Publications
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2016. Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity.. Proc Natl Acad Sci U S A.
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2016. A modeling method for increased precision and scope of directly measurable fluxes at a genome-scale.. Anal Chem.
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2016. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.. Nat Biotechnol. 34(8):828-837.
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2015. JSBML 1.0: providing a smorgasbord of options to encode systems biology models.. Bioinformatics.
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2015. Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC.. Front Microbiol. 6:958.
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2015. Prediction of intracellular metabolic states from extracellular metabolomic data.. Metabolomics. 11(3):603-619.
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2014. A Gapless, Unambiguous Genome Sequence of the Enterohemorrhagic Escherichia coli O157:H7 Strain EDL933.. Genome Announc. 2(4)
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2014. Improving collaboration by standardization efforts in systems biology.. Front Bioeng Biotechnol. 2:61.
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2014. Network reconstruction of platelet metabolism identifies metabolic signature for aspirin resistance.. Sci Rep. 4:3925.
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2013. Analysis of omics data with genome-scale models of metabolism.. Mol Biosyst. 9(2):167-74.
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2013. Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.. Mol Syst Biol. 9:661.
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2013. Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association.. Nat Commun. 4:2809.
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2013. A community-driven global reconstruction of human metabolism.. Nat Biotechnol.
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2013. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments.. Proc Natl Acad Sci U S A.
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2013. Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction.. Mol Syst Biol. 9:693.
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2013. GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data.. Bioinformatics.
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2013. Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity.. Biochem J. 449(2):427-35.
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2013. MS/MS networking guided analysis of molecule and gene cluster families.. Proc Natl Acad Sci U S A. 110(28):E2611-20.
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2013. Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites.. Biotechnol Adv. 32(2):255-268.
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2012. Comparative Analysis of Regulatory Elements between Escherichia coli and Klebsiella pneumoniae by Genome-Wide Transcription Start Site Profiling.. PLoS Genet. 8(8):e1002867.
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2012. Intracellular metabolite profiling of platelets: evaluation of extraction processes and chromatographic strategies.. J Chromatogr B Analyt Technol Biomed Life Sci. 898:111-20.
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2012. 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. 402(3):1183-98.
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2012. Systems biology of stored blood cells: can it help to extend the expiration date? J Proteomics. 76 Spec No.:163-7.
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2011. Adaptive Laboratory Evolution. Microbe.
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2011. A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.. Mol Syst Biol. 7:535.
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2011. Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli.. PLoS One. 6(10):e26172.
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2011. Deciphering the transcriptional regulatory logic of amino acid metabolism.. Nat Chem Biol. 8(1):65-71.
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2011. Elimination of thermodynamically infeasible loops in steady-state metabolic models.. Biophys J. 100(3):544-53.
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2011. Functional and metabolic effects of adaptive glycerol kinase (GLPK) mutants in Escherichia coli.. J Biol Chem. 286(26):23150-9.
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2011. The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions.. BMC Syst Biol. 5:155.
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2011. In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling.. Nat Rev Microbiol. 9(1):39-50.
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2011. Linkage of organic anion transporter-1 to metabolic pathways through integrated "omics"-driven network and functional analysis.. J Biol Chem. 286(36):31522-31.
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2011. Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism.. Mol Syst Biol. 7:518.
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2011. Microbial laboratory evolution in the era of genome-scale science.. Mol Syst Biol. 7:509.
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2011. The PurR regulon in Escherichia coli K-12 MG1655.. Nucleic Acids Res. 39(15):6456-64.
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2011. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.. Nat Protoc. 6(9):1290-307.
