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Group: MetabolicModeling - library [67 articles]

Recent papers posted by members of the MetabolicModeling group
  • Metabolic networks in motion: 13C-based flux analysis
    Mol Syst Biol, Vol. 2 (14 November 2006)
    by Uwe Sauer
    posted to sauer mfa flux-measurements by JeremyZucker to the group MetabolicModeling on 2008-07-18 02:51:54 as ** along with 2 people fishtank westoll
  • High-throughput phenomics: experimental methods for mapping fluxomes
    Current Opinion in Biotechnology, Vol. 15, No. 1. (February 2004), pp. 58-63.
    by Uwe Sauer
    posted to sauer flux-measurements fba experiments by JeremyZucker to the group MetabolicModeling on 2008-07-18 02:51:17 as **
  • The RAST Server: Rapid Annotations using Subsystems Technology
    BMC Genomics, Vol. 9 (08 February 2008), 75.
    by Ramy K Aziz, Daniela Bartels, Aaron A Best, Matthew Dejongh, Terrence Disz, Robert A Edwards, Kevin Formsma, Svetlana Gerdes, Elizabeth M Glass, Michael Kubal, Folker Meyer, Gary J Olsen, Robert Olson, Andrei L Osterman, Ross A Overbeek, Leslie K Mcneil, Daniel Paarmann, Tobias Paczian, Bruce Parrello, Gordon D Pusch, Claudia Reich, Rick Stevens, Olga Vassieva, Veronika Vonstein, Andreas Wilke, Olga Zagnitko
    posted to metabolic-reconstruction by JeremyZucker to the group MetabolicModeling on 2008-03-19 02:24:10 as ** along with 1 person klager
  • Evolutionary analysis of enzymes using Chisel.
    Bioinformatics, Vol. 23, No. 22. (15 November 2007), pp. 2961-2968.
    by AA Rodriguez, T Bompada, M Syed, PK Shah, N Maltsev
    posted to metabolic-reconstruction by JeremyZucker to the group MetabolicModeling on 2008-03-19 01:18:31 as **
  • Accelerating the reconstruction of genome-scale metabolic networks
    BMC Bioinformatics, Vol. 7 (13 June 2006), 296.
    by Richard A Notebaart, Frank HJ van Enckevort, Christof Francke, Roland J Siezen, Bas Teusink
    posted to metabolic-reconstruction by JeremyZucker to the group MetabolicModeling on 2008-02-08 00:21:34 as ** along with 2 people shung eweaver
  • The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks
    Mol Syst Biol, Vol. 3 (13 November 2007)
    by Sergio Grimbs, Joachim Selbig, Sascha Bulik, Hermann-Georg Holzhutter, Ralf Steuer
    posted to metabolic-models by JeremyZucker to the group MetabolicModeling on 2007-12-20 06:08:11 as ** along with 3 people cjeans zwang Ema
  • GSMN-TB: a web-based genome scale network model of Mycobacterium tuberculosis metabolism.
    Genome Biology, Vol. 8 (23 May 2007), R89.
    by Dany JV Beste, Tracy Hooper, Graham Stewart, Bushan Bonde, Claudio Avignone-Rossa, Michael Bushell, Paul Wheeler, Steffen Klamt, Andrzej M Kierzek, Johnjoe Mcfadden
    posted to metabolic-models tb by JeremyZucker to the group MetabolicModeling on 2007-12-14 21:15:31 as ** along with 1 person madhadron
  • Inverse metabolic engineering with phosphagen kinase systems improves the cellular energy state
    Metabolic Engineering, Vol. 6, No. 3. (July 2004), pp. 220-228.
    by Uwe Sauer, Uwe Schlattner
    posted to metabolic-engineering sauer by JeremyZucker to the group MetabolicModeling on 2007-11-18 06:21:42 as **
  • Assaying gene function by growth competition experiment
    Metabolic Engineering, Vol. 6, No. 3. (July 2004), pp. 212-219.
    by Joshua Merritt, Jeremy S Edwards
    posted to edwards metabolic-engineering by JeremyZucker to the group MetabolicModeling on 2007-11-18 06:20:59 as **
  • Strain improvement by metabolic engineering: lysine production as a case study for systems biology
    Current Opinion in Biotechnology, Vol. 16, No. 3. (June 2005), pp. 361-366.
    by Mattheos Koffas, Gregory Stephanopoulos
    posted to metabolic-engineering stephanopoulos by JeremyZucker to the group MetabolicModeling on 2007-11-18 06:14:36 as **
  • CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules.
