, Smethurst GJ, Hey Y, Okoniewski MJ et al. The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets - improving meta-analysis and prediction of prognosis. BMC Med Genomics 2008 Sep 21;1:42. PMID: 18803878
Fulp CT, Cho G, Marsh ED, Nasrallah IM et al. Identification of Arx transcriptional targets in the developing basal forebrain. Hum Mol Genet 2008 Dec 1;17(23):3740-60. PMID: 18799476
Zhang Y, Liu T, Meyer CA, Eeckhoute J et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008;9(9):R137. PMID: 18798982
Michael TP, Breton G, Hazen SP, Priest H et al. A morning-specific phytohormone gene expression program underlying rhythmic plant growth. PLoS Biol 2008 Sep 16;6(9):e225. PMID: 18798691
Rouchka EC, Phatak AW, Singh AV. Effect of single nucleotide polymorphisms on Affymetrix match-mismatch probe pairs. Bioinformation 2008 Jul 14;2(9):405-11. PMID: 18795114
Ptitsyn AA, Weil MM, Thamm DH. Systems biology approach to identification of biomarkers for metastatic progression in cancer. BMC Bioinformatics 2008 Aug 12;9 Suppl 9:S8. PMID: 18793472
Liu J, Li X, Dong GL, Zhang HW et al. In silico analysis and verification of S100 gene expression in gastric cancer. BMC Cancer 2008 Sep 16;8:261. PMID: 18793447
Cox ME, Gleave ME, Zakikhani M, Bell RH et al. Insulin receptor expression by human prostate cancers. Prostate 2009 Jan 1;69(1):33-40. PMID: 18785179
Akavia UD, Benayahu D. Meta-analysis and profiling of cardiac expression modules. Physiol Genomics 2008 Nov 12;35(3):305-15. PMID: 18780758
Shows KH, Shiang R. Regulation of the mouse Treacher Collins syndrome homolog (Tcof1) promoter through differential repression of constitutive expression. DNA Cell Biol 2008 Nov;27(11):589-600. PMID: 18771418
Rotter A, Hren M, Baebler S, Blejec A et al. Finding differentially expressed genes in two-channel DNA microarray datasets: how to increase reliability of data preprocessing. OMICS 2008 Sep;12(3):171-82. PMID: 18771401
Benoit M, Desnues B, Mege JL. Macrophage polarization in bacterial infections. J Immunol 2008 Sep 15;181(6):3733-9. PMID: 18768823
Konishi T. Data distribution of short oligonucleotide expression arrays and its application to the construction of a generalized intellectual framework. Stat Appl Genet Mol Biol 2008;7(1):Article25. PMID: 18764774
Goertzel B, Pennachin C, de Alvarenga Mudado M, de Souza Coelho L. Identifying the genes and genetic interrelationships underlying the impact of calorie restriction on maximum lifespan: an artificial intelligence-based approach. Rejuvenation Res 2008 Aug;11(4):735-48. PMID: 18729806
Eisenberg I, Novershtern N, Itzhaki Z, Becker-Cohen M et al. Mitochondrial processes are impaired in hereditary inclusion body myopathy. Hum Mol Genet 2008 Dec 1;17(23):3663-74. PMID: 18723858
Tanner SW, Agarwal P. Gene Vector Analysis (Geneva): a unified method to detect differentially-regulated gene sets and similar microarray experiments. BMC Bioinformatics 2008 Aug 22;9:348. PMID: 18721468
Bonte D, Lindvall C, Liu H, Dykema K et al. Cdc7-Dbf4 kinase overexpression in multiple cancers and tumor cell lines is correlated with p53 inactivation. Neoplasia 2008 Sep;10(9):920-31. PMID: 18714392
Martin KJ, Patrick DR, Bissell MJ, Fournier MV. Prognostic breast cancer signature identified from 3D culture model accurately predicts clinical outcome across independent datasets. PLoS One 2008 Aug 20;3(8):e2994. PMID: 18714348
Zheng G, Tu K, Yang Q, Xiong Y et al. ITFP: an integrated platform of mammalian transcription factors. Bioinformatics 2008 Oct 15;24(20):2416-7. PMID: 18713790
Magnusson B, Gummesson A, Glad CA, Goedecke JH et al. Cell death-inducing DFF45-like effector C is reduced by caloric restriction and regulates adipocyte lipid metabolism. Metabolism 2008 Sep;57(9):1307-13. PMID: 18702959
Ronchetti D, Lionetti M, Mosca L, Agnelli L et al. An integrative genomic approach reveals coordinated expression of intronic miR-335, miR-342, and miR-561 with deregulated host genes in multiple myeloma. BMC Med Genomics 2008 Aug 13;1:37. PMID: 18700954
Abu-Asab MS, Chaouchi M, Amri H. Phylogenetic modeling of heterogeneous gene-expression microarray data from cancerous specimens. OMICS 2008 Sep;12(3):183-99. PMID: 18699725
Lin YA, Chiang A, Lin R, Yao P et al. Methodologies for extracting functional pharmacogenomic experiments from international repository. AMIA Annu Symp Proc 2007 Oct 11;:463-7. PMID: 18693879
Rehrauer H, Schönmann S, Eberl L, Schlapbach R. PhyloDetect: a likelihood-based strategy for detecting microorganisms with diagnostic microarrays. Bioinformatics 2008 Aug 15;24(16):i83-9. PMID: 18689845
Ghosh D, Srivastava GP, Xu D, Schulz LC et al. A link between SIN1 (MAPKAP1) and poly(rC) binding protein 2 (PCBP2) in counteracting environmental stress. Proc Natl Acad Sci U S A 2008 Aug 19;105(33):11673-8. PMID: 18687895
van Vliet MH, Reyal F, Horlings HM, van de Vijver MJ et al. Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability. BMC Genomics 2008 Aug 6;9:375. PMID: 18684329
Adamo A, Pinney JW, Kunova A, Westhead DR et al. Heat stress enhances the accumulation of polyadenylated mitochondrial transcripts in Arabidopsis thaliana. PLoS One 2008 Aug 6;3(8):e2889. PMID: 18682831
Vinci G, Xia X, Veitia RA. Preservation of genes involved in sterol metabolism in cholesterol auxotrophs: facts and hypotheses. PLoS One 2008 Aug 6;3(8):e2883. PMID: 18682733
Williams PD, Lee JK, Theodorescu D. Molecular credentialing of rodent bladder carcinogenesis models. Neoplasia 2008 Aug;10(8):838-46. PMID: 18670642
Simcox A, Mitra S, Truesdell S, Paul L et al. Efficient genetic method for establishing Drosophila cell lines unlocks the potential to create lines of specific genotypes. PLoS Genet 2008 Aug 1;4(8):e1000142. PMID: 18670627
Wirapati P, Sotiriou C, Kunkel S, Farmer P et al. Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures. Breast Cancer Res 2008;10(4):R65. PMID: 18662380
Rouf R, Greytak S, Wooten EC, Wu J et al. Increased FOG-2 in failing myocardium disrupts thyroid hormone-dependent SERCA2 gene transcription. Circ Res 2008 Aug 29;103(5):493-501. PMID: 18658259
Grosso AR, Gomes AQ, Barbosa-Morais NL, Caldeira S et al. Tissue-specific splicing factor gene expression signatures. Nucleic Acids Res 2008 Sep;36(15):4823-32. PMID: 18653532
Svensson PA, Gabrielsson BG, Jernås M, Gummesson A et al. Regulation of human aldoketoreductase 1C3 (AKR1C3) gene expression in the adipose tissue. Cell Mol Biol Lett 2008;13(4):599-613. PMID: 18641923
Haibe-Kains B, Desmedt C, Sotiriou C, Bontempi G. A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all? Bioinformatics 2008 Oct 1;24(19):2200-8. PMID: 18635567
Yau C, Benz CC. Genes responsive to both oxidant stress and loss of estrogen receptor function identify a poor prognosis group of estrogen receptor positive primary breast cancers. Breast Cancer Res 2008;10(4):R61. PMID: 18631401
Martínez O, Reyes-Valdés MH. Defining diversity, specialization, and gene specificity in transcriptomes through information theory. Proc Natl Acad Sci U S A 2008 Jul 15;105(28):9709-14. PMID: 18606989
Hu J, Hu H, Li X. MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs. Nucleic Acids Res 2008 Aug;36(13):4488-97. PMID: 18606616
Chen X, Liang S, Zheng W, Liao Z et al. Meta-analysis of nasopharyngeal carcinoma microarray data explores mechanism of EBV-regulated neoplastic transformation. BMC Genomics 2008 Jul 7;9:322. PMID: 18605998
Chen HI, Hsu FH, Jiang Y, Tsai MH et al. A probe-density-based analysis method for array CGH data: simulation, normalization and centralization. Bioinformatics 2008 Aug 15;24(16):1749-56. PMID: 18603568
Casellas J, Varona L. Between-groups within-gene heterogeneity of residual variances in microarray gene expression data. BMC Genomics 2008 Jul 4;9:319. PMID: 18601719
Traka M, Gasper AV, Melchini A, Bacon JR et al. Broccoli consumption interacts with GSTM1 to perturb oncogenic signalling pathways in the prostate. PLoS One 2008 Jul 2;3(7):e2568. PMID: 18596959
Lippman ME, Rae JM, Chinnaiyan AM. An expression signature of estrogen-regulated genes predicts disease-free survival in tamoxifen-treated patients better than progesterone receptor status. Trans Am Clin Climatol Assoc 2008;119:77-90; discussion 90-2. PMID: 18596862
Macartney-Coxson DP, Hood KA, Shi HJ, Ward T et al. Metastatic susceptibility locus, an 8p hot-spot for tumour progression disrupted in colorectal liver metastases: 13 candidate genes examined at the DNA, mRNA and protein level. BMC Cancer 2008 Jul 1;8:187. PMID: 18590575
Ho JW, Stefani M, dos Remedios CG, Charleston MA. Differential variability analysis of gene expression and its application to human diseases. Bioinformatics 2008 Jul 1;24(13):i390-8. PMID: 18586739
Tempelman RJ. Statistical analysis of efficient unbalanced factorial designs for two-color microarray experiments. Int J Plant Genomics 2008;2008:584360. PMID: 18584033
Rakyan VK, Down TA, Thorne NP, Flicek P et al. An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res 2008 Sep;18(9):1518-29. PMID: 18577705
Park KW, Waki H, Villanueva CJ, Monticelli LA et al. Inhibitor of DNA binding 2 is a small molecule-inducible modulator of peroxisome proliferator-activated receptor-gamma expression and adipocyte differentiation. Mol Endocrinol 2008 Sep;22(9):2038-48. PMID: 18562627
Miozzi L, Piro RM, Rosa F, Ala U et al. Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data. PLoS One 2008 Jun 18;3(6):e2439. PMID: 18560577
Tomlins SA, Rhodes DR, Yu J, Varambally S et al. The role of SPINK1 in ETS rearrangement-negative prostate cancers. Cancer Cell 2008 Jun;13(6):519-28. PMID: 18538735
Palmer RD, Barbosa-Morais NL, Gooding EL, Muralidhar B et al. Pediatric malignant germ cell tumors show characteristic transcriptome profiles. Cancer Res 2008 Jun 1;68(11):4239-47. PMID: 18519683
Liu L, Liao GQ, He P, Zhu H et al. Detection of circulating cancer cells in lung cancer patients with a panel of marker genes. Biochem Biophys Res Commun 2008 Aug 8;372(4):756-60. PMID: 18514066
Sridhar S, Schembri F, Zeskind J, Shah V et al. Smoking-induced gene expression changes in the bronchial airway are reflected in nasal and buccal epithelium. BMC Genomics 2008 May 30;9:259. PMID: 18513428
Iakoubova O, Shepherd J, Sacks F. Association of the 719Arg variant of KIF6 with both increased risk of coronary events and with greater response to statin therapy. J Am Coll Cardiol 2008 Jun 3;51(22):2195; author reply 2195-6. PMID: 18510970
Foell JL, Max D, Giersberg C, Korholz D et al. Sensitivity of Hodgkin's lymphoma cell lines to the cell cycle inhibitor roscovitine. Anticancer Res 2008 Mar-Apr;28(2A):887-94. PMID: 18507033
Arya R, Lakhotia SC. Hsp60D is essential for caspase-mediated induced apoptosis in Drosophila melanogaster. Cell Stress Chaperones 2008 Dec;13(4):509-26. PMID: 18506601
Sun W, Yuan S, Li KC. Trait-trait dynamic interaction: 2D-trait eQTL mapping for genetic variation study. BMC Genomics 2008 May 23;9:242. PMID: 18498664
Ducray F, Idbaih A, de Reyniès A, Bièche I et al. Anaplastic oligodendrogliomas with 1p19q codeletion have a proneural gene expression profile. Mol Cancer 2008 May 20;7:41. PMID: 18492260
Vias M, Massie CE, East P, Scott H et al. Pro-neural transcription factors as cancer markers. BMC Med Genomics 2008 May 19;1:17. PMID: 18489756
Gotea V, Ovcharenko I. DiRE: identifying distant regulatory elements of co-expressed genes. Nucleic Acids Res 2008 Jul 1;36(Web Server issue):W133-9. PMID: 18487623
Arora A, Simpson DA. Individual mRNA expression profiles reveal the effects of specific microRNAs. Genome Biol 2008;9(5):R82. PMID: 18485210
