Student Publications

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O'Brien EJ, Monk JM, Palsson BO. "Using Genome-scale Models to Predict Biological Capabilities." Cell. 2015;161(5):971-87.
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.
Kim D, Hong J S-J, Qiu Y, et al. "Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling." PLoS Genet.. 2012;8(8):e1002867.
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.
Cho B-K, Federowicz S, Park Y-S, Zengler K, Palsson BØ. "Deciphering the transcriptional regulatory logic of amino acid metabolism." Nat. Chem. Biol.. 2012;8(1):65-71.
Thiele I, Fleming RMT, Que R, Bordbar A, Diep D, Palsson BO. "Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage." PLoS ONE. 2012;7(9):e45635.
Nam H, Lewis NE, Lerman JA, et al. "Network context and selection in the evolution to enzyme specificity." Science. 2012;337(6098):1101-4.
Johnson DBF, Wang C, Xu J, et al. "Release factor one is nonessential in Escherichia coli." ACS Chem. Biol.. 2012;7(8):1337-44.
Prindle A, Samayoa P, Razinkov I, Danino T, Tsimring LS, Hasty J. "A sensing array of radically coupled genetic 'biopixels'." Nature. 2012;481(7379):39-44.
Johnson DBF, Xu J, Shen Z, et al. "RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites." Nat. Chem. Biol.. 2011;7(11):779-86.
Lerman J, Palsson BO. "Microbiology. Topping off a multiscale balancing act." Science. 2010;330(6007):1058-9.
Feist AM, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, Palsson BØ. "Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli." Metab. Eng.. 2010;12(3):173-86.
Lewis NE, Hixson KK, Conrad TM, et al. "Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models." Mol. Syst. Biol.. 2010;6:390.
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.
Applebee KM, Herrgård MJ, Palsson BØ. "Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli." J. Bacteriol.. 2008;190(14):5087-94.
Covert MW, Xiao N, Chen TJ, Karr JR. "Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli." Bioinformatics. 2008;24(18):2044-50.
Luban S, Kihara D. "Comparative genomics of small RNAs in bacterial genomes." OMICS. 2007;11(1):58-73.
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.
Herring CD, Raghunathan A, Honisch C, et al. "Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale." Nat. Genet.. 2006;38(12):1406-12.
Joyce AR, Reed JL, White A, et al. "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J. Bacteriol.. 2006;188(23):8259-71.
Herrgård MJ, Fong SS, Palsson BØ. "Identification of genome-scale metabolic network models using experimentally measured flux profiles." PLoS Comput. Biol.. 2006;2(7):e72.