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Open Access

Lobenhofer EK, Auman JT, Blackshear PE, Boorman GA, Bushel PR, Cunningham ML, Fostel JM, Gerrish K, Heinloth AN, Irwin RD, Malarkey DE, Merrick BA, Sieber SO, Tucker CJ, Ward SM, Wilson RE, Hurban P, Tennant RW, Paules RS.
Gene expression response in target organ and whole blood varies as a function of target organ injury phenotype.
Genome Biol. 2008;9(6):R100.
[PubMed]
Diehn M, Nardini C, Wang DS, McGovern S, Jayaraman M, Liang Y, Aldape K, Cha S, Kuo MD.
Identification of noninvasive imaging surrogates for brain tumor gene-expression modules
Proc Natl Acad Sci U S A. 2008 Apr 1;105(13):5213-8.
[PubMed]
Rescan PY, Montfort J, Rallière C, Le Cam A, Esquerré D, Hugot K.
Dynamic gene expression in fish muscle during recovery growth induced by a fasting-refeeding schedule
BMC Genomics. 2007 Nov 28;8:438.
[PubMed]
Kim PM, Korbel JO, Gerstein MB.
Positive selection at the protein network periphery: Evaluation in terms of structural constraints and cellular context
Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20274-9.
[PubMed]
Campanaro S, Picelli S, Torregrossa R, Colluto L, Ceol M, Del Prete D, D'Angelo A, Valle G, Anglani F.
Genes involved in TGFβ1-driven epithelial-mesenchymal transition of renal epithelial cells are topologically related in the human interactome map
BMC Genomics. 2007 Oct 22;8:383.
[PubMed]
Baron D, Montfort J, Houlgatte R, Fostier A, Guiguen Y.
Androgen-induced masculinization in rainbow trout results in a marked dysregulation of early gonadal gene expression profiles
BMC Genomics. 2007 Oct 4;8:357.
[PubMed]
Fry RC, Navasumrit P, Valiathan C, Svensson JP, Hogan BJ, Luo M, Bhattacharya S, Kandjanapa K, Soontararuks S, Nookabkaew S, Mahidol C, Ruchirawat M, Samson LD.
Activation of Inflammation/NF-κB Signaling in Infants Born to Arsenic-Exposed Mothers
PLoS Genet. 2007 Nov 23;3(11):e207
[PubMed]
Gagné JP, Éthier C, Gagné P, Mercier G, Bonicalzi ME, Mes-Masson AM, Droit A, Winstall E, Isabelle M, Poirier GG.
Comparative proteome analysis of human epithelial ovarian cancer
Proteome Sci. 2007 Sep 24;5:16.
[PubMed]
Das D, Clark TA, Schweitzer A, Yamamoto M, Marr H, Arribere J, Minovitsky S, Poliakov A, Dubchak I, Blume JE, Conboy JG.
A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing.
Nucleic Acids Res. 2007;35(14):4845-57.
[PubMed]
Cui Y, McBride SJ, Boyd WA, Alper S, Freedman JH.
Toxicogenomic analysis of Caenorhabditis elegans reveals novel genes and pathways involved in the resistance to cadmium toxicity
Genome Biol. 2007 Jun 25;8(6):R122
[PubMed]
Hao Y, Sood S, Triadafilopoulos G, Kim JH, Wang Z, Sahbaie P, Omary MB, Lowe AW.
Gene expression changes associated with Barrett's esophagus and Barrett's-associated adenocarcinoma cell lines after acid or bile salt exposure.
BMC Gastroenterol. 2007 Jun 27;7:24.
[PubMed]
Torres A, Storey L, Anders M, Miller RL, Bulbulian BJ, Jin J, Raghavan S, Lee J, Slade HB, Birmachu W
Immune-mediated changes in actinic keratosis following topical treatment with imiquimod 5% cream
J Transl Med. 2007 Jan 26;5:7.
[PubMed]
Seung-Jae Noh, Kyooyeol Lee, Hyojung Paik and Cheol-Goo Hur
TISA: Tissue-specific Alternative Splicing in Human and Mouse Genes
DNA Res. 2006 Oct 31;13(5):229-43.
[PubMed]
Campagne F, Skrabanek L
Mining expressed sequence tags identifies cancer markers of clinical interest
BMC Bioinformatics. 2006 Nov 1;7:481.
[PubMed]
Lim MS, Elenitoba-Johnson KSJ
Mass Spectrometry-based Proteomic Studies of Human Anaplastic Large Cell Lymphoma
Mol Cell Proteomics. 2006 Oct;5(10):1787-98.
[Pubmed]
Giusti B, Fibbi G, Margheri F, Serrati S, Rossi L, Poggi F, Lapini I, Magi A, Del Rosso A, Cinelli M, Guiducci S, Kahaleh B, Bazzichi L, Bombardieri S, Matucci-Cerinic M, Gensini GF, Del Rosso M, Abbate R.
A model of anti-angiogenesis: differential transcriptosome profiling of microvascular endothelial cells from diffuse systemic sclerosis patients
Arthritis Res Ther. 2006;8(4):R115.
[PubMed]
Beldade P, Rudd S, Gruber JD, Long AD.
A wing expressed sequence tag resource for Bicyclus anynana butterflies, an evo-devo model
BMC GENOMICS 7: Art. No. 130 MAY 31 2006
[PubMed]
Dere E, Boverhof DR, Burgoon LD, Zacharewski TR.
In vivo - in vitro toxicogenomic comparison of TCDD-elicited gene expression in Hepa1c1c7 mouse hepatoma cells and C57BL/6 hepatic tissue
BMC Genomics. 2006 Apr 12;7:80.
[PubMed]
Fernandez-Cobo M, Holland JF, Pogo BG.
Transcription profiles of non-immortalized breast cancer cell lines
BMC Cancer. 2006 Apr 20;6:99.
[PubMed]
Wu CG, Budhu A, Chen S, Zhou X, Popescu NC, Valerie K, Wang XW.
Effect of hepatitis C virus core protein on the molecular profiling of human B lymphocytes
Mol Med. 2006 Jan-Mar;12(1-3):47-53.
[PubMed]
Pilch B, Mann M.
Large-scale and high-confidence proteomic analysis of human seminal plasma
Genome Biol. 2006;7(5):R40.
[PubMed]
Byron J. Gao, Obi L.Griffith, Martin Ester, Steven J.M. Jones
Discovering Significant OPSM Subspace Clusters in Massive Gene Expression Data
The 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 06), Philadelphia, USA, August 20-23, 2006.
Graudens E, Boulanger V, Mollard C, Mariage-Samson R, Barlet X, Gremy G, Couillault C, Lajemi M, Piatier-Tonneau D, Zaborski P, Eveno E, Auffray C, Imbeaud S.
Deciphering cellular states of innate tumor drug responses.
Genome Biol. 2006;7(3):R19.
[PubMed]
Pett MR, Herdman MT, Palmer RD, Yeo GS, Shivji MK, Stanley MA, Coleman N.
Selection of cervical keratinocytes containing integrated HPV16 associates with episome loss and an endogenous antiviral response.
