Published in Nat Rev Genet on April 01, 2010
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The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol (2008) 5.26
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Synthetic gene networks that count. Science (2009) 4.54
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Synthetic protein scaffolds provide modular control over metabolic flux. Nat Biotechnol (2009) 4.11
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Systems approach to refining genome annotation. Proc Natl Acad Sci U S A (2006) 3.58
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Reconstruction of cellular signalling networks and analysis of their properties. Nat Rev Mol Cell Biol (2005) 3.46
Variability and robustness in T cell activation from regulated heterogeneity in protein levels. Science (2008) 3.38
A synthetic gene-metabolic oscillator. Nature (2005) 3.26
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A comprehensive map of the toll-like receptor signaling network. Mol Syst Biol (2006) 2.89
The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks. Bioinformatics (2003) 2.88
Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc Natl Acad Sci U S A (2008) 2.85
The transcription unit architecture of the Escherichia coli genome. Nat Biotechnol (2009) 2.85
Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc Natl Acad Sci U S A (2005) 2.84
Modular organization of protein interaction networks. Bioinformatics (2006) 2.68
Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species. PLoS Biol (2009) 2.67
Systematic identification of functional orthologs based on protein network comparison. Genome Res (2006) 2.47
Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput Biol (2008) 2.46
Chemical combination effects predict connectivity in biological systems. Mol Syst Biol (2007) 2.42
Global analyses of sumoylated proteins in Saccharomyces cerevisiae. Induction of protein sumoylation by cellular stresses. J Biol Chem (2004) 2.27
Genetic screening for signal transduction in the era of network biology. Cell (2007) 2.19
Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data. J Biol Chem (2004) 2.19
Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Sci Signal (2009) 2.16
Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization. PLoS Comput Biol (2009) 2.14
Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. Genome Res (2006) 2.12
Dissection of the insulin signaling pathway via quantitative phosphoproteomics. Proc Natl Acad Sci U S A (2008) 2.11
Properties of developmental gene regulatory networks. Proc Natl Acad Sci U S A (2008) 2.05
Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. Sci Signal (2009) 2.04
Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks. BMC Syst Biol (2008) 2.02
A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189. PLoS Comput Biol (2009) 2.02
Accelerating the reconstruction of genome-scale metabolic networks. BMC Bioinformatics (2006) 1.97
Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metab Eng (2009) 1.96
Rapid evolution of functional complexity in a domain family. Sci Signal (2009) 1.85
Dynamic analysis of integrated signaling, metabolic, and regulatory networks. PLoS Comput Biol (2008) 1.81
Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proc Natl Acad Sci U S A (2009) 1.79
Influence of metabolic network structure and function on enzyme evolution. Genome Biol (2006) 1.79
Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target. Genes Dev (2009) 1.78
Synthetic ecosystems based on airborne inter- and intrakingdom communication. Proc Natl Acad Sci U S A (2007) 1.77
Systems-level interactions between insulin-EGF networks amplify mitogenic signaling. Mol Syst Biol (2009) 1.77
Genome-scale gene/reaction essentiality and synthetic lethality analysis. Mol Syst Biol (2009) 1.69
Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics (2006) 1.65
Hubba: hub objects analyzer--a framework of interactome hubs identification for network biology. Nucleic Acids Res (2008) 1.65
Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction. BMC Syst Biol (2009) 1.62
Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of Mus musculus. Biotechnol Prog (2005) 1.60
The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis. Biophys J (2004) 1.55
DOMINE: a database of protein domain interactions. Nucleic Acids Res (2007) 1.54
iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations. Genome Biol (2009) 1.53
Comparative genome-scale metabolic reconstruction and flux balance analysis of multiple Staphylococcus aureus genomes identify novel antimicrobial drug targets. J Bacteriol (2009) 1.51
Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli. Proc Natl Acad Sci U S A (2007) 1.49
Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major. Mol Syst Biol (2008) 1.49
Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS Comput Biol (2006) 1.48
Prediction of phenotype and gene expression for combinations of mutations. Mol Syst Biol (2007) 1.48
Design of artificial cell-cell communication using gene and metabolic networks. Proc Natl Acad Sci U S A (2004) 1.40
Redefining the p53 response element. Proc Natl Acad Sci U S A (2009) 1.36
Systems biology of SNPs. Mol Syst Biol (2006) 1.35
