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fishtank's library [186 articles]

Recent papers added to fishtank's library.
  • Development and validation of a spectral library searching method for peptide identification from MS/MS.
    Proteomics, Vol. 7, No. 5. (March 2007), pp. 655-667.
    by H Lam, EW Deutsch, JS Eddes, JK Eng, N King, SE Stein, R Aebersold
    posted to proteomics by fishtank on 2008-05-28 20:54:36 as ** along with 3 people jyuh nedwards olberd
  • Single-cell zeroth-order protein degradation enhances the robustness of synthetic oscillator
    Mol Syst Biol, Vol. 3 (31 July 2007)
    by Wilson W Wong, Tony Y Tsai, James C Liao
    posted to enzyme_optimization by fishtank on 2008-05-16 22:26:37 as read along with 2 people austin zwang
  • Microarray data analysis and mining approaches
    Brief Funct Genomic Proteomic (22 January 2008), elm034.
    by Francesca Cordero, Marco Botta, Raffaele A Calogero
    posted to microarray biomarkers by fishtank on 2008-05-16 22:21:51 as read along with 3 people jyuh jfr neveaire
  • Unravelling the regulatory structure of biochemical networks using stimulus response experiments and large-scale model selection
    Systems Biology, IEE Proceedings, Vol. 153, No. 4. (2006), pp. 275-285.
    by SA Wahl, MD Haunschild, M Oldiges, W Wiechert
    posted to rate_constants kinetic_simulation by fishtank on 2008-05-05 17:31:34 as read
  • PhyR Is Involved in the General Stress Response of Methylobacterium extorquens AM1
    J. Bacteriol., Vol. 190, No. 3. (1 February 2008), pp. 1027-1035.
    by Benjamin Gourion, Anne Francez-Charlot, Julia A Vorholt
    posted to am1 by fishtank on 2008-04-18 00:44:45 as read
  • The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
    PNAS, Vol. 97, No. 10. (9 May 2000), pp. 5528-5533.
    by JS Edwards, BO Palsson
    posted to ecoli_ppp fba by fishtank on 2008-04-18 00:37:11 as read along with 1 person tny
  • Conservation of the metabolomic response to starvation across two divergent microbes.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 51. (19 December 2006), pp. 19302-19307.
    by MJ Brauer, J Yuan, BD Bennett, W Lu, E Kimball, D Botstein, JD Rabinowitz
    posted to yeast by fishtank on 2008-04-18 00:34:23 as read
  • Design, construction and performance of the most efficient biomass producing E. coli bacterium
    Metabolic Engineering, Vol. 8, No. 6. (November 2006), pp. 628-638.
    by Cong T Trinh, Ross Carlson, Aaron Wlaschin, Friedrich Srienc
    posted to ecoli_ppp by fishtank on 2008-04-18 00:27:51 as read
  • Rational design of efficient organisms
    Journal of Biotechnology, Vol. 131, No. 2, Supplement 1. (September 2007), pp. S204-S204.
    by Cong T Trinh, Pornkamol Unrean, Friedrich Srienc
    posted to ecoli_ppp by fishtank on 2008-04-18 00:24:21 as read
  • Global metabolic response of Escherichia coli to gnd or zwf gene-knockout, based on 13C-labeling experiments and the measurement of enzyme activities
    Applied Microbiology and Biotechnology, Vol. 64, No. 1. (17 March 2004), pp. 91-98.
    by J Zhao, T Baba, H Mori, K Shimizu
    posted to ecoli_ppp by fishtank on 2008-04-17 23:55:03 as read
  • Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data.
    Nat Genet, Vol. 34, No. 2. (June 2003), pp. 166-176.
    by E Segal, M Shapira, A Regev, D Pe'er, D Botstein, D Koller, N Friedman
    posted to gene_regulation by fishtank on 2008-04-10 19:31:54 as read along with 13 people chrisamiller pkm tvdbulck dragonrez tuck bayesian wnpx tabu koller olympos dimatura karfunkel roys
  • Changing perspectives in yeast research nearly a decade after the genome sequence.
    Genome Res, Vol. 15, No. 12. (December 2005), pp. 1611-1619.
    by K Dolinski, D Botstein
    posted to yeast by fishtank on 2008-04-10 01:26:45 as read along with 3 people and 1 group lfriedl nirfriedman dmc kdl
  • If I only had a brain: exploring mouse brain images in the Allen Brain Atlas.