    FEBS Lett, Vol. 579, No. 21. (29 August 2005), pp. 4685-4691.
    by HJ Feldman, M Dumontier, S Ling, N Haider, CW Hogue
    posted to biopax metabolic-reconstruction semantic-web by JeremyZucker to the group MetabolicModeling on 2007-10-30 19:31:59 as **** along with 1 person kuhn
  • Use of genome-scale microbial models for metabolic engineering
    Current Opinion in Biotechnology, Vol. 15, No. 1. (February 2004), pp. 64-69.
    by Kiran R Patil, Mats Akesson, Jens Nielsen
    posted to metabolic-reconstruction by JeremyZucker to the group MetabolicModeling on 2007-10-30 00:52:13 as ** along with 1 person and 1 group claire2327 streptomyces
  • Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae.
    BMC Genomics, Vol. 5, No. 1. (8 September 2004)
    by NC Duarte, BØ Palsson, P Fu
    posted to fba palsson yeast by JeremyZucker to the group MetabolicModeling on 2007-10-28 22:14:56 as **
  • Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network.
    Genome Res, Vol. 13, No. 2. (February 2003), pp. 244-253.
    by J Förster, I Famili, P Fu, BØ Palsson, J Nielsen
    posted to fba metabolic-reconstruction palsson yeast by JeremyZucker to the group MetabolicModeling on 2007-10-28 22:12:19 as ** along with 7 people and 2 groups opheliav wnpx nirfriedman bsmagic gcalda jpoyatos edwardmorrissey Bioinformatics bioinplant
  • Thiolactomycin and related analogues as novel anti-mycobacterial agents targeting KasA and KasB condensing enzymes in Mycobacterium tuberculosis.
    J Biol Chem, Vol. 275, No. 22. (2 June 2000), pp. 16857-16864.
    by L Kremer, JD Douglas, AR Baulard, C Morehouse, MR Guy, D Alland, LG Dover, JH Lakey, WR Jacobs, PJ Brennan, DE Minnikin, GS Besra
    posted to drugs mycolic-acid tb thiolactomycin by JeremyZucker to the group MetabolicModeling on 2007-10-28 21:31:46 as **
  • The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: novel insights into drug mechanisms of action.
    J Biol Chem, Vol. 279, No. 38. (17 September 2004), pp. 40174-40184.
    by HI Boshoff, TG Myers, BR Copp, MR McNeil, MA Wilson, CE Barry
    posted to boshoff mycolic-acid tb by JeremyZucker to the group MetabolicModeling on 2007-10-28 21:24:59 as **
  • Pathway to synthesis and processing of mycolic acids in Mycobacterium tuberculosis.
    Clin Microbiol Rev, Vol. 18, No. 1. (January 2005), pp. 81-101.
    by K Takayama, C Wang, GS Besra
    posted to metabolic-reconstruction mycolic-acid tb by JeremyZucker to the group MetabolicModeling on 2007-10-28 21:15:18 as **
  • Flux Balance Analysis of Mycolic Acid Pathway: Targets for Anti-Tubercular Drugs
    PLoS Computational Biology, Vol. 1, No. 5. (1 October 2005), e46.
    by Karthik Raman, Preethi Rajagopalan, Nagasuma Chandra
    posted to eflux fba mycolic-acid by JeremyZucker to the group MetabolicModeling on 2007-10-28 20:12:41 as read along with 1 person madhadron
  • Cofactor engineering of intracellular CoA/acetyl-CoA and its effect on metabolic flux redistribution in Escherichia coli
    Metabolic Engineering, Vol. 6, No. 2. (April 2004), pp. 133-139.
    by Ravishankar V Vadali, George N Bennett, San
    posted to fba metabolic-engineering by JeremyZucker to the group MetabolicModeling on 2007-10-17 20:48:15 as **
  • Genome data mining of lactic acid bacteria: the impact of bioinformatics
    Current Opinion in Biotechnology, Vol. 15, No. 2. (April 2004), pp. 105-115.