Becker SA, Palsson BO. Context-specific metabolic networks are consistent with experiments. PLoS Comput Biol 2008 May 16;4(5):e1000082. PMID: 18483554
Okada K, Asai K. Expansion of signaling genes for adaptive immune system evolution in early vertebrates. BMC Genomics 2008 May 14;9:218. PMID: 18479507
Chen GK, Jorgenson E, Witte JS. An empirical evaluation of the common disease-common variant hypothesis. BMC Proc 2007;1 Suppl 1:S5. PMID: 18466549
Legewie S, Herzel H, Westerhoff HV, Blüthgen N. Recurrent design patterns in the feedback regulation of the mammalian signalling network. Mol Syst Biol 2008;4:190. PMID: 18463614
Ivliev AE, 't Hoen PA, Villerius MP, den Dunnen JT et al. Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data. Nucleic Acids Res 2008 Jul 1;36(Web Server issue):W327-31. PMID: 18463138
Kalathur RK, Gagniere N, Berthommier G, Poidevin L et al. RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina. BMC Genomics 2008 May 5;9:208. PMID: 18457592
Mosley JD, Keri RA. Cell cycle correlated genes dictate the prognostic power of breast cancer gene lists. BMC Med Genomics 2008 Apr 25;1:11. PMID: 18439262
Li H, Zhu D, Cook M. A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data. BMC Genomics 2008 Apr 24;9:188. PMID: 18435860
Foell JL, Hesse M, Volkmer I, Schmiedel BJ et al. Membrane-associated phospholipase A1 beta (LIPI) Is an Ewing tumour-associated cancer/testis antigen. Pediatr Blood Cancer 2008 Aug;51(2):228-34. PMID: 18435455
Dohmann EM, Levesque MP, De Veylder L, Reichardt I et al. The Arabidopsis COP9 signalosome is essential for G2 phase progression and genomic stability. Development 2008 Jun;135(11):2013-22. PMID: 18434413
Oti M, van Reeuwijk J, Huynen MA, Brunner HG. Conserved co-expression for candidate disease gene prioritization. BMC Bioinformatics 2008 Apr 23;9:208. PMID: 18433471
Cheng C, Li LM. Inferring microRNA activities by combining gene expression with microRNA target prediction. PLoS One 2008 Apr 23;3(4):e1989. PMID: 18431476
Kuner R, Barth AS, Ruschhaupt M, Buness A et al. Genomic analysis reveals poor separation of human cardiomyopathies of ischemic and nonischemic etiologies. Physiol Genomics 2008 Jun 12;34(1):88-94. PMID: 18430805
Crawford NP, Alsarraj J, Lukes L, Walker RC et al. Bromodomain 4 activation predicts breast cancer survival. Proc Natl Acad Sci U S A 2008 Apr 29;105(17):6380-5. PMID: 18427120
Tang H, Ross A, Capel B. Expression and functional analysis of Gm114, a putative mammalian ortholog of Drosophila bam. Dev Biol 2008 Jun 1;318(1):73-81. PMID: 18423593
Rondaij MG, Bierings R, van Agtmaal EL, Gijzen KA et al. Guanine exchange factor RalGDS mediates exocytosis of Weibel-Palade bodies from endothelial cells. Blood 2008 Jul 1;112(1):56-63. PMID: 18417737
Kim SY, Kim YS. A gene sets approach for identifying prognostic gene signatures for outcome prediction. BMC Genomics 2008 Apr 16;9:177. PMID: 18416850
Molenaar JJ, Ebus ME, Koster J, van Sluis P et al. Cyclin D1 and CDK4 activity contribute to the undifferentiated phenotype in neuroblastoma. Cancer Res 2008 Apr 15;68(8):2599-609. PMID: 18413728
Zhao XM, Wang RS, Chen L, Aihara K. Uncovering signal transduction networks from high-throughput data by integer linear programming. Nucleic Acids Res 2008 May;36(9):e48. PMID: 18411207
Xu B, Geerts D, Qian K, Zhang H et al. Myeloid ecotropic viral integration site 1 (MEIS) 1 involvement in embryonic implantation. Hum Reprod 2008 Jun;23(6):1394-406. PMID: 18408019
Bhattacharya A, De RK. Divisive Correlation Clustering Algorithm (DCCA) for grouping of genes: detecting varying patterns in expression profiles. Bioinformatics 2008 Jun 1;24(11):1359-66. PMID: 18407922
Hwang S, Son SW, Kim SC, Kim YJ et al. A protein interaction network associated with asthma. J Theor Biol 2008 Jun 21;252(4):722-31. PMID: 18395227
Roomets E, Kivelä T, Tyni T. Carnitine palmitoyltransferase I and Acyl-CoA dehydrogenase 9 in retina: insights of retinopathy in mitochondrial trifunctional protein defects. Invest Ophthalmol Vis Sci 2008 Apr;49(4):1660-4. PMID: 18385088
Greco D, Somervuo P, Di Lieto A, Raitila T et al. Physiology, pathology and relatedness of human tissues from gene expression meta-analysis. PLoS One 2008 Apr 2;3(4):e1880. PMID: 18382664
Xu H, Tang Y, Liu DZ, Ran R et al. Gene expression in peripheral blood differs after cardioembolic compared with large-vessel atherosclerotic stroke: biomarkers for the etiology of ischemic stroke. J Cereb Blood Flow Metab 2008 Jul;28(7):1320-8. PMID: 18382470
Hann CL, Daniel VC, Sugar EA, Dobromilskaya I et al. Therapeutic efficacy of ABT-737, a selective inhibitor of BCL-2, in small cell lung cancer. Cancer Res 2008 Apr 1;68(7):2321-8. PMID: 18381439
Nukiwa T, Suzuki T, Fukuhara T, Kikuchi T. Secretory leukocyte peptidase inhibitor and lung cancer. Cancer Sci 2008 May;99(5):849-55. PMID: 18380788
Rybaczyk LA, Bashaw MJ, Pathak DR, Huang K. An indicator of cancer: downregulation of monoamine oxidase-A in multiple organs and species. BMC Genomics 2008 Mar 20;9:134. PMID: 18366702
Astrand M, Mostad P, Rudemo M. Empirical Bayes models for multiple probe type microarrays at the probe level. BMC Bioinformatics 2008 Mar 20;9:156. PMID: 18366694
Thorrez L, Van Deun K, Tranchevent LC, Van Lommel L et al. Using ribosomal protein genes as reference: a tale of caution. PLoS One 2008 Mar 26;3(3):e1854. PMID: 18365009
Ivanov SV, Ivanova AV, Salnikow K, Timofeeva O et al. Two novel VHL targets, TGFBI (BIGH3) and its transactivator KLF10, are up-regulated in renal clear cell carcinoma and other tumors. Biochem Biophys Res Commun 2008 Jun 13;370(4):536-40. PMID: 18359287
Sharopova N. Plant simple sequence repeats: distribution, variation, and effects on gene expression. Genome 2008 Feb;51(2):79-90. PMID: 18356942
Creighton CJ. Multiple oncogenic pathway signatures show coordinate expression patterns in human prostate tumors. PLoS One 2008 Mar 19;3(3):e1816. PMID: 18350153
Liu B. Association of the dusp6 (mkp3) gene with mouse brain weight and forebrain structure. J Child Neurol 2008 Jun;23(6):624-7. PMID: 18344456
Rody A, Karn T, Ruckhäberle E, Müller V et al. Gene expression of topoisomerase II alpha (TOP2A) by microarray analysis is highly prognostic in estrogen receptor (ER) positive breast cancer. Breast Cancer Res Treat 2009 Feb;113(3):457-66. PMID: 18340528
Neptune ER, Podowski M, Calvi C, Cho JH et al. Targeted disruption of NeuroD, a proneural basic helix-loop-helix factor, impairs distal lung formation and neuroendocrine morphology in the neonatal lung. J Biol Chem 2008 Jul 25;283(30):21160-9. PMID: 18339630
Grundberg E, Brändström H, Lam KC, Gurd S et al. Systematic assessment of the human osteoblast transcriptome in resting and induced primary cells. Physiol Genomics 2008 May 13;33(3):301-11. PMID: 18334548
Hong SE, Park I, Cha H, Rho SH et al. Identification of mouse heart transcriptomic network sensitive to various heart diseases. Biotechnol J 2008 May;3(5):648-58. PMID: 18320566
Jupiter DC, VanBuren V. A visual data mining tool that facilitates reconstruction of transcription regulatory networks. PLoS One 2008 Mar 5;3(3):e1717. PMID: 18320038
Gallegos Ruiz MI, Floor K, Roepman P, Rodriguez JA et al. Integration of gene dosage and gene expression in non-small cell lung cancer, identification of HSP90 as potential target. PLoS One 2008 Mar 5;3(3):e0001722. PMID: 18320023
Hassane DC, Guzman ML, Corbett C, Li X et al. Discovery of agents that eradicate leukemia stem cells using an in silico screen of public gene expression data. Blood 2008 Jun 15;111(12):5654-62. PMID: 18305216
Fehrmann RS, de Jonge HJ, Ter Elst A, de Vries A et al. A new perspective on transcriptional system regulation (TSR): towards TSR profiling. PLoS One 2008 Feb 20;3(2):e1656. PMID: 18297136
Calogero RA, Quaglino E, Saviozzi S, Forni G et al. Oncoantigens as anti-tumor vaccination targets: the chance of a lucky strike? Cancer Immunol Immunother 2008 Nov;57(11):1685-94. PMID: 18286283
Tomlins SA, Laxman B, Varambally S, Cao X et al. Role of the TMPRSS2-ERG gene fusion in prostate cancer. Neoplasia 2008 Feb;10(2):177-88. PMID: 18283340
Cho H, Park C, Hwang IY, Han SB et al. Rgs5 targeting leads to chronic low blood pressure and a lean body habitus. Mol Cell Biol 2008 Apr;28(8):2590-7. PMID: 18268011
Pang H, Zhao H. Building pathway clusters from Random Forests classification using class votes. BMC Bioinformatics 2008 Feb 6;9:87. PMID: 18254968
Ye H, Yu T, Temam S, Ziober BL et al. Transcriptomic dissection of tongue squamous cell carcinoma. BMC Genomics 2008 Feb 6;9:69. PMID: 18254958
Toonen EJ, Barrera P, Radstake TR, van Riel PL et al. Gene expression profiling in rheumatoid arthritis: current concepts and future directions. Ann Rheum Dis 2008 Dec;67(12):1663-9. PMID: 18250114
Chesi M, Robbiani DF, Sebag M, Chng WJ et al. AID-dependent activation of a MYC transgene induces multiple myeloma in a conditional mouse model of post-germinal center malignancies. Cancer Cell 2008 Feb;13(2):167-80. PMID: 18242516
Rodriguez-Zas SL, Ko Y, Adams HA, Southey BR. Advancing the understanding of the embryo transcriptome co-regulation using meta-, functional, and gene network analysis tools. Reproduction 2008 Feb;135(2):213-24. PMID: 18239050
Rodriguez-Zas SL, Schellander K, Lewin HA. Biological interpretations of transcriptomic profiles in mammalian oocytes and embryos. Reproduction 2008 Feb;135(2):129-39. PMID: 18239044
Lee CK, Sunkin SM, Kuan C, Thompson CL et al. Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data. Genome Biol 2008 Jan 30;9(1):R23. PMID: 18234097
Dudley J, Butte AJ. Enabling integrative genomic analysis of high-impact human diseases through text mining. Pac Symp Biocomput 2008;:580-91. PMID: 18229717
Chen DP, Weber SC, Constantinou PS, Ferris TA et al. Novel integration of hospital electronic medical records and gene expression measurements to identify genetic markers of maturation. Pac Symp Biocomput 2008;:243-54. PMID: 18229690
Jen CH, Yang TP, Tung CY, Su SH et al. Signature Evaluation Tool (SET): a Java-based tool to evaluate and visualize the sample discrimination abilities of gene expression signatures. BMC Bioinformatics 2008 Jan 28;9:58. PMID: 18221568
Giangreco A, Qin M, Pintar JE, Watt FM. Epidermal stem cells are retained in vivo throughout skin aging. Aging Cell 2008 Mar;7(2):250-9. PMID: 18221414
Davids W, Zhang Z. The impact of horizontal gene transfer in shaping operons and protein interaction networks--direct evidence of preferential attachment. BMC Evol Biol 2008 Jan 24;8:23. PMID: 18218112
Zhu Y, Zhu Y, Xu W. EzArray: a web-based highly automated Affymetrix expression array data management and analysis system. BMC Bioinformatics 2008 Jan 24;9:46. PMID: 18218103
Wang Z, Hao Y, Lowe AW. The adenocarcinoma-associated antigen, AGR2, promotes tumor growth, cell migration, and cellular transformation. Cancer Res 2008 Jan 15;68(2):492-7. PMID: 18199544
Yang PH, Cheung WK, Peng Y, He ML et al. Makorin-2 is a neurogenesis inhibitor downstream of phosphatidylinositol 3-kinase/Akt (PI3K/Akt) signal. J Biol Chem 2008 Mar 28;283(13):8486-95. PMID: 18198183
Moran LB, Graeber MB. Towards a pathway definition of Parkinson's disease: a complex disorder with links to cancer, diabetes and inflammation. Neurogenetics 2008 Feb;9(1):1-13. PMID: 18196299
Bar-Joseph Z, Siegfried Z, Brandeis M, Brors B et al. Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells. Proc Natl Acad Sci U S A 2008 Jan 22;105(3):955-60. PMID: 18195366
Yagi T, Giallourakis C, Mohanty S, Scheidig C et al. Defective signal transduction in B lymphocytes lacking presenilin proteins. Proc Natl Acad Sci U S A 2008 Jan 22;105(3):979-84. PMID: 18195359