    Biology of the cell / under the auspices of the European Cell Biology Organization, Vol. 99, No. 7. (July 2007), pp. 403-409.
    by H Hochheiser, J Yanowitz
    posted to image_registration by fishtank on 2008-04-08 22:19:19 as **
  • Bayesian methods for proteomics
    PROTEOMICS, Vol. 9999, No. 9999. (2007), NA.
    by Gil Alterovitz, Jonathan Liu, Ehsan Afkhami, Marco F Ramoni
    posted to proteomics by fishtank on 2008-03-29 00:38:38 as ** along with 1 person jyuh
  • Systems Biology: Principles, Methods, and Concepts
    (20 November 2006)
    by Andrzej Konopka
    posted to book systems_biology by fishtank on 2008-03-26 16:09:37 as read
  • Implementation of Microarrays for Methylobacterium extorquens AM1
    OMICS: A Journal of Integrative Biology, Vol. 11, No. 4. (2007), pp. 325-340.
    by Yoko Okubo, Elizabeth Skovran, Xiaofeng Guo, Dhileep Sivam, Mary E Lidstrom
    posted to am1 by fishtank on 2008-03-25 23:00:39 as **
  • Formulating genome-scale kinetic models in the post-genome era
    Mol Syst Biol, Vol. 4 (4 March 2008)
    by Neema Jamshidi, Bernhard O Palsson
    posted to kinetic_simulation-review by fishtank on 2008-03-20 20:19:54 as read along with 1 person westoll
  • Is proteomics the new genomics?
    Cell, Vol. 130, No. 3. (10 August 2007), pp. 395-398.
    by J Cox, M Mann
    posted to proteomics by fishtank on 2008-02-23 01:27:58 as ** along with 3 people and 1 group grahamc oelemento Pao-Yang ParkinsonLab_at_MaRS
  • Methods, algorithms and tools in computational proteomics: A practical point of view.
    Proteomics, Vol. 7, No. 16. (August 2007), pp. 2815-2832.
    by R Matthiesen
    posted to proteomics by fishtank on 2008-02-23 01:22:42 as read along with 1 person jyuh
  • Qscore: an algorithm for evaluating SEQUEST database search results
    Journal of the American Society for Mass Spectrometry, Vol. 13, No. 4. (April 2002), pp. 378-386.
    by Roger E Moore, Mary K Young, Terry D Lee
    posted to proteomics by fishtank on 2008-02-23 00:41:28 as read
  • On the Attribution and Additivity of Binding Energies
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 78, No. 7. (1981), pp. 4046-4050.
    by William P Jencks
    posted to enzyme_optimization by fishtank on 2008-02-21 21:27:05 as read
  • Evolution of enzyme function and the development of catalytic efficiency.
    Biochemistry, Vol. 15, No. 25. (14 December 1976), pp. 5631-5640.
    by WJ Albery, JR Knowles
    posted to enzyme_optimization by fishtank on 2008-02-21 21:23:17 as read
  • Challenges in enzyme mechanism and energetics.
    Annu Rev Biochem, Vol. 72 (2003), pp. 517-571.
    by DA Kraut, KS Carroll, D Herschlag
    posted to enzyme_optimization by fishtank on 2008-02-21 21:07:58 as read along with 2 people and 1 group hlwoodcock livingthingdan livingthing
  • Catalysis, Binding and Enzyme-Substrate Complementarity
    Proceedings of the Royal Society of London. Series B, Biological Sciences, Vol. 187, No. 1089. (1974), pp. 397-407.
    by AR Fersht
    posted to enzyme_optimization by fishtank on 2008-02-21 20:59:55 as read
  • Computer simulations of enzyme catalysis: Finding out what has been optimized by evolution
    Proceedings of the National Academy of Sciences, Vol. 95, No. 11. (26 May 1998), pp. 5950-5955.
    by Arieh Warshel, Jan Florian
    posted to enzyme_optimization by fishtank on 2008-02-21 20:54:45 as read
  • Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases.
