Systems-level analysis of mechanisms regulating yeast metabolic flux

Metabolite concentrations, fluxes and free energies imply efficient enzyme usage

(2016) Junyoung O Park et al.   Nature Chemical Biology

A nested parallel experiment demonstrates differences in intensity-dependence between RNA-seq and microarrays

(2015) David G. Robinson et al.   NUCLEIC ACIDS RESEARCH

Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State Data

(2015) Luca Gerosa et al.   Cell Systems

Domain Organization, Catalysis and Regulation of Eukaryotic Cystathionine Beta-Synthases

(2014) Tomas Majtan et al.   PLoS One

Lost in Transition: Start-Up of Glycolysis Yields Subpopulations of Nongrowing Cells

(2014) J. H. van Heerden et al.   SCIENCE

Large-scale functional analysis of the roles of phosphorylation in yeast metabolic pathways

(2014) J. C. Schulz et al.   Science Signaling

Somewhat in control—the role of transcription in regulating microbial metabolic fluxes

(2013) Karl Kochanowski et al.   CURRENT OPINION IN BIOTECHNOLOGY

New types of experimental data shape the use of enzyme kinetics for dynamic network modeling

(2013) Katja Tummler et al.   FEBS Journal

A century of enzyme kinetic analysis, 1913 to 2013

(2013) Kenneth A. Johnson   FEBS LETTERS

Yeast Pif1 Helicase Exhibits a One-base-pair Stepping Mechanism for Unwinding Duplex DNA

(2013) Ramanagouda Ramanagoudr-Bhojappa et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins

(2013) Kaspar Valgepea et al.   Molecular BioSystems

Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast

(2013) G. G. Zampar et al.   Molecular Systems Biology

Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis

(2013) V. Chubukov et al.   Molecular Systems Biology

Coordination of bacterial proteome with metabolism by cyclic AMP signalling

(2013) Conghui You et al.   NATURE

Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo

(2013) Hannes Link et al.   NATURE BIOTECHNOLOGY

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Glycolytic strategy as a tradeoff between energy yield and protein cost

(2013) A. Flamholz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Consistent Estimation of Gibbs Energy Using Component Contributions

(2013) Elad Noor et al.   PLoS Computational Biology

Mechanism of Feedback Allosteric Inhibition of ATP Phosphoribosyltransferase

(2012) Sònia Pedreño et al.   BIOCHEMISTRY

Regulation of Yeast Pyruvate Kinase by Ultrasensitive Allostery Independent of Phosphorylation

(2012) Yi-Fan Xu et al.   MOLECULAR CELL

Stitching together Multiple Data Dimensions Reveals Interacting Metabolomic and Transcriptomic Networks That Modulate Cell Regulation

(2012) Jun Zhu et al.   PLOS BIOLOGY

Liquid Chromatography–High Resolution Mass Spectrometry Analysis of Fatty Acid Metabolism

(2011) Jurre J. Kamphorst et al.   ANALYTICAL CHEMISTRY

Regulation and control of metabolic fluxes in microbes

(2011) Luca Gerosa et al.   CURRENT OPINION IN BIOTECHNOLOGY

A flux-sensing mechanism could regulate the switch between respiration and fermentation

(2011) Daphne H. E. W. Huberts et al.   FEMS YEAST RESEARCH

Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics

(2011) R. Costenoble et al.   Molecular Systems Biology

Environmental and genetic perturbations reveal different networks of metabolic regulation

(2011) A. J. Greenberg et al.   Molecular Systems Biology

α-ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition

(2011) Christopher D Doucette et al.   Nature Chemical Biology

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model

(2010) K. Yizhak et al.   BIOINFORMATICS

Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity

(2010) Sarah-Maria Fendt et al.   Molecular Systems Biology

BRENDA, the enzyme information system in 2011

(2010) M. Scheer et al.   NUCLEIC ACIDS RESEARCH

Functional Organization of the S. cerevisiae Phosphorylation Network

(2009) Dorothea Fiedler et al.   CELL

rNMR: open source software for identifying and quantifying metabolites in NMR spectra

(2009) Ian A. Lewis et al.   MAGNETIC RESONANCE IN CHEMISTRY

Growth-limiting Intracellular Metabolites in Yeast Growing under Diverse Nutrient Limitations

(2009) Viktor M. Boer et al.   MOLECULAR BIOLOGY OF THE CELL

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

ChemmineR: a compound mining framework for R

(2008) Y. Cao et al.   BIOINFORMATICS

Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A

(2008) Paula Jouhten et al.   BMC Systems Biology

Pyruvate kinase M2 is a phosphotyrosine-binding protein

(2008) Heather R. Christofk et al.   NATURE

Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach

(2008) Bryson D Bennett et al.   Nature Protocols

Kinetic flux profiling for quantitation of cellular metabolic fluxes

(2008) Jie Yuan et al.   Nature Protocols

Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast

(2007) Matthew J. Brauer et al.   MOLECULAR BIOLOGY OF THE CELL