Publications
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2018. Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.. PLoS Comput Biol. 14(1):e1005895.
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2016. BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.. Nucleic Acids Res.
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2016. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism.. Cell Syst. 3(5):434-443.e8.
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2015. Do genome-scale models need exact solvers or clearer standards? Mol Syst Biol. 11(10):831.
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2015. Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways.. PLoS Comput Biol. 11(8):e1004321.
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2015. JSBML 1.0: providing a smorgasbord of options to encode systems biology models.. Bioinformatics.
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2015. A Markov chain model for N-linked protein glycosylation - towards a low-parameter tool for model-driven glycoengineering.. Metab Eng.
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2015. Optimizing eukaryotic cell hosts for protein production through systems biotechnology and genome-scale modeling.. Biotechnol J. 10(7):939-49.
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2014. Minimal metabolic pathway structure is consistent with associated biomolecular interactions.. Mol Syst Biol. 10(7):737.
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2014. Multi-Tissue Computational Modeling Analyzes Pathophysiology of Type 2 Diabetes in MKR Mice.. PLoS One. 9(7):e102319.
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2014. Systems glycobiology for glycoengineering.. Curr Opin Biotechnol. 30C:218-224.
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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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2012. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods.. Nat Rev Microbiol. 10(4):291-305.
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2012. In silico method for modelling metabolism and gene product expression at genome scale. Nat Commun. 3:929.
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2012. Network context and selection in the evolution to enzyme specificity.. Science. 337(6098):1101-4.
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2012. Proteomic analysis of Chinese hamster ovary cells.. J Proteome Res. 11(11):5265-76.
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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. The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line.. Nat Biotechnol. 29(8):735-41.
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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. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.. Nat Protoc. 6(9):1290-307.
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2011. The role of cellular objectives and selective pressures in metabolic pathway evolution.. Curr Opin Biotechnol. 22(4):595-600.
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2010. Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655.. Applied and environmental microbiology. 76(19):6529-40.
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2010. Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions.. Molecular systems biology. 6:422.
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2010. Large-scale in silico modeling of metabolic interactions between cell types in the human brain.. Nature biotechnology. 28(12):1279-85.
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2010. Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models.. Molecular systems biology. 6:390.
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2010. RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media.. Proceedings of the National Academy of Sciences of the United States of America. 107(47):20500-5.
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2009. Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content.. Journal of bacteriology. 191(11):3437-44.
