| | Other Issues: previous | next | latest | archiveDatabase HIP2: An online database of human plasma proteins from healthy individuals Sudipto Saha, Scott H Harrison, Changyu Shen, Haixu Tang, Predrag Radivojac, Randy J Arnold, Xiang Zhang, and Jake Yue Chen BMC Med Genomics. 2008; 1: 12. Published online 2008 April 25. doi: 10.1186/1755-8794-1-12.PMCID: PMC2396660 New Jersey Center for Tourette Syndrome Sharing Repository: methods and sample description Gary A Heiman, Robert A King, and Jay A Tischfield BMC Med Genomics. 2008; 1: 58. Published online 2008 November 26. doi: 10.1186/1755-8794-1-58.PMCID: PMC2605751 Research Articles Biomarker expression patterns that correlate with high grade features in treatment naive, organ-confined prostate cancer Timothy J McDonnell, Nikhil S Chari, Jeong Hee Cho-Vega, Patricia Troncoso, Xuemei Wang, Carlos E Bueso-Ramos, Kevin Coombes, Shawn Brisbay, Remigio Lopez, George Prendergast, Christopher Logothetis, and Kim-Anh Do BMC Med Genomics. 2008; 1: 1. Published online 2008 January 31. doi: 10.1186/1755-8794-1-1.PMCID: PMC2227949 Microarray analysis in B cells among siblings with/without MS - role for transcription factor TCF2 Jagannadha R Avasarala, Sridar V Chittur, Ajish D George, and John A Tine BMC Med Genomics. 2008; 1: 2. Published online 2008 January 31. doi: 10.1186/1755-8794-1-2.PMCID: PMC2227948 Tiling resolution array CGH and high density expression profiling of urothelial carcinomas delineate genomic amplicons and candidate target genes specific for advanced tumors Markus Heidenblad, David Lindgren, Tord Jonson, Fredrik Liedberg, Srinivas Veerla, Gunilla Chebil, Sigurdur Gudjonsson, Åke Borg, Wiking Månsson, and Mattias Höglund BMC Med Genomics. 2008; 1: 3. Published online 2008 January 31. doi: 10.1186/1755-8794-1-3.PMCID: PMC2227947 Comparing the old and new generation SELDI-TOF MS: implications for serum protein profiling Marie-Christine W Gast, Judith YMN Engwegen, Jan HM Schellens, and Jos H Beijnen BMC Med Genomics. 2008; 1: 4. Published online 2008 January 31. doi: 10.1186/1755-8794-1-4.PMCID: PMC2263070 Robust SNP genotyping by multiplex PCR and arrayed primer extension Mohua Podder, Jian Ruan, Ben W Tripp, Zane E Chu, and Scott J Tebbutt BMC Med Genomics. 2008; 1: 5. Published online 2008 January 31. doi: 10.1186/1755-8794-1-5.PMCID: PMC2266772 Midkine is a NF-κB-inducible gene that supports prostate cancer cell survival Zongbing You, Ying Dong, Xiangtian Kong, Laurel A Beckett, Regina Gandour-Edwards, and Jonathan Melamed BMC Med Genomics. 2008; 1: 6. Published online 2008 February 14. doi: 10.1186/1755-8794-1-6.PMCID: PMC2254643 Identification of molecular pathways affected by pterostilbene, a natural dimethylether analog of resveratrol Zhiqiang Pan, Ameeta K Agarwal, Tao Xu, Qin Feng, Scott R Baerson, Stephen O Duke, and Agnes M Rimando BMC Med Genomics. 2008; 1: 7. Published online 2008 March 20. doi: 10.1186/1755-8794-1-7.PMCID: PMC2330146 Identification of differentially expressed genes in fibroblasts derived from patients with Dupuytren's Contracture Latha Satish, William A LaFramboise, David B O'Gorman, Sandra Johnson, Benjamin Janto, Bing Siang Gan, Mark E Baratz, Fen Z Hu, J Christopher Post, Garth D Ehrlich, and Sandeep Kathju BMC Med Genomics. 