Student Publications

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Filters: Keyword is Sequence Analysis, Protein  [Clear All Filters]
2012
Prlić A, Yates A, Bliven SE, et al. "BioJava: an open-source framework for bioinformatics in 2012." Bioinformatics. 2012;28(20):2693-5.
Bliven S, Prlić A. "Circular permutation in proteins." PLoS Comput. Biol.. 2012;8(3):e1002445.
2009
Ng J, Bandeira N, Liu W-T, et al. "Dereplication and de novo sequencing of nonribosomal peptides." Nat. Methods. 2009;6(8):596-9.
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.
Kim S, Gupta N, Bandeira N, Pevzner PA. "Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra." Mol. Cell Proteomics. 2009;8(1):53-69.
2008
Pevzner PA, Kim S, Ng J. "Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"." Science. 2008;321(5892):1040; author reply 1040.
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.
Zhi D, Krishna SS, Cao H, Pevzner P, Godzik A. "Representing and comparing protein structures as paths in three-dimensional space." BMC Bioinformatics. 2006;7:460.
2005
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.
Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. "Identification of post-translational modifications via blind search of mass-spectra." Proc IEEE Comput Syst Bioinform Conf. 2005:157-66.
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.
2004
Raphael B, Zhi D, Tang H, Pevzner P. "A novel method for multiple alignment of sequences with repeated and shuffled elements." Genome Res.. 2004;14(11):2336-46.
2003
Price ND, Papin JA, Schilling CH, Palsson BO. "Genome-scale microbial in silico models: the constraints-based approach." Trends Biotechnol.. 2003;21(4):162-9.