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Computational prediction of human metabolic pathways from the complete human genome
Pedro Romero, Jonathan Wagg, Michelle L Green, Dale Kaiser, Markus Krummenacker, Peter D Karp
Genome Biol. 2005; 6(1): R2. Published online 2004 December 22. doi: 10.1186/gb-2004-6-1-r2
PMCID:
PMC549063
Abstract Full Text PDF–278K Supplementary Material

Is Cited by the Following 56 Articles in this Archive:

Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT
Rasmus Agren, Sergio Bordel, Adil Mardinoglu, Natapol Pornputtapong, Intawat Nookaew, Jens Nielsen
PLoS Comput Biol. 2012 May; 8(5): e1002518. Published online 2012 May 17. doi: 10.1371/journal.pcbi.1002518
PMCID:
PMC3355067
Abstract Full Text PDF–472K Supplementary Material
Novel search method for the discovery of functional relationships
Fidel Ramírez, Glenn Lawyer, Mario Albrecht
Bioinformatics. 2012 January 15; 28(2): 269–276. Published online 2011 December 16. doi: 10.1093/bioinformatics/btr631
PMCID:
PMC3259435
Abstract Full Text PDF–674K Supplementary Material
MMMDB: Mouse Multiple Tissue Metabolome Database
Masahiro Sugimoto, Satsuki Ikeda, Kanako Niigata, Masaru Tomita, Hideyo Sato, Tomoyoshi Soga
Nucleic Acids Res. 2012 January; 40(D1): D809–D814. Published online 2011 December 1. doi: 10.1093/nar/gkr1170
PMCID:
PMC3245187
Abstract Full Text PDF–2.1M
Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data
Alla Karnovsky, Terry Weymouth, Tim Hull, V. Glenn Tarcea, Giovanni Scardoni, Carlo Laudanna, Maureen A. Sartor, Kathleen A. Stringer, H. V. Jagadish, Charles Burant, Brian Athey, Gilbert S. Omenn
Bioinformatics. 2012 February 1; 28(3): 373–380. Published online 2011 November 30. doi: 10.1093/bioinformatics/btr661
PMCID:
PMC3268237
Free in PMC on 2013/02/01
DNAtraffic—a new database for systems biology of DNA dynamics during the cell life
Krzysztof Kuchta, Daniela Barszcz, Elzbieta Grzesiuk, Pawel Pomorski, Joanna Krwawicz
Nucleic Acids Res. 2012 January; 40(D1): D1235–D1240. Published online 2011 November 22. doi: 10.1093/nar/gkr962
PMCID:
PMC3245060
Abstract Full Text PDF–6.3M
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
Structural diversity of biologically interesting datasets: a scaffold analysis approach
Varun Khanna, Shoba Ranganathan
J Cheminform. 2011; 3: 30. Published online 2011 August 8. doi: 10.1186/1758-2946-3-30
PMCID:
PMC3179739
Abstract Full Text PDF–2.3M Supplementary Material
A metabolic model of the mitochondrion and its use in modelling diseases of the tricarboxylic acid cycle
Anthony C Smith, Alan J Robinson
BMC Syst Biol. 2011; 5: 102. Published online 2011 June 29. doi: 10.1186/1752-0509-5-102
PMCID:
PMC3152903
Abstract Full Text PDF–620K Supplementary Material
A Survey of Metabolic Databases Emphasizing the MetaCyc Family
Peter D. Karp, Ron Caspi
Arch Toxicol. Author manuscript; available in PMC 2012 September 1.
