Student Publications

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O'Brien EJ, Palsson BO. "Computing the functional proteome: recent progress and future prospects for genome-scale models." Curr. Opin. Biotechnol.. 2015;34:125-34.
Baycin-Hizal D, Tabb DL, Chaerkady R, et al. "Proteomic analysis of Chinese hamster ovary cells." J. Proteome Res.. 2012;11(11):5265-76.
Ho Sui SJ, Lo R, Fernandes AR, et al. "Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence." Int. J. Antimicrob. Agents. 2012;40(3):246-51.
Chang RL, Luo F, Johnson S, Scheuermann RH. "Deterministic graph-theoretic algorithm for detecting modules in biological interaction networks." Int J Bioinform Res Appl. 2010;6(2):101-19.
Chang RL, Xie L, Xie L, Bourne PE, Palsson BØ. "Drug off-target effects predicted using structural analysis in the context of a metabolic network model." PLoS Comput. Biol.. 2010;6(9):e1000938.
Wang H, Kakaradov B, Collins SR, et al. "A complex-based reconstruction of the Saccharomyces cerevisiae interactome." Mol. Cell Proteomics. 2009;8(6):1361-81.
Horler RSP, Butcher A, Papangelopoulos N, Ashton PD, Thomas GH. "EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations." Bioinformatics. 2009;25(2):163-6.
Li F, Thiele I, Jamshidi N, Palsson BØ. "Identification of potential pathway mediation targets in Toll-like receptor signaling." PLoS Comput. Biol.. 2009;5(2):e1000292.
Hawkins T, Chitale M, Luban S, Kihara D. "PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data." Proteins. 2009;74(3):566-82.
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.
Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP. "Discovery and revision of Arabidopsis genes by proteogenomics." Proc. Natl. Acad. Sci. U.S.A.. 2008;105(52):21034-8.
Bandyopadhyay S, Kelley R, Krogan NJ, Ideker T. "Functional maps of protein complexes from quantitative genetic interaction data." PLoS Comput. Biol.. 2008;4(4):e1000065.
Covert MW, Xiao N, Chen TJ, Karr JR. "Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli." Bioinformatics. 2008;24(18):2044-50.
Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, Zhou H. "A multidimensional chromatography technology for in-depth phosphoproteome analysis." Mol. Cell Proteomics. 2008;7(7):1389-96.
Payne SH, Yau M, Smolka MB, Tanner S, Zhou H, Bafna V. "Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis." J. Proteome Res.. 2008;7(8):3373-81.
Joyce AR, Palsson BØ. "The model organism as a system: integrating 'omics' data sets." Nat. Rev. Mol. Cell Biol.. 2006;7(3):198-210.
Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. "Identification of post-translational modifications by blind search of mass spectra." Nat. Biotechnol.. 2005;23(12):1562-7.