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JeremyZucker's library [97 articles]

Recent papers added to JeremyZucker's library.
  • Nutrient-related analysis of pathway/genome databases.
    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2001), pp. 471-482.
    by PR Romero, P Karp
    posted to symbolic-programming ecocyc biohacker by JeremyZucker on 2008-05-14 16:46:41 as **
  • Optimization based automated curation of metabolic reconstructions
    BMC Bioinformatics, Vol. 8 (20 June 2007), 212.
    by Vinay S Kumar, Madhukar S Dasika, Costas D Maranas
    posted to metabolic-reconstruction fba biohacker by JeremyZucker on 2008-05-14 16:32:50 as **
  • Experimental and Computational Assessment of Conditionally Essential Genes in Escherichia coli
    J. Bacteriol., Vol. 188, No. 23. (1 December 2006), pp. 8259-8271.
    by Andrew R Joyce, Jennifer L Reed, Aprilfawn White, Robert Edwards, Andrei Osterman, Tomoya Baba, Hirotada Mori, Scott A Lesely, Bernhard O Palsson, Sanjay Agarwalla
    posted to palsson metabolic-models fba ecoli biohacker by JeremyZucker on 2008-05-14 16:27:54 as ** along with 1 person lylu
  • Integrating high-throughput and computational data elucidates bacterial networks.
    Nature, Vol. 429, No. 6987. (6 May 2004), pp. 92-96.
    by MW Covert, EM Knight, JL Reed, MJ Herrgard, BO Palsson
    posted to metabolic-reconstruction metabolic-models fba biohacker by JeremyZucker on 2008-05-14 16:26:30 as ** along with 5 people and 2 groups Retchless lfriedl RMGraze alexg raiyar kdl steinmetzlab
  • Symbolic inference of xenobiotic metabolism.
    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2004), pp. 545-556.
    by DC McShan, M Updadhayaya, I Shah
    posted to symbolic-programming cheminformatics biohacker by JeremyZucker on 2008-05-14 16:18:15 as **
  • A gold standard set of mechanistically diverse enzyme superfamilies.
    Genome Biol, Vol. 7, No. 1. (2006)
    by SD Brown, JA Gerlt, JL Seffernick, PC Babbitt
    posted to functional-annotation metabolic-reconstruction by JeremyZucker on 2008-04-17 00:13:32 as ** along with 3 people and 1 group kuhn robert caporaso biomedical-nlp
  • New surveyor tools for charting microbial metabolic maps
    Nature Reviews Microbiology, Vol. 6, No. 2., pp. 156-161.
    by Rainer Breitling, Dennis Vitkup, Michael P Barrett
    posted to orphan-enzyme by JeremyZucker on 2008-04-03 00:12:07 as ** along with 2 people thomaskelder ptrobajo
  • Orphan enzymes could be an unexplored reservoir of new drug targets.
    Drug discovery today, Vol. 11, No. 7-8. (April 2006), pp. 300-305.
    by O Lespinet, B Labedan
    posted to orphan-enzyme by JeremyZucker on 2008-04-03 00:10:46 as **
  • Puzzling over orphan enzymes.
    Cellular and molecular life sciences : CMLS, Vol. 63, No. 5. (March 2006), pp. 517-523.
    by O Lespinet, B Labedan
    posted to orphan-enzyme by JeremyZucker on 2008-04-03 00:10:23 as **
  • ORENZA: a web resource for studying ORphan ENZyme Activities
    BMC Bioinformatics, Vol. 7 (06 October 2006), 436.
    by Olivier Lespinet, Bernard Labedan
    posted to orphan-enzyme by JeremyZucker on 2008-04-03 00:10:02 as ** along with 2 people tny dquest
  • Distribution of orphan metabolic activities
    Trends in Biotechnology, Vol. 25, No. 8. (August 2007), pp. 343-348.
    by Lifeng Chen, Dennis Vitkup
    posted to metabolic-reconstruction by JeremyZucker on 2008-04-03 00:09:21 as **
  • Evolutionary programming as a platform for in silico metabolic engineering.