Identification of potential pathway mediation targets in Toll-like receptor signaling. PLoS Comput Biol (2009) 1.30
A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicola. BMC Syst Biol (2009) 1.29
Genome-scale analysis of Mannheimia succiniciproducens metabolism. Biotechnol Bioeng (2007) 1.28
Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk. J Theor Biol (2004) 1.27
Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A (2007) 11.46
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 reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. BMC Microbiol (2005) 9.94
Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol (2004) 9.61
What is flux balance analysis? Nat Biotechnol (2010) 9.01
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res (2003) 7.22
A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc (2010) 6.64
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
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc (2011) 5.71
Applications of genome-scale metabolic reconstructions. Mol Syst Biol (2009) 5.54
Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol (2008) 5.36
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol (2008) 5.26
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol (2008) 4.55
Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet (2006) 4.44
Network-based prediction of human tissue-specific metabolism. Nat Biotechnol (2008) 4.39
A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011. Mol Syst Biol (2011) 4.03
A community-driven global reconstruction of human metabolism. Nat Biotechnol (2013) 3.89
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics (2010) 3.87
The model organism as a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol (2006) 3.69
Thirteen years of building constraint-based in silico models of Escherichia coli. J Bacteriol (2003) 3.52
Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat Genet (2004) 3.31
Experimental and computational assessment of conditionally essential genes in Escherichia coli. J Bacteriol (2006) 2.93
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The transcription unit architecture of the Escherichia coli genome. Nat Biotechnol (2009) 2.85
Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants. J Bacteriol (2005) 2.82
Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol (2006) 2.80
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Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. BMC Syst Biol (2007) 2.51
Reconstruction of microbial transcriptional regulatory networks. Curr Opin Biotechnol (2004) 2.47
Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism. Mol Syst Biol (2011) 2.44
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Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization. PLoS Comput Biol (2009) 2.14
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Large-scale in silico modeling of metabolic interactions between cell types in the human brain. Nat Biotechnol (2010) 1.85
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A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol (2008) 1.81
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Top-down analysis of temporal hierarchy in biochemical reaction networks. PLoS Comput Biol (2008) 1.29
Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling. PLoS Genet (2012) 1.29
The PurR regulon in Escherichia coli K-12 MG1655. Nucleic Acids Res (2011) 1.29
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RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media. Proc Natl Acad Sci U S A (2010) 1.27
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Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints. Biophys J (2006) 1.24
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Deciphering the transcriptional regulatory logic of amino acid metabolism. Nat Chem Biol (2011) 1.22
Metabolite coupling in genome-scale metabolic networks. BMC Bioinformatics (2006) 1.22
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Expa: a program for calculating extreme pathways in biochemical reaction networks. Bioinformatics (2004) 1.22
The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions. BMC Syst Biol (2011) 1.19
Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae. BMC Genomics (2004) 1.18
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De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads. PLoS One (2010) 1.15
Metabolic analysis of adaptive evolution for in silico-designed lactate-producing strains. Biotechnol Bioeng (2006) 1.14
Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS). Anal Bioanal Chem (2011) 1.14
High-throughput mutation detection underlying adaptive evolution of Escherichia coli-K12. Genome Res (2004) 1.14
Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli. PLoS Comput Biol (2007) 1.12
Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA. Microbiology (2006) 1.10
A genome-scale, constraint-based approach to systems biology of human metabolism. Mol Biosyst (2007) 1.08
Functional states of the genome-scale Escherichia coli transcriptional regulatory system. PLoS Comput Biol (2009) 1.06
Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain. Appl Environ Microbiol (2008) 1.06