Student Publications

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Price ND, Reed JL, Papin JA, Famili I, Palsson BO. "Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices." Biophys. J.. 2003;84(2 Pt 1):794-804.
Zhu X, Hart R, Chang M S, et al. "Analysis of the major patterns of B cell gene expression changes in response to short-term stimulation with 33 single ligands." J. Immunol.. 2004;173(12):7141-9.
Chandonia J-M, Hon G, Walker NS, et al. "The ASTRAL Compendium in 2004." Nucleic Acids Res.. 2004;32(Database issue):D189-92.
Covert MW, Leung TH, Gaston JE, Baltimore D. "Achieving stability of lipopolysaccharide-induced NF-kappaB activation." Science. 2005;309(5742):1854-7.
Tompa M, Li N, Bailey TL, et al. "Assessing computational tools for the discovery of transcription factor binding sites." Nat. Biotechnol.. 2005;23(1):137-44.
Chang MW, Lindstrom W, Olson AJ, Belew RK. "Analysis of HIV wild-type and mutant structures via in silico docking against diverse ligand libraries." J Chem Inf Model. 2007;47(3):1258-62.
Tanner S, Payne SH, Dasari S, et al. "Accurate annotation of peptide modifications through unrestrictive database search." J. Proteome Res.. 2008;7(1):170-81.
Rao F, Zhang L, Wessel J, et al. "Adrenergic polymorphism and the human stress response." Ann. N. Y. Acad. Sci.. 2008;1148:282-96.
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.
Ng J, Pevzner PA. "Algorithm for identification of fusion proteins via mass spectrometry." J. Proteome Res.. 2008;7(1):89-95.
Bechtel JM, Rajesh P, Ilikchyan I, et al. "The Alternative Splicing Mutation Database: a hub for investigations of alternative splicing using mutational evidence." BMC Res Notes. 2008;1:3.
Briedis KM, Starr A, Bourne PE. "Analysis of the human kinome using methods including fold recognition reveals two novel kinases." PLoS ONE. 2008;3(2):e1597.
Gendron JM, Pruneda-Paz JL, Doherty CJ, Gross AM, S Kang E, Kay SA. "Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor." Proc. Natl. Acad. Sci. U.S.A.. 2012;109(8):3167-72.
Arnold ES, Ling S-C, Huelga SC, et al. "ALS-linked TDP-43 mutations produce aberrant RNA splicing and adult-onset motor neuron disease without aggregation or loss of nuclear TDP-43." Proc. Natl. Acad. Sci. U.S.A.. 2013;110(8):E736-45.
Chang RL, Xie L, Bourne PE, Palsson BO. "Antibacterial mechanisms identified through structural systems pharmacology." BMC Syst Biol. 2013;7:102.
Castellana NE, Shen Z, He Y, et al. "An Automated Proteogenomic Method Utilizes Mass Spectrometry to Reveal Novel Genes in Zea mays." Mol. Cell Proteomics. 2013.
Ma H, Morey R, O'Neil RC, et al. "Abnormalities in human pluripotent cells due to reprogramming mechanisms." Nature. 2014;511(7508):177-83.
Lin MS, Cherny JJ, Fournier CT, Roth SJ, Krizanc D, Weir MP. "Assessment of MS/MS search algorithms with parent-protein profiling." J. Proteome Res.. 2014;13(4):1823-32.
Sauls JT, Buescher JM. "Assimilating genome-scale metabolic reconstructions with modelBorgifier." Bioinformatics. 2014.
Sauls JT, Li D, Jun S. "Adder and a coarse-grained approach to cell size homeostasis in bacteria." Curr. Opin. Cell Biol.. 2016;38:38-44.