Published in final edited form as: Arch Toxicol. 2011 September; 85(9): 1015–1033. Published online 2011 April 27. doi: 10.1007/s00204-011-0705-2
PMCID:
PMC3352032
Free in PMC on 2012/09/01
Consensus-Phenotype Integration of Transcriptomic and Metabolomic Data Implies a Role for Metabolism in the Chemosensitivity of Tumour Cells
Rachel Cavill, Atanas Kamburov, James K. Ellis, Toby J. Athersuch, Marcus S. C. Blagrove, Ralf Herwig, Timothy M. D. Ebbels, Hector C. Keun
PLoS Comput Biol. 2011 March; 7(3): e1001113. Published online 2011 March 31. doi: 10.1371/journal.pcbi.1001113
PMCID:
PMC3068923
Abstract Full Text PDF–2.1M Supplementary Material
Pathway Commons, a web resource for biological pathway data
Ethan G. Cerami, Benjamin E. Gross, Emek Demir, Igor Rodchenkov, Özgün Babur, Nadia Anwar, Nikolaus Schultz, Gary D. Bader, Chris Sander
Nucleic Acids Res. 2011 January; 39(Database issue): D685–D690. Published online 2010 November 10. doi: 10.1093/nar/gkq1039
PMCID:
PMC3013659
Abstract Full Text PDF–1.8M
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1
Martin I Sigurdsson, Neema Jamshidi, Eirikur Steingrimsson, Ines Thiele, Bernhard Ø Palsson
BMC Syst Biol. 2010; 4: 140. Published online 2010 October 19. doi: 10.1186/1752-0509-4-140
PMCID:
PMC2978158
Abstract Full Text PDF–675K Supplementary Material
Network analysis of human protein location
Gaurav Kumar, Shoba Ranganathan
BMC Bioinformatics. 2010; 11(Suppl 7): S9. Published online 2010 October 15. doi: 10.1186/1471-2105-11-S7-S9
PMCID:
PMC2957692
Abstract Full Text PDF–1.2M Supplementary Material
Gene regulatory network reveals oxidative stress as the underlying molecular mechanism of type 2 diabetes and hypertension
Jesmin, Mahbubur SM Rashid, Hasan Jamil, Raquel Hontecillas, Josep Bassaganya-Riera
BMC Med Genomics. 2010; 3: 45. Published online 2010 October 13. doi: 10.1186/1755-8794-3-45
PMCID:
PMC2965702
Abstract Full Text PDF–3.8M Supplementary Material
Prediction of human protein–protein interaction by a mixed Bayesian model and its application to exploring underlying cancer-related pathway crosstalk
Yan Xu, Wen Hu, Zhiqiang Chang, Huizi DuanMu, Shanzhen Zhang, Zhenqi Li, Zihui Li, Lili Yu, Xia Li
J R Soc Interface. 2011 April 6; 8(57): 555–567. Published online 2010 October 13. doi: 10.1098/rsif.2010.0384
PMCID:
PMC3061120
Abstract Full Text PDF–402K
BioPAX – A community standard for pathway data sharing
Emek Demir, Michael P. Cary, Suzanne Paley, Ken Fukuda, Christian Lemer, Imre Vastrik, Guanming Wu, Peter D’Eustachio, Carl Schaefer, Joanne Luciano, Frank Schacherer, Irma Martinez-Flores, Zhenjun Hu, Veronica Jimenez-Jacinto, Geeta Joshi-Tope, Kumaran Kandasamy, Alejandra C. Lopez-Fuentes, Huaiyu Mi, Elgar Pichler, Igor Rodchenkov, Andrea Splendiani, Sasha Tkachev, Jeremy Zucker, Gopal Gopinath, Harsha Rajasimha, Ranjani Ramakrishnan, Imran Shah, Mustafa Syed, Nadia Anwar, Ozgun Babur, Michael Blinov, Erik Brauner, Dan Corwin, Sylva Donaldson, Frank Gibbons, Robert Goldberg, Peter Hornbeck, Augustin Luna, Peter Murray-Rust, Eric Neumann, Oliver Reubenacker, Matthias Samwald, Martijn van Iersel, Sarala Wimalaratne, Keith Allen, Burk Braun, Michelle Whirl-Carrillo, Kam Dahlquist, Andrew Finney, Marc Gillespie, Elizabeth Glass, Li Gong, Robin Haw, Michael Honig, Olivier Hubaut, David Kane, Shiva Krupa, Martina Kutmon, Julie Leonard, Debbie Marks, David Merberg, Victoria Petri, Alex Pico, Dean Ravenscroft, Liya Ren, Nigam Shah, Margot Sunshine, Rebecca Tang, Ryan Whaley, Stan Letovksy, Kenneth H. Buetow, Andrey Rzhetsky, Vincent Schachter, Bruno S. Sobral, Ugur Dogrusoz, Shannon McWeeney, Mirit Aladjem, Ewan Birney, Julio Collado-Vides, Susumu Goto, Michael Hucka, Nicolas Le Novère, Natalia Maltsev, Akhilesh Pandey, Paul Thomas, Edgar Wingender, Peter D. Karp, Chris Sander, Gary D. Bader
Nat Biotechnol. Author manuscript; available in PMC 2011 March 9.
