Published in Bioinformatics on June 15, 2010
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Modeling cancer metabolism on a genome scale. Mol Syst Biol (2015) 0.92
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Metabolic consequences of oncogenic IDH mutations. Pharmacol Ther (2015) 0.90
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OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants. BMC Genomics (2013) 0.83
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Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models. BMC Bioinformatics (2013) 0.82
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Systems-level analysis of mechanisms regulating yeast metabolic flux. Science (2016) 0.80
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Mass spectrometry-based workflow for accurate quantification of Escherichia coli enzymes: how proteomics can play a key role in metabolic engineering. Mol Cell Proteomics (2014) 0.79
Improved genome annotation through untargeted detection of pathway-specific metabolites. BMC Genomics (2011) 0.79
Metabolic modeling of muscle metabolism identifies key reactions linked to insulin resistance phenotypes. Mol Metab (2015) 0.79
redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models. PLoS Comput Biol (2017) 0.79
A metabolite-centric view on flux distributions in genome-scale metabolic models. BMC Syst Biol (2013) 0.78
GAM: a web-service for integrated transcriptional and metabolic network analysis. Nucleic Acids Res (2016) 0.78
Forward Individualized Medicine from Personal Genomes to Interactomes. Front Physiol (2015) 0.78
A network-based approach for predicting key enzymes explaining metabolite abundance alterations in a disease phenotype. BMC Syst Biol (2013) 0.77
Systematic applications of metabolomics in metabolic engineering. Metabolites (2012) 0.77
Multi-omics approaches to disease. Genome Biol (2017) 0.76
Longitudinal omics modeling and integration in clinical metabonomics research: challenges in childhood metabolic health research. Front Mol Biosci (2015) 0.76
Sparsity as cellular objective to infer directed metabolic networks from steady-state metabolome data: a theoretical analysis. PLoS One (2013) 0.76
From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems. Cell Mol Life Sci (2015) 0.76
Evaluation of a genome-scale in silico metabolic model for Geobacter metallireducens by using proteomic data from a field biostimulation experiment. Appl Environ Microbiol (2012) 0.75
Physiologically Shrinking the Solution Space of a Saccharomyces cerevisiae Genome-Scale Model Suggests the Role of the Metabolic Network in Shaping Gene Expression Noise. PLoS One (2015) 0.75
Metabolic modeling of common Escherichia coli strains in human gut microbiome. Biomed Res Int (2014) 0.75
Construction of a genome-scale kinetic model of mycobacterium tuberculosis using generic rate equations. Metabolites (2012) 0.75
Model-based quantification of metabolic interactions from dynamic microbial-community data. PLoS One (2017) 0.75
Mass Defect-Based N,N-Dimethyl Leucine Labels for Quantitative Proteomics and Amine Metabolomics of Pancreatic Cancer Cells. Anal Chem (2017) 0.75
SBMLmod: a Python-based web application and web service for efficient data integration and model simulation. BMC Bioinformatics (2017) 0.75
The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization. PLoS Comput Biol (2016) 0.75
An overview of bioinformatics methods for modeling biological pathways in yeast. Brief Funct Genomics (2015) 0.75
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol (2007) 11.03
Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol (2004) 9.61
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Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol (2009) 8.36
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Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc (2007) 6.24
Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res (2004) 6.21
Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science (2007) 5.87
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The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol (2008) 5.26
Network-based prediction of human tissue-specific metabolism. Nat Biotechnol (2008) 4.39
Thermodynamics-based metabolic flux analysis. Biophys J (2006) 3.35
Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states. Genome Res (2005) 2.91
Context-specific metabolic networks are consistent with experiments. PLoS Comput Biol (2008) 2.90
OptStrain: a computational framework for redesign of microbial production systems. Genome Res (2004) 2.80
Fat synthesis in adipose tissue. An examination of stoichiometric constraints. Biochem J (1986) 2.68