    BMC Bioinformatics, Vol. 6 (2005)
    by KR Patil, I Rocha, J Förster, J Nielsen
    posted to evolution fba metabolic-engineering by JeremyZucker on 2008-04-02 22:53:19 as ** along with 1 person dylan77
  • Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism
    Genome Res., Vol. 15, No. 6. (1 June 2005), pp. 820-829.
    by Irina Borodina, Preben Krabben, Jens Nielsen
    posted to fba metabolic-reconstruction streptomyces by JeremyZucker on 2008-04-02 02:26:59 as ** along with 1 person lylu
  • Assessing the potential of mutational strategies to elicit new phenotypes in industrial strains
    Proceedings of the National Academy of Sciences, Vol. 105, No. 7. (19 February 2008), pp. 2319-2324.
    by Daniel Klein-Marcuschamer, Gregory Stephanopoulos
    posted to metabolic-engineering by JeremyZucker on 2008-03-25 21:21:11 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 on 2008-03-19 02:24:10 as ** along with 1 person and 1 group klager MetabolicModeling
  • 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 on 2008-03-19 01:18:31 as ** along with 1 group MetabolicModeling
  • Influence of metabolic network structure and function on enzyme evolution.
    Genome Biol, Vol. 7, No. 5. (9 May 2006)
    by Dennis Vitkup, Peter Kharchenko, Andreas Wagner
    posted to metabolic-reconstruction orphan-enzyme by JeremyZucker on 2008-02-08 00:22:48 as ** along with 2 people tny mdstobbe
  • 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 on 2008-02-08 00:21:34 as ** along with 2 people and 1 group shung eweaver MetabolicModeling
  • Identifying metabolic enzymes with multiple types of association evidence.
    BMC Bioinformatics, Vol. 7 (2006)
    by P Kharchenko, L Chen, Y Freund, D Vitkup, GM Church
    posted to metabolic-reconstruction by JeremyZucker on 2008-02-08 00:20:23 as ** along with 2 people koller shung
  • Predicting genes for orphan metabolic activities using phylogenetic profiles.
    Genome Biol, Vol. 7, No. 2. (2006)
    by L Chen, D Vitkup
    posted to fba metabolic-reconstruction by JeremyZucker on 2008-02-08 00:18:42 as ** along with 1 person shung
  • Expression dynamics of a cellular metabolic network
    Molecular Systems Biology, Vol. 1, No. 1. (02 August 2005), pp. msb4100023-E1-msb4100023-E6.
    by Peter Kharchenko, George M Church, Dennis Vitkup
    posted to no-tag by JeremyZucker on 2008-02-08 00:17:44 as ** along with 4 people pcahan1 gespim koller jpoyatos
  • Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: a quantitative analysis.
    Genetics, Vol. 174, No. 4. (December 2006), pp. 2229-2243.
    by L Nie, G Wu, W Zhang
    posted to gene-regulation by JeremyZucker on 2008-01-24 18:10:18 as **
  • Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: a multiple regression to identify sources of variations.
    Biochem Biophys Res Commun, Vol. 339, No. 2. (13 January 2006), pp. 603-610.
    by L Nie, G Wu, W Zhang
    posted to gene-regulation by JeremyZucker on 2008-01-24 18:09:30 as **
  • Comparing protein abundance and mRNA expression levels on a genomic scale.
    Genome Biol, Vol. 4, No. 9. (2003)
    by D Greenbaum, C Colangelo, K Williams, M Gerstein
    posted to gene-regulation by JeremyZucker on 2008-01-24 17:48:02 as ** along with 3 people and 1 group ihpark penka roys Nie
  • Prevention of upper limb symptoms and signs of nerve afflictions in computer operators: the effect of intervention by stretching
    Journal of Occupational Medicine and Toxicology, Vol. 3 (07 January 2008), 1.
    by Jorgen R Jepsen, Gert Thomsen
    posted to no-tag by JeremyZucker on 2008-01-17 22:43:19 as **
  • 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 on 2007-12-20 06:08:11 as ** along with 3 people and 1 group cjeans zwang Ema MetabolicModeling
  • 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 on 2007-12-14 21:15:30 as ** along with 1 person and 1 group madhadron MetabolicModeling
  • Genome-Wide Mapping of in Vivo Protein-DNA Interactions
    Science (31 May 2007), 1141319.
    by David S Johnson, Ali Mortazavi, Richard M Myers, Barbara Wold
    posted to chipseq by JeremyZucker on 2007-12-04 18:11:33 as **** along with 17 people and 5 groups aalibes balicea andersbj aswin kengg giovanni cjeans ghattem zwang epigenetics biomcgary george_g cabbagezs Jporci blobbybirdman caseybrown emptyhb Bioinformatics microRNA Marcotte_Lab UH - Computational Biology Myxo group
  • Extending Double Modulation: Combinatorial Rules for Identifying the Modulations Necessary for Determining Elasticities in Metabolic Pathways
    Journal of Theoretical Biology, Vol. 182, No. 3. (7 October 1996), pp. 361-369.
    by Christoph Giersch, Athel Cornish-Bowden
    posted to cornish-bowden metabolic-control-analysis metabolic-engineering by JeremyZucker on 2007-11-18 18:55:25 as **
  • Amino acid stabilization for cell-free protein synthesis by modification of the Escherichia coli genome.