Solé X, Hernández P, de Heredia ML, Armengol L et al. Genetic and genomic analysis modeling of germline c-MYC overexpression and cancer susceptibility. BMC Genomics 2008 Jan 11;9:12. PMID: 18190704
Tchagang AB, Tewfik AH, DeRycke MS, Skubitz KM et al. Early detection of ovarian cancer using group biomarkers. Mol Cancer Ther 2008 Jan;7(1):27-37. PMID: 18187805
Sharma M, Batra J, Mabalirajan U, Sharma S et al. A genetic variation in inositol polyphosphate 4 phosphatase a enhances susceptibility to asthma. Am J Respir Crit Care Med 2008 Apr 1;177(7):712-9. PMID: 18187694
Ertel A, Tozeren A. Switch-like genes populate cell communication pathways and are enriched for extracellular proteins. BMC Genomics 2008 Jan 4;9:3. PMID: 18177501
Lin SL, Chang D, Chiang A, Ying SY. Androgen receptor regulates CD168 expression and signaling in prostate cancer. Carcinogenesis 2008 Feb;29(2):282-90. PMID: 18174258
Helgeson BE, Tomlins SA, Shah N, Laxman B et al. Characterization of TMPRSS2:ETV5 and SLC45A3:ETV5 gene fusions in prostate cancer. Cancer Res 2008 Jan 1;68(1):73-80. PMID: 18172298
Tuller T, Kupiec M, Ruppin E. Determinants of protein abundance and translation efficiency in S. cerevisiae. PLoS Comput Biol 2007 Dec;3(12):e248. PMID: 18159940
Demetris AJ, Specht S, Nozaki I, Lunz JG 3rd et al. Small proline-rich proteins (SPRR) function as SH3 domain ligands, increase resistance to injury and are associated with epithelial-mesenchymal transition (EMT) in cholangiocytes. J Hepatol 2008 Feb;48(2):276-88. PMID: 18155796
Swindell WR. Comparative analysis of microarray data identifies common responses to caloric restriction among mouse tissues. Mech Ageing Dev 2008 Mar;129(3):138-53. PMID: 18155270
Camargo A, Azuaje F. Linking gene expression and functional network data in human heart failure. PLoS One 2007 Dec 19;2(12):e1347. PMID: 18094754
Jiang L, Yao M, Shi J, Shen P et al. Yin yang 1 directly regulates the transcription of RE-1 silencing transcription factor. J Neurosci Res 2008 May 1;86(6):1209-16. PMID: 18092359
Febbo PG, Mulligan MG, Slonina DA, Stegmaier K et al. Literature Lab: a method of automated literature interrogation to infer biology from microarray analysis. BMC Genomics 2007 Dec 18;8:461. PMID: 18088408
Gerbe F, Cox B, Rossant J, Chazaud C. Dynamic expression of Lrp2 pathway members reveals progressive epithelial differentiation of primitive endoderm in mouse blastocyst. Dev Biol 2008 Jan 15;313(2):594-602. PMID: 18083160
Chng WJ, Glebov O, Bergsagel PL, Kuehl WM. Genetic events in the pathogenesis of multiple myeloma. Best Pract Res Clin Haematol 2007 Dec;20(4):571-96. PMID: 18070707
Xue H, Xian B, Dong D, Xia K et al. A modular network model of aging. Mol Syst Biol 2007;3:147. PMID: 18059442
Ruckhäberle E, Rody A, Engels K, Gaetje R et al. Microarray analysis of altered sphingolipid metabolism reveals prognostic significance of sphingosine kinase 1 in breast cancer. Breast Cancer Res Treat 2008 Nov;112(1):41-52. PMID: 18058224
Arteaga-Salas JM, Zuzan H, Langdon WB, Upton GJ et al. An overview of image-processing methods for Affymetrix GeneChips. Brief Bioinform 2008 Jan;9(1):25-33. PMID: 18057073
Masotti D, Nardini C, Rossi S, Bonora E et al. TOM: enhancement and extension of a tool suite for in silico approaches to multigenic hereditary disorders. Bioinformatics 2008 Feb 1;24(3):428-9. PMID: 18048394
Seo DC, Sung JM, Cho HJ, Yi H et al. Gene expression profiling of cancer stem cell in human lung adenocarcinoma A549 cells. Mol Cancer 2007 Nov 22;6:75. PMID: 18034892
Hoshida Y, Brunet JP, Tamayo P, Golub TR et al. Subclass mapping: identifying common subtypes in independent disease data sets. PLoS One 2007 Nov 21;2(11):e1195. PMID: 18030330
Hsu SD, Chu CH, Tsou AP, Chen SJ et al. miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes. Nucleic Acids Res 2008 Jan;36(Database issue):D165-9. PMID: 18029362
Pavelka N, Fournier ML, Swanson SK, Pelizzola M et al. Statistical similarities between transcriptomics and quantitative shotgun proteomics data. Mol Cell Proteomics 2008 Apr;7(4):631-44. PMID: 18029349
Kim TM, Chung YJ, Rhyu MG, Jung MH. Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis. BMC Bioinformatics 2007 Nov 17;8:453. PMID: 18021416
Lalancette C, Thibault C, Bachand I, Caron N et al. Transcriptome analysis of bull semen with extreme nonreturn rate: use of suppression-subtractive hybridization to identify functional markers for fertility. Biol Reprod 2008 Apr;78(4):618-35. PMID: 18003951
Boursiac Y, Harper JF. The origin and function of calmodulin regulated Ca2+ pumps in plants. J Bioenerg Biomembr 2007 Dec;39(5-6):409-14. PMID: 18000746
Sturgill D, Zhang Y, Parisi M, Oliver B. Demasculinization of X chromosomes in the Drosophila genus. Nature 2007 Nov 8;450(7167):238-41. PMID: 17994090
Lu Y, Yi Y, Liu P, Wen W et al. Common human cancer genes discovered by integrated gene-expression analysis. PLoS One 2007 Nov 7;2(11):e1149. PMID: 17989776
Klebanov L, Chen L, Yakovlev A. Revisiting adverse effects of cross-hybridization in Affymetrix gene expression data: do they matter for correlation analysis? Biol Direct 2007 Nov 7;2:28. PMID: 17988401
Caspi A, Williams B, Kim-Cohen J, Craig IW et al. Moderation of breastfeeding effects on the IQ by genetic variation in fatty acid metabolism. Proc Natl Acad Sci U S A 2007 Nov 20;104(47):18860-5. PMID: 17984066
Kim SY, Kim JH, Lee HS, Noh SM et al. Meta- and gene set analysis of stomach cancer gene expression data. Mol Cells 2007 Oct 31;24(2):200-9. PMID: 17978572
Myllärniemi M, Lindholm P, Ryynänen MJ, Kliment CR et al. Gremlin-mediated decrease in bone morphogenetic protein signaling promotes pulmonary fibrosis. Am J Respir Crit Care Med 2008 Feb 1;177(3):321-9. PMID: 17975199
Geerts D, Wallick CJ, Koomoa DL, Koster J et al. Expression of prenylated Rab acceptor 1 domain family, member 2 (PRAF2) in neuroblastoma: correlation with clinical features, cellular localization, and cerulenin-mediated apoptosis regulation. Clin Cancer Res 2007 Nov 1;13(21):6312-9. PMID: 17975142
Ferguson BJ, Alexander C, Rossi SW, Liiv I et al. AIRE's CARD revealed, a new structure for central tolerance provokes transcriptional plasticity. J Biol Chem 2008 Jan 18;283(3):1723-31. PMID: 17974569
Chen R, Li L, Butte AJ. AILUN: reannotating gene expression data automatically. Nat Methods 2007 Nov;4(11):879. PMID: 17971777
Jongjaroenprasert W, Chanprasertyotin S, Butadej S, Nakasatien S et al. Association of genetic variants in GABRA3 gene and thyrotoxic hypokalaemic periodic paralysis in Thai population. Clin Endocrinol (Oxf) 2008 Apr;68(4):646-51. PMID: 17970773
Davis FP, Barkan DT, Eswar N, McKerrow JH et al. Host pathogen protein interactions predicted by comparative modeling. Protein Sci 2007 Dec;16(12):2585-96. PMID: 17965183
Gormley M, Dampier W, Ertel A, Karacali B et al. Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets. BMC Bioinformatics 2007 Oct 26;8:415. PMID: 17963508
Meir T, Dror R, Yu X, Qian J et al. Molecular characteristics of liver metastases from uveal melanoma. Invest Ophthalmol Vis Sci 2007 Nov;48(11):4890-6. PMID: 17962435
Strand AD, Baquet ZC, Aragaki AK, Holmans P et al. Expression profiling of Huntington's disease models suggests that brain-derived neurotrophic factor depletion plays a major role in striatal degeneration. J Neurosci 2007 Oct 24;27(43):11758-68. PMID: 17959817
Gosink MM, Petrie HT, Tsinoremas NF. Electronically subtracting expression patterns from a mixed cell population. Bioinformatics 2007 Dec 15;23(24):3328-34. PMID: 17956877
Jokic N, Ling YY, Ward RE, Michael-Titus AT et al. Retinoid receptors in chronic degeneration of the spinal cord: observations in a rat model of amyotrophic lateral sclerosis. J Neurochem 2007 Dec;103(5):1821-33. PMID: 17956549
Danko CG, McIlvain VA, Qin M, Knox BE et al. Bioinformatic identification of novel putative photoreceptor specific cis-elements. BMC Bioinformatics 2007 Oct 22;8:407. PMID: 17953763
Beach S, Tang H, Park S, Dhillon AS et al. Snail is a repressor of RKIP transcription in metastatic prostate cancer cells. Oncogene 2008 Apr 3;27(15):2243-8. PMID: 17952120
Crijns AP, de Graeff P, Geerts D, Ten Hoor KA et al. MEIS and PBX homeobox proteins in ovarian cancer. Eur J Cancer 2007 Nov;43(17):2495-505. PMID: 17949970
Foat BC, Tepper RG, Bussemaker HJ. TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors. Nucleic Acids Res 2008 Jan;36(Database issue):D125-31. PMID: 17947326
Nam S, Kim B, Shin S, Lee S. miRGator: an integrated system for functional annotation of microRNAs. Nucleic Acids Res 2008 Jan;36(Database issue):D159-64. PMID: 17942429
Chen J, Xu H, Aronow BJ, Jegga AG. Improved human disease candidate gene prioritization using mouse phenotype. BMC Bioinformatics 2007 Oct 16;8:392. PMID: 17939863
Obayashi T, Hayashi S, Shibaoka M, Saeki M et al. COXPRESdb: a database of coexpressed gene networks in mammals. Nucleic Acids Res 2008 Jan;36(Database issue):D77-82. PMID: 17932064
Costa IG, Roepcke S, Schliep A. Gene expression trees in lymphoid development. BMC Immunol 2007 Oct 9;8:25. PMID: 17925013
Zhang J, Ji Y, Zhang L. Extracting three-way gene interactions from microarray data. Bioinformatics 2007 Nov 1;23(21):2903-9. PMID: 17921496
Novershtern N, Itzhaki Z, Manor O, Friedman N et al. A functional and regulatory map of asthma. Am J Respir Cell Mol Biol 2008 Mar;38(3):324-36. PMID: 17921359
Wan X, Pavlidis P. Sharing and reusing gene expression profiling data in neuroscience. Neuroinformatics 2007 Fall;5(3):161-75. PMID: 17917127
Stirewalt DL, Meshinchi S, Kopecky KJ, Fan W et al. Identification of genes with abnormal expression changes in acute myeloid leukemia. Genes Chromosomes Cancer 2008 Jan;47(1):8-20. PMID: 17910043
Zilliox MJ, Irizarry RA. A gene expression bar code for microarray data. Nat Methods 2007 Nov;4(11):911-3. PMID: 17906632
Fujibuchi W, Kiseleva L, Taniguchi T, Harada H et al. CellMontage: similar expression profile search server. Bioinformatics 2007 Nov 15;23(22):3103-4. PMID: 17895274
Beane J, Sebastiani P, Liu G, Brody JS et al. Reversible and permanent effects of tobacco smoke exposure on airway epithelial gene expression. Genome Biol 2007;8(9):R201. PMID: 17894889
Yu JX, Sieuwerts AM, Zhang Y, Martens JW et al. Pathway analysis of gene signatures predicting metastasis of node-negative primary breast cancer. BMC Cancer 2007 Sep 25;7:182. PMID: 17894856
Gamberoni G, Lamma E, Lodo G, Marchesini J et al. Fun&Co: identification of key functional differences in transcriptomes. Bioinformatics 2007 Oct 15;23(20):2725-32. PMID: 17893090
Bianchetti L, Wu Y, Guerin E, Plewniak F et al. SAGETTARIUS: a program to reduce the number of tags mapped to multiple transcripts and to plan SAGE sequencing stages. Nucleic Acids Res 2007;35(18):e122. PMID: 17884916
Zhang Z, Chen D, Fenstermacher DA. Integrated analysis of independent gene expression microarray datasets improves the predictability of breast cancer outcome. BMC Genomics 2007 Sep 20;8:331. PMID: 17883867
Jørgensen TN, Roper E, Thurman JM, Marrack P et al. Type I interferon signaling is involved in the spontaneous development of lupus-like disease in B6.Nba2 and (B6.Nba2 x NZW)F(1) mice. Genes Immun 2007 Dec;8(8):653-62. PMID: 17882225
Gary-Gouy H, Sainz-Perez A, Marteau JB, Marfaing-Koka A et al. Natural phosphorylation of CD5 in chronic lymphocytic leukemia B cells and analysis of CD5-regulated genes in a B cell line suggest a role for CD5 in malignant phenotype. J Immunol 2007 Oct 1;179(7):4335-44. PMID: 17878328
Hipp J, Andersson KE, Kwon TG, Kwak EK et al. Microarray analysis of exstrophic human bladder smooth muscle. BJU Int 2008 Jan;101(1):100-5. PMID: 17868416