    Anal Chem, Vol. 76, No. 6. (15 March 2004), pp. 1664-1671.
    by RG Sadygov, H Liu, JR Yates
    posted to proteomics by fishtank on 2008-02-21 00:34:53 as read along with 1 person nedwards
  • Intensity-based protein identification by machine learning from a library of tandem mass spectra
    Nat Biotech, Vol. 22, No. 2. (February 2004), pp. 214-219.
    by Joshua E Elias, Francis D Gibbons, Oliver D King, Frederick P Roth, Steven P Gygi
    posted to proteomics by fishtank on 2008-02-21 00:22:47 as read
  • Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC-MS/MS) for Large-Scale Protein Analysis: The Yeast Proteome
    J. Proteome Res., Vol. 2, No. 1. (3 February 2003), pp. 43-50.
    by J Peng, JE Elias, CC Thoreen, LJ Licklider, SP Gygi
    posted to proteomics by fishtank on 2008-02-21 00:22:17 as read
  • Analysis and validation of proteomic data generated by tandem mass spectrometry
    Nat Meth, Vol. 4, No. 10. (October 2007), pp. 787-797.
    by Alexey Nesvizhskii, Olga Vitek, Ruedi Aebersold
    posted to proteomics by fishtank on 2008-02-21 00:20:49 as read along with 2 people jyuh nedwards
  • Software for computational peptide identification from MS-MS data
    Drug Discovery Today, Vol. 11, No. 13-14. (July 2006), pp. 595-600.
    by Changjiang Xu, Bin Ma
    posted to proteomics by fishtank on 2008-02-20 22:10:26 as read
  • Computational analysis of shotgun proteomics data
    Current Opinion in Chemical Biology, Vol. 9, No. 1. (February 2005), pp. 88-94.
    by Michael J Maccoss
    posted to proteomics by fishtank on 2008-02-20 22:08:57 as read
  • Simplified modelling of metabolic pathways for flux prediction and optimization: lessons from an in vitro reconstruction of the upper part of glycolysis.
    Biochem J, Vol. 396, No. 2. (1 June 2006), pp. 317-326.
    by JB Fiévet, C Dillmann, G Curien, D de Vienne
    posted to enzyme_optimization by fishtank on 2008-02-04 19:45:13 as **
  • Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data
    Theoretical Biology and Medical Modelling, Vol. 3 (15 December 2006), 42.
    by Wolfram Liebermeister, Edda Klipp
    posted to enzyme_optimization by fishtank on 2008-02-04 19:33:22 as ** along with 4 people and 1 group jyuh wnpx raiyar jrbanga steinmetzlab
  • Optimization of kinetic parameters of enzymes
    Biochemistry and Molecular Biology Education, Vol. 30, No. 3. (2002), pp. 184-188.
    by Reinhart Heinrich, Enrique Meléndez-Hevia, Héctor Cabezas
    posted to enzyme_optimization by fishtank on 2008-02-04 19:15:45 as **
  • Microarrays in breast cancer research and clinical practice--the future lies ahead.
    Endocr Relat Cancer, Vol. 13, No. 4. (December 2006), pp. 1017-1031.
    by SK Gruvberger-Saal, HE Cunliffe, KM Carr, IA Hedenfalk
    posted to biomarkers by fishtank on 2008-01-29 07:24:19 as read along with 2 people jfr waszak
  • Outcome signature genes in breast cancer: is there a unique set?
    Bioinformatics, Vol. 21, No. 2., 171.
    by Liat Ein-Dor, Itai Kela, Eytan Domany
    posted to biomarkers by fishtank on 2008-01-29 07:21:31 as read along with 2 people and 1 group winterschlaefer frohike Bioinformatics
  • Perspective: How to Make Microarray, Serial Analysis of Gene Expression, and Proteomic Relevant to Day-to-Day Endocrine Problems and Physiological Systems
    Endocrinology, Vol. 143, No. 6. (1 June 2002), pp. 1995-2001.
    by Denis Soulet, Serge Rivest
    posted to proteomics by fishtank on 2008-01-19 02:31:50 as read
  • Biostatistical Analysis (4th Edition)
    (08 October 1998)
    by Jerrold H Zar
    posted to no-tag by fishtank on 2008-01-17 19:43:20 as read
  • Stoichiometric model for evaluating the metabolic capabilities of the facultative methylotroph <I>Methylobacterium extorquens</I> AM1, with application to reconstruction of C<SUB><FONT SIZE='-1'>3</FONT></SUB> and C<SUB><FONT SIZE='-1'>4</FONT></SUB> metabolism
    Biotechnology and Bioengineering, Vol. 78, No. 3. (2002), pp. 296-312.
    by Stephen J Van Dien, Mary E Lidstrom
    posted to am1 by fishtank on 2008-01-14 20:09:46 as **
  • Reconstruction of C3 and C4 metabolism in Methylobacterium extorquens AM1 using transposon mutagenesis
    Microbiology, Vol. 149, No. 3. (1 March 2003), pp. 601-609.
    by Stephen J Van Dien, Yoko Okubo, Melinda T Hough, Natalia Korotkova, Tricia Taitano, Mary E Lidstrom
    posted to am1 am1_mutant by fishtank on 2008-01-14 20:03:38 as read
  • Genetics of the serine cycle in Methylobacterium extorquens AM1: cloning, sequence, mutation, and physiological effect of glyA, the gene for serine hydroxymethyltransferase.