2008; 1: 10. Published online 2008 April 23. doi: 10.1186/1755-8794-1-10.PMCID: PMC2377253 Cell cycle correlated genes dictate the prognostic power of breast cancer gene lists Jonathan D Mosley and Ruth A Keri BMC Med Genomics. 2008; 1: 11. Published online 2008 April 25. doi: 10.1186/1755-8794-1-11.PMCID: PMC2396170 The gene expression profiles of primary and metastatic melanoma yields a transition point of tumor progression and metastasis Adam I Riker, Steven A Enkemann, Oystein Fodstad, Suhu Liu, Suping Ren, Christopher Morris, Yaguang Xi, Paul Howell, Brandon Metge, Rajeev S Samant, Lalita A Shevde, Wenbin Li, Steven Eschrich, Adil Daud, Jingfang Ju, and Jaime Matta BMC Med Genomics. 2008; 1: 13. Published online 2008 April 28. doi: 10.1186/1755-8794-1-13.PMCID: PMC2408576 The role of the small intestine in the development of dietary fat-induced obesity and insulin resistance in C57BL/6J mice Nicole JW de Wit, Hanneke Bosch-Vermeulen, Philip J de Groot, Guido JEJ Hooiveld, Mechteld M Grootte Bromhaar, Jenny Jansen, Michael Müller, and Roelof van der Meer BMC Med Genomics. 2008; 1: 14. Published online 2008 May 6. doi: 10.1186/1755-8794-1-14.PMCID: PMC2396659 Classification of human cancers based on DNA copy number amplification modeling Samuel Myllykangas, Jarkko Tikka, Tom Böhling, Sakari Knuutila, and Jaakko Hollmén BMC Med Genomics. 2008; 1: 15. Published online 2008 May 14. doi: 10.1186/1755-8794-1-15.PMCID: PMC2397431 Investigating the complex genetic architecture of ankle-brachial index, a measure of peripheral arterial disease, in non-Hispanic whites Sharon LR Kardia, M Todd Greene, Eric Boerwinkle, Stephen T Turner, and Iftikhar J Kullo BMC Med Genomics. 2008; 1: 16. Published online 2008 May 15. doi: 10.1186/1755-8794-1-16.PMCID: PMC2412898 Pro-neural transcription factors as cancer markers Maria Vias, Charlie E Massie, Philip East, Helen Scott, Anne Warren, Zongxiang Zhou, Alexander Yu Nikitin, David E Neal, and Ian G Mills BMC Med Genomics. 2008; 1: 17. Published online 2008 May 19. doi: 10.1186/1755-8794-1-17.PMCID: PMC2413260 Whole genome identification of Mycobacterium tuberculosis vaccine candidates by comprehensive data mining and bioinformatic analyses Anat Zvi, Naomi Ariel, John Fulkerson, Jerald C Sadoff, and Avigdor Shafferman BMC Med Genomics. 2008; 1: 18. Published online 2008 May 28. doi: 10.1186/1755-8794-1-18.PMCID: PMC2442614 Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis Eleni M Tomazou, Vardhman K Rakyan, Gregory Lefebvre, Robert Andrews, Peter Ellis, David K Jackson, Cordelia Langford, Matthew D Francis, Liselotte Bäckdahl, Marcos Miretti, Penny Coggill, Diego Ottaviani, Denise Sheer, Adele Murrell, and Stephan Beck BMC Med Genomics. 2008; 1: 19. Published online 2008 May 30. doi: 10.1186/1755-8794-1-19.PMCID: PMC2430202 Generation of a non-small cell lung cancer transcriptome microarray Austin Tanney, Gavin R Oliver, Vadim Farztdinov, Richard D Kennedy, Jude M Mulligan, Ciaran E Fulton, Susan M Farragher, John K Field, Patrick G Johnston, D Paul Harkin, Vitali Proutski, and Karl A Mulligan BMC Med Genomics. 2008; 1: 20. Published online 2008 May 30. doi: 10.1186/1755-8794-1-20.PMCID: PMC2426710 Association of ABCB1 genetic variants with renal function in Africans and in Caucasians Murielle Bochud, Chin B Eap, Marc Maillard, Toby Johnson, Peter Vollenweider, Pascal Bovet, Robert C Elston, Sven Bergmann, Jacques S Beckmann, Dawn M Waterworth, Vincent Mooser, Anne Gabriel, and Michel Burnier BMC Med Genomics. 