Li H, Sun Y, Zhan M. Analysis of gene coexpression by B-spline based CoD estimation. EURASIP J Bioinform Syst Biol 2007;:49478. PMID: 17846662
Ucar D, Neuhaus I, Ross-MacDonald P, Tilford C et al. Construction of a reference gene association network from multiple profiling data: application to data analysis. Bioinformatics 2007 Oct 15;23(20):2716-24. PMID: 17846039
Möller-Levet CS, West CM, Miller CJ. Exploiting sample variability to enhance multivariate analysis of microarray data. Bioinformatics 2007 Oct 15;23(20):2733-40. PMID: 17827205
Xie RL, Liu L, Mitra P, Stein JL et al. Transcriptional activation of the histone nuclear factor P (HiNF-P) gene by HiNF-P and its cyclin E/CDK2 responsive co-factor p220NPAT defines a novel autoregulatory loop at the G1/S phase transition. Gene 2007 Nov 1;402(1-2):94-102. PMID: 17826007
Gorlov IP, Meyer P, Liloglou T, Myles J et al. Seizure 6-like (SEZ6L) gene and risk for lung cancer. Cancer Res 2007 Sep 1;67(17):8406-11. PMID: 17804757
Jarboe JS, Johnson KR, Choi Y, Lonser RR et al. Expression of interleukin-13 receptor alpha2 in glioblastoma multiforme: implications for targeted therapies. Cancer Res 2007 Sep 1;67(17):7983-6. PMID: 17804706
Alberstein M, Amit M, Vaknin K, O'Donnell A et al. Regulation of transcription of the RNA splicing factor hSlu7 by Elk-1 and Sp1 affects alternative splicing. RNA 2007 Nov;13(11):1988-99. PMID: 17804646
Ottolenghi C, Pelosi E, Tran J, Colombino M et al. Loss of Wnt4 and Foxl2 leads to female-to-male sex reversal extending to germ cells. Hum Mol Genet 2007 Dec 1;16(23):2795-804. PMID: 17728319
Hibbs MA, Hess DC, Myers CL, Huttenhower C et al. Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics 2007 Oct 15;23(20):2692-9. PMID: 17724061
Clement TM, Anway MD, Uzumcu M, Skinner MK. Regulation of the gonadal transcriptome during sex determination and testis morphogenesis: comparative candidate genes. Reproduction 2007 Sep;134(3):455-72. PMID: 17709564
Ferg M, Sanges R, Gehrig J, Kiss J et al. The TATA-binding protein regulates maternal mRNA degradation and differential zygotic transcription in zebrafish. EMBO J 2007 Sep 5;26(17):3945-56. PMID: 17703193
Tian F, Zhang H, Zhang X, Song C et al. miRAS: a data processing system for miRNA expression profiling study. BMC Bioinformatics 2007 Aug 4;8:285. PMID: 17683571
Tomlins SA, Laxman B, Dhanasekaran SM, Helgeson BE et al. Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer. Nature 2007 Aug 2;448(7153):595-9. PMID: 17671502
Kim B, Lee HJ, Choi HY, Shin Y et al. Clinical validity of the lung cancer biomarkers identified by bioinformatics analysis of public expression data. Cancer Res 2007 Aug 1;67(15):7431-8. PMID: 17671213
Axelsen JB, Lotem J, Sachs L, Domany E. Genes overexpressed in different human solid cancers exhibit different tissue-specific expression profiles. Proc Natl Acad Sci U S A 2007 Aug 7;104(32):13122-7. PMID: 17664417
Chen M, Kendziorski C. A statistical framework for expression quantitative trait loci mapping. Genetics 2007 Oct;177(2):761-71. PMID: 17660576
Fujibuchi W, Kato T. Classification of heterogeneous microarray data by maximum entropy kernel. BMC Bioinformatics 2007 Jul 26;8:267. PMID: 17651507
Song L, Bedo J, Borgwardt KM, Gretton A et al. Gene selection via the BAHSIC family of algorithms. Bioinformatics 2007 Jul 1;23(13):i490-8. PMID: 17646335
Shiga M, Takigawa I, Mamitsuka H. Annotating gene function by combining expression data with a modular gene network. Bioinformatics 2007 Jul 1;23(13):i468-78. PMID: 17646332
Lim WK, Wang K, Lefebvre C, Califano A. Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. Bioinformatics 2007 Jul 1;23(13):i282-8. PMID: 17646307
Huang Y, Li H, Hu H, Yan X et al. Systematic discovery of functional modules and context-specific functional annotation of human genome. Bioinformatics 2007 Jul 1;23(13):i222-9. PMID: 17646300
Green ML, Karp PD. Using genome-context data to identify specific types of functional associations in pathway/genome databases. Bioinformatics 2007 Jul 1;23(13):i205-11. PMID: 17646298
Dyer MD, Murali TM, Sobral BW. Computational prediction of host-pathogen protein-protein interactions. Bioinformatics 2007 Jul 1;23(13):i159-66. PMID: 17646292
Pemberton TJ, Li FY, Oka S, Mendoza-Fandino GA et al. Identification of novel genes expressed during mouse tooth development by microarray gene expression analysis. Dev Dyn 2007 Aug;236(8):2245-57. PMID: 17626284
Wu M, Min C, Wang X, Yu Z et al. Repression of BCL2 by the tumor suppressor activity of the lysyl oxidase propeptide inhibits transformed phenotype of lung and pancreatic cancer cells. Cancer Res 2007 Jul 1;67(13):6278-85. PMID: 17616686
Paulson KE, Rieger-Christ K, McDevitt MA, Kuperwasser C et al. Alterations of the HBP1 transcriptional repressor are associated with invasive breast cancer. Cancer Res 2007 Jul 1;67(13):6136-45. PMID: 17616670
Scott MS, Barton GJ. Probabilistic prediction and ranking of human protein-protein interactions. BMC Bioinformatics 2007 Jul 5;8:239. PMID: 17615067
Yi Y, Li C, Miller C, George AL Jr. Strategy for encoding and comparison of gene expression signatures. Genome Biol 2007;8(7):R133. PMID: 17612401
McElwee JJ, Schuster E, Blanc E, Piper MD et al. Evolutionary conservation of regulated longevity assurance mechanisms. Genome Biol 2007;8(7):R132. PMID: 17612391
Jenner MW, Leone PE, Walker BA, Ross FM et al. Gene mapping and expression analysis of 16q loss of heterozygosity identifies WWOX and CYLD as being important in determining clinical outcome in multiple myeloma. Blood 2007 Nov 1;110(9):3291-300. PMID: 17609426
Smith SC, Oxford G, Baras AS, Owens C et al. Expression of ral GTPases, their effectors, and activators in human bladder cancer. Clin Cancer Res 2007 Jul 1;13(13):3803-13. PMID: 17606711
Yap DY, Smith DK, Zhang XW, Hill J. Using biomarker signature patterns for an mRNA molecular diagnostic of mouse embryonic stem cell differentiation state. BMC Genomics 2007 Jul 3;8:210. PMID: 17605829
Huang J, Hao P, Zhang YL, Deng FX et al. Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS). BMC Genomics 2007 Jul 2;8:207. PMID: 17601345
Lu ZH, Wright JD, Belt B, Cardiff RD et al. Hypoxia-inducible factor-1 facilitates cervical cancer progression in human papillomavirus type 16 transgenic mice. Am J Pathol 2007 Aug;171(2):667-81. PMID: 17600126
Oeder S, Mages J, Flicek P, Lang R. Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets. BMC Genomics 2007 Jun 28;8:200. PMID: 17598913
Singh AV, Knudsen KB, Knudsen TB. Integrative analysis of the mouse embryonic transcriptome. Bioinformation 2007 Apr 10;1(10):406-13. PMID: 17597930
Holst CR, Bou-Reslan H, Gore BB, Wong K et al. Secreted sulfatases Sulf1 and Sulf2 have overlapping yet essential roles in mouse neonatal survival. PLoS One 2007 Jun 27;2(6):e575. PMID: 17593974
Hu Z, Ng DM, Yamada T, Chen C et al. VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Res 2007 Jul;35(Web Server issue):W625-32. PMID: 17586824
Sarangi A, Bupp K, Roth MJ. Identification of a retroviral receptor used by an envelope protein derived by peptide library screening. Proc Natl Acad Sci U S A 2007 Jun 26;104(26):11032-7. PMID: 17581869
Hirst M, Delaney A, Rogers SA, Schnerch A et al. LongSAGE profiling of nine human embryonic stem cell lines. Genome Biol 2007;8(6):R113. PMID: 17570852
Day A, Carlson MR, Dong J, O'Connor BD et al. Celsius: a community resource for Affymetrix microarray data. Genome Biol 2007;8(6):R112. PMID: 17570842
Elnitski LL, Shah P, Moreland RT, Umayam L et al. The ENCODEdb portal: simplified access to ENCODE Consortium data. Genome Res 2007 Jun;17(6):954-9. PMID: 17568011
Calabria AR, Shusta EV. A genomic comparison of in vivo and in vitro brain microvascular endothelial cells. J Cereb Blood Flow Metab 2008 Jan;28(1):135-48. PMID: 17565361
Harrison AP, Johnston CE, Orengo CA. Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips. BMC Bioinformatics 2007 Jun 11;8:195. PMID: 17562008
Tsang J, Zhu J, van Oudenaarden A. MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol Cell 2007 Jun 8;26(5):753-67. PMID: 17560377
Yu H, Wang F, Tu K, Xie L et al. Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data. BMC Bioinformatics 2007 Jun 11;8:194. PMID: 17559689
Shephard EA, Chandan P, Stevanovic-Walker M, Edwards M et al. Alternative promoters and repetitive DNA elements define the species-dependent tissue-specific expression of the FMO1 genes of human and mouse. Biochem J 2007 Sep 15;406(3):491-9. PMID: 17547558
Warnat P, Oberthuer A, Fischer M, Westermann F et al. Cross-study analysis of gene expression data for intermediate neuroblastoma identifies two biological subtypes. BMC Cancer 2007 May 25;7:89. PMID: 17531100
Schmid CD, Sengstag T, Bucher P, Delorenzi M. MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data. Nucleic Acids Res 2007 Jul;35(Web Server issue):W201-5. PMID: 17526516
Luan Y, Li H. Group additive regression models for genomic data analysis. Biostatistics 2008 Jan;9(1):100-13. PMID: 17513311
Kapur K, Xing Y, Ouyang Z, Wong WH. Exon arrays provide accurate assessments of gene expression. Genome Biol 2007;8(5):R82. PMID: 17504534
Ott LW, Resing KA, Sizemore AW, Heyen JW et al. Tumor Necrosis Factor-alpha- and interleukin-1-induced cellular responses: coupling proteomic and genomic information. J Proteome Res 2007 Jun;6(6):2176-85. PMID: 17503796
Maine GN, Burstein E. COMMD proteins: COMMing to the scene. Cell Mol Life Sci 2007 Aug;64(15):1997-2005. PMID: 17497243
Davis S, Meltzer PS. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics 2007 Jul 15;23(14):1846-7. PMID: 17496320
Hardie WD, Korfhagen TR, Sartor MA, Prestridge A et al. Genomic profile of matrix and vasculature remodeling in TGF-alpha induced pulmonary fibrosis. Am J Respir Cell Mol Biol 2007 Sep;37(3):309-21. PMID: 17496152
Henz SR, Cumbie JS, Kasschau KD, Lohmann JU et al. Distinct expression patterns of natural antisense transcripts in Arabidopsis. Plant Physiol 2007 Jul;144(3):1247-55. PMID: 17496106
Herschkowitz JI, Simin K, Weigman VJ, Mikaelian I et al. Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors. Genome Biol 2007;8(5):R76. PMID: 17493263
Hertzberg L, Izraeli S, Domany E. STOP: searching for transcription factor motifs using gene expression. Bioinformatics 2007 Jul 15;23(14):1737-43. PMID: 17488754
Nilsson B, Håkansson P, Johansson M, Nelander S et al. Threshold-free high-power methods for the ontological analysis of genome-wide gene-expression studies. Genome Biol 2007;8(5):R74. PMID: 17488501
Wei Z, Li H. A Markov random field model for network-based analysis of genomic data. Bioinformatics 2007 Jun 15;23(12):1537-44. PMID: 17483504
Chalmel F, Rolland AD, Niederhauser-Wiederkehr C, Chung SS et al. The conserved transcriptome in human and rodent male gametogenesis. Proc Natl Acad Sci U S A 2007 May 15;104(20):8346-51. PMID: 17483452
Reimand J, Kull M, Peterson H, Hansen J et al. g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res 2007 Jul;35(Web Server issue):W193-200. PMID: 17478515
Sukhdeo K, Mani M, Zhang Y, Dutta J et al. Targeting the beta-catenin/TCF transcriptional complex in the treatment of multiple myeloma. Proc Natl Acad Sci U S A 2007 May 1;104(18):7516-21. PMID: 17452641
Alberts R, Terpstra P, Hardonk M, Bystrykh LV et al. A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat. BMC Bioinformatics 2007 Apr 20;8:132. PMID: 17448222
Arredouani MS, Franco F, Imrich A, Fedulov A et al. Scavenger Receptors SR-AI/II and MARCO limit pulmonary dendritic cell migration and allergic airway inflammation. J Immunol 2007 May 1;178(9):5912-20. PMID: 17442975