P NATL ACAD SCI USA 103 (10): 3822-3827 MAR 7 2006
[PubMed]
Shou J, Bull CM, Li L, Qian HR, Wei T, Luo S, Perkins D, Solenberg PJ, Tan SL, Chen XY, Roehm NW, Wolos JA, Onyia JE.
Identification of blood biomarkers of rheumatoid arthritis by transcript profiling of peripheral blood mononuclear cells from the rat collagen-induced arthritis model.
Arthritis Res Ther. 2006 Jan 10;8(1):R28
[PubMed]
Gene Ontology Consortium
The Gene Ontology (GO) project in 2006
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D322-6.
[PubMed]
Crockett DK, Lin Z, Vaughn CP, Lim MS, Elenitoba-Johnson KS.
Identification of proteins from formalin-fixed paraffin-embedded cells by LC-MS/MS
LAB INVEST 85 (11): 1405-1415 NOV 2005
[PubMed]
McNutt MC, Tongbai R, Cui W, Collins I, Freebern WJ, Montano I, Haggerty CM, Chandramouli G, Gardner K.
Human promoter genomic composition demonstrates non-random groupings that reflect general cellular function
BMC BIOINFORMATICS 6: Art. No. 259 OCT 18 2005
[PubMed]
Frigessi A, van de Wiel MA, Holden M, Svendsrud DH, Glad IK, Lyng H.
Genome-wide estimation of transcript concentrations from spotted cDNA microarray data
Nucleic Acids Res. 2005 Oct 4;33(17):e143.
[PubMed]
Lomax J
Get ready to GO! A biologist's guide to the Gene Ontology
BRIEF BIOINFORM 6 (3): 298-304 SEP 2005
[PubMed]
Campanaro S, Vezzi A, Vitulo N, Lauro FM, D'Angelo M, Simonato F, Cestaro A, Malacrida G, Bertoloni G, Valle G, Bartlett DH.
Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains
BMC GENOMICS 6: Art. No. 122 SEP 14 2005
[PubMed]
Sandberg R, Ernberg I.
The molecular portrait of in vitro growth by meta-analysis of gene-expression profiles
Genome Biol. 2005;6(8):R65. Epub 2005 Jul 27.
[PubMed]
Chen YF, Shin SJ, Lin SR
Ets1 Was Significantly Activated by ERK1/2 in Mutant K-ras Stably Transfected Human Adrenocortical Cells
DNA Cell Biol. 2005 Feb;24(2):126-32.
[PubMed]
Anderle P, Sengstag T, Mutch DM, Rumbo M, Praz V, Mansourian R, Delorenzi M, Williamson G, Roberts MA.
Changes in the transcriptional profile of transporters in the intestine along the anterior-posterior and crypt-villus axes
BMC GENOMICS 6: Art. No. 69 MAY 10 2005
[PubMed]
Shah V, Sridhar S, Beane J, Brody JS, Spira A.
SIEGE: Smoking induced epithelial gene expression database
NUCLEIC ACIDS RES 33: D573-D579 Sp. Iss. SI JAN 1 2005
[PubMed]
Halaschek-Wiener J, Khattra JS, McKay S, Pouzyrev A, Stott JM, Yang GS, Holt RA, Jones SJ, Marra MA, Brooks-Wilson AR, Riddle DL.
Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression
GENOME RES 15 (5): 603-615 MAY 2005
[PubMed]
Yan W, Lee H, Yi EC, Reiss D, Shannon P, Kwieciszewski BK, Coito C, Li XJ, Keller A, Eng J, Galitski T, Goodlett DR, Aebersold R, Katze MG
System-based proteomic analysis of the interferon response in human liver cells
Genome Biol. 2004;5(8):R54. Epub 2004 Jul 22
[PubMed]
Annereau JP, Szakacs G, Tucker CJ, Arciello A, Cardarelli C, Collins J, Grissom S, Zeeberg BR, Reinhold W, Weinstein JN, Pommier Y, Paules RS, and Gottesman MM
Analysis of ATP-Binding Cassette Transporter Expression in Drug-Selected Cell Lines by a Microarray Dedicated to Multidrug Resistance.
Mol Pharmacol. 2004 Dec;66(6):1397-405. Epub 2004 Sep 01.
[PubMed]
Stevens EV, Posadas EM, Davidson B, Kohn EC.
Proteomics in cancer
ANN ONCOL 15: 167-171 Suppl. 4 2004
[PubMed]
Wang X, Wang M, Amarzguioui M, Liu F, Fodstad O, Prydz H.
Downregulation of tissue factor by RNA interference in human melanoma Lox-L cells reduces pulmonary metastasis in nude mice
INT J CANCER 112 (6): 994-1002 DEC 20 2004
[PubMed]
Gracey AY, Fraser EJ, Li W, Fang Y, Taylor RR, Rogers J, Brass A, Cossins AR.
Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate
P NATL ACAD SCI USA 101 (48): 16970-16975 NOV 30 2004
[PubMed]
Midori A. Harris and Helen Parkinson
Standards and Ontologies for Functional Genomics 2
Comparative and Functional Genomics Volume 5 (2004), Issue 8, Pages 618-622
Subscriptions Required (available to NIH online)
Talvinen K, Tuikkala J, Nevalainen O, Rantanen A, HirsimŠki P, Sundstršm J, Kronqvist P.
Proliferation marker securin identifies favourable outcome in invasive ductal breast cancer
Br J Cancer. 2008 Jul 22;99(2):335-40.
[PubMed]
Yang S, Liu T, Li S, Zhang X, Ding Q, Que H, Yan X, Wei K, Liu S.
Comparative proteomic analysis of brains of naturally aging mice.
Neuroscience. 2008 Jun 26;154(3):1107-20.
[PubMed]
Pohjanvirta R, Boutros PC, Moffat ID, LindŽn J, Wendelin D, Okey AB
Genome-wide effects of acute progressive feed restriction in liver and white adipose tissue
Toxicol Appl Pharmacol. 2008 Jul 1;230(1):41-56.
[PubMed]
Nordgard SH, Johansen FE, Alnaes GI, Bucher E, SyvŠnen AC, Naume B, B¿rresen-Dale AL, Kristensen VN.
Genome-wide analysis identifies 16q deletion associated with survival, molecular subtypes, mRNA expression, and germline haplotypes in breast cancer patients
Genes Chromosomes Cancer. 2008 Aug;47(8):680-96.
[PubMed]
Ruden DM, Jamison DC, Zeeberg BR, Garfinkel MD, Weinstein JN, Rasouli P, Lu X
The EDGE hypothesis: epigenetically directed genetic errors in repeat-containing proteins (RCPs) involved in evolution, neuroendocrine signaling, and cancer.
Front Neuroendocrinol. 2008 Jun;29(3):428-44.
[PubMed]
Jeffrey H. Ringrose, Rienk E. Jeeninga, Ben Berkhout, and Dave Speijer
Proteomic Studies Reveal Coordinated Changes in T-Cell Expression Patterns upon Infection with Human Immunodeficiency Virus Type 1
J Virol. 2008 May;82(9):4320-30.
