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icases's library [55 articles]

Recent papers added to icases's library.
  • Using the stress response to monitor process control: pathways to more effective bioremediation
    Current Opinion in Biotechnology, Vol. 17, No. 3. (June 2006), pp. 285-290.
    by Terry C Hazen, David A Stahl
    posted to biodegradation by icases on 2008-06-09 11:31:48 as **
  • The potential of metabolomics tools in bioremediation studies.
    Omics : a journal of integrative biology, Vol. 11, No. 3. (2007), pp. 305-313.
    by SG Villas-Bôas, P Bruheim
    posted to biodegradation by icases on 2008-06-09 11:12:58 as **
  • Genomics for environmental microbiology
    Current Opinion in Biotechnology, Vol. 17, No. 3. (June 2006), pp. 229-235.
    by Adam M Deutschbauer, Dylan Chivian, Adam P Arkin
    posted to biodegradation by icases on 2008-06-09 11:11:14 as **
  • Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays.
    Appl Environ Microbiol, Vol. 70, No. 7. (July 2004), pp. 4303-4317.
    by SK Rhee, X Liu, L Wu, SC Chong, X Wan, J Zhou
    posted to biodegradation by icases on 2008-06-09 10:59:29 as ** along with 1 person mcox
  • Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1.
    PLoS genetics, Vol. 2, No. 12. (December 2006)
    by EF Mongodin, N Shapir, SC Daugherty, RT DeBoy, JB Emerson, A Shvartzbeyn, D Radune, J Vamathevan, F Riggs, V Grinberg, H Khouri, LP Wackett, KE Nelson, MJ Sadowsky
    posted to biodegradation by icases on 2008-06-09 10:58:35 as **
  • The organization of the microbial biodegradation network from a systems-biology perspective.
    EMBO Rep, Vol. 4, No. 10. (October 2003), pp. 994-999.
    by F Pazos, A Valencia, V De Lorenzo
    posted to biodegradation by icases on 2008-06-09 10:56:33 as **
  • Accessing microbial diversity for bioremediation and environmental restoration
    Trends in Biotechnology, Vol. 23, No. 3. (March 2005), pp. 135-142.
    by Debarati Paul, Gunjan Pandey, Janmejay Pandey, Rakesh K Jain
    posted to biodegradation by icases on 2008-06-09 10:49:56 as **
  • Microbial Pathway Prediction: A Functional Group Approach
    J. Chem. Inf. Comput. Sci., Vol. 43, No. 3. (27 May 2003), pp. 1051-1057.
    by BK Hou, LP Wackett, LBM Ellis
    posted to biodegradation by icases on 2008-06-09 10:47:55 as **
  • BSD: the Biodegradative Strain Database.
    Nucleic Acids Res, Vol. 31, No. 1. (1 January 2003), pp. 152-155.
    by JW Urbance, J Cole, P Saxman, JM Tiedje
    posted to biodegradation by icases on 2008-06-09 10:47:00 as ** along with 1 person saxman
  • The environmental fate of organic pollutants through the global microbial metabolism
    Mol Syst Biol, Vol. 3 (5 June 2007)
    by Manuel J Gomez, Florencio Pazos, Francisco J Guijarro, Victor de Lorenzo, Alfonso Valencia
    posted to biodegradation by icases on 2008-06-09 10:37:39 as **
  • The Biodegradation Network, a New Scenario for Computational Systems Biology Research
    Computational Methods in Systems Biology (2005), pp. 252-256.
    by Florencio Pazos, David Guijas, Manuel J Gomez, Almudena Trigo, Victor de Lorenzo, Alfonso Valencia
    posted to biodegradation by icases on 2008-06-09 10:35:31 as **
  • Novel biocatalysis by database mining
    Current Opinion in Biotechnology, Vol. 15, No. 4. (August 2004), pp. 280-284.
