Publications

Author Title [ Year(Asc)]
Filters: Author is Palsson, Bernhard Ø  [Clear All Filters]
2013
Hyduke DR, Lewis NE, Palsson BØ.  2013.  Analysis of omics data with genome-scale models of metabolism.. Mol Biosyst. 9(2):167-74.
McCloskey D, Palsson BØ, Feist AM.  2013.  Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.. Mol Syst Biol. 9:661.
Nagarajan H, Embree M, Rotaru A-E, Shrestha PM, Feist AM, Palsson BØ, Lovley DR, Zengler K.  2013.  Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association.. Nat Commun. 4:2809.
Thiele I, Swainston N, Fleming RMT, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD et al..  2013.  A community-driven global reconstruction of human metabolism.. Nat Biotechnol.
Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, Feist AM, Palsson BØ.  2013.  Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments.. Proc Natl Acad Sci U S A.
O'Brien EJ, Lerman JA, Chang RL, Hyduke DR, Palsson BØ.  2013.  Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction.. Mol Syst Biol. 9:693.
Schmidt BJ, Ebrahim A, Metz TO, Adkins JN, Palsson BØ, Hyduke DR.  2013.  GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data.. Bioinformatics.
Rolfsson O, Paglia G, Magnusdóttir M, Palsson BØ, Thiele I.  2013.  Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity.. Biochem J. 449(2):427-35.
Nguyen D D, Wu C-H, Moree WJ, Lamsa A, Medema MH, Zhao X, Gavilan RG, Aparicio M, Atencio L, Jackson C et al..  2013.  MS/MS networking guided analysis of molecule and gene cluster families.. Proc Natl Acad Sci U S A. 110(28):E2611-20.
Hwang K-S, Kim H U, Charusanti P, Palsson BØ, Lee S Y.  2013.  Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites.. Biotechnol Adv. 32(2):255-268.
2011
Palsson BØ.  2011.  Adaptive Laboratory Evolution. Microbe.
Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist AM, Palsson BØ.  2011.  A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.. Mol Syst Biol. 7:535.
Lee D-H, Feist AM, Barrett CL, Palsson BØ.  2011.  Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli.. PLoS One. 6(10):e26172.
Cho B-K, Federowicz S, Park Y-S, Zengler K, Palsson BØ.  2011.  Deciphering the transcriptional regulatory logic of amino acid metabolism.. Nat Chem Biol. 8(1):65-71.
Schellenberger J, Lewis NE, Palsson BØ.  2011.  Elimination of thermodynamically infeasible loops in steady-state metabolic models.. Biophys J. 100(3):544-53.
Applebee KM, Joyce AR, Conrad TM, Pettigrew DW, Palsson BØ.  2011.  Functional and metabolic effects of adaptive glycerol kinase (GLPK) mutants in Escherichia coli.. J Biol Chem. 286(26):23150-9.
Rolfsson O, Palsson BØ, Thiele I.  2011.  The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions.. BMC Syst Biol. 5:155.
Mahadevan R, Palsson BØ, Lovley DR.  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.
Ahn S-Y, Jamshidi N, Mo ML, Wu W, Eraly SA, Dnyanmote A, Bush KT, Gallegos TF, Sweet DH, Palsson BØ et al..  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.
Chang RL, Ghamsari L, Manichaikul A, Hom EFY, Balaji S, Fu W, Shen Y, Hao T, Palsson BØ, Salehi-Ashtiani K et al..  2011.  Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism.. Mol Syst Biol. 7:518.
Conrad TM, Lewis NE, Palsson BØ.  2011.  Microbial laboratory evolution in the era of genome-scale science.. Mol Syst Biol. 7:509.
Cho B-K, Federowicz SA, Embree M, Park Y-S, Kim D, Palsson BØ.  2011.  The PurR regulon in Escherichia coli K-12 MG1655.. Nucleic Acids Res. 39(15):6456-64.
Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S et al..  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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