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MatchMiner: a tool for batch navigation among gene and gene product identifiers
Kimberly J Bussey, David Kane, Margot Sunshine, Sudar Narasimhan, Satoshi Nishizuka, William C Reinhold, Barry Zeeberg, Ajay, John N Weinstein
Genome Biol. 2003; 4(4): R27. Published online 2003 March 25. doi: 10.1186/gb-2003-4-4-r27
PMCID:
PMC154578
Abstract Full Text PDF–447K
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 Is Cited by the Following 49 Articles in this Archive:
Identifier mapping performance for integrating transcriptomics and proteomics experimental results
Roger S Day, Kevin K McDade, Uma R Chandran, Alex Lisovich, Thomas P Conrads, Brian L Hood, VS Kumar Kolli, David Kirchner, Traci Litzi, G Larry Maxwell
BMC Bioinformatics. 2011; 12: 213. Published online 2011 May 27. doi: 10.1186/1471-2105-12-213
PMCID:
PMC3124437
Abstract Full Text PDF–2.1M
Microbiota Modulate Host Gene Expression via MicroRNAs
Guillaume Dalmasso, Hang Thi Thu Nguyen, Yutao Yan, Hamed Laroui, Moiz A. Charania, Saravanan Ayyadurai, Shanthi V. Sitaraman, Didier Merlin
PLoS One. 2011; 6(4): e19293. Published online 2011 April 29. doi: 10.1371/journal.pone.0019293
PMCID:
PMC3084815
Abstract Full Text PDF–291K Supplementary Material
Do Two Machine-Learning Based Prognostic Signatures for Breast Cancer Capture the Same Biological Processes?
Yotam Drier, Eytan Domany
PLoS One. 2011; 6(3): e17795. Published online 2011 March 14. doi: 10.1371/journal.pone.0017795
PMCID:
PMC3056769
Abstract Full Text PDF–107K Supplementary Material
Schizophrenia and vitamin D related genes could have been subject to latitude-driven adaptation
Roberto Amato, Michele Pinelli, Antonella Monticelli, Gennaro Miele, Sergio Cocozza
BMC Evol Biol. 2010; 10: 351. Published online 2010 November 11. doi: 10.1186/1471-2148-10-351
PMCID:
PMC2996405
Abstract Full Text PDF–1.4M Supplementary Material
Module-based prediction approach for robust inter-study predictions in microarray data
Zhibao Mi, Kui Shen, Nan Song, Chunrong Cheng, Chi Song, Naftali Kaminski, George C. Tseng
Bioinformatics. 2010 October 15; 26(20): 2586–2593. Published online 2010 August 17. doi: 10.1093/bioinformatics/btq472
PMCID:
PMC2951088
Abstract Full Text PDF–622K Supplementary Material
MicroRNAs determine human intestinal epithelial cell fate
Guillaume Dalmasso, Hang Thi Thu Nguyen, Yutao Yan, Hamed Laroui, Shanthi Srinivasan, Shanthi V Sitaraman, Didier Merlin
Differentiation. Author manuscript; available in PMC 2011 September 1.
Published in final edited form as: Differentiation. 2010 Sep–Oct; 80(2-3): 147–154. Published online 2010 July 17. doi: 10.1016/j.diff.2010.06.005
PMCID:
PMC2943016
Abstract Full Text PDF–1.3M Supplementary Material
The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services
Martijn P van Iersel, Alexander R Pico, Thomas Kelder, Jianjiong Gao, Isaac Ho, Kristina Hanspers, Bruce R Conklin, Chris T Evelo
BMC Bioinformatics. 2010; 11: 5. Published online 2010 January 4. doi: 10.1186/1471-2105-11-5
PMCID:
PMC2824678
Abstract Full Text PDF–299K Supplementary Material
Differential expression of apoptotic genes PDIA3 and MAP3K5 distinguishes between low- and high-risk prostate cancer
Nicole Chui Pressinotti, Helmut Klocker, Georg Schäfer, Van-Duc Luu, Markus Ruschhaupt, Ruprecht Kuner, Eberhard Steiner, Annemarie Poustka, Georg Bartsch, Holger Sültmann
Mol Cancer. 2009; 8: 130. Published online 2009 December 27. doi: 10.1186/1476-4598-8-130
PMCID:
PMC2807430
Abstract Full Text PDF–1.7M Supplementary Material
Impact of biospecimens handling on biomarker research in breast cancer
Loris De Cecco, Valeria Musella, Silvia Veneroni, Vera Cappelletti, Italia Bongarzone, Maurizio Callari, Barbara Valeri, Marco A Pierotti, Maria Grazia Daidone
BMC Cancer. 2009; 9: 409. Published online 2009 November 24. doi: 10.1186/1471-2407-9-409
PMCID:
PMC2787533
Abstract Full Text PDF–1.1M
Acquisition of the contractile phenotype by murine arterial smooth muscle cells depends on the Mir143/145 gene cluster
Thomas Boettger, Nadine Beetz, Sawa Kostin, Johanna Schneider, Marcus Krüger, Lutz Hein, Thomas Braun
J Clin Invest. 2009 September 1; 119(9): 2634–2647. Published online 2009 August 17. doi: 10.1172/JCI38864
PMCID:
PMC2735940
Abstract Full Text PDF–4.6M Supplementary Material
WebArrayDB: cross-platform microarray data analysis and public data repository
Xiao-Qin Xia, Michael McClelland, Steffen Porwollik, Wenzhi Song, Xianling Cong, Yipeng Wang
Bioinformatics. 2009 September 15; 25(18): 2425–2429. Published online 2009 July 14. doi: 10.1093/bioinformatics/btp430
PMCID:
PMC2735672
Abstract Full Text PDF–304K
ProGMap: an integrated annotation resource for protein orthology
Arnold Kuzniar, Ke Lin, Ying He, Harm Nijveen, Sándor Pongor, Jack A. M. Leunissen
Nucleic Acids Res. 2009 July 1; 37(Web Server issue): W428–W434. Published online 2009 July 1. doi: 10.1093/nar/gkp462
PMCID:
PMC2703891
Abstract Full Text PDF–4.8M
How Do Human Cells React to the Absence of Mitochondrial DNA?