    by Lawrence P Wackett
    posted to biodegradation by icases on 2008-06-09 10:34:03 as **
  • MetaRouter: bioinformatics for bioremediation.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by F Pazos, D Guijas, A Valencia, V De Lorenzo
    posted to biodegradation by icases on 2008-06-09 10:33:10 as **
  • Thermodynamics of enzyme-catalyzed reactions--a database for quantitative biochemistry
    Bioinformatics, Vol. 20, No. 16. (1 November 2004), pp. 2874-2877.
    by Robert N Goldberg, Yadu B Tewari, Talapady N Bhat
    posted to biodegradation by icases on 2008-06-09 10:31:44 as ** along with 1 person csanford
  • OptStrain: A computational framework for redesign of microbial production systems
    Genome Res., Vol. 14, No. 11. (1 November 2004), pp. 2367-2376.
    by Priti Pharkya, Anthony P Burgard, Costas D Maranas
    posted to biodegradation by icases on 2008-06-09 10:31:05 as **
  • Bacterial Transcriptional Regulators for Degradation Pathways of Aromatic Compounds
    Microbiol. Mol. Biol. Rev., Vol. 68, No. 3. (1 September 2004), pp. 474-500.
    by David Tropel, Jan R van der Meer
    posted to biodegradation by icases on 2008-06-09 10:30:31 as **
  • The University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining
    Nucl. Acids Res., Vol. 31, No. 1. (1 January 2003), pp. 262-265.
    by Lynda B Ellis, Bo K Hou, Wenjun Kang, Lawrence P Wackett
    posted to biodegradation by icases on 2008-06-09 10:29:56 as **
  • Exploring the microbial biodegradation and biotransformation gene pool
    Trends in Biotechnology, Vol. 23, No. 10. (October 2005), pp. 497-506.
    by Teca C Galvão, William W Mohn, Víctor de Lorenzo
    posted to biodegradation by icases on 2008-06-09 10:28:51 as **
  • The University of Minnesota Biocatalysis/Biodegradation Database: the first decade.
    Nucleic acids research, Vol. 34, No. Database issue. (1 January 2006)
    by LB Ellis, D Roe, LP Wackett
    posted to biodegradation by icases on 2008-06-09 10:27:48 as **
  • Evolution of catabolic pathways: Genomic insights into microbial s-triazine metabolism.
    Journal of bacteriology, Vol. 189, No. 3. (February 2007), pp. 674-682.
    by N Shapir, EF Mongodin, MJ Sadowsky, SC Daugherty, KE Nelson, LP Wackett
    posted to biodegradation by icases on 2008-06-09 10:27:19 as **
  • Pathways to discovering new microbial metabolism for functional genomics and biotechnology.
    Advances in applied microbiology, Vol. 61 (2007), pp. 219-232.
    by LP Wackett
    posted to biodegradation by icases on 2008-06-09 10:26:49 as **
  • The University of Minnesota pathway prediction system: predicting metabolic logic
    Nucl. Acids Res. (4 June 2008), gkn315.
    by Lynda B Ellis, Junfeng Gao, Kathrin Fenner, Lawrence P Wackett
    posted to biodegradation by icases on 2008-06-09 10:24:38 as **
  • Tools for Visually Exploring Biological Networks.
    Bioinformatics (25 August 2007)
    by Matthew Suderman, Michael Hallett
    posted to network by icases on 2007-08-28 23:11:32 as ** along with 12 people and 3 groups hryk AlexanderPico schuylrp jyuh dullhunk sebastien_vigneau grahamc sgoetz cabbagezs cerami loopback007 Pao-Yang ParkinsonLab_at_MaRS TNT Cancer_Stem_Cells
  • Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE).
    Genome Res, Vol. 17, No. 6. (June 2007), pp. 910-916.
    by AA Bhinge, J Kim, GM Euskirchen, M Snyder, VR Iyer
    posted to binding eukariot genome-wide site by icases on 2007-08-01 14:03:22 as ** along with 2 people and 1 group ghattem levydavid01 TNT
  • Design of gene circuits: lessons from bacteria.