    J. Bacteriol., Vol. 176, No. 21. (1 November 1994), pp. 6759-6762.
    by LV Chistoserdova, ME Lidstrom
    posted to am1 am1_enzymes by fishtank on 2008-01-14 19:44:18 as read
  • Formaldehyde-Detoxifying Role of the Tetrahydromethanopterin-Linked Pathway in Methylobacterium extorquens AM1
    J. Bacteriol., Vol. 185, No. 24. (15 December 2003), pp. 7160-7168.
    by Christopher J Marx, Ludmila Chistoserdova, Mary E Lidstrom
    posted to am1 am1_enzymes by fishtank on 2008-01-14 19:29:25 as read
  • Identification of a Fourth Formate Dehydrogenase in Methylobacterium extorquens AM1 and Confirmation of the Essential Role of Formate Oxidation in Methylotrophy
    J. Bacteriol., Vol. 189, No. 24. (15 December 2007), pp. 9076-9081.
    by Ludmila Chistoserdova, Gregory J Crowther, Julia A Vorholt, Elizabeth Skovran, Jean-Charles Portais, Mary E Lidstrom
    posted to am1 am1_enzymes by fishtank on 2007-12-27 23:11:59 as read
  • Purification and characterization of hydroxypyruvate reductase from the facultative methylotroph Methylobacterium extorquens AM1.
    J Bacteriol, Vol. 173, No. 22. (November 1991), pp. 7228-7232.
    by LV Chistoserdova, ME Lidstrom
    posted to am1_enzymes by fishtank on 2007-12-18 00:07:50 as read
  • Characterization of the formyltransferase from Methylobacterium extorquens AM1
    European Journal of Biochemistry, Vol. 268, No. 17. (2001), pp. 4769-4775.
    by Barbara K Pomper, Julia A Vorholt
    posted to am1_enzymes by fishtank on 2007-12-17 23:58:59 as read
  • Novel formaldehyde-activating enzyme in Methylobacterium extorquens AM1 required for growth on methanol.
    J Bacteriol, Vol. 182, No. 23. (December 2000), pp. 6645-6650.
    by JA Vorholt, CJ Marx, ME Lidstrom, RK Thauer
    posted to am1_enzymes by fishtank on 2007-12-17 23:46:09 as read
  • The tungsten-containing formate dehydrogenase from Methylobacterium extorquens AM1: Purification and properties
    European Journal of Biochemistry, Vol. 270, No. 2. (2003), pp. 325-333.
    by Markus Laukel, Ludmila Chistoserdova, Mary E Lidstrom, Julia A Vorholt
    posted to am1_enzymes by fishtank on 2007-12-17 23:35:15 as **
  • Multiple Formate Dehydrogenase Enzymes in the Facultative Methylotroph Methylobacterium extorquens AM1 Are Dispensable for Growth on Methanol
    J. Bacteriol., Vol. 186, No. 1. (1 January 2004), pp. 22-28.
    by Ludmila Chistoserdova, Markus Laukel, Jean-Charles Portais, Julia A Vorholt, Mary E Lidstrom
    posted to am1_enzymes by fishtank on 2007-12-17 23:34:29 as **
  • A methenyl tetrahydromethanopterin cyclohydrolase and a methenyl tetrahydrofolate cyclohydrolase in Methylobacterium extorquens AM1
    European Journal of Biochemistry, Vol. 261, No. 2. (1999), pp. 475-480.
    by Barbara K Pomper, Julia A Vorholt, Ludmila Chistoserdova, Mary E Lidstrom, Rudolf K Thauer
    posted to am1_enzymes by fishtank on 2007-12-17 23:32:29 as **
  • The NADP-Dependent Methylene Tetrahydromethanopterin Dehydrogenase in Methylobacterium extorquens AM1
    J. Bacteriol., Vol. 180, No. 20. (15 October 1998), pp. 5351-5356.
    by Julia A Vorholt, Ludmila Chistoserdova, Mary E Lidstrom, Rudolf K Thauer
    posted to am1_enzymes by fishtank on 2007-12-17 23:26:00 as **
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