[PubMed]
Chang YC, Lin SY, Liang SY, Pan KT, Chou CC, Chen CH, Liao CL, Khoo KH, Meng TC.
Tyrosine Phosphoproteomics and Identification of Substrates of Protein Tyrosine Phosphatase dPTP61F in Drosophila S2 Cells by Mass Spectrometry-Based Substrate Trapping Strategy
J Proteome Res. 2008 Mar 7;7(3):1055-1066.
[PubMed]
Wilson-Grady JT, Villén J, Gygi SP.
Phosphoproteome Analysis of Fission Yeast
J Proteome Res. 2008 Mar;7(3):1088-97.
[PubMed]
Finney GL, Blackler AR, Hoopmann MR, Canterbury JD, Wu CC, Maccoss MJ.
Label-Free Comparative Analysis of Proteomics Mixtures Using Chromatographic Alignment of High-Resolution muLC-MS Data
Anal Chem. 2008 Feb 15;80(4):961-71.
[PubMed]
Michalak P, Malone JH.
Testis-derived microRNA profiles of African clawed frogs (Xenopus) and their sterile hybrids
Genomics. 2008 Feb;91(2):158-64.
[PubMed]
Delneri D, Hoyle DC, Gkargkas K, Cross EJ, Rash B, Zeef L, Leong HS, Davey HM, Hayes A, Kell DB, Griffith GW, Oliver SG.
Identification and characterization of high-flux-control genes of yeast through competition analyses in continuous cultures
Nat Genet. 2008 Jan;40(1):113-7
[PubMed]
Zougman A, Pilch B, Podtelejnikov A, Kiehntopf M, Schnabel C, Kumar C, Mann M.
Integrated Analysis of the Cerebrospinal Fluid Peptidome and Proteome
J Proteome Res. 2008 Jan;7(1):386-99.
[PubMed]
TA Wynn
Cellular and molecular mechanisms of fibrosis
J Pathol. 2008 Jan;214(2):199-210.
[PubMed]
Gao H, Fält S, Sandelin A, Gustafsson JA, Dahlman-Wright K.
Genome-Wide Identification of Estrogen Receptor {alpha}-Binding Sites in Mouse Liver
Mol Endocrinol. 2008 Jan;22(1):10-22.
[PubMed]
Young AN, Master VA, Paner GP, Wang MD, Amin MB.
Renal epithelial neoplasms: diagnostic applications of gene expression profiling
Adv Anat Pathol. 2008 Jan;15(1):28-38.
[PubMed]
Wei Shi, Wanlei Zhou and Dakang Xu
Identifying cis-regulatory elements by statistical analysis and phylogenetic footprinting and analyzing their coexistence and related gene ontology
Physiol Genomics. 2007 Nov 14;31(3):374-84.
[PubMed]
Heller G, Schmidt WM, Ziegler B, Holzer S, Müllauer L, Bilban M, Zielinski CC, Drach J, Zöchbauer-Müller S.
Genome-wide transcriptional response to 5-aza-2'-deoxycytidine and trichostatin a in multiple myeloma cells
Cancer Res. 2008 Jan 1;68(1):44-54.
[PubMed]
Woods CG, Kosyk O, Bradford BU, Ross PK, Burns AM, Cunningham ML, Qu P, Ibrahim JG, Rusyn I.
Time course investigation of PPARα- and Kupffer cell-dependent effects of WY-14,643 in mouse liver using microarray gene expression
Toxicol Appl Pharmacol. 2007 Dec 15;225(3):267-77
[PubMed]
Trempus CS, Dang H, Humble MM, Wei SJ, Gerdes MJ, Morris RJ, Bortner CD, Cotsarelis G, Tennant RW.
Comprehensive Microarray Transcriptome Profiling of CD34-Enriched Mouse Keratinocyte Stem Cells
J Invest Dermatol. 2007 Dec;127(12):2904-7.
[PubMed]
Haque T, Faury D, Albrecht S, Lopez-Aguilar E, Hauser P, Garami M, HanzŽly Z, Bogn‡r L, Del Maestro RF, Atkinson J, Nantel A, Jabado N.
Gene Expression Profiling from Formalin-Fixed Paraffin-Embedded Tumors of Pediatric Glioblastoma
Clin Cancer Res. 2007 Nov 1;13(21):6284-92.
[PubMed]
Torres A, Storey L, Anders M, Miller RL, Bulbulian BJ, Jin J, Raghavan S, Lee J, Slade HB, Birmachu W.
Microarray analysis of aberrant gene expression in actinic keratosis: effect of the Toll-like receptor-7 agonist imiquimod
Br J Dermatol. 2007 Dec;157(6):1132-47.
[PubMed]
Wallentine JC, Kim KK, Seiler CE 3rd, Vaughn CP, Crockett DK, Tripp SR, Elenitoba-Johnson KS, Lim MS.
Comprehensive identification of proteins in Hodgkin lymphoma-derived ReedÐSternberg cells by LC-MS/MS
LABORATORY INVESTIGATION 87 (11): 1113-1124 NOV 2007
[PubMed]
Blanding CR, Simmons SJ, Casati P, Walbot V, Stapleton AE.
Coordinated regulation of maize genes during increasing exposure to ultraviolet radiation: identification of ultraviolet-responsive genes, functional processes and associated potential promoter motifs.
Plant Biotechnol J. 2007 Nov;5(6):677-95.
[PubMed]
Newbold RR, Jefferson WN, Grissom SF, Padilla-Banks E, Snyder RJ, Lobenhofer EK.
Developmental exposure to diethylstilbestrol alters uterine gene expression that may be associated with uterine neoplasia later in life
Mol Carcinog. 2007 Sep;46(9):783-96.
[PubMed]
Zhan M, Yamaza H, Sun Y, Sinclair J, Li H, Zou S.
Temporal and spatial transcriptional profiles of aging in Drosophila melanogaster
Genome Res. 2007 Aug;17(8):1236-43.
[PubMed]
Kroes RA, Burgdorf J, Otto NJ, Panksepp J, Moskal JR.
Social defeat, a paradigm of depression in rats that elicits 22-kHz vocalizations, preferentially activates the cholinergic signaling pathway in the periaqueductal gray.
Behav Brain Res. 2007 Sep 4;182(2):290-300.
[PubMed]
Beyer RP, Fry RC, Lasarev MR, McConnachie LA, Meira LB, Palmer VS, Powell CL, Ross PK, Bammler TK, Bradford BU, Cranson AB, Cunningham ML, Fannin RD, Higgins GM, Hurban P, Kayton RJ, Kerr KF, Kosyk O, Lobenhofer EK, Sieber SO, Vliet PA, Weis BK, Wolfinger R, Woods CG, Freedman JH, Linney E, Kaufmann WK, Kavanagh TJ, Paules RS, Rusyn I, Samson LD, Spencer PS, Suk W, Tennant RJ, Zarbl H; Members of the Toxicogenomics Research Consortium
Multicenter Study of Acetaminophen Hepatotoxicity Reveals the Importance of Biological Endpoints in Genomic Analyses
Toxicol Sci. 2007 Sep;99(1):326-37.