    by Roland J Siezen, Frank H van Enckevort, Michiel Kleerebezem, Bas Teusink
    posted to metabolic-models metabolic-reconstruction by JeremyZucker to the group MetabolicModeling on 2007-10-17 20:47:29 as ** along with 1 person fnekrep
  • Functional ingredient production: application of global metabolic models
    Current Opinion in Biotechnology, Vol. 16, No. 2. (April 2005), pp. 190-197.
    by Eddy J Smid, Douwe Molenaar, Jeroen Hugenholtz, Willem M Vos, Bas Teusink
    posted to fba metabolic-engineering metabolic-models by JeremyZucker to the group MetabolicModeling on 2007-10-17 19:45:32 as **
  • Metabolic Engineering in the -omics Era: Elucidating and Modulating Regulatory Networks.
    Microbiol Mol Biol Rev, Vol. 69, No. 2. (June 2005), pp. 197-216.
    by GN Vemuri, AA Aristidou
    posted to fba metabolic-engineering omics regulatory-networks by JeremyZucker to the group MetabolicModeling on 2007-10-17 19:43:40 as ** along with 3 people operon kuhn athleem
  • Global physiological understanding and metabolic engineering of microorganisms based on omics studies
    Applied Microbiology and Biotechnology, Vol. 68, No. 5. (2005), pp. 567-579.
    by S Park, S Lee, J Cho, T Kim, J Lee, J Park, MJ Han
    posted to fba metabolic-engineering metabolic-reconstruction by JeremyZucker to the group MetabolicModeling on 2007-10-17 19:42:09 as **
  • Fluxome analysis using GC-MS
    Microbial Cell Factories, Vol. 6 (07 February 2007), 6.
    by Christoph Wittmann
    posted to fba gc-ms metabo metabolic-engineering metabolic-reconstruction by JeremyZucker to the group MetabolicModeling on 2007-10-17 19:39:39 as **
  • Metabolic pathway analysis for rational design of L-methionine production by Escherichia coli and Corynebacterium glutamicum
    Metabolic Engineering, Vol. 8, No. 4. (July 2006), pp. 353-369.
    by Jens O Kromer, Christoph Wittmann, Hartwig Schroder, Elmar Heinzle
    posted to fba metabolic-reconstruction by JeremyZucker to the group MetabolicModeling on 2007-10-17 19:36:07 as **
  • Whole genome protein domain analysis using a new method for domain clustering.
    Comput Chem, Vol. 23, No. 3-4. (15 June 1999), pp. 333-340.
    by J Gouzy, F Corpet, D Kahn
    posted to genomics fba debugging-the-bug by JeremyZucker to the group MetabolicModeling on 2007-09-21 21:17:33 as **
  • Enzyme-specific profiles for genome annotation: PRIAM.
    Nucleic Acids Res, Vol. 31, No. 22. (15 November 2003), pp. 6633-6639.
    by C Claudel-Renard, C Chevalet, T Faraut, D Kahn
    posted to fba debugging-the-bug by JeremyZucker to the group MetabolicModeling on 2007-09-21 21:16:18 as read along with 5 people labedan Ayest eweaver gelack shung
  • Functional genomic hypothesis generation and experimentation by a robot scientist.
    Nature, Vol. 427, No. 6971. (15 January 2004), pp. 247-252.
    by RD King, KE Whelan, FM Jones, PG Reiser, CH Bryant, SH Muggleton, DB Kell, SG Oliver
    posted to ai agi by JeremyZucker to the group MetabolicModeling on 2007-08-11 01:19:38 as *** along with 7 people and 4 groups dbk tmmurali yas jtbates tabu samal dullhunk streptomyces dbk-lab T_lab triplehelix
  • Length, time, and energy scales of photosystems.
    Adv Protein Chem, Vol. 63 (2003), pp. 71-109.
    by CC Moser, CC Page, RJ Cogdell, J Barber, CA Wraight, PL Dutton
    posted to photosynthesis by JeremyZucker to the group MetabolicModeling on 2007-08-10 20:31:56 as **
  • Conservation of Expression and Sequence of Metabolic Genes Is Reflected by Activity Across Metabolic States.