2008; 1: 21. Published online 2008 June 2. doi: 10.1186/1755-8794-1-21.PMCID: PMC2424071 Worldwide population differentiation at disease-associated SNPs Sean Myles, Dan Davison, Jeffrey Barrett, Mark Stoneking, and Nic Timpson BMC Med Genomics. 2008; 1: 22. Published online 2008 June 4. doi: 10.1186/1755-8794-1-22.PMCID: PMC2440747 A genome-wide search replicates evidence of a quantitative trait locus for circulating angiotensin I-converting enzyme (ACE) unlinked to the ACE gene Colin A McKenzie, Xiaofeng Zhu, Terrence E Forrester, Amy Luke, Adebowale A Adeyemo, Nourdine Bouzekri, and Richard S Cooper BMC Med Genomics. 2008; 1: 23. Published online 2008 June 10. doi: 10.1186/1755-8794-1-23.PMCID: PMC2442613 Genome wide SNP comparative analysis between EGFR and KRAS mutated NSCLC and characterization of two models of oncogenic cooperation in non-small cell lung carcinoma Hélène Blons, Karine Pallier, Delphine Le Corre, Claire Danel, Maxime Tremblay-Gravel, Claude Houdayer, Elizabeth Fabre-Guillevin, Marc Riquet, Philippe Dessen, and Pierre Laurent-Puig BMC Med Genomics. 2008; 1: 25. Published online 2008 June 12. doi: 10.1186/1755-8794-1-25.PMCID: PMC2527324 Whole genome assessment of the retinal response to diabetes reveals a progressive neurovascular inflammatory response Robert M Brucklacher, Kruti M Patel, Heather D VanGuilder, Georgina V Bixler, Alistair J Barber, David A Antonetti, Cheng-Mao Lin, Kathryn F LaNoue, Thomas W Gardner, Sarah K Bronson, and Willard M Freeman BMC Med Genomics. 2008; 1: 26. Published online 2008 June 13. doi: 10.1186/1755-8794-1-26.PMCID: PMC2442612 Molecular analysis of the vaginal response to estrogens in the ovariectomized rat and postmenopausal woman Scott A Jelinsky, Sung E Choe, Judy S Crabtree, Monette M Cotreau, Ewa Wilson, Kathryn Saraf, Andrew J Dorner, Eugene L Brown, Bryan J Peano, Xiaochun Zhang, Richard C Winneker, and Heather A Harris BMC Med Genomics. 2008; 1: 27. Published online 2008 June 25. doi: 10.1186/1755-8794-1-27.PMCID: PMC2453134 Pathway analysis reveals functional convergence of gene expression profiles in breast cancer Ronglai Shen, Arul M Chinnaiyan, and Debashis Ghosh BMC Med Genomics. 2008; 1: 28. Published online 2008 June 27. doi: 10.1186/1755-8794-1-28.PMCID: PMC2447843 Characterization of global transcription profile of normal and HPV-immortalized keratinocytes and their response to TNF treatment Lara Termini, Enrique Boccardo, Gustavo H Esteves, Roberto Hirata, Jr, Waleska K Martins, Anna Estela L Colo, E Jordão Neves, Luisa Lina Villa, and Luiz FL Reis BMC Med Genomics. 2008; 1: 29. Published online 2008 June 27. doi: 10.1186/1755-8794-1-29.PMCID: PMC2459201 Gene expression in periodontal tissues following treatment Thomas Beikler, Ulrike Peters, Karola Prior, Martin Eisenacher, and Thomas F Flemmig BMC Med Genomics. 2008; 1: 30. Published online 2008 July 7. doi: 10.1186/1755-8794-1-30.PMCID: PMC2491649 Increased cell motility and invasion upon knockdown of lipolysis stimulated lipoprotein receptor (LSR) in SW780 bladder cancer cells Malene Herbsleb, Karin Birkenkamp-Demtroder, Thomas Thykjaer, Carsten Wiuf, Anne-Mette K Hein, Torben F Ørntoft, and Lars Dyrskjøt BMC Med Genomics. 