Montano M, Flanagan JN, Jiang L, Sebastiani P et al. Transcriptional profiling of testosterone-regulated genes in the skeletal muscle of human immunodeficiency virus-infected men experiencing weight loss. J Clin Endocrinol Metab 2007 Jul;92(7):2793-802. PMID: 17440010
Graham RR, Kyogoku C, Sigurdsson S, Vlasova IA et al. Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus. Proc Natl Acad Sci U S A 2007 Apr 17;104(16):6758-63. PMID: 17412832
Al-Shahrour F, Arbiza L, Dopazo H, Huerta-Cepas J et al. From genes to functional classes in the study of biological systems. BMC Bioinformatics 2007 Apr 3;8:114. PMID: 17407596
Park WD, Stegall MD. A meta-analysis of kidney microarray datasets: investigation of cytokine gene detection and correlation with rt-PCR and detection thresholds. BMC Genomics 2007 Mar 30;8:88. PMID: 17397532
Hanada K, Zhang X, Borevitz JO, Li WH et al. A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection. Genome Res 2007 May;17(5):632-40. PMID: 17395691
Chandramouli A, Shi J, Feng Y, Holubec H et al. Haploinsufficiency of the cdc2l gene contributes to skin cancer development in mice. Carcinogenesis 2007 Sep;28(9):2028-35. PMID: 17389615
Simmen FA, Xiao R, Velarde MC, Nicholson RD et al. Dysregulation of intestinal crypt cell proliferation and villus cell migration in mice lacking Kruppel-like factor 9. Am J Physiol Gastrointest Liver Physiol 2007 Jun;292(6):G1757-69. PMID: 17379758
Ernst C, Sequeira A, Klempan T, Ernst N et al. Confirmation of region-specific patterns of gene expression in the human brain. Neurogenetics 2007 Aug;8(3):219-24. PMID: 17375343
Agnelli L, Fabris S, Bicciato S, Basso D et al. Upregulation of translational machinery and distinct genetic subgroups characterise hyperdiploidy in multiple myeloma. Br J Haematol 2007 Feb;136(4):565-73. PMID: 17367409
Inaoka H, Fukuoka Y, Kohane IS. Evidence of spatially bound gene regulation in Mus musculus: decreased gene expression proximal to microRNA genomic location. Proc Natl Acad Sci U S A 2007 Mar 20;104(12):5020-5. PMID: 17360362
Truntzer C, Mercier C, Estève J, Gautier C et al. Importance of data structure in comparing two dimension reduction methods for classification of microarray gene expression data. BMC Bioinformatics 2007 Mar 13;8:90. PMID: 17355634
Itoh Y, Melamed E, Yang X, Kampf K et al. Dosage compensation is less effective in birds than in mammals. J Biol 2007;6(1):2. PMID: 17352797
Pedemonte E, Benvenuto F, Casazza S, Mancardi G et al. The molecular signature of therapeutic mesenchymal stem cells exposes the architecture of the hematopoietic stem cell niche synapse. BMC Genomics 2007 Mar 6;8:65. PMID: 17341312
Jia Z, Xu S. Mapping quantitative trait loci for expression abundance. Genetics 2007 May;176(1):611-23. PMID: 17339210
Talavera D, Vogel C, Orozco M, Teichmann SA et al. The (in)dependence of alternative splicing and gene duplication. PLoS Comput Biol 2007 Mar 2;3(3):e33. PMID: 17335345
O'Shaughnessy PJ, Abel M, Charlton HM, Hu B et al. Altered expression of genes involved in regulation of vitamin A metabolism, solute transportation, and cytoskeletal function in the androgen-insensitive tfm mouse testis. Endocrinology 2007 Jun;148(6):2914-24. PMID: 17332066
Crasto CJ, Masiar P, Miller PL. NeuroExtract: facilitating neuroscience-oriented retrieval from broadly-focused bioscience databases using text-based query mediation. J Am Med Inform Assoc 2007 May-Jun;14(3):355-60. PMID: 17329721
Buckanovich RJ, Sasaroli D, O'Brien-Jenkins A, Botbyl J et al. Tumor vascular proteins as biomarkers in ovarian cancer. J Clin Oncol 2007 Mar 1;25(7):852-61. PMID: 17327606
Platts AE, Dix DJ, Chemes HE, Thompson KE et al. Success and failure in human spermatogenesis as revealed by teratozoospermic RNAs. Hum Mol Genet 2007 Apr 1;16(7):763-73. PMID: 17327269
Ergün A, Lawrence CA, Kohanski MA, Brennan TA et al. A network biology approach to prostate cancer. Mol Syst Biol 2007;3:82. PMID: 17299418
Murray DB, Beckmann M, Kitano H. Regulation of yeast oscillatory dynamics. Proc Natl Acad Sci U S A 2007 Feb 13;104(7):2241-6. PMID: 17284613
Turley RS, Finger EC, Hempel N, How T et al. The type III transforming growth factor-beta receptor as a novel tumor suppressor gene in prostate cancer. Cancer Res 2007 Feb 1;67(3):1090-8. PMID: 17283142
Duarte NC, Becker SA, Jamshidi N, Thiele I et al. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A 2007 Feb 6;104(6):1777-82. PMID: 17267599
Bonig H, Priestley GV, Oehler V, Papayannopoulou T. Hematopoietic progenitor cells (HPC) from mobilized peripheral blood display enhanced migration and marrow homing compared to steady-state bone marrow HPC. Exp Hematol 2007 Feb;35(2):326-34. PMID: 17258081
Cheng CW, Bielby H, Licence D, Smith SK et al. Quantitative cellular and molecular analysis of the effect of progesterone withdrawal in a murine model of decidualization. Biol Reprod 2007 May;76(5):871-83. PMID: 17251523
Butte AJ, Chen R. Finding disease-related genomic experiments within an international repository: first steps in translational bioinformatics. AMIA Annu Symp Proc 2006;:106-10. PMID: 17238312
Choi JK, Kim SC. Environmental effects on gene expression phenotype have regional biases in the human genome. Genetics 2007 Apr;175(4):1607-13. PMID: 17237506
Shi Y, Mitchell T, Bar-Joseph Z. Inferring pairwise regulatory relationships from multiple time series datasets. Bioinformatics 2007 Mar 15;23(6):755-63. PMID: 17237067
Yoneya T, Mamitsuka H. A hidden Markov model-based approach for identifying timing differences in gene expression under different experimental factors. Bioinformatics 2007 Apr 1;23(7):842-9. PMID: 17237042
Stalteri MA, Harrison AP. Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips. BMC Bioinformatics 2007 Jan 15;8:13. PMID: 17224057
Riz I, Akimov SS, Eaker SS, Baxter KK et al. TLX1/HOX11-induced hematopoietic differentiation blockade. Oncogene 2007 Jun 14;26(28):4115-23. PMID: 17213805
Chong A, Zhang Z, Choi KP, Choudhary V et al. Promoter profiling and coexpression data analysis identifies 24 novel genes that are coregulated with AMPA receptor genes, GRIAs. Genomics 2007 Mar;89(3):378-84. PMID: 17208408
Brass DM, Tomfohr J, Yang IV, Schwartz DA. Using mouse genomics to understand idiopathic interstitial fibrosis. Proc Am Thorac Soc 2007 Jan;4(1):92-100. PMID: 17202297
Studer SM, Kaminski N. Towards systems biology of human pulmonary fibrosis. Proc Am Thorac Soc 2007 Jan;4(1):85-91. PMID: 17202296
Kolpakov F, Poroikov V, Sharipov R, Kondrakhin Y et al. CYCLONET--an integrated database on cell cycle regulation and carcinogenesis. Nucleic Acids Res 2007 Jan;35(Database issue):D550-6. PMID: 17202170
Hurt EM, Thomas SB, Peng B, Farrar WL. Integrated molecular profiling of SOD2 expression in multiple myeloma. Blood 2007 May 1;109(9):3953-62. PMID: 17192397
Chari R, Lockwood WW, Coe BP, Chu A et al. SIGMA: a system for integrative genomic microarray analysis of cancer genomes. BMC Genomics 2006 Dec 27;7:324. PMID: 17192189
Ramsey VG, Doherty JM, Chen CC, Stappenbeck TS et al. The maturation of mucus-secreting gastric epithelial progenitors into digestive-enzyme secreting zymogenic cells requires Mist1. Development 2007 Jan;134(1):211-22. PMID: 17164426
McRae AF, Matigian NA, Vadlamudi L, Mulley JC et al. Replicated effects of sex and genotype on gene expression in human lymphoblastoid cell lines. Hum Mol Genet 2007 Feb 15;16(4):364-73. PMID: 17164263
Bosco EE, Wang Y, Xu H, Zilfou JT et al. The retinoblastoma tumor suppressor modifies the therapeutic response of breast cancer. J Clin Invest 2007 Jan;117(1):218-28. PMID: 17160137
Carey VJ, Morgan M, Falcon S, Lazarus R et al. GGtools: analysis of genetics of gene expression in bioconductor. Bioinformatics 2007 Feb 15;23(4):522-3. PMID: 17158513
Liu D, Brockman JM, Dass B, Hutchins LN et al. Systematic variation in mRNA 3'-processing signals during mouse spermatogenesis. Nucleic Acids Res 2007;35(1):234-46. PMID: 17158511
Zapala MA, Schork NJ. Multivariate regression analysis of distance matrices for testing associations between gene expression patterns and related variables. Proc Natl Acad Sci U S A 2006 Dec 19;103(51):19430-5. PMID: 17146048
Nguyen LN, Holdren MS, Nguyen AP, Furuya MH et al. Sorting nexin 1 down-regulation promotes colon tumorigenesis. Clin Cancer Res 2006 Dec 1;12(23):6952-9. PMID: 17145813
Forton JT, Udalova IA, Campino S, Rockett KA et al. Localization of a long-range cis-regulatory element of IL13 by allelic transcript ratio mapping. Genome Res 2007 Jan;17(1):82-7. PMID: 17135570
Saxena V, Orgill D, Kohane I. Absolute enrichment: gene set enrichment analysis for homeostatic systems. Nucleic Acids Res 2006;34(22):e151. PMID: 17130162
Jeffery IB, Madden SF, McGettigan PA, Perrière G et al. Integrating transcription factor binding site information with gene expression datasets. Bioinformatics 2007 Feb 1;23(3):298-305. PMID: 17127681
Sternlicht MD, Dunning AM, Moore DH, Pharoah PD et al. Prognostic value of PAI1 in invasive breast cancer: evidence that tumor-specific factors are more important than genetic variation in regulating PAI1 expression. Cancer Epidemiol Biomarkers Prev 2006 Nov;15(11):2107-14. PMID: 17119035
Kel A, Voss N, Jauregui R, Kel-Margoulis O et al. Beyond microarrays: find key transcription factors controlling signal transduction pathways. BMC Bioinformatics 2006 Sep 6;7 Suppl 2:S13. PMID: 17118134
DeVoss J, Hou Y, Johannes K, Lu W et al. Spontaneous autoimmunity prevented by thymic expression of a single self-antigen. J Exp Med 2006 Nov 27;203(12):2727-35. PMID: 17116738
Kim YC, Jung YC, Xuan Z, Dong H et al. Pan-genome isolation of low abundance transcripts using SAGE tag. FEBS Lett 2006 Dec 11;580(28-29):6721-9. PMID: 17113583
Pujana MA, Ruiz A, Badenas C, Puig-Butille JA et al. Molecular characterization of a t(9;12)(p21;q13) balanced chromosome translocation in combination with integrative genomics analysis identifies C9orf14 as a candidate tumor-suppressor. Genes Chromosomes Cancer 2007 Feb;46(2):155-62. PMID: 17099875
Bao L, Zhou M, Wu L, Lu L et al. PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. Nucleic Acids Res 2007 Jan;35(Database issue):D51-4. PMID: 17099235
Kopitar-Jerala N. The role of cystatins in cells of the immune system. FEBS Lett 2006 Nov 27;580(27):6295-301. PMID: 17098233
Balko JM, Potti A, Saunders C, Stromberg A et al. Gene expression patterns that predict sensitivity to epidermal growth factor receptor tyrosine kinase inhibitors in lung cancer cell lines and human lung tumors. BMC Genomics 2006 Nov 10;7:289. PMID: 17096850
Pan F, Chiu CH, Pulapura S, Mehan MR et al. Gene Aging Nexus: a web database and data mining platform for microarray data on aging. Nucleic Acids Res 2007 Jan;35(Database issue):D756-9. PMID: 17090592
Liu F, Park PJ, Lai W, Maher E et al. A genome-wide screen reveals functional gene clusters in the cancer genome and identifies EphA2 as a mitogen in glioblastoma. Cancer Res 2006 Nov 15;66(22):10815-23. PMID: 17090523
Romualdi C, De Pittà C, Tombolan L, Bortoluzzi S et al. Defining the gene expression signature of rhabdomyosarcoma by meta-analysis. BMC Genomics 2006 Nov 7;7:287. PMID: 17090319
Campagne F, Skrabanek L. Mining expressed sequence tags identifies cancer markers of clinical interest. BMC Bioinformatics 2006 Nov 1;7:481. PMID: 17078886
Thompson DM, Parker R. Cytoplasmic decay of intergenic transcripts in Saccharomyces cerevisiae. Mol Cell Biol 2007 Jan;27(1):92-101. PMID: 17074811
Farkas IJ, Wu C, Chennubhotla C, Bahar I et al. Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae. BMC Bioinformatics 2006 Oct 28;7:478. PMID: 17069658
Cheung TH, Kwan YL, Hamady M, Liu X. Unraveling transcriptional control and cis-regulatory codes using the software suite GeneACT. Genome Biol 2006;7(10):R97. PMID: 17064417