    Metab Eng, Vol. 6, No. 3. (July 2004), pp. 197-203.
    by N Michel-Reydellet, K Calhoun, J Swartz
    posted to metabolic-engineering michel-reydellet by JeremyZucker on 2007-11-18 06:23:12 as ** along with 1 person Odi
  • Stoichiometric network constraints on xylose metabolism by recombinant Saccharomyces cerevisiae
    Metabolic Engineering, Vol. 6, No. 3. (July 2004), pp. 229-238.
    by Yong-Su Jin, Thomas W Jeffries
    posted to jin metabolic-engineering by JeremyZucker on 2007-11-18 06:22:27 as **
  • 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 on 2007-11-18 06:21:42 as ** along with 1 group MetabolicModeling
  • 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 on 2007-11-18 06:20:59 as ** along with 1 group MetabolicModeling
  • 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 on 2007-11-18 06:14:36 as ** along with 1 group MetabolicModeling
  • 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 on 2007-10-30 19:31:58 as **** along with 1 person and 1 group kuhn MetabolicModeling
  • Modeling and simulation: tools for metabolic engineering
    Journal of Biotechnology, Vol. 94, No. 1. (14 March 2002), pp. 37-63.
    by Wolfgang Wiechert
    posted to fba metabolic-engineering metabolic-models by JeremyZucker on 2007-10-30 00:54:11 as **
  • 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-engineering metabolic-reconstruction by JeremyZucker on 2007-10-30 00:52:13 as ** along with 1 person and 2 groups claire2327 streptomyces MetabolicModeling
  • Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae.
    Genome Res, Vol. 16, No. 5. (May 2006), pp. 627-635.
    by MJ Herrgård, BS Lee, V Portnoy, BØ Palsson
    posted to fba gene-regulation palsson regulatory-networks yeast by JeremyZucker on 2007-10-28 22:15:45 as ** along with 7 people and 3 groups nickluscombe aswin kengg koller raiyar cjeans edwardmorrissey EBI-regulation steinmetzlab Plantandetc
  • 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 on 2007-10-28 22:14:56 as ** along with 1 group MetabolicModeling
  • Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network.
    Proc Natl Acad Sci U S A, Vol. 100, No. 23. (11 November 2003), pp. 13134-13139.
    by I Famili, J Forster, J Nielsen, BO Palsson
    posted to fba palsson yeast by JeremyZucker on 2007-10-28 22:13:30 as ** along with 1 person koller
  • 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 on 2007-10-28 22:12:19 as ** along with 7 people and 3 groups opheliav wnpx nirfriedman bsmagic gcalda jpoyatos edwardmorrissey Bioinformatics bioinplant MetabolicModeling
  • 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 on 2007-10-28 21:31:46 as ** along with 1 group MetabolicModeling
  • 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 on 2007-10-28 21:24:59 as ** along with 1 group MetabolicModeling
  • 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 on 2007-10-28 21:15:18 as ** along with 1 group MetabolicModeling
  • 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 on 2007-10-28 20:12:41 as read along with 1 person and 1 group madhadron MetabolicModeling
  • e-Science and biological pathway semantics.
    BMC Bioinformatics, Vol. 8 Suppl 3 (2007)
    by JS Luciano, RD Stevens
    posted to biopax semantic-web by JeremyZucker on 2007-10-17 21:26:03 as ** along with 6 people dansullivanblk alanrw jyuh dullhunk bootsy tral
  • In silico biotechnology: Era of reconstruction and interrogation
    Current Opinion in Biotechnology, Vol. 15, No. 1. (February 2004), pp. 50-51.
    by Bernhard O Palsson
    posted to fba metabolic-reconstruction palsson by JeremyZucker on 2007-10-17 20:59:36 as **
  • In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments.
    Appl Environ Microbiol, Vol. 71, No. 11. (November 2005), pp. 7253-7262.
    by B Teusink, FH van Enckevort, C Francke, A Wiersma, A Wegkamp, EJ Smid, RJ Siezen
    posted to fba metabolic-reconstruction by JeremyZucker on 2007-10-17 20:58:32 as **
  • Impact of `ome' analyses on inverse metabolic engineering
    Metabolic Engineering, Vol. 6, No. 3. (July 2004), pp. 204-211.
    by Christoffer Bro, Jens Nielsen
    posted to metabolic-engineering omics by JeremyZucker on 2007-10-17 20:57:32 as **
  • 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 on 2007-10-17 20:48:15 as ** along with 1 group MetabolicModeling
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