A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes

[1]  Ronan M. T. Fleming,et al.  A community-driven global reconstruction of human metabolism , 2013, Nature Biotechnology.

[2]  H. Westerhoff,et al.  Why in vivo may not equal in vitro – new effectors revealed by measurement of enzymatic activities under the same in vivo‐like assay conditions , 2012, The FEBS journal.

[3]  I. Nookaew,et al.  Fifteen years of large scale metabolic modeling of yeast: developments and impacts. , 2012, Biotechnology advances.

[4]  Neil Swainston,et al.  Improving metabolic flux predictions using absolute gene expression data , 2012, BMC Systems Biology.

[5]  Pedro Mendes,et al.  Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network , 2012, BMC Systems Biology.

[6]  K. Elliott Epistemic and methodological iteration in scientific research , 2012 .

[7]  Hans V. Westerhoff,et al.  Testing Biochemistry Revisited: How In Vivo Metabolism Can Be Understood from In Vitro Enzyme Kinetics , 2012, PLoS Comput. Biol..

[8]  Douglas B. Kell,et al.  The genetic control of growth rate: a systems biology study in yeast , 2012, BMC Systems Biology.

[9]  S. Oliver,et al.  Protein production in Saccharomyces cerevisiae for systems biology studies. , 2011, Methods in enzymology.

[10]  Michel Dumontier,et al.  Controlled vocabularies and semantics in systems biology , 2011, Molecular systems biology.

[11]  Duygu Dikicioglu,et al.  How yeast re-programmes its transcriptional profile in response to different nutrient impulses , 2011, BMC Systems Biology.

[12]  Evangelos Simeonidis,et al.  Building a kinetic model of trehalose biosynthesis in Saccharomyces cerevisiae. , 2011, Methods in enzymology.

[13]  Christopher G. Knight,et al.  Absolute Quantification of the Glycolytic Pathway in Yeast: , 2011, Molecular & Cellular Proteomics.

[14]  N. Malys,et al.  Towards a full quantitative description of yeast metabolism a systematic approach for estimating the kinetic parameters of isoenzymes under in vivo like conditions. , 2011, Methods in enzymology.

[15]  Neil Swainston,et al.  A QconCAT informatics pipeline for the analysis, visualization and sharing of absolute quantitative proteomics data , 2011, Proteomics.

[16]  Warwick B Dunn,et al.  Sample preparation related to the intracellular metabolome of yeast methods for quenching, extraction, and metabolite quantitation. , 2011, Methods in enzymology.

[17]  Karin Lanthaler,et al.  The use of continuous culture in systems biology investigations. , 2011, Methods in enzymology.

[18]  H. Westerhoff,et al.  A probabilistic approach to identify putative drug targets in biochemical networks , 2011, Journal of The Royal Society Interface.

[19]  David S. Broomhead,et al.  Systematic integration of experimental data and models in systems biology , 2010, BMC Bioinformatics.

[20]  Edda Klipp,et al.  Parameter Balancing in Kinetic Models of Cell Metabolism , 2010, The journal of physical chemistry. B.

[21]  Neil Swainston,et al.  Further developments towards a genome-scale metabolic model of yeast , 2010, BMC Systems Biology.

[22]  Alan T. Bull,et al.  The renaissance of continuous culture in the post-genomics age , 2010, Journal of Industrial Microbiology & Biotechnology.

[23]  Neil Swainston,et al.  Enzyme kinetics informatics: from instrument to browser , 2010, The FEBS journal.

[24]  Norman W. Paton,et al.  Integrative Information Management for Systems Biology , 2010, DILS.

[25]  Melanie I. Stefan,et al.  BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models , 2010, BMC Systems Biology.

[26]  Hidde de Jong,et al.  Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria , 2010, BMC Systems Biology.

[27]  Evangelos Simeonidis,et al.  Systems Biology: The elements and principles of Life , 2009, FEBS letters.

[28]  Joshua D. Knowles,et al.  Development and performance of a gas chromatography-time-of-flight mass spectrometry analysis for large-scale nontargeted metabolomic studies of human serum. , 2009, Analytical chemistry.

[29]  Neil Swainston,et al.  libAnnotationSBML: a library for exploiting SBML annotations , 2009, Bioinform..

