Publications

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Fu W, Paglia G, Magnúsdóttir M, Steinarsdóttir EA, Gudmundsson S, Palsson BO, Andrésson OS, Brynjólfsson S.  2014.  Effects of abiotic stressors on lutein production in the green microalga Dunaliella salina.. Microb Cell Fact. 13(1):3.
Fu W, Guðmundsson O, Paglia G, Herjólfsson G, Andrésson OS, Palsson BO, Brynjólfsson S.  2013.  Enhancement of carotenoid biosynthesis in the green microalga Dunaliella salina with light-emitting diodes and adaptive laboratory evolution.. Appl Microbiol Biotechnol. 97(6):2395-403.
Fu W, Magnúsdóttir M, Brynjólfson S, Palsson BO, Paglia G.  2012.  UPLC-UV-MS(E) analysis for quantification and identification of major carotenoid and chlorophyll species in algae.. Anal Bioanal Chem. 404(10):3145-54.
Fu W, Gudmundsson O, Feist AM, Herjolfsson G, Brynjolfsson S, Palsson BO.  2012.  Maximizing biomass productivity and cell density of Chlorella vulgaris by using light-emitting diode-based photobioreactor.. J Biotechnol.
Francis K, Palsson BØ.  1997.  Effective intercellular communication distances are determined by the relative time constants for cyto/chemokine secretion and diffusion.. Proceedings of the National Academy of Sciences of the United States of America. 94(23):12258-62.
Francis K, Ramakrishna R, Holloway W, Palsson BØ.  1998.  Two new pseudopod morphologies displayed by the human hematopoietic KG1a progenitor cell line and by primary human CD34(+) cells.. Blood. 92(10):3616-23.
Francis K, Palsson BØ, Donahue J, Fong S, Carrier E.  2002.  Murine Sca-1(+)/Lin(-) cells and human KG1a cells exhibit multiple pseudopod morphologies during migration.. Experimental hematology. 30(5):460-3.
Fouts DE, Matthias MA, Adhikarla H, Adler B, Amorim-Santos L, Berg DE, Bulach D, Buschiazzo A, Chang Y-F, Galloway RL et al..  2016.  What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira. PLoS Negl Trop Dis. 10(2):e0004403.
Förster J, Famili I, Palsson BØ, Nielsen J.  2003.  Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae.. Omics : a journal of integrative biology. 7(2):193-202.
Förster J, Famili I, Fu P, Palsson BØ, Nielsen J.  2003.  Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network.. Genome research. 13(2):244-53.
Fong S, Marciniak JY, Palsson BØ.  2003.  Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model.. Journal of bacteriology. 185(21):6400-8.
Fong S, Joyce AR, Palsson BØ.  2005.  Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states.. Genome research. 15(10):1365-72.
Fong S, Nanchen A, Palsson BØ, Sauer U.  2006.  Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes.. The Journal of biological chemistry. 281(12):8024-33.
Fong S, Palsson BØ.  2004.  Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes.. Nature genetics. 36(10):1056-8.
Fong S, Joyce AR, Palsson BØ.  2005.  The econometrics of evolution.. Nature chemical biology. 1(4):191-2.
Fong NL, Lerman JA, Lam I, Palsson BO, Charusanti P.  2013.  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. 342(1):62-9.
Fong S, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, Palsson BØ.  2005.  In silico design and adaptive evolution of Escherichia coli for production of lactic acid.. Biotechnology and bioengineering. 91(5):643-8.
Fleming RMT, Maes CM, Saunders MA, Ye Y, Palsson BØ.  2012.  A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks.. J Theor Biol. 292:71-7.
Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BØ.  2007.  A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.. Molecular systems biology. 3:121.
Feist AM, Palsson BØ.  2008.  The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli.. Nature biotechnology. 26(6):659-67.
Feist AM, Palsson BO.  2016.  What do cells actually want? Genome Biol. 17(1):110.
Feist AM, Herrgard MJ, Thiele I, Reed JL, Palsson BØ.  2009.  Reconstruction of biochemical networks in microorganisms.. Nature reviews. Microbiology. 7(2):129-43.
Feist AM, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, Palsson BØ.  2010.  Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli.. Metabolic engineering. 12(3):173-86.
Feist AM, Nagarajan H, Rotaru A-E, Tremblay P-L, Zhang T, Nevin KP, Lovley DR, Zengler K.  2014.  Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in Geobacter metallireducens.. PLoS Comput Biol. 10(4):e1003575.
Feist AM, Scholten JCM, Palsson BØ, Brockman FJ, Ideker T.  2006.  Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri.. Molecular systems biology. 2:2006.0004.
Feist AM, Palsson BØ.  2010.  The biomass objective function.. Current opinion in microbiology. 13(3):344-9.
Federowicz S, Kim D, Ebrahim A, Lerman J, Nagarajan H, Cho B-K, Zengler K, Palsson B.  2014.  Determining the control circuitry of redox metabolism at the genome-scale.. PLoS Genet. 10(4):e1004264.
Fang X, Sastry A, Mih N, Kim D, Tan J, Yurkovich JT, Lloyd CJ, Gao Y, Yang L, Palsson BO.  2017.  Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities.. Proc Natl Acad Sci U S A.
Fang X, Monk JM, Mih N, Du B, Sastry AV, Kavvas E, Seif Y, Smarr L, Palsson BO.  2018.  Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa.. BMC Syst Biol. 12(1):66.
Famili I, Forster J, Nielsen J, Palsson BØ.  2003.  Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network.. Proceedings of the National Academy of Sciences of the United States of America. 100(23):13134-9.
Famili I, Palsson BØ.  2003.  The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools.. Biophysical journal. 85(1):16-26.
Famili I, Mahadevan R, Palsson BØ.  2005.  k-Cone analysis: determining all candidate values for kinetic parameters on a network scale.. Biophysical journal. 88(3):1616-25.
Famili I, Palsson BØ.  2003.  Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices.. Journal of theoretical biology. 224(1):87-96.

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