[PubMed]
Gatti D, Maki A, Chesler EJ, Kirova R, Kosyk O, Lu L, Manly KF, Williams RW, Perkins A, Langston MA, Threadgill DW, Rusyn I.
Genome-level analysis of genetic regulation of liver gene expression networks
Hepatology. 2007 Aug;46(2):548-57.
[PubMed]
Niculescu MD, da Costa KA, Fischer LM, Zeisel SH.
Lymphocyte gene expression in subjects fed a low-choline diet differs between those who develop organ dysfunction and those who do not
Am J Clin Nutr. 2007 Jul;86(1):230-9.
[PubMed]
Goh SH, Josleyn M, Lee YT, Danner RL, Gherman RB, Cam MC, Miller JL.
The human reticulocyte transcriptome
Physiol Genomics. 2007 Jul 18;30(2):172-8.
[PubMed]
Philibert RA, Ryu GY, Yoon JG, Sandhu H, Hollenbeck N, Gunter T, Barkhurst A, Adams W, Madan A.
Transcriptional profiling of subjects from the Iowa adoption studies.
Am J Med Genet B Neuropsychiatr Genet. 2007 Jul 5;144(5):683-90.
[PubMed]
Langille MG, Clark DV.
Parent genes of retrotransposition-generated gene duplicates in Drosophila melanogaster have distinct expression profiles
Genomics. 2007 Sep;90(3):334-43.
[PubMed]
Dong MQ, Venable JD, Au N, Xu T, Park SK, Cociorva D, Johnson JR, Dillin A, Yates JR 3rd.
Quantitative Mass Spectrometry Identifies Insulin Signaling Targets in C. elegans
Science. 2007 Aug 3;317(5838):660-3.
[PubMed]
Feng Y, Sun B, Li X, Zhang L, Niu Y, Xiao C, Ning L, Fang Z, Wang Y, Zhang L, Cheng J, Zhang W, Hao X.
Differentially expressed genes between primary cancer and paired lymph node metastases predict clinical outcome of node-positive breast cancer patients
Breast Cancer Res Treat. 2007 Jul;103(3):319-29.
[PubMed]
Shin S, Sun Y, Liu Y, Khaner H, Svant S, Cai J, Xu QX, Davidson BP, Stice SL, Smith AK, Goldman SA, Reubinoff BE, Zhan M, Rao MS, Chesnut JD.
Whole Genome Analysis of Human Neural Stem Cells Derived from Embryonic Stem Cells and Stem and Progenitor Cells Isolated from Fetal Tissue
Stem Cells. 2007 May;25(5):1298-306.
[PubMed]
Patel MJ, Liu W, Sykes MC, Ward NE, Risin SA, Risin D, Jo H.
Identification of mechanosensitive genes in osteoblasts by comparative microarray studies using the rotating wall vessel and the random positioning machine
J Cell Biochem. 2007 Jun 1;101(3):587-99.
[PubMed]
Conway AM, James AB, Zang J, Morris BJ.
Regulation of neuronal cdc20 (p55cdc) expression by the plasticity-related transcription factor zif268
Synapse. 2007 Jun;61(6):463-8.
[PubMed]
Schumacher JA, Crockett DK, Elenitoba-Johnson KS, Lim MS.
Evaluation of enrichment techniques for mass spectrometry: identification of tyrosine phosphoproteins in cancer cells
J Mol Diagn. 2007 Apr;9(2):169-77.
[PubMed]
Faury D, Nantel A, Dunn SE, Guiot MC, Haque T, Hauser P, Garami M, Bognar L, Hanzely Z, Liberski PP, Lopez-Aguilar E, Valera ET, Tone LG, Carret AS, Del Maestro RF, Gleave M, Montes JL, Pietsch T, Albrecht S, Jabado N
Molecular Profiling Identifies Prognostic Subgroups of Pediatric Glioblastoma and Shows Increased YB-1 Expression in Tumors
J Clin Oncol. 2007 Apr 1;25(10):1196-208.
[PubMed]
Buchholz DR, Heimeier RA, Das B, Washington T, Shi YB.
Pairing morphology with gene expression in thyroid hormone-induced intestinal remodeling and identification of a core set of TH-induced genes across tadpole tissues
Dev Biol. 2007 Mar 15;303(2):576-90.
[PubMed]
Lujian Liao, Julie Pilotte, Tao Xu, Catherine C. L. Wong, Gerald M. Edelman, Peter Vanderklish, and John R. Yates, III
BDNF Induces Widespread Changes in Synaptic Protein Content and Up-Regulates Components of the Translation Machinery: An Analysis Using High-Throughput Proteomics
J Proteome Res. 2007 Mar;6(3):1059-71.
[PubMed]
Jiang X, Jiang X, Feng S, Tian R, Ye M, Zou H
Development of Efficient Protein Extraction Methods for Shotgun Proteome Analysis of Formalin-Fixed Tissues
J Proteome Res. 2007 Mar;6(3):1038-47.
[PubMed]
Munton RP, Tweedie-Cullen R, Livingstone-Zatchej M, Weinandy F, Waidelich M, Longo D, Gehrig P, Potthast F, Rutishauser D, Gerrits B, Panse C, Schlapbach R, Mansuy IM
Qualitative and Quantitative Analyses of Protein Phosphorylation in Naive and Stimulated Mouse Synaptosomal Preparations
Mol Cell Proteomics. 2007 Feb;6(2):283-93.
[PubMed]
Wagner W, Wein F, Roderburg C, Saffrich R, Faber A, Krause U, Schubert M, Benes V, Eckstein V, Maul H, Ho AD
Adhesion of hematopoietic progenitor cells to human mesenchymal stem cells as a model for cell?cell interaction
Exp Hematol. 2007 Feb;35(2):314-25.
[PubMed]
Fagerstrom-Billai F, Durand-Dubief M, Ekwall K, Wright AP
Individual Subunits of the Ssn6-Tup11/12 Corepressor Are Selectively Required for Repression of Different Target Genes
Mol Cell Biol. 2007 Feb;27(3):1069-82.
[PubMed]
Schubert-Unkmeir A, Sokolova O, Panzner U, Eigenthaler M, Frosch M
Gene Expression Pattern in Human Brain Endothelial Cells in Response to Neisseria meningitidis
Infect Immun. 2007 Feb;75(2):899-914.
[PubMed]
Scott DiGuistini, Steven G. Ralph, Young W. Lim, Robert Holt, Steven Jones, Jšrg Bohlmann, Colette Breuil
Generation and annotation of lodgepole pine and oleoresin-induced expressed sequences from the blue-stain fungus Ophiostoma clavigerum, a Mountain Pine Beetle-associated pathogen
FEMS MICROBIOLOGY LETTERS 267 (2): 151-158 FEB 2007
P Laiho, A Kokko, S Vanharanta, R Salovaara, H Sammalkorpi, H JŠrvinen, J-P Mecklin, T J Karttunen, K Tuppurainen, V Davalos, S Schwartz Jr, D Arango, M J MŠkinen and L A Aaltonen
Serrated carcinomas form a subclass of colorectal cancer with distinct molecular basis
Oncogene. 2007 Jan 11;26(2):312-20.
