Student Publications

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Ma H, Morey R, O'Neil RC, et al. "Abnormalities in human pluripotent cells due to reprogramming mechanisms." Nature. 2014;511(7508):177-83.
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.
Covert MW, Leung TH, Gaston JE, Baltimore D. "Achieving stability of lipopolysaccharide-induced NF-kappaB activation." Science. 2005;309(5742):1854-7.
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.
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.
Wilmarth PA, Tanner S, Dasari S, et al. "Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility?" J. Proteome Res.. 2006;5(10):2554-66.
Ng J, Pevzner PA. "Algorithm for identification of fusion proteins via mass spectrometry." J. Proteome Res.. 2008;7(1):89-95.
Jones NC, Zhi D, Raphael BJ. "AliWABA: alignment on the web through an A-Bruijn approach." Nucleic Acids Res.. 2006;34(Web Server issue):W613-6.
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.
Wu J, Okamura D, Li M, et al. "An alternative pluripotent state confers interspecies chimaeric competency." Nature. 2015;521(7552):316-21.
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.
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.
Gross AM, Kreisberg JF, Ideker T. "Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer Types." PLoS ONE. 2015;10(11):e0142618.
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.
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.
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.
Chang RL, Xie L, Bourne PE, Palsson BO. "Antibacterial mechanisms identified through structural systems pharmacology." BMC Syst Biol. 2013;7:102.
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.
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.
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.
Chandonia J-M, Hon G, Walker NS, et al. "The ASTRAL Compendium in 2004." Nucleic Acids Res.. 2004;32(Database issue):D189-92.
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.