Metabolite concentrations, fluxes and free energies imply efficient enzyme usage

Avoiding Misannotation of In-Source Fragmentation Products as Cellular Metabolites in Liquid Chromatography–Mass Spectrometry-Based Metabolomics

(2015) Yi-Fan Xu et al.   ANALYTICAL CHEMISTRY

Visual account of protein investment in cellular functions

(2014) W. Liebermeister et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) Kaspar Valgepea et al.   Molecular BioSystems

Glutamine-driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxia

(2013) J. Fan et al.   Molecular Systems Biology

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa 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

13CFLUX2—high-performance software suite for 13C-metabolic flux analysis

(2012) Michael Weitzel et al.   BIOINFORMATICS

Quantitative Assignment of Reaction Directionality in a Multicompartmental Human Metabolic Reconstruction

(2012) H.S. Haraldsdóttir et al.   BIOPHYSICAL JOURNAL

Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins

(2012) Tamar Geiger et al.   MOLECULAR & CELLULAR PROTEOMICS

Ultrasensitive regulation of anapleurosis via allosteric activation of PEP carboxylase

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

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA

(2012) Ida Schomburg et al.   NUCLEIC ACIDS RESEARCH

Elimination of Thermodynamically Infeasible Loops in Steady-State Metabolic Models

(2011) Jan Schellenberger et al.   BIOPHYSICAL JOURNAL

Metabolomic Analysis via Reversed-Phase Ion-Pairing Liquid Chromatography Coupled to a Stand Alone Orbitrap Mass Spectrometer

(2010) Wenyun Lu et al.   ANALYTICAL CHEMISTRY

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

Measuring enzyme activities under standardized in vivo-like conditions for systems biology

(2010) Karen van Eunen et al.   FEBS Journal

Quantitative assignment of reaction directionality in constraint-based models of metabolism: Application to Escherichia coli

(2009) R.M.T. Fleming et al.   BIOPHYSICAL CHEMISTRY

Influence of uncertainties in pH, pMg, activity coefficients, metabolite concentrations, and other factors on the analysis of the thermodynamic feasibility of metabolic pathways

(2009) Vojislav Vojinović et al.   BIOTECHNOLOGY AND BIOENGINEERING

Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli

(2009) Bryson D Bennett et al.   Nature Chemical Biology

Ensemble Modeling of Metabolic Networks

(2008) Linh M. Tran et al.   BIOPHYSICAL JOURNAL

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

(2008) Lyris M. F. de Godoy et al.   NATURE

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

(2008) Bryson D Bennett et al.   Nature Protocols