Student Publications

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Filters: Keyword is Proteomics  [Clear All Filters]
2014
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.
2010
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.
Lewis NE, Hixson KK, Conrad TM, et al. "Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models." Mol. Syst. Biol.. 2010;6:390.
2008
Ng J, Pevzner PA. "Algorithm for identification of fusion proteins via mass spectrometry." J. Proteome Res.. 2008;7(1):89-95.
Frank AM, Bandeira N, Shen Z, et al. "Clustering millions of tandem mass spectra." J. Proteome Res.. 2008;7(1):113-22.
Gupta N, Benhamida J, Bhargava V, et al. "Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes." Genome Res.. 2008;18(7):1133-42.
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.
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.
Kim S, Gupta N, Pevzner PA. "Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases." J. Proteome Res.. 2008;7(8):3354-63.
2007
Kim T H, Barrera LO, Ren B. "ChIP-chip for genome-wide analysis of protein binding in mammalian cells." Curr Protoc Mol Biol. 2007;Chapter 21:Unit 21.13.
Tanner S, Shen Z, Ng J, et al. "Improving gene annotation using peptide mass spectrometry." Genome Res.. 2007;17(2):231-9.
Cline MS, Smoot M, Cerami E, et al. "Integration of biological networks and gene expression data using Cytoscape." Nat Protoc. 2007;2(10):2366-82.
Gupta N, Tanner S, Jaitly N, et al. "Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation." Genome Res.. 2007;17(9):1362-77.
2006
Suthram S, Shlomi T, Ruppin E, Sharan R, Ideker T. "A direct comparison of protein interaction confidence assignment schemes." BMC Bioinformatics. 2006;7:360.
Vosseller K, Trinidad JC, Chalkley RJ, et al. "O-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry." Mol. Cell Proteomics. 2006;5(5):923-34.