    Nat Rev Genet, Vol. 5, No. 1. (January 2004), pp. 34-42.
    by ME Wall, WS Hlavacek, MA Savageau
    posted to bacteria dynamics evolution transcription by icases on 2007-05-31 16:36:46 as ** along with 4 people and 2 groups rklancer monod jjray dbikard TNT SynBioSys
  • Network motifs: theory and experimental approaches
    Nature Reviews Genetics, Vol. 8, No. 6., pp. 450-461.
    by Uri Alon
    posted to network transcription by icases on 2007-05-20 11:38:23 as ** along with 13 people and 3 groups aalibes cmmorel jtaylor dbikard margaritis shigepong zwang grinfish Pascalichouchou xingxu karfunkel vietanh0 haarcuba TNT Centre de Recherches Interdisciplinaires SynBioSys
  • Assessing performance of orthology detection strategies applied to eukaryotic genomes.
    PLoS ONE, Vol. 2 (2007)
    by F Chen, AJ Mackey, JK Vermunt, DS Roos
    posted to eukatior evolution orthologs by icases on 2007-04-20 07:54:40 as ** along with 6 people and 3 groups operon rvosa indigoviolet stajich cjeans winterschlaefer EisenLab FAB-lab TNT
  • Internal Versus External Effector and Transcription Factor Gene Pairs Differ in Their Relative Chromosomal Position in Escherichia coli.
    J Mol Biol (12 January 2007)
    by Sarath Chandra C Janga, Heladia Salgado, Julio Collado-Vides, Agustino Martínez-Antonio
    posted to bacteria transcription by icases on 2007-03-01 09:50:44 as ** along with 1 group TNT
  • Inferring Pairwise Regulatory Relationships from Multiple Time Series Datasets.
    Bioinformatics (19 January 2007)
    by Yanxin Shi, Tom Mitchell, Ziv Bar-Joseph
    posted to regulation network modelling by icases on 2007-02-11 14:49:41 as ***** along with 1 group TNT
  • Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae.
    Nat Biotechnol, Vol. 22, No. 1. (January 2004), pp. 86-92.
    by J Ihmels, R Levy, N Barkai
    posted to yeast transcription regulation pathways evolution eukariot by icases on 2007-02-05 18:54:16 as **** along with 6 people and 4 groups hryk adepace nickluscombe koller arne shung EisenLab EBI-regulation TNT dIEMoSIRIS
  • Metabolic modeling of microbial strains in silico.
    Trends Biochem Sci, Vol. 26, No. 3. (March 2001), pp. 179-186.
    by MW Covert, CH Schilling, I Famili, JS Edwards, II Goryanin, E Selkov, BO Palsson
    posted to simulation prediction pathways network metabolism metabolic bacteria by icases on 2007-01-26 17:36:46 as ** along with 1 person and 2 groups raiyar steinmetzlab TNT
  • Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions.
    BMC Bioinformatics, Vol. 1 (2000)
    by JS Edwards, BO Palsson
    posted to simulation prediction pathways network metabolism bacteria by icases on 2007-01-26 17:36:11 as ** along with 1 person and 2 groups raiyar steinmetzlab TNT
  • Modeling the Evolution of Protein Domain Architectures Using Maximum Parsimony
    Journal of Molecular Biology, Vol. 366, No. 1. (9 February 2007), pp. 307-315.
    by Jessica H Fong, Lewis Y Geer, Anna R Panchenko, Stephen H Bryant
    posted to metabolism evolution bacteria by icases on 2007-01-26 17:34:18 as **** along with 5 people and 3 groups marcius tny choonpeng redelings zwang BioinfoCIPF SGU-CIPF TNT
  • Transcriptional regulation of protein complexes within and across species
    PNAS, Vol. 104, No. 4. (23 January 2007), pp. 1283-1288.
    by Kai Tan, Tomer Shlomi, Hoda Feizi, Trey Ideker, Roded Sharan
    posted to transcription regulation network evolution by icases on 2007-01-25 19:33:03 as ***** along with 4 people and 2 groups carlk nickluscombe zwang dylan77 EBI-regulation TNT
  • Role of NtrC in biofilm formation via controlling expression of the gene encoding an ADP-glycero-manno-heptose-6-epimerase in the pathogenic bacterium, Vibrio vulnificus
    Molecular Microbiology, Vol. 63, No. 2. (January 2007), pp. 559-574.