[PubMed]
Edward K. Lobenhofer, Gary A. Boorman, Kenneth L. Phillips, Alexandra N. Heinloth, David E. Malarkey, Pamela E. Blackshear, Christopher Houle and Patrick Hurban
Application of visualization tools to the analysis of histopathological data enhances biological insight and interpretation.
Toxicol Pathol. 2006;34(7):921-8.
[PubMed]
Bingyun Sun, Jeffrey A. Ranish, Angelita G. Utleg, James T. White, Xiaowei Yan, Biaoyang Lin and Leroy Hood
Shotgun Glycopeptide Capture Approach Coupled with Mass Spectrometry for Comprehensive Glycoproteomics
Mol Cell Proteomics. 2007 Jan;6(1):141-9.
[PubMed]
ven Klaschika, Ihsan Gursela and Dennis M. Klinman
CpG-mediated changes in gene expression in murine spleen cells identified by microarray analysis
Mol Immunol. 2007 Feb;44(6):1095-104.
[PubMed]
Boverhof DR, Burgoon LD, Tashiro C, Sharratt B, Chittim B, Harkema JR, Mendrick DL, Zacharewski TR
Comparative Toxicogenomic Analysis of the Hepatotoxic Effects of TCDD in Sprague Dawley Rats and C57BL/6 Mice
Toxicol Sci. 2006 Dec;94(2):398-416.
[PubMed]
Patke A, Mecklenbrauker I, Erdjument-Bromage H, Tempst P, Tarakhovsky A.
BAFF controls B cell metabolic fitness through a PKCbeta- and Akt-dependent mechanism.
J Exp Med. 2006 Oct 30;203(11):2551-62.
[PubMed]
Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, and Mann M.
Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks
Cell. 2006 Nov 3;127(3):635-48.
[PubMed]
Green RF, Moore C.
Incorporating genetic analyses into birth defects cluster investigations: Strategies for identifying candidate genes
Birth Defects Res A Clin Mol Teratol. 2006 Nov;76(11):798-810.
[PubMed]
Dopazo J
Functional Interpretation of Microarray Experiments
OMICS. 2006 Fall;10(3):398-410.
[PubMed]
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Modulation of pro- and antiapoptotic molecules in double-positive (CD4+CD8+) thymocytes following dexamethasone treatment
J Pharmacol Exp Ther. 2006 Nov;319(2):887-97.
[PubMed]
Bachtiary B, Boutros PC, Pintilie M, Shi W, Bastianutto C, Li JH, Schwock J, Zhang W, Penn LZ, Jurisica I, Fyles A, Liu FF.
Gene expression profiling in cervical cancer: an exploration of intratumor heterogeneity
Clin Cancer Res. 2006 Oct 1;12(19):5632-40.
[PubMed]
Antonov AV, Mewes HW
Complex Functionality of Gene Groups Identified from High-throughput Data
J Mol Biol. 2006 Oct 13;363(1):289-96.
[PubMed]
Jason A. Wall, Jing Wei, Mimi Ly, Peter Belmont, Joshua J. Martindale, Diem Tran, Jun Sun, Wenqiong J. Chen, Wen Yu, Paul Oeller, Steve Briggs, Asa B. Gustafsson, M. R. Sayen, Roberta A. Gottlieb, and Christopher C. Glembotski
Alterations in oxidative phosphorylation complex proteins in the hearts of transgenic mice that overexpress the p38 MAP kinase activator, MAP kinase kinase 6
Am J Physiol Heart Circ Physiol. 2006 Nov;291(5):H2462-72.
[PubMed]
Guo L, Lobenhofer EK, Wang C, Shippy R, Harris SC, Zhang L, Mei N, Chen T, Herman D, Goodsaid FM, Hurban P, Phillips KL, Xu J, Deng X, Sun YA, Tong W, Dragan YP, Shi L.
Rat toxicogenomic study reveals analytical consistency across microarray platforms
Nat Biotechnol. 2006 Sep 8;24(9):1162-1169
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Hong Sun, Geir Skogerbo, and Runsheng Chen
Conserved distances between vertebrate highly conserved elements.
Hum Mol Genet. 2006 Oct 1;15(19):2911-22.
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Expression Profiling Identifies Three Pathways Altered in Cellular Immortalization: Interferon, Cell Cycle, and Cytoskeleton
J GERONTOL A-BIOL 61 (9): 879-889 SEP 2006
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Microarrays: a monitoring tool for transplant patients?
TRANSPLANT INT 19 (10): 775-788 OCT 2006
[PubMed]
Jerry M. Wright, Christian A. Merlo, Jeffrey B. Reynolds, Pamela L. Zeitlin, Joe G. N. Garcia, William B. Guggino and Michael P. Boyle
Respiratory Epithelial Gene Expression in Patients with Mild and Severe Cystic Fibrosis Lung Disease
AM J RESP CELL MOL 35 (3): 327-336 SEP 2006
[PubMed]
Melanson JE, Avery SL, and Pinto DM
High-coverage quantitative proteomics using amine-specific isotopic labeling
PROTEOMICS 6 (16): 4466-4474 AUG 2006
[PubMed]
Joseph R. Moskal, Roger A. Kroes, Nigel J. Otto, Omid Rahimi, Brenda J. Claiborne
Distinct patterns of gene expression in the left and right hippocampal formation of developing rats
HIPPOCAMPUS 16 (8): 629-634 2006
[PubMed]
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A mammalian promoter model links cis elements to genetic networks
Biochem Biophys Res Commun. 2006 Aug 18;347(1):166-77.
[PubMed]
Joseph Riss, Chand Khanna, Seongjoon Koo, Gadisetti V.R. Chandramouli, Howard H. Yang, Ying Hu, David E. Kleiner, Andreas Rosenwald, Carl F. Schaefer, Shmuel A. Ben-Sasson1, Liming Yang, John Powell, David W. Kane, Robert A. Star, Olga Aprelikova, Kristin Bauer, James R. Vasselli, Jodi K. Maranchie, Kurt W. Kohn, Ken H. Buetow, W. Marston Linehan, John N. Weinstein, Maxwell P. Lee, Richard D. Klausner and J. Carl Barrett
Cancers as Wounds that Do Not Heal: Differences and Similarities between Renal Regeneration/Repair and Renal Cell Carcinoma
Cancer Research 66, 7216-7224, July 15, 2006
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Biological microarray interpretation: The rules of engagement
Biochim Biophys Acta. 2006 Jul;1759(7):319-27.
[PubMed]
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Informatics-assisted Protein Profiling in a Transgenic Mouse Model of Amyotrophic Lateral Sclerosis.
2006 Jul;5(7):1233-1244.
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Celecoxib Treatment Alters the Gene Expression Profile of Normal Colonic Mucosa.
Cancer Epidemiol Biomarkers Prev. 2006 Jul;15(7):1382-91.
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Selective identification of newly synthesized proteins in mammalian cells using bioorthogonal noncanonical amino acid tagging (BONCAT)
Proc Natl Acad Sci U S A. 2006 Jun 20;103(25):9482-7.
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Minghsun Liu, Stephen J Popper, Kathleen H Rubins and David A Relman
Early days: genomics and human responses to infection
Curr Opin Microbiol. 2006 Jun;9(3):312-9.