    PLoS Comput Biol, Vol. 2, No. 8. (18 August 2006)
    by Yonatan Bilu, Tomer Shlomi, Naama Barkai, Eytan Ruppin
    posted to fba by JeremyZucker to the group MetabolicModeling on 2007-08-09 04:41:50 as ** along with 2 people and 1 group nickluscombe edwardmorrissey EBI-regulation
  • In silico gene function prediction using ontology-based pattern identification
    Bioinformatics, Vol. 21, No. 7. (01 April 2005), pp. 1237-1245.
    by Zhou Yingyao, A Young, Santrosyan Andrey, Chen Kaisheng, Yan S Frank, A Winzeler
    posted to plasmo by JeremyZucker to the group MetabolicModeling on 2007-08-03 22:54:59 as **
  • Polysaccharide biosynthesis locus required for virulence of Bacteroides fragilis.
    Infect Immun, Vol. 69, No. 7. (July 2001), pp. 4342-4350.
    by MJ Coyne, AO Tzianabos, BC Mallory, VJ Carey, DL Kasper, LE Comstock
    posted to pneu nonhousekeeping by JeremyZucker to the group MetabolicModeling on 2007-05-15 19:45:28 as **
  • The Control of Flux: 21 Years On
    by H Kacser
    edited by D Fell
    posted to fba by JeremyZucker to the group MetabolicModeling on 2007-05-14 19:30:26 as **
  • BIOSYNTHESIS AND ASSEMBLY OF CAPSULAR POLYSACCHARIDES IN ESCHERICHIA COLI - Annual Review of Biochemistry, 75(1):39 - Abstract
    posted to ecoli capsule by abrandes to the group MetabolicModeling on 2007-05-08 22:27:59 as ***
  • Characterization and quantification of C-polysaccharide in Streptococcus pneumoniae capsular polysaccharide preparations
    Analytical Biochemistry, Vol. 336, No. 2. (15 January 2005), pp. 262-272.
    by Qiuwei Xu, Chitrananda Abeygunawardana, Assunta S Ng, Annie W Sturgess, Bryan J Harmon, Jr Hennessey
    posted to pneumo capsule by abrandes to the group MetabolicModeling on 2007-05-08 20:47:32 as ***
  • LINUCS: linear notation for unique description of carbohydrate sequences.
    Carbohydr Res, Vol. 336, No. 1. (1 November 2001), pp. 1-11.
    by A Bohne-Lang, E Lang, T Förster, CW von der Lieth
    posted to glyco by abrandes to the group MetabolicModeling on 2007-05-08 20:05:40 as ***
  • Chlorophyll a oxygenase (CAO) is involved in chlorophyll b formation from chlorophyll a.
    Proc Natl Acad Sci U S A, Vol. 95, No. 21. (13 October 1998), pp. 12719-12723.
    by A Tanaka, H Ito, R Tanaka, NK Tanaka, K Yoshida, K Okada
    posted to photosynthesis cyanobacteria chlorophyll by JeremyZucker to the group MetabolicModeling on 2007-04-30 19:40:24 as **
  • Cloning and functional expression of the gene encoding the key enzyme for chlorophyll b biosynthesis (CAO) from Arabidopsis thaliana.
    Plant J, Vol. 21, No. 3. (February 2000), pp. 305-310.
    by U Oster, R Tanaka, A Tanaka, W Rüdiger
    posted to photosynthesis cyanobacteria chlorophyll by JeremyZucker to the group MetabolicModeling on 2007-04-30 19:39:14 as **
  • Genetic analysis of chlorophyll biosynthesis.
    Annu Rev Genet, Vol. 31 (1997), pp. 61-89.
    by JY Suzuki, DW Bollivar, CE Bauer
    posted to photosynthesis cyanobacteria by JeremyZucker to the group MetabolicModeling on 2007-04-30 18:55:37 as **
  • Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome.
    Proc Natl Acad Sci U S A, Vol. 100, No. 17. (19 August 2003), pp. 10020-10025.
    by A Dufresne, M Salanoubat, F Partensky, F Artiguenave, IM Axmann, V Barbe, S Duprat, MY Galperin, EV Koonin, F Le Gall, KS Makarova, M Ostrowski, S Oztas, C Robert, IB Rogozin, DJ Scanlan, N Tandeau de Marsac, J Weissenbach, P Wincker, YI Wolf, WR Hess
    posted to photosynthesis cyanobacteria by JeremyZucker to the group MetabolicModeling on 2007-04-30 18:43:07 as read along with 1 person and 2 groups jwm Radiation_Damage Stressosome
  • Synthesis of chlorophyll b: Localization of chlorophyllide a oxygenase and discovery of a stable radical in the catalytic subunit
    posted to photosynthesis cyanobacteria by JeremyZucker to the group MetabolicModeling on 2007-04-30 18:27:24 as **
  • The photosynthetic apparatus of Prochlorococcus: Insights through comparative genomics.