Rossana Mineri, Norman Pavelka, Erika Fernandez-Vizarra, Paola Ricciardi-Castagnoli, Massimo Zeviani, Valeria Tiranti
PLoS ONE. 2009; 4(5): e5713. Published online 2009 May 28. doi: 10.1371/journal.pone.0005713
PMCID:
PMC2683933
Abstract Full Text PDF–274K Supplementary Material
Ratio adjustment and calibration scheme for gene-wise normalization to enhance microarray inter-study prediction
Chunrong Cheng, Kui Shen, Chi Song, Jianhua Luo, George C. Tseng
Bioinformatics. 2009 July 1; 25(13): 1655–1661. Published online 2009 May 4. doi: 10.1093/bioinformatics/btp292
PMCID:
PMC2732320
Abstract Full Text PDF–555K Supplementary Material
The gene expression signature of genomic instability in breast cancer is an independent predictor of clinical outcome
Jens K. Habermann, Jana Doering, Sampsa Hautaniemi, Uwe J. Roblick, Nana K. Bündgen, Daniel Nicorici, Ulrike Kronenwett, Shruti Rathnagiriswaran, Rama K. R. Mettu, Yan Ma, Stefan Krüger, Hans-Peter Bruch, Gert Auer, Nancy L. Guo, Thomas Ried
Int J Cancer. Author manuscript; available in PMC 2010 April 1.
Published in final edited form as: Int J Cancer. 2009 April 1; 124(7): 1552–1564. doi: 10.1002/ijc.24017
PMCID:
PMC2707256
Abstract Full Text PDF–861K Supplementary Material
Post-Translational Regulation of Oct4 Transcriptional Activity
Jonathan P. Saxe, Alexey Tomilin, Hans R. Schöler, Kathrin Plath, Jing Huang
PLoS ONE. 2009; 4(2): e4467. Published online 2009 February 16. doi: 10.1371/journal.pone.0004467
PMCID:
PMC2637973
Abstract Full Text PDF–484K Supplementary Material
ArrayIDer: automated structural re-annotation pipeline for DNA microarrays
Bart HJ van den Berg, Jay H Konieczka, Fiona M McCarthy, Shane C Burgess
BMC Bioinformatics. 2009; 10: 30. Published online 2009 January 23. doi: 10.1186/1471-2105-10-30
PMCID:
PMC2636773
Abstract Full Text PDF–385K
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
Da Wei Huang, Brad T. Sherman, Richard A. Lempicki
Nucleic Acids Res. 2009 January; 37(1): 1–13. Published online 2009 January. doi: 10.1093/nar/gkn923
PMCID:
PMC2615629
Abstract Full Text PDF–239K Supplementary Material
An integrative genomic and proteomic approach to chemosensitivity prediction
Yan Ma, Zhenyu Ding, Yong Qian, Ying-Wooi Wan, Kursad Tosun, Xianglin Shi, Vincent Castranova, E. James Harner, Nancy I. Guo
Int J Oncol. Author manuscript; available in PMC 2010 January 1.
Published in final edited form as: Int J Oncol. 2009 January; 34(1): 107–115. doi: 10.3892/ijo_00000134
PMCID:
PMC2667126
Abstract Full Text PDF–803K Supplementary Material
Confirmation of gene expression-based prediction of survival in non-small cell lung cancer
Nancy L. Guo, Ying-Wooi Wan, Kursad Tosun, Hong Lin, Zola Msiska, Daniel C. Flynn, Scot C. Remick, Val Vallyathan, Afshin Dowlati, Xianglin Shi, Vincent Castranova, David G. Beer, Yong Qian
Clin Cancer Res. Author manuscript; available in PMC 2009 December 15.
