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

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

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

Indirect and suboptimal control of gene expression is widespread in bacteria

(2013) M. N. Price et al.   Molecular Systems Biology

Functioning of a metabolic flux sensor in Escherichia coli

(2013) K. Kochanowski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Metabolic Footprinting of Mutant Libraries to Map Metabolite Utilization to Genotype

(2012) Richard Baran et al.   ACS Chemical Biology

Ultrasensitive regulation of anapleurosis via allosteric activation of PEP carboxylase

(2012) Yi-Fan Xu et al.   Nature Chemical Biology

Rethinking glycolysis: on the biochemical logic of metabolic pathways

(2012) Arren Bar-Even et al.   Nature Chemical Biology

Regulatory architecture determines optimal regulation of gene expression in metabolic pathways

(2012) V. Chubukov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism

(2012) J. M. Buescher et al.   SCIENCE

Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

(2012) P. Nicolas et al.   SCIENCE

High-Throughput, Accurate Mass Metabolome Profiling of Cellular Extracts by Flow Injection–Time-of-Flight Mass Spectrometry

(2011) Tobias Fuhrer et al.   ANALYTICAL CHEMISTRY

Regulation and control of metabolic fluxes in microbes

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

Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli

(2011) B. R. B. Haverkorn van Rijsewijk et al.   Molecular Systems Biology

13C Metabolic Flux Analysis Identifies an Unusual Route for Pyruvate Dissimilation in Mycobacteria which Requires Isocitrate Lyase and Carbon Dioxide Fixation

(2011) Dany J. V. Beste et al.   PLoS Pathogens

Ultrahigh Performance Liquid Chromatography−Tandem Mass Spectrometry Method for Fast and Robust Quantification of Anionic and Aromatic Metabolites

(2010) Joerg Martin Buescher et al.   ANALYTICAL CHEMISTRY

Extensive In Vivo Metabolite-Protein Interactions Revealed by Large-Scale Systematic Analyses

(2010) Xiyan Li et al.   CELL

Complex coordination of multi-scale cellular responses to environmental stress

(2010) Luís L. Fonseca et al.   Molecular BioSystems

A systematic screen for protein–lipid interactions in Saccharomyces cerevisiae

(2010) Oriol Gallego et al.   Molecular Systems Biology

Acetylation of Metabolic Enzymes Coordinates Carbon Source Utilization and Metabolic Flux

(2010) Q. Wang et al.   SCIENCE

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

Phosphoproteomic Analysis Reveals Interconnected System-Wide Responses to Perturbations of Kinases and Phosphatases in Yeast

(2010) B. Bodenmiller et al.   Science Signaling

Achieving Optimal Growth through Product Feedback Inhibition in Metabolism

(2010) Sidhartha Goyal et al.   PLoS Computational Biology

Growth Rate-Dependent Global Effects on Gene Expression in Bacteria

(2009) Stefan Klumpp et al.   CELL

Time-dependent regulation analysis dissects shifts between metabolic and gene-expression regulation during nitrogen starvation in baker’s yeast

(2009) Karen van Eunen et al.   FEBS Journal

Metabolic Fluxes during Strong Carbon Catabolite Repression by Malate inBacillus subtilis

(2009) Roelco J. Kleijn et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Shifts in growth strategies reflect tradeoffs in cellular economics

(2009) Douwe Molenaar et al.   Molecular Systems Biology

Metabolic reconfiguration precedes transcriptional regulation in the antioxidant response

(2009) Markus Ralser et al.   NATURE BIOTECHNOLOGY

13C-based metabolic flux analysis

(2009) Nicola Zamboni et al.   Nature Protocols

Getting Started in Gene Expression Microarray Analysis

(2009) Donna K. Slonim et al.   PLoS Computational Biology

Dynamics of Glycolytic Regulation during Adaptation of Saccharomyces cerevisiae to Fermentative Metabolism

(2008) J. van den Brink et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Dissecting Enzyme Regulation by Multiple Allosteric Effectors: Nucleotide Regulation of Aspartate Transcarbamoylase†

(2008) Joshua D. Rabinowitz et al.   BIOCHEMISTRY

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

Principles of transcriptional regulation and evolution of the metabolic system in E. coli

(2008) A. S.N. Seshasayee et al.   GENOME RESEARCH

CcpN Controls Central Carbon Fluxes in Bacillus subtilis

(2008) S. Tannler et al.   JOURNAL OF BACTERIOLOGY

Quantitative Analysis of the High Temperature-induced Glycolytic Flux Increase inSaccharomyces cerevisiaeReveals Dominant Metabolic Regulation

(2008) Jarne Postmus et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Maintenance metabolism and carbon fluxes in Bacillus species

(2008) Simon Tännler et al.   Microbial Cell Factories

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Mixed and diverse metabolic and gene-expression regulation of the glycolytic and fermentative pathways in response to aHXK2deletion inSaccharomyces cerevisiae

(2007) Sergio Rossell et al.   FEMS YEAST RESEARCH