[30]  D. Kell,et al.  Mass Spectrometry Tools and Metabolite-specific Databases for Molecular Identification in Metabolomics , 2009 .

[31]  Joshua D. Knowles,et al.  Development of a robust and repeatable UPLC-MS method for the long-term metabolomic study of human serum. , 2009, Analytical chemistry.

[32]  Stefan Hoops,et al.  Enzyme kinetics and computational modeling for systems biology. , 2009, Methods in enzymology.

[33]  Markus J. Herrgård,et al.  A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology , 2008, Nature Biotechnology.

[34]  E. Nevoigt,et al.  Progress in Metabolic Engineering of Saccharomyces cerevisiae , 2008, Microbiology and Molecular Biology Reviews.

[35]  Jens Nielsen,et al.  Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae. , 2008, FEMS yeast research.

[36]  Mike Tyers,et al.  The size of the nucleus increases as yeast cells grow. , 2007, Molecular biology of the cell.

[37]  P. Mendes,et al.  Comparison of sampling techniques for parallel analysis of transcript and metabolite levels in Saccharomyces cerevisiae , 2007, Yeast.

[38]  Mudita Singhal,et al.  COPASI - a COmplex PAthway SImulator , 2006, Bioinform..

[39]  Sophia Ananiadou,et al.  Text mining and its potential applications in systems biology. , 2006, Trends in biotechnology.

[40]  Dagmar Iber,et al.  The mechanism of cell differentiation in Bacillus subtilis , 2006, Nature.

[41]  D. Kell Metabolomics, modelling and machine learning in systems biology – towards an understanding of the languages of cells , 2006, The FEBS journal.

[42]  Douglas B Kell,et al.  Theodor Bücher Lecture. Metabolomics, modelling and machine learning in systems biology - towards an understanding of the languages of cells. Delivered on 3 July 2005 at the 30th FEBS Congress and the 9th IUBMB conference in Budapest. , 2006, The FEBS journal.

[43]  T. Hughes,et al.  Mapping pathways and phenotypes by systematic gene overexpression. , 2006, Molecular cell.

[44]  B. Palsson Systems Biology: Properties of Reconstructed Networks , 2006 .

[45]  Nigel W. Hardy,et al.  MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics , 2006, BMC Bioinformatics.

[46]  Hugh D. Spence,et al.  Minimum information requested in the annotation of biochemical models (MIRIAM) , 2005, Nature Biotechnology.

[47]  Mark Gerstein,et al.  Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. , 2005, Genes & development.

[48]  Barbara M. Bakker,et al.  Experimental and in Silico Analyses of Glycolytic Flux Control in Bloodstream Form Trypanosoma brucei* , 2005, Journal of Biological Chemistry.

[49]  R. Beynon,et al.  Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides , 2005, Nature Methods.

[50]  Douglas B. Kell,et al.  The role of modeling in systems biology , 2005 .

[51]  Jacky L. Snoep,et al.  Web-based kinetic modelling using JWS Online , 2004, Bioinform..

[52]  D. Kell Metabolomics and systems biology: making sense of the soup. , 2004, Current opinion in microbiology.

[53]  Douglas B. Kell,et al.  Comparative Genomic Assessment of Novel Broad-Spectrum Targets for Antibacterial Drugs , 2004, Comparative and functional genomics.

[54]  B. Birren,et al.  Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae , 2004, Nature.

[55]  Douglas B. Kell,et al.  Quantifying heterogeneity: flow cytometry of bacterial cultures , 1991, Antonie van Leeuwenhoek.

[56]  D. Tollervey,et al.  The 'scavenger' m7GpppX pyrophosphatase activity of Dcs1 modulates nutrient-induced responses in yeast. , 2004, Nucleic acids research.

[57]  D. Kell,et al.  Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era. , 2004, BioEssays : news and reviews in molecular, cellular and developmental biology.

[58]  E. O’Shea,et al.  Global analysis of protein expression in yeast , 2003, Nature.

[59]  K. Takeo,et al.  Quantitative three-dimensional structural analysis of Exophiala dermatitidis yeast cells by freeze-substitution and serial ultrathin sectioning. , 2003, Journal of electron microscopy.