Dynamic simulation of the human red blood cell metabolic network. Bioinformatics (2001) 1.92
Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts. FEMS Yeast Res (2005) 1.65
Integration of metabolome data with metabolic networks reveals reporter reactions. Mol Syst Biol (2006) 1.60
Determinants of protein abundance and translation efficiency in S. cerevisiae. PLoS Comput Biol (2007) 1.60
Integration of gene expression data into genome-scale metabolic models. Metab Eng (2004) 1.59
Predicting metabolic biomarkers of human inborn errors of metabolism. Mol Syst Biol (2009) 1.59
Comparative genome-scale metabolic reconstruction and flux balance analysis of multiple Staphylococcus aureus genomes identify novel antimicrobial drug targets. J Bacteriol (2009) 1.51
Unraveling the complexity of flux regulation: a new method demonstrated for nutrient starvation in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2006) 1.45
Illuminating drug discovery with biological pathways. FEBS Lett (2005) 1.22
An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments. BMC Bioinformatics (2008) 1.12
Transcriptional regulation of protein complexes within and across species. Proc Natl Acad Sci U S A (2007) 7.07
Medical sequencing at the extremes of human body mass. Am J Hum Genet (2007) 5.61
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol (2008) 4.55
Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science (2012) 4.41
Network-based prediction of human tissue-specific metabolism. Nat Biotechnol (2008) 4.39
Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase. Nature (2011) 4.32
A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods (2006) 3.95
Associating genes and protein complexes with disease via network propagation. PLoS Comput Biol (2010) 3.65
Predicting selective drug targets in cancer through metabolic networks. Mol Syst Biol (2011) 3.65
A key role for mitochondrial gatekeeper pyruvate dehydrogenase in oncogene-induced senescence. Nature (2013) 3.46
Translation efficiency is determined by both codon bias and folding energy. Proc Natl Acad Sci U S A (2010) 3.40
Multiple knockout analysis of genetic robustness in the yeast metabolic network. Nat Genet (2006) 3.25
PREDICT: a method for inferring novel drug indications with application to personalized medicine. Mol Syst Biol (2011) 3.22
Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc Natl Acad Sci U S A (2005) 2.99
Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol Syst Biol (2010) 2.60
The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters. Biochemistry (2011) 2.42
Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science (2012) 2.38
Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proc Natl Acad Sci U S A (2008) 2.23
A genome-scale computational study of the interplay between transcriptional regulation and metabolism. Mol Syst Biol (2007) 2.15
Actor-critic models of the basal ganglia: new anatomical and computational perspectives. Neural Netw (2002) 2.12
Systems biology standards--the community speaks. Nat Biotechnol (2007) 2.09
The evolution of modularity in bacterial metabolic networks. Proc Natl Acad Sci U S A (2008) 1.96
The large-scale organization of the bacterial network of ecological co-occurrence interactions. Nucleic Acids Res (2010) 1.75
Competitive and cooperative metabolic interactions in bacterial communities. Nat Commun (2011) 1.75
Glycolytic strategy as a tradeoff between energy yield and protein cost. Proc Natl Acad Sci U S A (2013) 1.75
Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity. Proc Natl Acad Sci U S A (2011) 1.68
Genome-scale metabolic modeling elucidates the role of proliferative adaptation in causing the Warburg effect. PLoS Comput Biol (2011) 1.66
Annotation and merging of SBML models with semanticSBML. Bioinformatics (2009) 1.62
Composite effects of gene determinants on the translation speed and density of ribosomes. Genome Biol (2011) 1.61
Determinants of protein abundance and translation efficiency in S. cerevisiae. PLoS Comput Biol (2007) 1.60
SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics (2007) 1.60
Direct evolution of genetic robustness in microRNA. Proc Natl Acad Sci U S A (2006) 1.59
Predicting metabolic biomarkers of human inborn errors of metabolism. Mol Syst Biol (2009) 1.59
A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics (2006) 1.56
Glutamine-driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxia. Mol Syst Biol (2013) 1.56
Enhancing the prioritization of disease-causing genes through tissue specific protein interaction networks. PLoS Comput Biol (2012) 1.51
Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways. Bioinformatics (2009) 1.51
QPath: a method for querying pathways in a protein-protein interaction network. BMC Bioinformatics (2006) 1.46