2008; 1: 31. Published online 2008 July 22. doi: 10.1186/1755-8794-1-31.PMCID: PMC2492871 My sister's keeper?: genomic research and the identifiability of siblings Christopher A Cassa, Brian Schmidt, Isaac S Kohane, and Kenneth D Mandl BMC Med Genomics. 2008; 1: 32. Published online 2008 July 25. doi: 10.1186/1755-8794-1-32.PMCID: PMC2503988 Influence of monolayer, spheroid, and tumor growth conditions on chromosome 3 gene expression in tumorigenic epithelial ovarian cancer cell lines Neal AL Cody, Magdalena Zietarska, Ali Filali-Mouhim, Diane M Provencher, Anne-Marie Mes-Masson, and Patricia N Tonin BMC Med Genomics. 2008; 1: 34. Published online 2008 August 7. doi: 10.1186/1755-8794-1-34.PMCID: PMC2519080 Role of Caveolin 1, E-Cadherin, Enolase 2 and PKCalpha on resistance to methotrexate in human HT29 colon cancer cells Elisabet Selga, Cristina Morales, Véronique Noé, Miguel A Peinado, and Carlos J Ciudad BMC Med Genomics. 2008; 1: 35. Published online 2008 August 11. doi: 10.1186/1755-8794-1-35.PMCID: PMC2527490 Differential expression of genes mapping to recurrently abnormal chromosomal regions characterize neuroblastic tumours with distinct ploidy status Cinzia Lavarino, Idoia Garcia, Carlos Mackintosh, Nai-Kong V Cheung, Gema Domenech, José Ríos, Noelia Perez, Eva Rodríguez, Carmen de Torres, William L Gerald, Esperanza Tuset, Sandra Acosta, Helena Beleta, Enrique de Álava, and Jaume Mora BMC Med Genomics. 2008; 1: 36. Published online 2008 August 13. doi: 10.1186/1755-8794-1-36.PMCID: PMC2531130 An integrative genomic approach reveals coordinated expression of intronic miR-335, miR-342, and miR-561 with deregulated host genes in multiple myeloma Domenica Ronchetti, Marta Lionetti, Laura Mosca, Luca Agnelli, Adrian Andronache, Sonia Fabris, Giorgio Lambertenghi Deliliers, and Antonino Neri BMC Med Genomics. 2008; 1: 37. Published online 2008 August 13. doi: 10.1186/1755-8794-1-37.PMCID: PMC2531129 Tobacco use induces anti-apoptotic, proliferative patterns of gene expression in circulating leukocytes of Caucasian males Peter C Charles, Brian D Alder, Eleanor G Hilliard, Jonathan C Schisler, Robert E Lineberger, Joel S Parker, Sabeen Mapara, Samuel S Wu, Andrea Portbury, Cam Patterson, and George A Stouffer BMC Med Genomics. 2008; 1: 38. Published online 2008 August 18. doi: 10.1186/1755-8794-1-38.PMCID: PMC2531187 Identification of a gene signature in cell cycle pathway for breast cancer prognosis using gene expression profiling data Jiangang Liu, Andrew Campen, Shuguang Huang, Sheng-Bin Peng, Xiang Ye, Mathew Palakal, A Keith Dunker, Yuni Xia, and Shuyu Li BMC Med Genomics. 2008; 1: 39. Published online 2008 September 11. doi: 10.1186/1755-8794-1-39.PMCID: PMC2551605 Transcriptomic signature of Bexarotene (Rexinoid LGD1069) on mammary gland from three transgenic mouse mammary cancer models Martin C Abba, Yuhui Hu, Carla C Levy, Sally Gaddis, Frances S Kittrell, Yun Zhang, Jamal Hill, Reid P Bissonnette, Daniel Medina, Powel H Brown, and C Marcelo Aldaz BMC Med Genomics. 2008; 1: 40. Published online 2008 September 11. doi: 10.1186/1755-8794-1-40.PMCID: PMC2563021 A high confidence, manually validated human blood plasma protein reference set Susann Schenk, Gary J Schoenhals, Gustavo de Souza, and Matthias Mann BMC Med Genomics. 2008; 1: 41. Published online 2008 September 15. doi: 10.1186/1755-8794-1-41.PMCID: PMC2563020 The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets – improving meta-analysis and prediction of prognosis Andrew H Sims, Graeme J Smethurst, Yvonne Hey, Michal J Okoniewski, Stuart D Pepper, Anthony Howell, Crispin J Miller, and Robert B Clarke BMC Med Genomics. 