Published in final edited form as: Nat Biotechnol. 2010 September; 28(9): 935–942. Published online 2010 September 9. doi: 10.1038/nbt.1666
PMCID:
PMC3001121
Abstract Full Text PDF–574K Supplementary Material
Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism
Livnat Jerby, Tomer Shlomi, Eytan Ruppin
Mol Syst Biol. 2010; 6: 401. Published online 2010 September 7. doi: 10.1038/msb.2010.56
PMCID:
PMC2964116
Abstract Full Text PDF–1.3M Supplementary Material
Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network
Germán Plata, Tzu-Lin Hsiao, Kellen L Olszewski, Manuel Llinás, Dennis Vitkup
Mol Syst Biol. 2010; 6: 408. Published online 2010 September 7. doi: 10.1038/msb.2010.60
PMCID:
PMC2964117
Abstract Full Text PDF–515K Supplementary Material
Compartmentalization of the Edinburgh Human Metabolic Network
Tong Hao, Hong-Wu Ma, Xue-Ming Zhao, Igor Goryanin
BMC Bioinformatics. 2010; 11: 393. Published online 2010 July 22. doi: 10.1186/1471-2105-11-393
PMCID:
PMC2918583
Abstract Full Text PDF–819K Supplementary Material
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function
David Warde-Farley, Sylva L. Donaldson, Ovi Comes, Khalid Zuberi, Rashad Badrawi, Pauline Chao, Max Franz, Chris Grouios, Farzana Kazi, Christian Tannus Lopes, Anson Maitland, Sara Mostafavi, Jason Montojo, Quentin Shao, George Wright, Gary D. Bader, Quaid Morris
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W214–W220. Published online 2010 June 21. doi: 10.1093/nar/gkq537
PMCID:
PMC2896186
Abstract Full Text PDF–8.6M Supplementary Material
MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks
Ludovic Cottret, David Wildridge, Florence Vinson, Michael P. Barrett, Hubert Charles, Marie-France Sagot, Fabien Jourdan
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W132–W137. Published online 2010 May 5. doi: 10.1093/nar/gkq312
PMCID:
PMC2896158
Abstract Full Text PDF–3.3M
Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis
Henning Redestig, Miyako Kusano, Atsushi Fukushima, Fumio Matsuda, Kazuki Saito, Masanori Arita
BMC Bioinformatics. 2010; 11: 214. Published online 2010 April 29. doi: 10.1186/1471-2105-11-214
PMCID:
PMC2879285
Abstract Full Text PDF–760K Supplementary Material
Improved Microarray-Based Decision Support with Graph Encoded Interactome Data
Anneleen Daemen, Marco Signoretto, Olivier Gevaert, Johan A. K. Suykens, Bart De Moor
PLoS One. 2010; 5(4): e10225. Published online 2010 April 19. doi: 10.1371/journal.pone.0010225
PMCID:
PMC2856685
Abstract Full Text PDF–957K
Use of reconstituted metabolic networks to assist in metabolomic data visualization and mining
Fabien Jourdan, Ludovic Cottret, Laurence Huc, David Wildridge, Richard Scheltema, Anne Hillenweck, Michael P. Barrett, Daniel Zalko, David G. Watson, Laurent Debrauwer
Metabolomics. 2010 June; 6(2): 312–321. Published online 2010 January 6. doi: 10.1007/s11306-009-0196-9
PMCID:
PMC2874485
Abstract Full Text PDF–790K Supplementary Material
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
Ron Caspi, Tomer Altman, Joseph M. Dale, Kate Dreher, Carol A. Fulcher, Fred Gilham, Pallavi Kaipa, Athikkattuvalasu S. Karthikeyan, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller, Suzanne Paley, Liviu Popescu, Anuradha Pujar, Alexander G. Shearer, Peifen Zhang, Peter D. Karp
Nucleic Acids Res. 2010 January; 38(Database issue): D473–D479. Published online 2010 January. doi: 10.1093/nar/gkp875
PMCID:
PMC2808959
Abstract Full Text PDF–3.7M
HPD: an online integrated human pathway database enabling systems biology studies
Sudhir R Chowbina, Xiaogang Wu, Fan Zhang, Peter M Li, Ragini Pandey, Harini N Kasamsetty, Jake Y Chen
BMC Bioinformatics. 2009; 10(Suppl 11): S5. Published online 2009 October 8. doi: 10.1186/1471-2105-10-S11-S5
PMCID:
PMC3226194
Abstract Full Text PDF–6.2M Supplementary Material
HPD: an online integrated human pathway database enabling systems biology studies
Sudhir R Chowbina, Xiaogang Wu, Fan Zhang, Peter M Li, Ragini Pandey, Harini N Kasamsetty, Jake Y Chen
BMC Bioinformatics. 2009; 10(Suppl 11): S5. Published online 2009 October 8. doi: 10.1186/1471-2105-10-S11-S5
PMCID:
PMC3226194
Abstract Full Text PDF–6.2M Supplementary Material
A Mapping of Drug Space from the Viewpoint of Small Molecule Metabolism
James Corey Adams, Michael J. Keiser, Li Basuino, Henry F. Chambers, Deok-Sun Lee, Olaf G. Wiest, Patricia C. Babbitt
PLoS Comput Biol. 2009 August; 5(8): e1000474. Published online 2009 August 21. doi: 10.1371/journal.pcbi.1000474
PMCID:
PMC2727484
Abstract Full Text PDF–1.0M Supplementary Material
MouseCyc: a curated biochemical pathways database for the laboratory mouse
Alexei V Evsikov, Mary E Dolan, Michael P Genrich, Emily Patek, Carol J Bult
Genome Biol. 2009; 10(8): R84. Published online 2009 August 14. doi: 10.1186/gb-2009-10-8-r84
PMCID:
PMC2745765
Abstract Full Text PDF–966K Supplementary Material
The conservation and evolutionary modularity of metabolism
José M Peregrín-Alvarez, Chris Sanford, John Parkinson
Genome Biol. 2009; 10(6): R63. Published online 2009 June 12. doi: 10.1186/gb-2009-10-6-r63
PMCID:
PMC2718497
Abstract Full Text PDF–1.0M Supplementary Material
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