Li S, Li YH, Wei T, Su EW et al. Too much data, but little inter-changeability: a lesson learned from mining public data on tissue specificity of gene expression. Biol Direct 2006 Oct 25;1:33. PMID: 17064414
Ziober AF, Patel KR, Alawi F, Gimotty P et al. Identification of a gene signature for rapid screening of oral squamous cell carcinoma. Clin Cancer Res 2006 Oct 15;12(20 Pt 1):5960-71. PMID: 17062667
Barth AS, Kuner R, Buness A, Ruschhaupt M et al. Identification of a common gene expression signature in dilated cardiomyopathy across independent microarray studies. J Am Coll Cardiol 2006 Oct 17;48(8):1610-7. PMID: 17045896
Levine DM, Haynor DR, Castle JC, Stepaniants SB et al. Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways. Genome Biol 2006;7(10):R93. PMID: 17044931
Agarwal S, Harada J, Schreifels J, Lech P et al. Isolation, characterization, and genetic complementation of a cellular mutant resistant to retroviral infection. Proc Natl Acad Sci U S A 2006 Oct 24;103(43):15933-8. PMID: 17043244
Yoon S, Yang Y, Choi J, Seong J. Large scale data mining approach for gene-specific standardization of microarray gene expression data. Bioinformatics 2006 Dec 1;22(23):2898-904. PMID: 17032674
Wormald S, Hilton DJ, Smyth GK, Speed TP. Proximal genomic localization of STAT1 binding and regulated transcriptional activity. BMC Genomics 2006 Oct 11;7:254. PMID: 17032459
Mendoza G, Pemberton TJ, Lee K, Scarel-Caminaga R et al. A new locus for autosomal dominant amelogenesis imperfecta on chromosome 8q24.3. Hum Genet 2007 Jan;120(5):653-62. PMID: 17024372
Fonseca R, Van Wier SA, Chng WJ, Ketterling R et al. Prognostic value of chromosome 1q21 gain by fluorescent in situ hybridization and increase CKS1B expression in myeloma. Leukemia 2006 Nov;20(11):2034-40. PMID: 17024118
Hever A, Roth RB, Hevezi PA, Lee J et al. Molecular characterization of human adenomyosis. Mol Hum Reprod 2006 Dec;12(12):737-48. PMID: 17020905
Carroll JS, Meyer CA, Song J, Li W et al. Genome-wide analysis of estrogen receptor binding sites. Nat Genet 2006 Nov;38(11):1289-97. PMID: 17013392
Huttenhower C, Hibbs M, Myers C, Troyanskaya OG. A scalable method for integration and functional analysis of multiple microarray datasets. Bioinformatics 2006 Dec 1;22(23):2890-7. PMID: 17005538
Paananen J, Storvik M, Wong G. CROPPER: a metagene creator resource for cross-platform and cross-species compendium studies. BMC Bioinformatics 2006 Sep 22;7:418. PMID: 16995941
Harvatine KJ, Bauman DE. SREBP1 and thyroid hormone responsive spot 14 (S14) are involved in the regulation of bovine mammary lipid synthesis during diet-induced milk fat depression and treatment with CLA. J Nutr 2006 Oct;136(10):2468-74. PMID: 16988111
Dolan ME, Holden CC, Beard MK, Bult CJ. Genomes as geography: using GIS technology to build interactive genome feature maps. BMC Bioinformatics 2006 Sep 19;7:416. PMID: 16984652
Sahni J, Nelson B, Scharenberg AM. SLC41A2 encodes a plasma-membrane Mg2+ transporter. Biochem J 2007 Jan 15;401(2):505-13. PMID: 16984228
Stahlman MT, Besnard V, Wert SE, Weaver TE et al. Expression of ABCA3 in developing lung and other tissues. J Histochem Cytochem 2007 Jan;55(1):71-83. PMID: 16982851
Sutherland HG, Newton K, Brownstein DG, Holmes MC et al. Disruption of Ledgf/Psip1 results in perinatal mortality and homeotic skeletal transformations. Mol Cell Biol 2006 Oct;26(19):7201-10. PMID: 16980622
Mullins JJ, Mullins LJ, Dunbar DR, Brammar WJ et al. Identification of a human ortholog of the mouse Dcpp gene locus, encoding a novel member of the CSP-1/Dcpp salivary protein family. Physiol Genomics 2006 Dec 13;28(1):129-40. PMID: 16954406
Irizarry RA, Cope LM, Wu Z. Feature-level exploration of a published Affymetrix GeneChip control dataset. Genome Biol 2006;7(8):404. PMID: 16953902
Vinther J, Hedegaard MM, Gardner PP, Andersen JS et al. Identification of miRNA targets with stable isotope labeling by amino acids in cell culture. Nucleic Acids Res 2006;34(16):e107. PMID: 16945957
Lohoff FW, Dahl JP, Ferraro TN, Arnold SE et al. Variations in the vesicular monoamine transporter 1 gene (VMAT1/SLC18A1) are associated with bipolar i disorder. Neuropsychopharmacology 2006 Dec;31(12):2739-47. PMID: 16936705
Moalic Y, Blanchard Y, Félix H, Jestin A. Porcine endogenous retrovirus integration sites in the human genome: features in common with those of murine leukemia virus. J Virol 2006 Nov;80(22):10980-8. PMID: 16928752
Radde N, Gebert J, Forst CV. Systematic component selection for gene-network refinement. Bioinformatics 2006 Nov 1;22(21):2674-80. PMID: 16926218
Wang XS, Zhang Z, Wang HC, Cai JL et al. Rapid identification of UCA1 as a very sensitive and specific unique marker for human bladder carcinoma. Clin Cancer Res 2006 Aug 15;12(16):4851-8. PMID: 16914571
Ge X, Wu Q, Jung YC, Chen J et al. A large quantity of novel human antisense transcripts detected by LongSAGE. Bioinformatics 2006 Oct 15;22(20):2475-9. PMID: 16895931
Hung MS, Avner P, Rogner UC. Identification of the transcription factor ARNTL2 as a candidate gene for the type 1 diabetes locus Idd6. Hum Mol Genet 2006 Sep 15;15(18):2732-42. PMID: 16893914
Georgieva L, Moskvina V, Peirce T, Norton N et al. Convergent evidence that oligodendrocyte lineage transcription factor 2 (OLIG2) and interacting genes influence susceptibility to schizophrenia. Proc Natl Acad Sci U S A 2006 Aug 15;103(33):12469-74. PMID: 16891421
Itman C, Mendis S, Barakat B, Loveland KL. All in the family: TGF-beta family action in testis development. Reproduction 2006 Aug;132(2):233-46. PMID: 16885532
Jeffery IB, Higgins DG, Culhane AC. Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data. BMC Bioinformatics 2006 Jul 26;7:359. PMID: 16872483
Lu X, Zhang X. The effect of GeneChip gene definitions on the microarray study of cancers. Bioessays 2006 Jul;28(7):739-46. PMID: 16850407
Wang YP, Liang L, Han BC, Quan Y et al. GEPS: the Gene Expression Pattern Scanner. Nucleic Acids Res 2006 Jul 1;34(Web Server issue):W492-7. PMID: 16845057
Rossi S, Masotti D, Nardini C, Bonora E et al. TOM: a web-based integrated approach for identification of candidate disease genes. Nucleic Acids Res 2006 Jul 1;34(Web Server issue):W285-92. PMID: 16845011
Papana A, Ishwaran H. CART variance stabilization and regularization for high-throughput genomic data. Bioinformatics 2006 Sep 15;22(18):2254-61. PMID: 16844707
Siddiqui AS, Delaney AD, Schnerch A, Griffith OL et al. Sequence biases in large scale gene expression profiling data. Nucleic Acids Res 2006 Jul 13;34(12):e83. PMID: 16840527
Nam D, Kim SB, Kim SK, Yang S et al. ADGO: analysis of differentially expressed gene sets using composite GO annotation. Bioinformatics 2006 Sep 15;22(18):2249-53. PMID: 16837524
Kim SY, Kim Y. Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data. BMC Bioinformatics 2006 Jul 4;7:330. PMID: 16817975
Koli K, Myllärniemi M, Vuorinen K, Salmenkivi K et al. Bone morphogenetic protein-4 inhibitor gremlin is overexpressed in idiopathic pulmonary fibrosis. Am J Pathol 2006 Jul;169(1):61-71. PMID: 16816361
Laule O, Hirsch-Hoffmann M, Hruz T, Gruissem W et al. Web-based analysis of the mouse transcriptome using Genevestigator. BMC Bioinformatics 2006 Jun 21;7:311. PMID: 16790046
Lewinski MK, Yamashita M, Emerman M, Ciuffi A et al. Retroviral DNA integration: viral and cellular determinants of target-site selection. PLoS Pathog 2006 Jun;2(6):e60. PMID: 16789841
Hong SE, Rho SH, Yeom YI, Kim do H. HCNet: a database of heart and calcium functional network. Bioinformatics 2006 Aug 15;22(16):2053-4. PMID: 16787974
Yin H, Radomska HS, Tenen DG, Glass J. Down regulation of PSA by C/EBPalpha is associated with loss of AR expression and inhibition of PSA promoter activity in the LNCaP cell line. BMC Cancer 2006 Jun 14;6:158. PMID: 16774685
Wei Z, Li H. Nonparametric pathway-based regression models for analysis of genomic data. Biostatistics 2007 Apr;8(2):265-84. PMID: 16772399
Sun M, Hurst LD, Carmichael GG, Chen J. Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcriptionand organismic complexity. Genome Res 2006 Jul;16(7):922-33. PMID: 16769979
Brown AL, Wilkinson CR, Waterman SR, Kok CH et al. Genetic regulators of myelopoiesis and leukemic signaling identified by gene profiling and linear modeling. J Leukoc Biol 2006 Aug;80(2):433-47. PMID: 16769770
Sémon M, Duret L. Evolutionary origin and maintenance of coexpressed gene clusters in mammals. Mol Biol Evol 2006 Sep;23(9):1715-23. PMID: 16757654
Elbez Y, Farkash-Amar S, Simon I. An analysis of intra array repeats: the good, the bad and the non informative. BMC Genomics 2006 Jun 5;7:136. PMID: 16753054
Wiese C, Rolletschek A, Kania G, Navarrete-Santos A et al. Signals from embryonic fibroblasts induce adult intestinal epithelial cells to form nestin-positive cells with proliferation and multilineage differentiation capacity in vitro. Stem Cells 2006 Sep;24(9):2085-97. PMID: 16741226
Kaminski N, Rosas IO. Gene expression profiling as a window into idiopathic pulmonary fibrosis pathogenesis: can we identify the right target genes? Proc Am Thorac Soc 2006 Jun;3(4):339-44. PMID: 16738198
Ponomarev I, Maiya R, Harnett MT, Schafer GL et al. Transcriptional signatures of cellular plasticity in mice lacking the alpha1 subunit of GABAA receptors. J Neurosci 2006 May 24;26(21):5673-83. PMID: 16723524
Knowles DG, McLysaght A. High rate of recent intron gain and loss in simultaneously duplicated Arabidopsis genes. Mol Biol Evol 2006 Aug;23(8):1548-57. PMID: 16720694
Legendre M, Ritchie W, Lopez F, Gautheret D. Differential repression of alternative transcripts: a screen for miRNA targets. PLoS Comput Biol 2006 May;2(5):e43. PMID: 16699595
Montano M, Rarick M, Sebastiani P, Brinkmann P et al. Gene-expression profiling of HIV-1 infection and perinatal transmission in Botswana. Genes Immun 2006 Jun;7(4):298-309. PMID: 16691187
Calcagno AM, Ludwig JA, Fostel JM, Gottesman MM et al. Comparison of drug transporter levels in normal colon, colon cancer, and Caco-2 cells: impact on drug disposition and discovery. Mol Pharm 2006 Jan-Feb;3(1):87-93. PMID: 16686373
Malcomber ST, Kellogg EA. Evolution of unisexual flowers in grasses (Poaceae) and the putative sex-determination gene, TASSELSEED2 (TS2). New Phytol 2006;170(4):885-99. PMID: 16684246
Frith MC, Forrest AR, Nourbakhsh E, Pang KC et al. The abundance of short proteins in the mammalian proteome. PLoS Genet 2006 Apr;2(4):e52. PMID: 16683031
Khan RL, Gonye GE, Gao G, Schwaber JS. A universal reference sample derived from clone vector for improved detection of differential gene expression. BMC Genomics 2006 May 5;7:109. PMID: 16677381
Radmacher MD, Marcucci G, Ruppert AS, Mrózek K et al. Independent confirmation of a prognostic gene-expression signature in adult acute myeloid leukemia with a normal karyotype: a Cancer and Leukemia Group B study. Blood 2006 Sep 1;108(5):1677-83. PMID: 16670265
Dunne J, Cullmann C, Ritter M, Soria NM et al. siRNA-mediated AML1/MTG8 depletion affects differentiation and proliferation-associated gene expression in t(8;21)-positive cell lines and primary AML blasts. Oncogene 2006 Oct 5;25(45):6067-78. PMID: 16652140
Grasberger H, Refetoff S. Identification of the maturation factor for dual oxidase. Evolution of an eukaryotic operon equivalent. J Biol Chem 2006 Jul 7;281(27):18269-72. PMID: 16651268
Yu H, Jiang H, Zhou Q, Yang J et al. Origination and evolution of a human-specific transmembrane protein gene, c1orf37-dup. Hum Mol Genet 2006 Jun 1;15(11):1870-5. PMID: 16644869
Soupene E, Kuypers FA. Identification of an erythroid ATP-dependent aminophospholipid transporter. Br J Haematol 2006 May;133(4):436-8. PMID: 16643453