2008; 1: 42. Published online 2008 September 21. doi: 10.1186/1755-8794-1-42.PMCID: PMC2563019 Regulatory subunits of PKA define an axis of cellular proliferation/differentiation in ovarian cancer cells Chris Cheadle, Maria Nesterova, Tonya Watkins, Kathleen C Barnes, John C Hall, Antony Rosen, Kevin G Becker, and Yoon S Cho-Chung BMC Med Genomics. 2008; 1: 43. Published online 2008 September 26. doi: 10.1186/1755-8794-1-43.PMCID: PMC2577111 A genome-wide association study for late-onset Alzheimer's disease using DNA pooling Richard Abraham, Valentina Moskvina, Rebecca Sims, Paul Hollingworth, Angharad Morgan, Lyudmila Georgieva, Kimberley Dowzell, Sven Cichon, Axel M Hillmer, Michael C O'Donovan, Julie Williams, Michael J Owen, and George Kirov BMC Med Genomics. 2008; 1: 44. Published online 2008 September 29. doi: 10.1186/1755-8794-1-44.PMCID: PMC2570675 Gene expression in BMPR2 mutation carriers with and without evidence of Pulmonary Arterial Hypertension suggests pathways relevant to disease penetrance James West, Joy Cogan, Mark Geraci, Linda Robinson, John Newman, John A Phillips, Kirk Lane, Barbara Meyrick, and Jim Loyd BMC Med Genomics. 2008; 1: 45. Published online 2008 September 29. doi: 10.1186/1755-8794-1-45.PMCID: PMC2561034 A systems biology approach to construct the gene regulatory network of systemic inflammation via microarray and databases mining Bor-Sen Chen, Shih-Kuang Yang, Chung-Yu Lan, and Yung-Jen Chuang BMC Med Genomics. 2008; 1: 46. Published online 2008 September 30. doi: 10.1186/1755-8794-1-46.PMCID: PMC2567339 DNA methylation changes in ovarian cancer are cumulative with disease progression and identify tumor stage George S Watts, Bernard W Futscher, Nicholas Holtan, Koen DeGeest, Frederick E Domann, and Stephen L Rose BMC Med Genomics. 2008; 1: 47. Published online 2008 September 30. doi: 10.1186/1755-8794-1-47.PMCID: PMC2566571 The Comparative Toxicogenomics Database facilitates identification and understanding of chemical-gene-disease associations: arsenic as a case study Allan P Davis, Cynthia G Murphy, Michael C Rosenstein, Thomas C Wiegers, and Carolyn J Mattingly BMC Med Genomics. 2008; 1: 48. Published online 2008 October 9. doi: 10.1186/1755-8794-1-48.PMCID: PMC2576347 The molecular basis of genistein-induced mitotic arrest and exit of self-renewal in embryonal carcinoma and primary cancer cell lines Christian RA Regenbrecht, Marc Jung, Hans Lehrach, and James Adjaye BMC Med Genomics. 2008; 1: 49. Published online 2008 October 10. doi: 10.1186/1755-8794-1-49.PMCID: PMC2577110 Multiplex ligation-dependent probe amplification for genetic screening in autism spectrum disorders: Efficient identification of known microduplications and identification of a novel microduplication in ASMT Guiqing Cai, Lisa Edelmann, Juliet E Goldsmith, Ninette Cohen, Alisa Nakamine, Jennifer G Reichert, Ellen J Hoffman, Danielle M Zurawiecki, Jeremy M Silverman, Eric Hollander, Latha Soorya, Evdokia Anagnostou, Catalina Betancur, and Joseph D Buxbaum BMC Med Genomics. 