    Photosynth Res, Vol. 70, No. 1. (2001), pp. 53-71.
    by WR Hess, G Rocap, CS Ting, F Larimer, S Stilwagen, J Lamerdin, SW Chisholm
    posted to photosynthesis cyanobacteria by JeremyZucker to the group MetabolicModeling on 2007-04-21 01:24:31 as **
  • Identification of Chlorophyllide a Oxygenase in the Prochlorococcus Genome by a Comparative Genomic Approach --
    Plant and Cell Physiology, Vol. 47, No. 12., 1622.
    by Satoh A Tanaka
    posted to photosynthesis cyanobacteria by JeremyZucker to the group MetabolicModeling on 2007-04-21 01:24:03 as **
  • Prochlorococcus marinus Chisholm et al. 1992 subsp. pastoris subsp. nov. strain PCC 9511, the first axenic chlorophyll a(2)/b(2)-containing cyanobacterium (Oxyphotobacteria) --
    International Journal of Systematic and Evolutionary Microbiology, Vol. 50, No. 5., 1833.
    by Rippka
    posted to photosynthesis cyanobacteria by JeremyZucker to the group MetabolicModeling on 2007-04-21 01:22:55 as **
  • Identification of a Vinyl Reductase Gene for Chlorophyll Synthesis in Arabidopsis thaliana and Implications for the Evolution of Prochlorococcus Species -- Nagata et al. 17 (1): 233 -- THE PLANT CELL
    THE PLANT CELL, Vol. 17, No. 1., 233.
    by Nagata
    posted to photosynthesis cyanobacteria by JeremyZucker to the group MetabolicModeling on 2007-04-21 01:21:24 as **
  • In Vivo Regulation of Glutamine Synthetase Activity in the Marine Chlorophyll b-Containing Cyanobacterium Prochlorococcus sp. Strain PCC 9511 (Oxyphotobacteria)
    Applied and Environmental Microbiology, Vol. 67, No. 5., 2202.
    by El Alaoui
    posted to gene-regulation enzyme cyanobacteria by JeremyZucker to the group MetabolicModeling on 2007-03-27 21:44:51 as **
  • In Silico Atomic Tracing by Substrate-Product Relationships in Escherichia coli Intermediary Metabolism
    Genome Research, Vol. 13, No. 11., 2455.
    by -- Arita
    posted to fba ecoli arita by JeremyZucker to the group MetabolicModeling on 2007-03-24 05:07:19 as ****
  • Metabolic modeling of a mutualistic microbial community.
    Mol Syst Biol, Vol. 3 (2007)
    by S Stolyar, S Van Dien, KL Hillesland, N Pinel, TJ Lie, JA Leigh, DA Stahl
    posted to fba by JeremyZucker to the group MetabolicModeling on 2007-03-24 04:58:25 as **** along with 4 people and 1 group athleem aswin OriginalLurch cjeans clab
  • Dynamic modeling of the central carbon metabolism of <I>Escherichia coli</I>
    Biotechnology and Bioengineering, Vol. 79, No. 1. (2002), pp. 53-73.
    by Christophe Chassagnole, Naruemol Noisommit-Rizzi, Joachim W Schmid, Klaus Mauch, Matthias Reuss
    posted to no-tag by JeremyZucker to the group MetabolicModeling on 2007-03-07 00:13:39 as **** along with 1 person abrandes
  • Variant tricarboxylic acid cycle in Mycobacterium tuberculosis: Identification of alpha-ketoglutarate decarboxylase -- Tian et al. 102 (30): 10670 -- Proceedings of the National Academy of Sciences
    by J Tian, R Bryk, M Itoh, M Suematsu, C Nathan
    posted to ecoli enzyme fba kinetics tb tca vmax by JeremyZucker to the group MetabolicModeling on 2007-03-06 23:14:45 as ****
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