Published in final edited form as: Clin Cancer Res. 2008 December 15; 14(24): 8213–8220. doi: 10.1158/1078-0432.CCR-08-0095
PMCID:
PMC2605664
Abstract Full Text PDF–1.8M Supplementary Material
CRONOS: the cross-reference navigation server
Brigitte Waegele, Irmtraud Dunger-Kaltenbach, Gisela Fobo, Corinna Montrone, H.-Werner Mewes, Andreas Ruepp
Bioinformatics. 2009 January 1; 25(1): 141–143. Published online 2008 November 13. doi: 10.1093/bioinformatics/btn590
PMCID:
PMC2638938
Abstract Full Text PDF–124K Supplementary Material
A miRNA Signature of Prion Induced Neurodegeneration
Reuben Saba, Chelsey D. Goodman, Rhiannon L. C. H. Huzarewich, Catherine Robertson, Stephanie A. Booth
PLoS ONE. 2008; 3(11): e3652. Published online 2008 November 6. doi: 10.1371/journal.pone.0003652
PMCID:
PMC2575400
Abstract Full Text PDF–752K Supplementary Material
DAVID gene ID conversion tool
Da Wei Huang, Brad T Sherman, Robert Stephens, Michael W Baseler, H Clifford Lane, Richard A Lempicki
Bioinformation. 2008; 2(10): 428–430. Published online 2008 July 30.
PMCID:
PMC2561161
Abstract Full Text PDF–101K Supplementary Material
Using transcriptional profiling to develop a diagnostic test of operational tolerance in liver transplant recipients
Marc Martínez-Llordella, Juan José Lozano, Isabel Puig-Pey, Giuseppe Orlando, Giuseppe Tisone, Jan Lerut, Carlos Benítez, Jose Antonio Pons, Pascual Parrilla, Pablo Ramírez, Miquel Bruguera, Antoni Rimola, Alberto Sánchez-Fueyo
J Clin Invest. 2008 August 1; 118(8): 2845–2857. Published online 2008 July 24. doi: 10.1172/JCI35342
PMCID:
PMC2483684
Abstract Full Text PDF–1.5M Supplementary Material
GenCLiP: a software program for clustering gene lists by literature profiling and constructing gene co-occurrence networks related to custom keywords
Zhong-Xi Huang, Hui-Yong Tian, Zhen-Fu Hu, Yi-Bo Zhou, Jin Zhao, Kai-Tai Yao
BMC Bioinformatics. 2008; 9: 308. Published online 2008 July 13. doi: 10.1186/1471-2105-9-308
PMCID:
PMC2483997
Abstract Full Text PDF–692K Supplementary Material
Regulation of Multiple Core Spliceosomal Proteins by Alternative Splicing-Coupled Nonsense-Mediated mRNA Decay
Arneet L. Saltzman, Yoon Ki Kim, Qun Pan, Matthew M. Fagnani, Lynne E. Maquat, Benjamin J. Blencowe
Mol Cell Biol. 2008 July; 28(13): 4320–4330. Published online 2008 April 28. doi: 10.1128/MCB.00361-08
PMCID:
PMC2447145
Abstract Full Text PDF–493K Supplementary Material
Application of a correlation correction factor in a microarray cross-platform reproducibility study
Kellie J Archer, Catherine I Dumur, G Scott Taylor, Michael D Chaplin, Anthony Guiseppi-Elie, Geraldine Grant, Andrea Ferreira-Gonzalez, Carleton T Garrett
BMC Bioinformatics. 2007; 8: 447. Published online 2007 November 15. doi: 10.1186/1471-2105-8-447
PMCID:
PMC2211756
Abstract Full Text PDF–443K
Genes involved in TGFβ1-driven epithelial-mesenchymal transition of renal epithelial cells are topologically related in the human interactome map
Stefano Campanaro, Simone Picelli, Rossella Torregrossa, Laura Colluto, Monica Ceol, Dorella Del Prete, Angela D'Angelo, Giorgio Valle, Franca Anglani
BMC Genomics. 2007; 8: 383. Published online 2007 October 22. doi: 10.1186/1471-2164-8-383
PMCID:
PMC2174485
Abstract Full Text PDF–2.5M Supplementary Material
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases
Richard G Côté, Philip Jones, Lennart Martens, Samuel Kerrien, Florian Reisinger, Quan Lin, Rasko Leinonen, Rolf Apweiler, Henning Hermjakob
BMC Bioinformatics. 2007; 8: 401. Published online 2007 October 18. doi: 10.1186/1471-2105-8-401
PMCID:
PMC2151082
Abstract Full Text PDF–888K
Portraits of breast cancer progression
Gul S Dalgin, Gabriela Alexe, Daniel Scanfeld, Pablo Tamayo, Jill P Mesirov, Shridar Ganesan, Charles DeLisi, Gyan Bhanot
BMC Bioinformatics. 2007; 8: 291. Published online 2007 August 6. doi: 10.1186/1471-2105-8-291
PMCID:
PMC1978212
Abstract Full Text PDF–5.0M Supplementary Material
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