    by Kim, Han-Suk, Lee, Mi-Ae, Chun, Se-Jin, Park, Soon-Jung, Lee, Kyu-Ho
    posted to sigma54 regulation promoter bacteria by icases on 2007-01-24 21:44:31 as ** along with 1 group TNT
  • Regulators of expression of the oligopeptide permease A proteins of Borrelia burgdorferi.
    J Bacteriol (19 January 2007)
    by Melisa Medrano, Yanpeng Ding, Xing-Guo G Wang, Peng Lu, Jenifer Coburn, Linden T T Hu
    posted to sigma54 regulation promoter bacteria by icases on 2007-01-24 21:42:13 as ** along with 1 group TNT
  • Aire deficient mice develop multiple features of APECED phenotype and show altered immune response.
    Hum Mol Genet, Vol. 11, No. 4. (15 February 2002), pp. 397-409.
    by C Ramsey, O Winqvist, L Puhakka, M Halonen, A Moro, O Kämpe, P Eskelin, M Pelto-Huikko, L Peltonen
    posted to apeced aire by icases on 2007-01-24 10:57:15 as ** along with 1 group TNT
  • Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles
    PLoS Biology, Vol. 5, No. 1. (1 January 2007), e8.
    by Jeremiah J Faith, Boris Hayete, Joshua T Thaden, Ilaria Mogno, Jamey Wierzbowski, Guillaume Cottarel, Simon Kasif, James J Collins, Timothy S Gardner
    posted to trsncription transciption regulation promoter network bacteria by icases on 2007-01-12 01:06:15 as ** along with 5 people and 2 groups jfr teuder nickluscombe aswin heliopais EBI-regulation TNT
  • Characterization of extracellular proteins produced by Aeromonas hydrophila AH-1.
    Proteomics (4 January 2007)
    by Hong Bing B Yu, Rasvinder Kaur, Simin Lim, Xian Hui H Wang, Ka Yin Y Leung
    posted to bacteria sigma54 by icases on 2007-01-06 19:23:31 as ** along with 1 group TNT
  • Analysis of Growth of Lactobacillus plantarum WCFS1 on a Complex Medium Using a Genome-scale Metabolic Model.
    J Biol Chem, Vol. 281, No. 52. (29 December 2006), pp. 40041-40048.
    by Bas Teusink, Anne Wiersma, Douwe Molenaar, Christof Francke, Willem M M de Vos, Roland J J Siezen, Eddy J J Smid
    posted to bacteria metabolism network prediction simulation by icases on 2006-12-26 23:36:24 as ** along with 1 group TNT
  • Assessing computational tools for the discovery of transcription factor binding sites
    Nature Biotechnology, Vol. 23, No. 1. (06 January 2005), pp. 137-144.
    by Martin Tompa, Nan Li, Timothy L Bailey, George M Church, Bart D De Moor, Eleazar Eskin, Alexander V Favorov, Martin C Frith, Yutao Fu, James J Kent, Vsevolod J Makeev, Andrei A Mironov, William S Noble, Giulio Pavesi, Graziano Pesole, Mireille Régnier, Nicolas Simonis, Saurabh Sinha, Gert Thijs, Jacques v van Helden, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye, Zhou Zhu
    posted to prediction promoter transciption by icases on 2006-12-20 16:27:03 as ***** along with 23 people and 6 groups nuin ep161302 ana barry aalibes aprasad jfr tuck chad_davis lyongu tabu dquest neveaire ranb johncumbers noano xiaobeizhao olympos GustavoLacerda nklee mdimon dandaman vietanh0 structural_bioinformatics Biostatistics Computational-Genomics Bioinformatics Neuroscience TNT
  • Applied bioinformatics for the identification of regulatory elements.
