Student Publications

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Dixon-Salazar TJ, Silhavy JL, Udpa N, et al. "Exome sequencing can improve diagnosis and alter patient management." Sci Transl Med. 2012;4(138):138ra78.
Doan S, Lin K-W, Conway M, et al. "PhenDisco: phenotype discovery system for the database of genotypes and phenotypes." J Am Med Inform Assoc. 2013.
Dost B, Shlomi T, Gupta N, Ruppin E, Bafna V, Sharan R. "QNet: a tool for querying protein interaction networks." J. Comput. Biol.. 2008;15(7):913-25.
Duarte NC, Becker SA, Jamshidi N, et al. "Global reconstruction of the human metabolic network based on genomic and bibliomic data." Proc. Natl. Acad. Sci. U.S.A.. 2007;104(6):1777-82.
Duarte NC, Herrgård MJ, Palsson BØ. "Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model." Genome Res.. 2004;14(7):1298-309.
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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.
Edwards JS, Covert M, Palsson B. "Metabolic modelling of microbes: the flux-balance approach." Environ. Microbiol.. 2002;4(3):133-40.
Embree M, Nagarajan H, Movahedi N, Chitsaz H, Zengler K. "Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community." ISME J. 2013.
Birney E, Stamatoyannopoulos JA, Dutta A, et al. "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project." Nature. 2007;447(7146):799-816.
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Famili I, Mahadevan R, Palsson BO. "k-Cone analysis: determining all candidate values for kinetic parameters on a network scale." Biophys. J.. 2005;88(3):1616-25.
Famili I, Palsson BO. "Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices." J. Theor. Biol.. 2003;224(1):87-96.
Famili I, Palsson BO. "The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools." Biophys. J.. 2003;85(1):16-26.
Famili I, Forster J, Nielsen J, Palsson BO. "Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network." Proc. Natl. Acad. Sci. U.S.A.. 2003;100(23):13134-9.
Feist AM, Herrgård MJ, Thiele I, Reed JL, Palsson BØ. "Reconstruction of biochemical networks in microorganisms." Nat. Rev. Microbiol.. 2009;7(2):129-43.
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.
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.
Feldman KE, Loriaux PM, Saito M, et al. "Ex vivo innate immune cytokine signature of enhanced risk of relapsing brucellosis." PLoS Negl Trop Dis. 2013;7(9):e2424.
Feupe S F, Frias PF, Mednick SC, McDevitt EA, Heintzman ND. "Nocturnal continuous glucose and sleep stage data in adults with type 1 diabetes in real-world conditions." J Diabetes Sci Technol. 2013;7(5):1337-45.
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.
Fong SS, Joyce AR, Palsson BØ. "The econometrics of evolution." Nat. Chem. Biol.. 2005;1(4):191-2.
Fong SS, Joyce AR, Palsson BØ. "Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states." Genome Res.. 2005;15(10):1365-72.
Förster J, Famili I, Palsson BO, Nielsen J. "Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae." OMICS. 2003;7(2):193-202.
Förster J, Famili I, Fu P, Palsson BØ, Nielsen J. "Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network." Genome Res.. 2003;13(2):244-53.
Fossum E, Friedel CC, Rajagopala SV, et al. "Evolutionarily conserved herpesviral protein interaction networks." PLoS Pathog.. 2009;5(9):e1000570.
Fox-Walsh K, Davis-Turak J, Zhou Y, Li H, Fu X-D. "A multiplex RNA-seq strategy to profile poly(A+) RNA: application to analysis of transcription response and 3' end formation." Genomics. 2011;98(4):266-71.

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