Published in Curr Opin Biotechnol on August 23, 2006
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Experimental and computational assessment of conditionally essential genes in Escherichia coli. J Bacteriol (2006) 2.93
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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
Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J Biol Chem (2002) 2.74
Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states. Genome Res (2004) 2.71
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
Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation. Proc Natl Acad Sci U S A (2007) 2.43
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Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet. J Biol Chem (2004) 2.26
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Systems metabolic engineering of Escherichia coli for L-threonine production. Mol Syst Biol (2007) 2.18
Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nat Chem Biol (2012) 2.17
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
Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation. Appl Environ Microbiol (2005) 2.13
MS/MS networking guided analysis of molecule and gene cluster families. Proc Natl Acad Sci U S A (2013) 2.12
Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. Genome Res (2006) 2.12
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Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays. J Bacteriol (2005) 2.06
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Diagnostic accuracy of ultrasound and 18-F-FDG PET or PET/CT for patients with suspected recurrent papillary thyroid carcinoma. Ultrasound Med Biol (2010) 2.04
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Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli. Proc Natl Acad Sci U S A (2008) 1.99
Systems biotechnology for strain improvement. Trends Biotechnol (2005) 1.98
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Drug off-target effects predicted using structural analysis in the context of a metabolic network model. PLoS Comput Biol (2010) 1.97
Ultrasonographic screening for detection of thyroid cancer in patients with Graves' disease. Clin Endocrinol (Oxf) (2004) 1.96
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Extreme pathways and Kirchhoff's second law. Biophys J (2002) 1.95
Use of randomized sampling for analysis of metabolic networks. J Biol Chem (2008) 1.92
Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Mol Syst Biol (2010) 1.86
Large-scale in silico modeling of metabolic interactions between cell types in the human brain. Nat Biotechnol (2010) 1.85
Systematizing the generation of missing metabolic knowledge. Biotechnol Bioeng (2010) 1.85
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol (2008) 1.81
Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. Mol Syst Biol (2013) 1.80
Microbial laboratory evolution in the era of genome-scale science. Mol Syst Biol (2011) 1.78
Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nat Biotechnol (2013) 1.76
The outcomes of first reoperation for locoregionally recurrent/persistent papillary thyroid carcinoma in patients who initially underwent total thyroidectomy and remnant ablation. J Clin Endocrinol Metab (2011) 1.74
Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome Res (2002) 1.72
Reconciling gene expression data with known genome-scale regulatory network structures. Genome Res (2003) 1.65
Elimination of thermodynamically infeasible loops in steady-state metabolic models. Biophys J (2011) 1.64
Formulating genome-scale kinetic models in the post-genome era. Mol Syst Biol (2008) 1.64
Extreme pathway lengths and reaction participation in genome-scale metabolic networks. Genome Res (2002) 1.64
The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens. Nat Biotechnol (2004) 1.64
The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli. BMC Genomics (2011) 1.63
Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association. Nat Commun (2013) 1.62
Microbial production of short-chain alkanes. Nature (2013) 1.61
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Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction. Mol Syst Biol (2013) 1.58
Native-sized recombinant spider silk protein produced in metabolically engineered Escherichia coli results in a strong fiber. Proc Natl Acad Sci U S A (2010) 1.51
Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery. Mol Syst Biol (2011) 1.50
Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1,2-propanediol. Appl Environ Microbiol (2010) 1.41
Detection of the most common corneal dystrophies caused by BIGH3 gene point mutations using a multispot gold-capped nanoparticle array chip. Anal Chem (2010) 1.41
Recent advances in reconstruction and applications of genome-scale metabolic models. Curr Opin Biotechnol (2011) 1.41
MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis. Bioinformatics (2003) 1.40
Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide. Ecosal Plus (2010) 1.39
Towards genome-scale signalling network reconstructions. Nat Rev Genet (2010) 1.39
Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Proc Natl Acad Sci U S A (2013) 1.39
Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery. Biophys J (2010) 1.38
Structural and operational complexity of the Geobacter sulfurreducens genome. Genome Res (2010) 1.37
Comparative multi-omics systems analysis of Escherichia coli strains B and K-12. Genome Biol (2012) 1.37
Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli. J Bacteriol (2008) 1.37
Metabolic engineering of Escherichia coli for the production of polylactic acid and its copolymers. Biotechnol Bioeng (2010) 1.36
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. BMC Syst Biol (2010) 1.35
Identification and characterization of a new enoyl coenzyme A hydratase involved in biosynthesis of medium-chain-length polyhydroxyalkanoates in recombinant Escherichia coli. J Bacteriol (2003) 1.35
Systems biology of SNPs. Mol Syst Biol (2006) 1.35