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High recovery HPLC separation of lipid rafts for membrane proteome analysis.
J Proteome Res. 2006 Jun;5(6):1301-12.
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Morin RD, Chang E, Petrescu A, Liao N, Griffith M, Kirkpatrick R, Butterfield YS, Young AC, Stott J, Barber S, Babakaiff R, Dickson MC, Matsuo C, Wong D, Yang GS, Smailus DE, Wetherby KD, Kwong PN, Grimwood J, Brinkley CP 3rd, Brown-John M, Reddix-Dugue ND, Mayo M, Schmutz J, Beland J, Park M, Gibson S, Olson T, Bouffard GG, Tsai M, Featherstone R, Chand S, Siddiqui AS, Jang W, Lee E, Klein SL, Blakesley RW, Zeeberg BR, Narasimhan S, Weinstein JN, Pennacchio CP, Myers RM, Green ED, Wagner L, Gerhard DS, Marra MA, Jones SJ, Holt RA.
Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling.
Genome Res. 2006 Jun;16(6):796-803.
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Vaughn CP, Crockett DK, Lin Z, Lim MS, Elenitoba-Johnson KS.
Identification of proteins released by follicular lymphoma-derived cells using a mass spectrometry-based approach
Proteomics. 2006 May;6(10):3223-30.
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Andreu-Vieyra C, Lin YN, Matzuk MM.
Mining the oocyte transcriptome.
Trends Endocrinol Metab. 2006 May-Jun;17(4):136-43.
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Tsai JR, Chong IW, Chen CC, Lin SR, Sheu CC, Hwang JJ.
Mitogen-activated protein kinase pathway was significantly activated in human bronchial epithelial cells by nicotine.
DNA Cell Biol. 2006 May;25(5):312-22.
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Gao H, Bryzgalova G, Hedman E, Khan A, Efendic S, Gustafsson JA, Dahlman-Wright K.
Long-term administration of estradiol decreases expression of hepatic lipogenic genes and improves insulin sensitivity in ob/ob mice: a possible mechanism is through direct regulation of signal transducer and activator of transcription 3.
Mol Endocrinol. 2006 Jun;20(6):1287-99.
[PubMed]
Bussey KJ, Chin K, Lababidi S, Reimers M, Reinhold WC, Kuo WL, Gwadry F, Ajay, Kouros-Mehr H, Fridlyand J, Jain A, Collins C, Nishizuka S, Tonon G, Roschke A, Gehlhaus K, Kirsch I, Scudiero DA, Gray JW, Weinstein JN.
Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel
Mol Cancer Ther. 2006 Apr;5(4):853-67.
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Kainou T, Shinzato T, Sasaki K, Mitsui Y, Giga-Hama Y, Kumagai H, Uemura H.
Spsgt1, a new essential gene of Schizosaccharomyces pombe, is involved in carbohydrate metabolism.
Yeast. 2006 Jan 15;23(1):35-53.
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Zhang T, Stilwell JL, Gerion D, Ding L, Elboudwarej O, Cooke PA, Gray JW, Alivisatos AP, Chen FF.
Cellular Effect of High Doses of Silica-Coated Quantum Dot Profiled with High Throughput Gene Expression Analysis and High Content Cellomics Measurements.
NANO LETT 6 (4): 800-808 APR 2006
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Andersson KB, Florholmen G, Winer LH, Tonnessen T, Christensen G.
Regulation of neuronal type genes in congestive heart failure rats.
Acta Physiol (Oxf). 2006 Jan;186(1):17-27.
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Transcriptional profiling of reporter genes used for molecular imaging of embryonic stem cell transplantation.
Physiol Genomics. 2006 Mar 13;25(1):29-38. Epub 2006 Jan 3.
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Yan J, Burman A, Nichols C, Alila L, Showe LC, Showe MK, Boyer BB, Barnes BM, Marr TG.
Detection of differential gene expression in brown adipose tissue of hibernating arctic ground squirrels with mouse microarrays.
PHYSIOL GENOMICS 25 (2): 346-353 APR 13 2006
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Vascular bed-targeted in vivo gene delivery using tropism-modified adeno-associated viruses.
MOL THER 13 (4): 683-693 APR 2006
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Hansson SR, Chen Y, Brodszki J, Chen M, Hernandez-Andrade E, Inman JM, Kozhich OA, Larsson I, Marsal K, Medstrand P, Xiang CC, Brownstein MJ.
Gene expression profiling of human placentas from preeclamptic and normotensive pregnancies.
MOL HUM REPROD 12 (3): 169-179 MAR 2006
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Azadi S, Paquet-Durand F, Medstrand P, van Veen T, Ekstrom PA.
Up-regulation and increased phosphorylation of protein kinase C (PKC) delta, mu and theta in the degenerating rd1 mouse retina.
MOL CELL NEUROSCI 31 (4): 759-773 APR 2006
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Forner F, Foster LJ, Campanaro S, Valle G, Mann M.
Quantitative proteomic comparison of rat mitochondria from muscle, heart, and liver.
MOL CELL PROTEOMICS 5 (4): 608-619 APR 2006
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Innes CL, Heinloth AN, Flores KG, Sieber SO, Deming PB, Bushel PR, Kaufmann WK, Paules RS.
ATM requirement in gene expression responses to ionizing radiation in human lymphoblasts and fibroblasts.
Mol Cancer Res. 2006 Mar;4(3):197-207.
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Das B, Cai L, Carter MG, Piao YL, Sharov AA, Ko MS, Brown DD.
Gene expression changes at metamorphosis induced by thyroid hormone in Xenopus laevis tadpoles.
DEV BIOL 291 (2): 342-355 MAR 15 2006
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Stewart JJ, White JT, Yan X, Collins S, Drescher CW, Urban ND, Hood L, Lin B.
Proteins associated with Cisplatin resistance in ovarian cancer cells identified by quantitative proteomic technology and integrated with mRNA expression levels.
MOL CELL PROTEOMICS 5 (3): 433-443 MAR 2006
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Ballester B, Ramuz O, Gisselbrecht C, Doucet G, Loi L, Loriod B, Bertucci F, Bouabdallah R, Devilard E, Carbuccia N, Mozziconacci MJ, Birnbaum D, Brousset P, Berger F, Salles G, Briere J, Houlgatte R, Gaulard P, Xerri L.
Gene expression profiling identifies molecular subgroups among nodal peripheral T-cell lymphomas.
Oncogene. 2006 Mar 9;25(10):1560-70.
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Welch KD, Reilly TP, Bourdi M, Hays T, Pise-Masison CA, Radonovich MF, Brady JN, Dix DJ, Pohl LR.
Genomic Identification of Potential Risk Factors during Acetaminophen-Induced Liver Disease in Susceptible and Resistant Strains of Mice.
Chem Res Toxicol. 2006 Feb 20;19(2):223-233.
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Kokko A, Ylisaukko-Oja SS, Kiuru M, Takatalo MS, Salmikangas P, Tuimala J, Arango D, Karhu A, Aaltonen LA, Jantti J.
