Student Publications

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Friedmann-Morvinski D, Bhargava V, Gupta S, Verma IM, Subramaniam S. "Identification of therapeutic targets for glioblastoma by network analysis." Oncogene. 2015.
Frank A, Tanner S, Bafna V, Pevzner P. "Peptide sequence tags for fast database search in mass-spectrometry." J. Proteome Res.. 2005;4(4):1287-95.
Frank AM, Bandeira N, Shen Z, et al. "Clustering millions of tandem mass spectra." J. Proteome Res.. 2008;7(1):113-22.
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.
Fossum E, Friedel CC, Rajagopala SV, et al. "Evolutionarily conserved herpesviral protein interaction networks." PLoS Pathog.. 2009;5(9):e1000570.
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.
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.
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.
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.
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.
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.
Feist AM, Herrgård MJ, Thiele I, Reed JL, Palsson BØ. "Reconstruction of biochemical networks in microorganisms." Nat. Rev. Microbiol.. 2009;7(2):129-43.
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.
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, 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.