2008; 1: 50. Published online 2008 October 16. doi: 10.1186/1755-8794-1-50.PMCID: PMC2588447 Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age Yohan Lee, Adrienne C Scheck, Timothy F Cloughesy, Albert Lai, Jun Dong, Haumith K Farooqi, Linda M Liau, Steve Horvath, Paul S Mischel, and Stanley F Nelson BMC Med Genomics. 2008; 1: 52. Published online 2008 October 21. doi: 10.1186/1755-8794-1-52.PMCID: PMC2596165 A global transcriptional view of apoptosis in human T-cell activation Min Wang, Dirk Windgassen, and Eleftherios T Papoutsakis BMC Med Genomics. 2008; 1: 53. Published online 2008 October 23. doi: 10.1186/1755-8794-1-53.PMCID: PMC2600644 The distinctive gastric fluid proteome in gastric cancer reveals a multi-biomarker diagnostic profile Oi Lian Kon, Tai-Tung Yip, Meng Fatt Ho, Weng Hoong Chan, Wai Keong Wong, Soo Yong Tan, Wai Har Ng, Siok Yuen Kam, Alvin KH Eng, Patrick Ho, Rosa Viner, Hock Soo Ong, and M Priyanthi Kumarasinghe BMC Med Genomics. 2008; 1: 54. Published online 2008 October 25. doi: 10.1186/1755-8794-1-54.PMCID: PMC2584050 Pathways affected by asbestos exposure in normal and tumour tissue of lung cancer patients Salla Ruosaari, Tuija Hienonen-Kempas, Anne Puustinen, Virinder K Sarhadi, Jaakko Hollmén, Sakari Knuutila, Juha Saharinen, Harriet Wikman, and Sisko Anttila BMC Med Genomics. 2008; 1: 55. Published online 2008 November 11. doi: 10.1186/1755-8794-1-55.PMCID: PMC2612681 Discovery of DNA methylation markers in cervical cancer using relaxation ranking Maté Ongenaert, G Bea A Wisman, Haukeline H Volders, Alice J Koning, Ate GJ van der Zee, Wim van Criekinge, and Ed Schuuring BMC Med Genomics. 2008; 1: 57. Published online 2008 November 24. doi: 10.1186/1755-8794-1-57.PMCID: PMC2605750 Carboplatin-induced gene expression changes in vitro are prognostic of survival in epithelial ovarian cancer Panagiotis A Konstantinopoulos, Elena Fountzilas, Kamana Pillay, Luiz F Zerbini, Towia A Libermann, Stephen A Cannistra, and Dimitrios Spentzos BMC Med Genomics. 2008; 1: 59. Published online 2008 November 28. doi: 10.1186/1755-8794-1-59.PMCID: PMC2613398 Technical Advances Predictive gene lists for breast cancer prognosis: A topographic visualisation study Mingmanas Sivaraksa and David Lowe BMC Med Genomics. 2008; 1: 8. Published online 2008 April 17. doi: 10.1186/1755-8794-1-8.PMCID: PMC2375896 Expression profiling with RNA from formalin-fixed, paraffin-embedded material Andrea Oberli, Vlad Popovici, Mauro Delorenzi, Anna Baltzer, Janine Antonov, Sybille Matthey, Stefan Aebi, Hans Jörg Altermatt, and Rolf Jaggi BMC Med Genomics. 2008; 1: 9. Published online 2008 April 19. doi: 10.1186/1755-8794-1-9.PMCID: PMC2359756 Genotyping panel for assessing response to cancer chemotherapy Zunyan Dai, Audrey C Papp, Danxin Wang, Heather Hampel, and Wolfgang Sadee BMC Med Genomics. 2008; 1: 24. Published online 2008 June 11. doi: 10.1186/1755-8794-1-24.PMCID: PMC2442111 An approach to analyse the specific impact of rapamycin on mRNA-ribosome association Raphael Genolet, Tanguy Araud, Laetitia Maillard, Pascale Jaquier-Gubler, and Joseph Curran BMC Med Genomics. 2008; 1: 33. Published online 2008 August 1. doi: 10.1186/1755-8794-1-33.PMCID: PMC2533349 Expression-based Pathway Signature Analysis (EPSA): Mining publicly available microarray data for insight into human disease Jessica D Tenenbaum, Michael G Walker, Paul J Utz, and Atul J Butte BMC Med Genomics. 2008; 1: 51. Published online 2008 October 20. doi: 10.1186/1755-8794-1-51.PMCID: PMC2588448 |