[60]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[61]  Mark Johnston,et al.  Yeast genome duplication was followed by asynchronous differentiation of duplicated genes , 2003, Nature.

[62]  Johann M. Rohwer,et al.  Metabolic Control Analysis of Glycerol Synthesis in Saccharomyces cerevisiae , 2002, Applied and Environmental Microbiology.

[63]  D. Kell,et al.  Schemes of flux control in a model of Saccharomyces cerevisiae glycolysis. , 2002, European journal of biochemistry.

[64]  Z. Gu,et al.  Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. , 2002, Molecular biology and evolution.

[65]  J. Nielsen,et al.  Fuel ethanol production from lignocellulose: a challenge for metabolic engineering and process integration , 2001, Applied Microbiology and Biotechnology.

[66]  V. Pancholi,et al.  Multifunctional α-enolase: its role in diseases , 2001, Cellular and Molecular Life Sciences CMLS.

[67]  A. Minton,et al.  The Influence of Macromolecular Crowding and Macromolecular Confinement on Biochemical Reactions in Physiological Media* , 2001, The Journal of Biological Chemistry.

[68]  Barbara M. Bakker,et al.  Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. , 2000, European journal of biochemistry.

[69]  J. Pronk,et al.  Fermentative capacity in high‐cell‐density fed‐batch cultures of baker's yeast , 2000, Biotechnology and bioengineering.

[70]  J. Hauf,et al.  Simultaneous genomic overexpression of seven glycolytic enzymes in the yeast Saccharomyces cerevisiae. , 2000, Enzyme and microbial technology.

[71]  W. Jakoby New Beer in an Old Bottle: Eduard Buchner and the Growth of Biochemical Knowledge. Edited by Athel Cornish-Bowden. Universitat de Valencia, Valencia, 1997, 252 pp. , 1999 .

[72]  H. Westerhoff,et al.  The danger of metabolic pathways with turbo design. , 1998, Trends in biochemical sciences.

[73]  K. H. Wolfe,et al.  Molecular evidence for an ancient duplication of the entire yeast genome , 1997, Nature.

[74]  D. Kell,et al.  Flow cytometry and cell sorting of heterogeneous microbial populations: the importance of single-cell analyses. , 1996, Microbiological reviews.

[75]  D. Fell Understanding the Control of Metabolism , 1996 .

[76]  H M Davey,et al.  Oscillatory, stochastic and chaotic growth rate fluctuations in permittistatically controlled yeast cultures. , 1996, Bio Systems.

[77]  H. Kacser,et al.  The control of flux. , 1995, Biochemical Society transactions.

[78]  Douglas B. Kell,et al.  Metabolic Channeling in Organized Enzyme Systems: Experiments and Models , 1995 .

[79]  W. A. Scheffers,et al.  Effects of oxygen limitation on sugar metabolism in yeasts: a continuous-culture study of the Kluyver effect. , 1994, Microbiology.

[80]  Christopher L. Davey,et al.  THE PERMITTISTAT : A NOVEL TYPE OF TURBIDOSTAT , 1991 .

[81]  L. Lebioda,et al.  Mechanism of enolase: the crystal structure of enolase-Mg2(+)-2-phosphoglycerate/phosphoenolpyruvate complex at 2.2-A resolution. , 1991, Biochemistry.

[82]  O. Ward,et al.  Reductive biotransformations of organic compounds by cells or enzymes of yeast. , 1990, Enzyme and microbial technology.

[83]  Douglas B. Kell,et al.  Dielectric permittivity of microbial suspensions at radio frequencies: a novel method for the real-time estimation of microbial biomass , 1987 .

[84]  A. Cornish-Bowden,et al.  Control analysis of metabolic systems , 1985 .

[85]  J. Yamashita,et al.  Theoretical and experimental analyses of coupled enzyme reactions. , 1983, Journal of biochemistry.

[86]  H. Kacser,et al.  The molecular basis of dominance. , 1981, Genetics.

[87]  J. Adams The interrelationship of cell growth and division in haploid and diploid cells of Saccharomyces cerevisiae. , 1977, Experimental cell research.

[88]  R. L. Weiss,et al.  The relationship between enzyme activity, cell geometry, and fitness in Saccharomyces cerevisiae. , 1975, Proceedings of the National Academy of Sciences of the United States of America.