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KEGG spider: interpretation of genomics data in the context of the global gene metabolic network
Alexey V Antonov, Sabine Dietmann, Hans W Mewes
Genome Biol. 2008; 9(12): R179. Published online 2008 December 18. doi: 10.1186/gb-2008-9-12-r179
PMCID:
PMC2646283
Abstract Full Text PDF–330K Supplementary Material
 Is Cited by the Following 18 Articles in this Archive:
Critical assessment of human metabolic pathway databases: a stepping stone for future integration
Miranda D Stobbe, Sander M Houten, Gerbert A Jansen, Antoine HC van Kampen, Perry D Moerland
BMC Syst Biol. 2011; 5: 165. Published online 2011 October 14. doi: 10.1186/1752-0509-5-165
PMCID:
PMC3271347
Abstract Full Text PDF–994K Supplementary Material
The Implications of Relationships between Human Diseases and Metabolic Subpathways
Xia Li, Chunquan Li, Desi Shang, Jing Li, Junwei Han, Yingbo Miao, Yan Wang, Qianghu Wang, Wei Li, Chao Wu, Yunpeng Zhang, Xiang Li, Qianlan Yao
PLoS One. 2011; 6(6): e21131. Published online 2011 June 17. doi: 10.1371/journal.pone.0021131
PMCID:
PMC3117879
Abstract Full Text PDF–2.2M Supplementary Material
g:Profiler—a web server for functional interpretation of gene lists (2011 update)
Jüri Reimand, Tambet Arak, Jaak Vilo
Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W307–W315. Published online 2011 June 6. doi: 10.1093/nar/gkr378
PMCID:
PMC3125778
Abstract Full Text PDF–5.9M
Path finding methods accounting for stoichiometry in metabolic networks
Jon Pey, Joaquín Prada, John E Beasley, Francisco J Planes
Genome Biol. 2011; 12(5): R49. Published online 2011 May 27. doi: 10.1186/gb-2011-12-5-r49
PMCID:
PMC3219972
Abstract Full Text PDF–642K Supplementary Material
BioProfiling.de: analytical web portal for high-throughput cell biology
Alexey V. Antonov
Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W323–W327. Published online 2011 May 23. doi: 10.1093/nar/gkr372
PMCID:
PMC3125774
Abstract Full Text PDF–215K
A complement receptor C5a antagonist regulates epithelial to mesenchymal transition and crystallin expression after lens cataract surgery in mice
Rinako Suetsugu-Maki, Nobuyasu Maki, Timothy P. Fox, Kenta Nakamura, Richard Cowper.Solari, Craig R. Tomlinson, Hongchang Qu, John D. Lambris, Panagiotis A. Tsonis
Mol Vis. 2011; 17: 949–964. Published online 2011 April 19.
PMCID:
PMC3084220
Abstract Full Text PDF–1.0M
Bioinformatics Analysis of Macrophages Exposed to Porphyromonas gingivalis: Implications in Acute vs. Chronic Infections
Wen-Han Yu, Han Hu, Qingde Zhou, Yu Xia, Salomon Amar
PLoS One. 2010; 5(12): e15613. Published online 2010 December 23. doi: 10.1371/journal.pone.0015613
PMCID:
PMC3009741
Abstract Full Text PDF–298K Supplementary Material
MIPS: curated databases and comprehensive secondary data resources in 2010
H. Werner Mewes, Andreas Ruepp, Fabian Theis, Thomas Rattei, Mathias Walter, Dmitrij Frishman, Karsten Suhre, Manuel Spannagl, Klaus F.X. Mayer, Volker Stümpflen, Alexey Antonov
Nucleic Acids Res. 2011 January; 39(Database issue): D220–D224. Published online 2010 November 24. doi: 10.1093/nar/gkq1157
PMCID:
PMC3013725
Abstract Full Text PDF–1.1M
The early asthmatic response is associated with glycolysis, calcium binding and mitochondria activity as revealed by proteomic analysis in rats
Yu-Dong Xu, Jian-Mei Cui, Yu Wang, Lei-Miao Yin, Chang-Ke Gao, Yan-Yan Liu, Yong-Qing Yang
Respir Res. 2010; 11(1): 107. Published online 2010 August 6. doi: 10.1186/1465-9921-11-107
PMCID:
PMC2925830
Abstract Full Text PDF–1.3M Supplementary Material
CCancer: a bird’s eye view on gene lists reported in cancer-related studies
Sabine Dietmann, Wanseon Lee, Philip Wong, Igor Rodchenkov, Alexey V. Antonov
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W118–W123. Published online 2010 June 5. doi: 10.1093/nar/gkq515
PMCID:
PMC2896190
Abstract Full Text PDF–97K
R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases
Alexey V. Antonov, Esther E. Schmidt, Sabine Dietmann, Maria Krestyaninova, Henning Hermjakob
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W78–W83. Published online 2010 June 2. doi: 10.1093/nar/gkq482
PMCID:
PMC2896180
Abstract Full Text PDF–2.7M
Construction of a large scale integrated map of macrophage pathogen recognition and effector systems
Sobia Raza, Neil McDerment, Paul A Lacaze, Kevin Robertson, Steven Watterson, Ying Chen, Michael Chisholm, George Eleftheriadis, Stephanie Monk, Maire O'Sullivan, Arran Turnbull, Douglas Roy, Athanasios Theocharidis, Peter Ghazal, Tom C Freeman
BMC Syst Biol. 2010; 4: 63. Published online 2010 May 14. doi: 10.1186/1752-0509-4-63
PMCID:
PMC2892459
Abstract Full Text PDF–6.5M Supplementary Material
Seasonal proteomic changes reveal molecular adaptations to preserve and replenish liver proteins during ground squirrel hibernation
L. Elaine Epperson, James C. Rose, Hannah V. Carey, Sandra L. Martin
Am J Physiol Regul Integr Comp Physiol. 2010 February; 298(2): R329–R340. Published online 2009 November 18. doi: 10.1152/ajpregu.00416.2009
PMCID:
PMC2828287
Abstract Full Text Supplementary Material
SubpathwayMiner: a software package for flexible identification of pathways
Chunquan Li, Xia Li, Yingbo Miao, Qianghu Wang, Wei Jiang, Chun Xu, Jing Li, Junwei Han, Fan Zhang, Binsheng Gong, Liangde Xu
Nucleic Acids Res. 2009 October; 37(19): e131. Published online 2009 October. doi: 10.1093/nar/gkp667
PMCID:
PMC2770656
Abstract Full Text PDF–6.8M
GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists
Alexey V. Antonov, Sabine Dietmann, Philip Wong, Dominik Lutter, Hans W. Mewes
Nucleic Acids Res. 2009 July 1; 37(Web Server issue): W323–W328. Published online 2009 July 1. doi: 10.1093/nar/gkp313
PMCID:
PMC2703952
Abstract Full Text PDF–94K
PathExpress update: the enzyme neighbourhood method of associating gene-expression data with metabolic pathways
Nicolas Goffard, Tancred Frickey, Georg Weiller
Nucleic Acids Res. 2009 July 1; 37(Web Server issue): W335–W339. Published online 2009 July 1. doi: 10.1093/nar/gkp432
PMCID:
PMC2703986
Abstract Full Text PDF–330K
ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii
Patrick May, Jan-Ole Christian, Stefan Kempa, Dirk Walther
BMC Genomics. 2009; 10: 209. Published online 2009 May 4. doi: 10.1186/1471-2164-10-209
PMCID:
PMC2688524
Abstract Full Text PDF–815K Supplementary Material
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