Student Publications

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Ebrahim A, Lerman JA, Palsson BO, Hyduke DR. "COBRApy: COnstraints-Based Reconstruction and Analysis for Python." BMC Syst Biol. 2013;7:74.
Fong NL, Lerman JA, Lam I, Palsson BO, Charusanti P. "Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant." FEMS Microbiol. Lett.. 2013;342(1):62-9.
Chang RL, Andrews K, Kim D, Li Z, Godzik A, Palsson BO. "Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli." Science. 2013;340(6137):1220-3.
Lewis NE, Nagarajan H, Palsson BO. "Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods." Nat. Rev. Microbiol.. 2012;10(4):291-305.
Nam H, Lewis NE, Lerman JA, et al. "Network context and selection in the evolution to enzyme specificity." Science. 2012;337(6098):1101-4.
Orth JD, Conrad TM, Na J, et al. "A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011." Mol. Syst. Biol.. 2011;7:535.
Charusanti P, Chauhan S, McAteer K, et al. "An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92." BMC Syst Biol. 2011;5:163.
Chang RL, Ghamsari L, Manichaikul A, et al. "Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism." Mol. Syst. Biol.. 2011;7:518.
Cho B-K, Federowicz SA, Embree M, Park Y-S, Kim D, Palsson BØ. "The PurR regulon in Escherichia coli K-12 MG1655." Nucleic Acids Res.. 2011;39(15):6456-64.
Chang RL, Xie L, Xie L, Bourne PE, Palsson BØ. "Drug off-target effects predicted using structural analysis in the context of a metabolic network model." PLoS Comput. Biol.. 2010;6(9):e1000938.
Mo ML, Palsson BO, Herrgård MJ. "Connecting extracellular metabolomic measurements to intracellular flux states in yeast." BMC Syst Biol. 2009;3:37.
Barrett CL, Herrgard MJ, Palsson B. "Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation." BMC Syst Biol. 2009;3:30.
Terzer M, Maynard ND, Covert MW, Stelling J. "Genome-scale metabolic networks." Wiley Interdiscip Rev Syst Biol Med. 2009;1(3):285-97.
Portnoy VA, Herrgård MJ, Palsson BØ. "Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain." Appl. Environ. Microbiol.. 2008;74(24):7561-9.
Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, Zhou H. "A multidimensional chromatography technology for in-depth phosphoproteome analysis." Mol. Cell Proteomics. 2008;7(7):1389-96.
Shlomi T, Cabili MN, Herrgård MJ, Palsson BØ, Ruppin E. "Network-based prediction of human tissue-specific metabolism." Nat. Biotechnol.. 2008;26(9):1003-10.
Feist AM, Henry CS, Reed JL, et al. "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol. Syst. Biol.. 2007;3:121.
Hua Q, Joyce AR, Palsson BØ, Fong SS. "Metabolic characterization of Escherichia coli strains adapted to growth on lactate." Appl. Environ. Microbiol.. 2007;73(14):4639-47.
Cho B-K, Charusanti P, Herrgård MJ, Palsson BO. "Microbial regulatory and metabolic networks." Curr. Opin. Biotechnol.. 2007;18(4):360-4.
Becker SA, Feist AM, Mo ML, Hannum G, Palsson BØ, Herrgard MJ. "Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox." Nat Protoc. 2007;2(3):727-38.