Modeling tumor predisposing FH mutations in yeast: Effects on fumarase activity, growth phenotype and gene expression profile.
Int J Cancer. 2006 Mar 15;118(6):1340-5.
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Bryzgalova G, Gao H, Ahren B, Zierath JR, Galuska D, Steiler TL, Dahlman-Wright K, Nilsson S, Gustafsson JA, Efendic S, Khan A.
Evidence that oestrogen receptor-alpha plays an important role in the regulation of glucose homeostasis in mice: insulin sensitivity in the liver.
Diabetologia. 2006 Mar;49(3):588-97.
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Ciuffi A, Mitchell RS, Hoffmann C, Leipzig J, Shinn P, Ecker JR, Bushman FD.
Integration Site Selection by HIV-Based Vectors in Dividing and Growth-Arrested IMR-90 Lung Fibroblasts
Molecular Therapy Volume 13, Issue 2 , February 2006, Pages 366-373
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Deng DX, Tsalenko A, Vailaya A, Ben-Dor A, Kundu R, Estay I, Tabibiazar R, Kincaid R, Yakhini Z, Bruhn L, Quertermous T.
Differences in vascular bed disease susceptibility reflect differences in gene expression response to atherogenic stimuli.
CIRC RES 98 (2): 200-208 FEB 3 2006
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Vanharanta S, Pollard PJ, Lehtonen HJ, Laiho P, Sjoberg J, Leminen A, Aittomaki K, Arola J, Kruhoffer M, Orntoft TF, Tomlinson IP, Kiuru M, Arango D, Aaltonen LA.
Distinct expression profile in fumarate-hydratase-deficient uterine fibroids
HUM MOL GENET 15 (1): 97-103 JAN 1 2006
[PubMed]
Yin-Goen Q, Dale J, Yang WL, Phan J, Moffitt R, Petros JA, Datta MW, Amin MB, Wang MD, Young AN.
Advances in molecular classification of renal neoplasms
HISTOL HISTOPATHOL 21 (3): 325-339 MAR 2006
[PubMed]
Nathalie Tijet, Paul C. Boutros, Ivy D. Moffat, Allan B. Okey, Jouko Tuomisto, and Raimo Pohjanvirta
Aryl hydrocarbon receptor regulates distinct dioxin-dependent and dioxin-independent gene batteries
MOL PHARMACOL 69 (1): 140-153 JAN 2006
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Dillon GP, Feltwell T, Skelton JP, Ashton PD, Coulson PS, Quail MA, Nikolaidou-Katsaridou N, Wilson RA, Ivens AC.
Microarray analysis identifies genes preferentially expressed in the lung schistosomulum of Schistosoma mansoni
Int J Parasitol. 2006 Jan;36(1):1-8. Epub 2005 Nov 15.
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Kroes RA, Panksepp J, Burgdorf J, Otto NJ, Moskal JR.
Modeling depression: social dominance-submission gene expression patterns in rat neocortex
Neuroscience. 2006;137(1):37-49. Epub 2005 Nov 11.
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Wagner RA, Tabibiazar R, Liao A, Quertermous T.
Genome-wide expression dynamics during mouse embryonic development reveal similarities to Drosophila development
Dev Biol. 2005 Dec 15;288(2):595-611.
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Sullivan CJ, Teal TH, Luttrell IP, Tran KB, Peters MA, Wessells H.
Microarray analysis reveals novel gene expression changes associated with erectile dysfunction in diabetic rats
PHYSIOL GENOMICS 23 (2): 192-205 OCT 17 2005
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Williams DR, Epperson LE, Li W, Hughes MA, Taylor R, Rogers J, Martin SL, Cossins AR, Gracey AY.
Seasonally hibernating phenotype assessed through transcript screening
PHYSIOL GENOMICS 24 (1): 13-22 DEC 14 2005
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Berglund P, Stighall M, Jirstrom K, Borgquist S, Sjolander A, Hedenfalk I, Landberg G.
Cyclin E overexpression obstructs infiltrative behavior in breast cancer: A novel role reflected in the growth pattern of medullary breast cancers.
CANCER RES 65 (21): 9727-9734 NOV 1 2005
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Powell CL, Kosyk O, Bradford BU, Parker JS, Lobenhofer EK, Denda A, Uematsu F, Nakae D, Rusyn I.
Temporal correlation of pathology and DNA damage with gene expression in a choline-deficient model of rat liver injury
HEPATOLOGY 42 (5): 1137-1147 NOV 2005
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James AB, Conway AM, Morris BJ.
Genomic profiling of the neuronal target genes of the plasticity-related transcription factor-Zif268
J NEUROCHEM 95 (3): 796-810 NOV 2005
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Buchholz M, Braun M, Heidenblut A, Kestler HA, Kloppel G, Schmiegel W, Hahn SA, Luttges J, Gress TM.
Transcriptome analysis of microdissected pancreatic intraepithelial neoplastic lesions
ONCOGENE 24 (44): 6626-6636 OCT 6 2005
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Vanharanta S, Wortham NC, Laiho P, Sjoberg J, Aittomaki K, Arola J, Tomlinson IP, Karhu A, Arango D, Aaltonen LA.
7q deletion mapping and expression profiling in uterine fibroids
ONCOGENE 24 (43): 6545-6554 SEP 2005
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Dieguez-Acuna FJ, Gerber SA, Kodama S, Elias JE, Beausoleil SA, Faustman D, Gygi SP.
Characterization of mouse spleen cells by subtractive proteomics
MOL CELL PROTEOMICS 4 (10): 1459-1470 OCT 2005
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Ule J, Ule A, Spencer J, Williams A, Hu JS, Cline M, Wang H, Clark T, Fraser C, Ruggiu M, Zeeberg BR, Kane D, Weinstein JN, Blume J, Darnell RB.
Nova regulates brain-specific splicing to shape the synapse
NAT GENET 37 (8): 844-852 AUG 2005
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Ding LH, Shingyoji M, Chen F, Chatterjee A, Kasai KE, Chen DJ.
Gene expression profiles of normal human fibroblasts after exposure to ionizing radiation: A comparative study of low and high doses
RADIAT RES 164 (1): 17-26 JUL 2005
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Skotheim RI, Lind GE, Monni O, Nesland JM, Abeler VM, Fossa SD, Duale N, Brunborg G, Kallioniemi O, Andrews PW, Lothe RA.
Differentiation of human embryonal carcinomas in vitro and in vivo reveals expression profiles relevant to normal development
CANCER RES 65 (13): 5588-5598 JUL 1 2005
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Staib F, Robles AI, Varticovski L, Wang XW, Zeeberg BR, Sirotin M, Zhurkin VB, Hofseth LJ, Hussain SP, Weinstein JN, Galle PR, Harris CC.
The p53 tumor suppressor network is a key responder to microenvironmental components of chronic inflammatory stress
Cancer Res. 2005 Nov 15;65(22):10255-64.
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Sandhu C, Connor M, Kislinger T, Slingerland J, Emili A.
Global protein shotgun expression profiling of proliferating MCF-7 breast cancer cells
J PROTEOME RES 4 (3): 674-689 MAY-JUN 2005
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Vos JB, van Sterkenburg MA, Rabe KF, Schalkwijk J, Hiemstra PS, Datson NA.