    Nat Rev Genet, Vol. 5, No. 4. (April 2004), pp. 276-287.
    by WW Wasserman, A Sandelin
    posted to prediction promoter regulation transciption by icases on 2006-12-20 15:21:04 as ***** along with 15 people and 8 groups mariakmejia ana chad_davis moborg gpalidwor dchughes nickluscombe johncumbers giovanni xiaobeizhao bertelsen Stew nklee jdiezperezj ArtemPankin structural_bioinformatics Bioinformatics EisenLab G4ID EBI-regulation GeschwindLab TNT Genetics-of-Gambling
  • Stable evolutionary signal in a Yeast protein interaction network.
    BMC Evol Biol, Vol. 6 (2006)
    by S Wuchty, AL Barabási, MT Ferdig
    posted to interaction network protein yeast by icases on 2006-12-18 11:40:33 as ** along with 1 person and 1 group tuck TNT
  • The AauR-AauS two-component system regulates uptake and metabolism of acidic amino acids in Pseudomonas putida.
    Appl Environ Microbiol, Vol. 72, No. 10. (October 2006), pp. 6569-6577.
    by AM Sonawane, B Singh, KH Röhm
    posted to bacteria regulation sigma54 transciption by icases on 2006-12-18 11:38:08 as ** along with 1 group TNT
  • Adaptive evolution of bacterial metabolic networks by horizontal gene transfer
    Nature Genetics, Vol. 37, No. 12. (20 November 2005), pp. 1372-1375.
    by Csaba Pál, Balázs Papp, Martin J Lercher
    posted to evolution metabolic metabolism network by icases on 2006-12-17 10:47:12 as ** along with 3 people and 1 group michaelbarton knaseanka tny TNT
  • An integrated view of protein evolution
    Nature Reviews Genetics, Vol. 7, No. 5., pp. 337-348.
    by Csaba Pál, Balázs Papp, Martin J Lercher
    posted to evolution metabolic network by icases on 2006-12-17 10:46:23 as ** along with 6 people and 2 groups dayjm tny entropy markbothwell BioNica mingzhi Bothwellab TNT
  • Chance and necessity in the evolution of minimal metabolic networks
    Nature, Vol. 440, No. 7084., pp. 667-670.
    by Csaba Pã¡l, Balã¡zs Papp, Martin J Lercher, Pã©ter Csermely, Stephen G Oliver, Laurence D Hurst
    posted to evolution metabolic metabolism network by icases on 2006-12-17 10:45:23 as ** along with 8 people and 2 groups michaelbarton okarsligil Borelli ccots nirfriedman rabu mikaelhuss edwardmorrissey Bioinformatics TNT
  • Variability and memory of protein levels in human cells
    Nature (19 November 2006)
    by Alex Sigal, Ron Milo, Ariel Cohen, Naama Geva-Zatorsky, Yael Klein, Yuvalal Liron, Nitzan Rosenfeld, Tamar Danon, Natalie Perzov, Uri Alon
    posted to dynamics eukariot network by icases on 2006-12-15 13:43:25 as ** along with 4 people and 3 groups jjray marcius margaritis cjeans BioinfoCIPF SGU-CIPF TNT
  • Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae
    BMC Bioinformatics, Vol. 7 (28 October 2006), 478.
    by Illes J Farkas, Chuang Wu, Chakra Chennubhotla, Ivet Bahar, Zoltan N Oltvai
    posted to network trsncription yeast by icases on 2006-12-14 10:11:26 as *** along with 1 person and 1 group SeungjoonOh TNT
  • Selection for Unequal Densities of σ70 Promoter-Like Signals in Different Regions of Large Bacterial Genomes
    PLoS Genetics, Vol. 2, No. 11. (1 November 2006), e185.
    by Araceli M Huerta, Pilar M Francino, Enrique Morett, Julio Collado-Vides
    posted to evolution promoter trsncription by icases on 2006-12-14 10:10:39 as *** along with 2 people and 1 group Retchless discreteonyxorb TNT
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