Graham RR, Kozyrev SV, Baechler EC, Reddy MV et al. A common haplotype of interferon regulatory factor 5 (IRF5) regulates splicing and expression and is associated with increased risk of systemic lupus erythematosus. Nat Genet 2006 May;38(5):550-5. PMID: 16642019
Daniel VC, Peacock CD, Watkins DN. Developmental signalling pathways in lung cancer. Respirology 2006 May;11(3):234-40. PMID: 16635080
Boyer LA, Plath K, Zeitlinger J, Brambrink T et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 2006 May 18;441(7091):349-53. PMID: 16625203
Albers CJ, Jansen RC, Kok J, Kuipers OP et al. SIMAGE: simulation of DNA-microarray gene expression data. BMC Bioinformatics 2006 Apr 13;7:205. PMID: 16613602
Yuan Z, Tie A, Tarnopolsky M, Bakovic M. Genomic organization, promoter activity, and expression of the human choline transporter-like protein 1. Physiol Genomics 2006 Jun 16;26(1):76-90. PMID: 16609143
van Haaften RI, Schroen B, Janssen BJ, van Erk A et al. Biologically relevant effects of mRNA amplification on gene expression profiles. BMC Bioinformatics 2006 Apr 11;7:200. PMID: 16608515
Yu X, Griffith WC, Hanspers K, Dillman JF 3rd et al. A system-based approach to interpret dose- and time-dependent microarray data: quantitative integration of gene ontology analysis for risk assessment. Toxicol Sci 2006 Aug;92(2):560-77. PMID: 16601082
Ruzanov P, Jones SJ. An interactive tool for visualization of relationships between gene expression profiles. BMC Bioinformatics 2006 Apr 6;7:193. PMID: 16600045
Saarela J, Kallio SP, Chen D, Montpetit A et al. PRKCA and multiple sclerosis: association in two independent populations. PLoS Genet 2006 Mar;2(3):e42. PMID: 16596167
Calvo S, Jain M, Xie X, Sheth SA et al. Systematic identification of human mitochondrial disease genes through integrative genomics. Nat Genet 2006 May;38(5):576-82. PMID: 16582907
Hoen DR, Park KC, Elrouby N, Yu Z et al. Transposon-mediated expansion and diversification of a family of ULP-like genes. Mol Biol Evol 2006 Jun;23(6):1254-68. PMID: 16581939
Missirlis F, Holmberg S, Georgieva T, Dunkov BC et al. Characterization of mitochondrial ferritin in Drosophila. Proc Natl Acad Sci U S A 2006 Apr 11;103(15):5893-8. PMID: 16571656
Robertson KP, Smith CJ, Gough AM, Rocha ER. Characterization of Bacteroides fragilis hemolysins and regulation and synergistic interactions of HlyA and HlyB. Infect Immun 2006 Apr;74(4):2304-16. PMID: 16552061
Gao G, Zhong Y, Guo A, Zhu Q et al. DRTF: a database of rice transcription factors. Bioinformatics 2006 May 15;22(10):1286-7. PMID: 16551659
Byrnes JK, Morris GP, Li WH. Reorganization of adjacent gene relationships in yeast genomes by whole-genome duplication and gene deletion. Mol Biol Evol 2006 Jun;23(6):1136-43. PMID: 16527865
Inaoka H, Fukuoka Y, Kohane IS. Lower expression of genes near microRNA in C. elegans germline. BMC Bioinformatics 2006 Mar 6;7:112. PMID: 16519803
Pesaresi P, Masiero S, Eubel H, Braun HP et al. Nuclear photosynthetic gene expression is synergistically modulated by rates of protein synthesis in chloroplasts and mitochondria. Plant Cell 2006 Apr;18(4):970-91. PMID: 16517761
Gupta V, Parisi M, Sturgill D, Nuttall R et al. Global analysis of X-chromosome dosage compensation. J Biol 2006;5(1):3. PMID: 16507155
Page GP, Edwards JW, Gadbury GL, Yelisetti P et al. The PowerAtlas: a power and sample size atlas for microarray experimental design and research. BMC Bioinformatics 2006 Feb 22;7:84. PMID: 16504070
Bourquin JP, Subramanian A, Langebrake C, Reinhardt D et al. Identification of distinct molecular phenotypes in acute megakaryoblastic leukemia by gene expression profiling. Proc Natl Acad Sci U S A 2006 Feb 28;103(9):3339-44. PMID: 16492768
Sood P, Krek A, Zavolan M, Macino G et al. Cell-type-specific signatures of microRNAs on target mRNA expression. Proc Natl Acad Sci U S A 2006 Feb 21;103(8):2746-51. PMID: 16477010
Xiong H. Non-linear tests for identifying differentially expressed genes or genetic networks. Bioinformatics 2006 Apr 15;22(8):919-23. PMID: 16473873
Borghei A, Ouyang YB, Westmuckett AD, Marcello MR et al. Targeted disruption of tyrosylprotein sulfotransferase-2, an enzyme that catalyzes post-translational protein tyrosine O-sulfation, causes male infertility. J Biol Chem 2006 Apr 7;281(14):9423-31. PMID: 16469738
Murdoch S, Djuric U, Mazhar B, Seoud M et al. Mutations in NALP7 cause recurrent hydatidiform moles and reproductive wastage in humans. Nat Genet 2006 Mar;38(3):300-2. PMID: 16462743
McClintick JN, Edenberg HJ. Effects of filtering by Present call on analysis of microarray experiments. BMC Bioinformatics 2006 Jan 31;7:49. PMID: 16448562
Seo J, Gordish-Dressman H, Hoffman EP. An interactive power analysis tool for microarray hypothesis testing and generation. Bioinformatics 2006 Apr 1;22(7):808-14. PMID: 16418236
Price MN, Arkin AP, Alm EJ. OpWise: operons aid the identification of differentially expressed genes in bacterial microarray experiments. BMC Bioinformatics 2006 Jan 13;7:19. PMID: 16412220
Norris AW, Kahn CR. Analysis of gene expression in pathophysiological states: balancing false discovery and false negative rates. Proc Natl Acad Sci U S A 2006 Jan 17;103(3):649-53. PMID: 16407153
Butte AJ, Kohane IS. Creation and implications of a phenome-genome network. Nat Biotechnol 2006 Jan;24(1):55-62. PMID: 16404398
Wang X, Zhao H, Xu Q, Jin W et al. HPtaa database-potential target genes for clinical diagnosis and immunotherapy of human carcinoma. Nucleic Acids Res 2006 Jan 1;34(Database issue):D607-12. PMID: 16381942
Platts AE, Moldenhauer JS, Fayz B, Wang D et al. LARaLink 2.0: a comprehensive aid to basic and clinical cytogenetic research. Genet Test 2005 Winter;9(4):334-41. PMID: 16379548
Newkirk HL, Knoll JH, Rogan PK. Distortion of quantitative genomic and expression hybridization by Cot-1 DNA: mitigation of this effect. Nucleic Acids Res 2005 Dec 14;33(22):e191. PMID: 16356923
Crawford GE, Holt IE, Whittle J, Webb BD et al. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res 2006 Jan;16(1):123-31. PMID: 16344561
Hothorn T, Bühlmann P, Dudoit S, Molinaro A et al. Survival ensembles. Biostatistics 2006 Jul;7(3):355-73. PMID: 16344280
Argraves GL, Jani S, Barth JL, Argraves WS. ArrayQuest: a web resource for the analysis of DNA microarray data. BMC Bioinformatics 2005 Dec 1;6:287. PMID: 16321157
Chen Q, Qian K, Yan C. Cloning of cDNAs with PDCD2(C) domain and their expressions during apoptosis of HEK293T cells. Mol Cell Biochem 2005 Dec;280(1-2):185-91. PMID: 16311922
Dai M, Wang P, Boyd AD, Kostov G et al. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res 2005 Nov 10;33(20):e175. PMID: 16284200
Li H, Zhan M. Systematic intervention of transcription for identifying network response to disease and cellular phenotypes. Bioinformatics 2006 Jan 1;22(1):96-102. PMID: 16278241
Balagopal P, Olney R, Darmaun D, Mougey E et al. Oxandrolone enhances skeletal muscle myosin synthesis and alters global gene expression profile in Duchenne muscular dystrophy. Am J Physiol Endocrinol Metab 2006 Mar;290(3):E530-9. PMID: 16263771
Van Winkle LJ, Tesch JK, Shah A, Campione AL. System B0,+ amino acid transport regulates the penetration stage of blastocyst implantation with possible long-term developmental consequences through adulthood. Hum Reprod Update 2006 Mar-Apr;12(2):145-57. PMID: 16251251
Pritlove DC, Gu M, Boyd CA, Randeva HS et al. Novel placental expression of 2,3-bisphosphoglycerate mutase. Placenta 2006 Aug;27(8):924-7. PMID: 16246416
Chiu RW, Chan CW, Zhong XY, Lapaire O et al. Fetal rhesus D mRNA is not detectable in maternal plasma. Clin Chem 2005 Nov;51(11):2210-1. PMID: 16244308
Hughes AL. Consistent across-tissue signatures of differential gene expression in Crohn's disease. Immunogenetics 2005 Nov;57(10):709-16. PMID: 16189665
Hodanová K, Majewski J, Kublová M, Vyletal P et al. Mapping of a new candidate locus for uromodulin-associated kidney disease (UAKD) to chromosome 1q41. Kidney Int 2005 Oct;68(4):1472-82. PMID: 16164624
Wolfe CJ, Kohane IS, Butte AJ. Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. BMC Bioinformatics 2005 Sep 14;6:227. PMID: 16162296
Sczyrba A, Beckstette M, Brivanlou AH, Giegerich R et al. XenDB: full length cDNA prediction and cross species mapping in Xenopus laevis. BMC Genomics 2005 Sep 14;6:123. PMID: 16162280
Enver T, Soneji S, Joshi C, Brown J et al. Cellular differentiation hierarchies in normal and culture-adapted human embryonic stem cells. Hum Mol Genet 2005 Nov 1;14(21):3129-40. PMID: 16159889
Miller LD, Smeds J, George J, Vega VB et al. An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci U S A 2005 Sep 20;102(38):13550-5. PMID: 16141321
Watanabe H, Nonoguchi K, Sakurai T, Masuda T et al. A novel protein Depp, which is induced by progesterone in human endometrial stromal cells activates Elk-1 transcription factor. Mol Hum Reprod 2005 Jul;11(7):471-6. PMID: 16123073
Drukker M, Katchman H, Katz G, Even-Tov Friedman S et al. Human embryonic stem cells and their differentiated derivatives are less susceptible to immune rejection than adult cells. Stem Cells 2006 Feb;24(2):221-9. PMID: 16109762
Dybbs M, Ngai J, Kaplan JM. Using microarrays to facilitate positional cloning: identification of tomosyn as an inhibitor of neurosecretion. PLoS Genet 2005 Jul;1(1):6-16. PMID: 16103915
Dawson K, Rodriguez RL, Malyj W. Sample phenotype clusters in high-density oligonucleotide microarray data sets are revealed using Isomap, a nonlinear algorithm. BMC Bioinformatics 2005 Aug 2;6:195. PMID: 16076401
Fisher JS, Ju JS, Oppelt PJ, Smith JL et al. Muscle contractions, AICAR, and insulin cause phosphorylation of an AMPK-related kinase. Am J Physiol Endocrinol Metab 2005 Dec;289(6):E986-92. PMID: 16030062
Garge NR, Page GP, Sprague AP, Gorman BS et al. Reproducible clusters from microarray research: whither? BMC Bioinformatics 2005 Jul 15;6 Suppl 2:S10. PMID: 16026595
Stangeland B, Nestestog R, Grini PE, Skrbo N et al. Molecular analysis of Arabidopsis endosperm and embryo promoter trap lines: reporter-gene expression can result from T-DNA insertions in antisense orientation, in introns and in intergenic regions, in addition to sense insertion at the 5' end of genes. J Exp Bot 2005 Sep;56(419):2495-505. PMID: 16014362
Qian J, Esumi N, Chen Y, Wang Q et al. Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation. Nucleic Acids Res 2005;33(11):3479-91. PMID: 15967807
Jen CH, Michalopoulos I, Westhead DR, Meyer P. Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation. Genome Biol 2005;6(6):R51. PMID: 15960803
Reid JF, Lusa L, De Cecco L, Coradini D et al. Limits of predictive models using microarray data for breast cancer clinical treatment outcome. J Natl Cancer Inst 2005 Jun 15;97(12):927-30. PMID: 15956654
Kim SY, Volsky DJ. PAGE: parametric analysis of gene set enrichment. BMC Bioinformatics 2005 Jun 8;6:144. PMID: 15941488
Persson S, Wei H, Milne J, Page GP et al. Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proc Natl Acad Sci U S A 2005 Jun 14;102(24):8633-8. PMID: 15932943
Hu J, Zou F, Wright FA. Practical FDR-based sample size calculations in microarray experiments. Bioinformatics 2005 Aug 1;21(15):3264-72. PMID: 15932903
Blaveri E, Simko JP, Korkola JE, Brewer JL et al. Bladder cancer outcome and subtype classification by gene expression. Clin Cancer Res 2005 Jun 1;11(11):4044-55. PMID: 15930339
Jiang T, Keating AE. AVID: an integrative framework for discovering functional relationships among proteins. BMC Bioinformatics 2005 Jun 1;6:136. PMID: 15929793