Transcriptional response of bronchial epithelial cells to Pseudomonas aeruginosa: identification of early mediators of host defense
PHYSIOL GENOMICS 21 (3): 324-336 MAY 11 2005
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Karlsson G, Liu Y, Larsson J, Goumans MJ, Lee JS, Thorgeirsson SS, Ringner M, Karlsson S.
Gene expression profiling demonstrates that TGF-beta 1 signals exclusively through receptor complexes involving Alk5 and identifies targets of TGF-beta signaling
PHYSIOL GENOMICS 21 (3): 396-403 MAY 11 2005
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Handfield M, Mans JJ, Zheng G, Lopez MC, Mao S, Progulske-Fox A, Narasimhan G, Baker HV, Lamont RJ.
Distinct transcriptional profiles characterize oral epithelium-microbiota interactions
CELL MICROBIOL 7 (6): 811-823 JUN 2005
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Niculescu MD, Craciunescu CN, Zeisel SH.
Gene expression profiling of choline-deprived neural precursor cells isolated from mouse brain
MOL BRAIN RES 134 (2): 309-322 APR 4 2005
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Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A.
Reverse engineering of regulatory networks in human B cells
NAT GENET 37 (4): 382-390 APR 2005
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Nielsen PA, Olsen JV, Podtelejnikov AV, Andersen JR, Mann M, Wisniewski JR.
Proteomic mapping of brain plasma membrane proteins
MOL CELL PROTEOMICS 4 (4): 402-408 APR 2005
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Cai J, Ash D, Kotch LE, Jabs EW, Attie-Bitach T, Auge J, Mattei G, Etchevers H, Vekemans M, Korshunova Y, Tidwell R, Messina DN, Winston JB, Lovett M.
Gene expression in pharyngeal arch 1 during human embryonic development
HUM MOL GENET 14 (7): 903-912 APR 1 2005
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Hanifi-Moghaddam P, Gielen SC, Kloosterboer HJ, De Gooyer ME, Sijbers AM, van Gool AJ, Smid M, Moorhouse M, van Wijk FH, Burger CW, Blok LJ.
Molecular portrait of the progestagenic and estrogenic actions of tibolone: Behavior of cellular networks in response to tibolone
J CLIN ENDOCR METAB 90 (2): 973-983 FEB 2005
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Wagner RA, Tabibiazar R, Liao A, Quertermous T.
Genome-wide expression profiling of a cardiac pressure overload model identifies major metabolic and signaling pathway responses
J MOL CELL CARDIOL 37 (6): 1159-1170 DEC 2004
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El-Etr SH, Mueller A, Tompkins LS, Falkow S, Merrell DS.
Phosphorylation-independent effects of CagA during interaction between Helicobacter pylori and T84 polarized monolayers
J INFECT DIS 190 (8): 1516-1523 OCT 15 2004
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Lu J, Qian J, Izvolsky KI, Cardoso WV.
Global analysis of genes differentially expressed in branching and non-branching regions of the mouse embryonic lung
DEV BIOL 273 (2): 418-435 SEP 15 2004
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Boutros PC, Moffat ID, Franc MA, Tijet N, Tuomisto J, Pohjanvirta R, Okey AB.
Dioxin-responsive AHRE-II gene battery: identification by phylogenetic footprinting
BIOCHEM BIOPH RES CO 321 (3): 707-715 AUG 27 2004
[PubMed]
Subscriptions Required (not available to NIH online)
Yoshida Y, Miyamoto M, Bo X, Yaoita E, Yamamoto T
Overview of Kidney and Urine Proteome Databases
Contrib Nephrol. 2008;160:186-97.
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Rivera E, Flores I, Rivera E, Appleyard CB
Molecular profiling of a rat model of colitis: Validation of known inflammatory genes and identification of novel disease-associated targets
NFLAMMATORY BOWEL DISEASES 12 (10): 950-966 OCT 2006
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Sievertzon M, Nilsson P, Lundeberg J.
Improving reliability and performance of DNA microarrays.
Expert Rev Mol Diagn. 2006 May;6(3):481-92.
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Butcher JT, Tressel S, Johnson T, Turner D, Sorescu G, Jo H, Nerem RM.
Transcriptional profiles of valvular and vascular endothelial cells reveal phenotypic differences - Influence of shear stress
ARTERIOSCL THROM VAS 26 (1): 69-77 JAN 2006
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Massa V, Cabrera RM, Menegola E, Giavini E, Finnell RH.
Valproic acid-induced skeletal malformations: associated gene expression cascades
PHARMACOGENET GENOM 15 (11): 787-800 NOV 2005
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Gissel C, Voolstra C, Doss MX, Koehler CI, Winkler J, Hescheler J, Sachinidis A.
An optimized embryonic stem cell model for consistent gene expression and developmental studies - A fundamental study
THROMB HAEMOSTASIS 94 (4): 719-727 OCT 2005
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Chen R, Yi EC, Donohoe S, Pan S, Eng J, Cooke K, Crispin DA, Lane Z, Goodlett DR, Bronner MP, Aebersold R, Brentnall TA.
Pancreatic cancer proteome: The proteins that underlie invasion, metastasis, and immunologic escape
GASTROENTEROLOGY 129 (4): 1187-1197 OCT 2005
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Buchholz M, Kestler HA, Holzmann K, Ellenrieder V, Schneiderhan W, Siech M, Adler G, Bachem MG, Gress TM.
Transcriptome analysis of human hepatic and pancreatic stellate cells: organ-specific variations of a common transcriptional phenotype
J MOL MED-JMM 83 (10): 795-805 OCT 2005
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Arango D, Laiho P, Kokko A, Alhopuro P, Sammalkorpi H, Salovaara R, Nicorici D, Hautaniemi S, Alazzouzi H, Mecklin JP, Jarvinen H, Hemminki A, Astola J, Schwartz S Jr, Aaltonen LA.
Gene-expression profiling predicts recurrence in Dukes' C colorectal cancer
GASTROENTEROLOGY 129 (3): 874-884 SEP 2005 (login required)
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Brors B.
Microarray annotation and biological information on function
METHOD INFORM MED 44 (3): 468-472 2005
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Anderle P, Rumbo M, Sierro F, Mansourian R, Michetti P, Roberts MA, Kraehenbuhl JP.
Novel markers of the human follicle-associated epithelium identified by genomic profiling and microdissection
GASTROENTEROLOGY 129 (1): 321-327 JUL 2005 (login required)
[PubMed]
Tangrea MA, Wallis BS, Gillespie JW, Gannot G, Emmert-Buck MR, Chuaqui RF.
Novel proteomic approaches for tissue analysis
EXPERT REV PROTEOMIC 1 (2): 185-192 AUG 2004 (login required)
[PubMed]
Mueller A, Merrell DS, Grimm J, Falkow S.
Profiling of microdissected gastric epithelial cells reveals a cell type-specific response to Helicobacter pylori infection
GASTROENTEROLOGY 127 (5): 1446-1462 NOV 2004
[PubMed]

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