Metabolic-network-driven analysis of bacterial ecological strategies. Genome Biol (2009) 1.44
Unsupervised learning of natural languages. Proc Natl Acad Sci U S A (2005) 1.44
Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages. Nucleic Acids Res (2010) 1.42
INDI: a computational framework for inferring drug interactions and their associated recommendations. Mol Syst Biol (2012) 1.40
Toward accurate reconstruction of functional protein networks. Mol Syst Biol (2009) 1.40
From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions. Mol Syst Biol (2008) 1.35
iMAT: an integrative metabolic analysis tool. Bioinformatics (2010) 1.32
QNet: a tool for querying protein interaction networks. J Comput Biol (2008) 1.32
Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm. Nucleic Acids Res (2006) 1.29
Genome-scale analysis of translation elongation with a ribosome flow model. PLoS Comput Biol (2011) 1.29
A systems-level approach to mapping the telomere length maintenance gene circuitry. Mol Syst Biol (2008) 1.27
Association between translation efficiency and horizontal gene transfer within microbial communities. Nucleic Acids Res (2011) 1.24
Combining drug and gene similarity measures for drug-target elucidation. J Comput Biol (2011) 1.23
Gene expression of Caenorhabditis elegans neurons carries information on their synaptic connectivity. PLoS Comput Biol (2006) 1.21
A genome-wide screen for essential yeast genes that affect telomere length maintenance. Nucleic Acids Res (2009) 1.20
Increased microRNA activity in human cancers. PLoS One (2009) 1.18
Systematic identification of gene annotation errors in the widely used yeast mutation collections. Nat Methods (2012) 1.17
Systematic construction of kinetic models from genome-scale metabolic networks. PLoS One (2013) 1.16
Pepitope: epitope mapping from affinity-selected peptides. Bioinformatics (2007) 1.16
Integrative genomic analysis identifies isoleucine and CodY as regulators of Listeria monocytogenes virulence. PLoS Genet (2012) 1.14
Mathematical modeling of intracellular signaling pathways. BMC Neurosci (2006) 1.14
Fatty acid labeling from glutamine in hypoxia can be explained by isotope exchange without net reductive isocitrate dehydrogenase (IDH) flux. J Biol Chem (2013) 1.13
Metabolic associations of reduced proliferation and oxidative stress in advanced breast cancer. Cancer Res (2012) 1.13
SBMLmerge, a system for combining biochemical network models. Genome Inform (2006) 1.12
A quantitative study of the Hog1 MAPK response to fluctuating osmotic stress in Saccharomyces cerevisiae. PLoS One (2010) 1.11
Structural robustness of metabolic networks with respect to multiple knockouts. J Theor Biol (2007) 1.11
Feature selection via coalitional game theory. Neural Comput (2007) 1.11
ANAT: a tool for constructing and analyzing functional protein networks. Sci Signal (2011) 1.11
Network-based prediction of metabolic enzymes' subcellular localization. Bioinformatics (2009) 1.10
Spanning high-dimensional expression space using ribosome-binding site combinatorics. Nucleic Acids Res (2013) 1.08
Meta-analysis of gene expression data: a predictor-based approach. Bioinformatics (2007) 1.07
Prediction of microbial growth rate versus biomass yield by a metabolic network with kinetic parameters. PLoS Comput Biol (2012) 1.07
Selection for translation efficiency on synonymous polymorphisms in recent human evolution. Genome Biol Evol (2011) 1.05
Functional representation of enzymes by specific peptides. PLoS Comput Biol (2007) 1.05
Reconstructing ancestral gene content by coevolution. Genome Res (2009) 1.04
Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes. Nucleic Acids Res (2006) 1.02
Gene expression in the rodent brain is associated with its regional connectivity. PLoS Comput Biol (2011) 1.02
Model-based identification of drug targets that revert disrupted metabolism and its application to ageing. Nat Commun (2013) 1.01
Fair attribution of functional contribution in artificial and biological networks. Neural Comput (2004) 1.01
Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states. PLoS Comput Biol (2006) 1.00
Environmental stresses disrupt telomere length homeostasis. PLoS Genet (2013) 1.00
Predicting drug targets and biomarkers of cancer via genome-scale metabolic modeling. Clin Cancer Res (2012) 1.00
Retrieval, alignment, and clustering of computational models based on semantic annotations. Mol Syst Biol (2011) 0.99
Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species. PLoS Comput Biol (2010) 0.99
p53 promotes the expression of gluconeogenesis-related genes and enhances hepatic glucose production. Cancer Metab (2013) 0.98
Constraint-based functional similarity of metabolic genes: going beyond network topology. Bioinformatics (2007) 0.98