Kliman RM, Bernal CA. Unusual usage of AGG and TTG codons in humans and their viruses. Gene 2005 Jun 6;352:92-9. PMID: 15922516
Larsson O, Wahlestedt C, Timmons JA. Considerations when using the significance analysis of microarrays (SAM) algorithm. BMC Bioinformatics 2005 May 29;6:129. PMID: 15921534
Vasta V, Sonnenburg WK, Yan C, Soderling SH et al. Identification of a new variant of PDE1A calmodulin-stimulated cyclic nucleotide phosphodiesterase expressed in mouse sperm. Biol Reprod 2005 Oct;73(4):598-609. PMID: 15901640
Chen SH, Babichev Y, Rodrigues N, Voskas D et al. Gene expression analysis of Tek/Tie2 signaling. Physiol Genomics 2005 Jul 14;22(2):257-67. PMID: 15899944
Wang H, He X, Band M, Wilson C et al. A study of inter-lab and inter-platform agreement of DNA microarray data. BMC Genomics 2005 May 11;6:71. PMID: 15888200
Park SG, Kim HJ, Min YH, Choi EC et al. Human lysyl-tRNA synthetase is secreted to trigger proinflammatory response. Proc Natl Acad Sci U S A 2005 May 3;102(18):6356-61. PMID: 15851690
Ozyildirim AM, Wistow GJ, Gao J, Wang J et al. The lacrimal gland transcriptome is an unusually rich source of rare and poorly characterized gene transcripts. Invest Ophthalmol Vis Sci 2005 May;46(5):1572-80. PMID: 15851553
Mercer SE, Ewton DZ, Deng X, Lim S et al. Mirk/Dyrk1B mediates survival during the differentiation of C2C12 myoblasts. J Biol Chem 2005 Jul 8;280(27):25788-801. PMID: 15851482
Zhou S, Liu Y, Weng J, Kong L et al. Expression profiles of mouse dendritic cell sarcoma are similar to those of hematopoietic stem cells or progenitors by clustering and principal component analyses. Biochem Biophys Res Commun 2005 May 27;331(1):194-202. PMID: 15845378
Cabusora L, Sutton E, Fulmer A, Forst CV. Differential network expression during drug and stress response. Bioinformatics 2005 Jun 15;21(12):2898-905. PMID: 15840709
Bing N, Hoeschele I. Genetical genomics analysis of a yeast segregant population for transcription network inference. Genetics 2005 Jun;170(2):533-42. PMID: 15781693
Bazzini C, Vezzoli V, Sironi C, Dossena S et al. Thiazide-sensitive NaCl-cotransporter in the intestine: possible role of hydrochlorothiazide in the intestinal Ca2+ uptake. J Biol Chem 2005 May 20;280(20):19902-10. PMID: 15781471
Boyle J. Gene-Expression Omnibus integration and clustering tools in SeqExpress. Bioinformatics 2005 May 15;21(10):2550-1. PMID: 15746290
Yant SR, Wu X, Huang Y, Garrison B et al. High-resolution genome-wide mapping of transposon integration in mammals. Mol Cell Biol 2005 Mar;25(6):2085-94. PMID: 15743807
Nakai H, Wu X, Fuess S, Storm TA et al. Large-scale molecular characterization of adeno-associated virus vector integration in mouse liver. J Virol 2005 Mar;79(6):3606-14. PMID: 15731255
Adamia S, Reiman T, Crainie M, Mant MJ et al. Intronic splicing of hyaluronan synthase 1 (HAS1): a biologically relevant indicator of poor outcome in multiple myeloma. Blood 2005 Jun 15;105(12):4836-44. PMID: 15731173
Lu T, Costello CM, Croucher PJ, Häsler R et al. Can Zipf's law be adapted to normalize microarrays? BMC Bioinformatics 2005 Feb 23;6:37. PMID: 15727680
Scott MS, Perkins T, Bunnell S, Pepin F et al. Identifying regulatory subnetworks for a set of genes. Mol Cell Proteomics 2005 May;4(5):683-92. PMID: 15722371
Michiels S, Koscielny S, Hill C. Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet 2005 Feb 5-11;365(9458):488-92. PMID: 15705458
Singh AV, Knudsen KB, Knudsen TB. Computational systems analysis of developmental toxicity: design, development and implementation of a Birth Defects Systems Manager (BDSM). Reprod Toxicol 2005 Jan-Feb;19(3):421-39. PMID: 15686875
Vinterbo SA, Kim EY, Ohno-Machado L. Small, fuzzy and interpretable gene expression based classifiers. Bioinformatics 2005 May 1;21(9):1964-70. PMID: 15661797
Brockington M, Torelli S, Prandini P, Boito C et al. Localization and functional analysis of the LARGE family of glycosyltransferases: significance for muscular dystrophy. Hum Mol Genet 2005 Mar 1;14(5):657-65. PMID: 15661757
Staswick PE, Serban B, Rowe M, Tiryaki I et al. Characterization of an Arabidopsis enzyme family that conjugates amino acids to indole-3-acetic acid. Plant Cell 2005 Feb;17(2):616-27. PMID: 15659623
Sengoelge G, Luo W, Fine D, Perschl AM et al. A SAGE-based comparison between glomerular and aortic endothelial cells. Am J Physiol Renal Physiol 2005 Jun;288(6):F1290-300. PMID: 15657302
Zhou XJ, Kao MC, Huang H, Wong A et al. Functional annotation and network reconstruction through cross-platform integration of microarray data. Nat Biotechnol 2005 Feb;23(2):238-43. PMID: 15654329
Shen D, He J, Chang HR. In silico identification of breast cancer genes by combined multiple high throughput analyses. Int J Mol Med 2005 Feb;15(2):205-12. PMID: 15647832
Tanino M, Debily MA, Tamura T, Hishiki T et al. The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms. Nucleic Acids Res 2005 Jan 1;33(Database issue):D567-72. PMID: 15608263
Sémon M, Mouchiroud D, Duret L. Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance. Hum Mol Genet 2005 Feb 1;14(3):421-7. PMID: 15590696
Panepucci RA, Siufi JL, Silva WA Jr, Proto-Siquiera R et al. Comparison of gene expression of umbilical cord vein and bone marrow-derived mesenchymal stem cells. Stem Cells 2004;22(7):1263-78. PMID: 15579645
Rico-Bautista E, Greenhalgh CJ, Tollet-Egnell P, Hilton DJ et al. Suppressor of cytokine signaling-2 deficiency induces molecular and metabolic changes that partially overlap with growth hormone-dependent effects. Mol Endocrinol 2005 Mar;19(3):781-93. PMID: 15563548
Rodwell GE, Sonu R, Zahn JM, Lund J et al. A transcriptional profile of aging in the human kidney. PLoS Biol 2004 Dec;2(12):e427. PMID: 15562319
Shima N, Munroe RJ, Schimenti JC. The mouse genomic instability mutation chaos1 is an allele of Polq that exhibits genetic interaction with Atm. Mol Cell Biol 2004 Dec;24(23):10381-9. PMID: 15542845
Cheng KW, Lahad JP, Kuo WL, Lapuk A et al. The RAB25 small GTPase determines aggressiveness of ovarian and breast cancers. Nat Med 2004 Nov;10(11):1251-6. PMID: 15502842
Robinson SJ, Cram DJ, Lewis CT, Parkin IA. Maximizing the efficacy of SAGE analysis identifies novel transcripts in Arabidopsis. Plant Physiol 2004 Oct;136(2):3223-33. PMID: 15489285
Narezkina A, Taganov KD, Litwin S, Stoyanova R et al. Genome-wide analyses of avian sarcoma virus integration sites. J Virol 2004 Nov;78(21):11656-63. PMID: 15479807
Ott S, Hansen A, Kim SY, Miyano S. Superiority of network motifs over optimal networks and an application to the revelation of gene network evolution. Bioinformatics 2005 Jan 15;21(2):227-38. PMID: 15377501
Zerbini LF, Wang Y, Czibere A, Correa RG et al. NF-kappa B-mediated repression of growth arrest- and DNA-damage-inducible proteins 45alpha and gamma is essential for cancer cell survival. Proc Natl Acad Sci U S A 2004 Sep 14;101(37):13618-23. PMID: 15353598
Kim RD, Park PJ. Improving identification of differentially expressed genes in microarray studies using information from public databases. Genome Biol 2004;5(9):R70. PMID: 15345054
Tasheva ES, Ke A, Conrad GW. Analysis of the expression of chondroadherin in mouse ocular and non-ocular tissues. Mol Vis 2004 Aug 18;10:544-54. PMID: 15332017
Reverter A, McWilliam SM, Barris W, Dalrymple BP. A rapid method for computationally inferring transcriptome coverage and microarray sensitivity. Bioinformatics 2005 Jan 1;21(1):80-9. PMID: 15308544
Jordan IK, Mariño-Ramírez L, Wolf YI, Koonin EV. Conservation and coevolution in the scale-free human gene coexpression network. Mol Biol Evol 2004 Nov;21(11):2058-70. PMID: 15282333
Comeron JM. Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence. Genetics 2004 Jul;167(3):1293-304. PMID: 15280243
Puffenberger EG, Hu-Lince D, Parod JM, Craig DW et al. Mapping of sudden infant death with dysgenesis of the testes syndrome (SIDDT) by a SNP genome scan and identification of TSPYL loss of function. Proc Natl Acad Sci U S A 2004 Aug 10;101(32):11689-94. PMID: 15273283
Huopaniemi L, Kolmer M, Niittymäki J, Pelto-Huikko M et al. Inflammation-induced transcriptional regulation of Golgi transporters required for the synthesis of sulfo sLex glycan epitopes. Glycobiology 2004 Dec;14(12):1285-94. PMID: 15269183
Middendorf M, Kundaje A, Wiggins C, Freund Y et al. Predicting genetic regulatory response using classification. Bioinformatics 2004 Aug 4;20 Suppl 1:i232-40. PMID: 15262804
Volinia S, Evangelisti R, Francioso F, Arcelli D et al. GOAL: automated Gene Ontology analysis of expression profiles. Nucleic Acids Res 2004 Jul 1;32(Web Server issue):W492-9. PMID: 15215435
Haverty PM, Frith MC, Weng Z. CARRIE web service: automated transcriptional regulatory network inference and interactive analysis. Nucleic Acids Res 2004 Jul 1;32(Web Server issue):W213-6. PMID: 15215383
Lee HK, Hsu AK, Sajdak J, Qin J et al. Coexpression analysis of human genes across many microarray data sets. Genome Res 2004 Jun;14(6):1085-94. PMID: 15173114
Smid M, Dorssers LC. GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms. Bioinformatics 2004 Nov 1;20(16):2618-25. PMID: 15130934
Cheadle C, Cho-Chung YS, Becker KG, Vawter MP. Application of z-score transformation to Affymetrix data. Appl Bioinformatics 2003;2(4):209-17. PMID: 15130792
Laderoute KR, Calaoagan JM, Knapp M, Johnson RS. Glucose utilization is essential for hypoxia-inducible factor 1 alpha-dependent phosphorylation of c-Jun. Mol Cell Biol 2004 May;24(10):4128-37. PMID: 15121835
Challacombe JF, Rechtsteiner A, Gottardo R, Rocha LM et al. Evaluation of the host transcriptional response to human cytomegalovirus infection. Physiol Genomics 2004 Jun 17;18(1):51-62. PMID: 15069167
Vitt U, Gietzen D, Stevens K, Wingrove J et al. Identification of candidate disease genes by EST alignments, synteny, and expression and verification of Ensembl genes on rat chromosome 1q43-54. Genome Res 2004 Apr;14(4):640-50. PMID: 15060005
Oue N, Hamai Y, Mitani Y, Matsumura S et al. Gene expression profile of gastric carcinoma: identification of genes and tags potentially involved in invasion, metastasis, and carcinogenesis by serial analysis of gene expression. Cancer Res 2004 Apr 1;64(7):2397-405. PMID: 15059891
Walter-Yohrling J, Cao X, Callahan M, Weber W et al. Identification of genes expressed in malignant cells that promote invasion. Cancer Res 2003 Dec 15;63(24):8939-47. PMID: 14695211
Divina P, Forejt J. The Mouse SAGE Site: database of public mouse SAGE libraries. Nucleic Acids Res 2004 Jan 1;32(Database issue):D482-3. PMID: 14681462
Gómez-Merino FC, Brearley CA, Ornatowska M, Abdel-Haliem ME et al. AtDGK2, a novel diacylglycerol kinase from Arabidopsis thaliana, phosphorylates 1-stearoyl-2-arachidonoyl-sn-glycerol and 1,2-dioleoyl-sn-glycerol and exhibits cold-inducible gene expression. J Biol Chem 2004 Feb 27;279(9):8230-41. PMID: 14665624
Wu X, Li Y, Crise B, Burgess SM. Transcription start regions in the human genome are favored targets for MLV integration. Science 2003 Jun 13;300(5626):1749-51. PMID: 12805549
Olivero M, Ruggiero T, Coltella N, Maffe' A et al. Amplification of repeat-containing transcribed sequences (ARTS): a transcriptome fingerprinting strategy to detect functionally relevant microsatellite mutations in cancer. Nucleic Acids Res 2003 Apr 1;31(7):e33. PMID: 12655021
Hauser MA, Li YJ, Takeuchi S, Walters R et al. Genomic convergence: identifying candidate genes for Parkinson's disease by combining serial analysis of gene expression and genetic linkage. Hum Mol Genet 2003 Mar 15;12(6):671-7. PMID: 12620972

Recent PubMed publications that cite deposit of data in GEO. Please report omitted publications to geo@ncbi.nlm.nih.gov

Total number of citations: