Student Publications

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Kim J, Levy E, Ferbrache A, et al. "MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure." Bioinformatics. 2014;30(19):2826-7.
Prlić A, Yates A, Bliven SE, et al. "BioJava: an open-source framework for bioinformatics in 2012." Bioinformatics. 2012;28(20):2693-5.
He Y, Zhang Y, Zheng G, Wei C. "CTF: a CRF-based transcription factor binding sites finding system." BMC Genomics. 2012;13 Suppl 8:S18.
Hu M, Deng K, Selvaraj S, Qin Z, Ren B, Liu JS. "HiCNorm: removing biases in Hi-C data via Poisson regression." Bioinformatics. 2012;28(23):3131-3.
Chaisson MJ, Tesler G. "Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory." BMC Bioinformatics. 2012;13:238.
Prlic A, Bliven S, Rose PW, et al. "Pre-calculated protein structure alignments at the RCSB PDB website." Bioinformatics. 2010;26(23):2983-5.
Brinza D, Schultz M, Tesler G, Bafna V. "RAPID detection of gene-gene interactions in genome-wide association studies." Bioinformatics. 2010;26(22):2856-62.
Tsai K-C, Teng L-W, Shao Y-M, et al. "The first pharmacophore model for potent NF-kappaB inhibitors." Bioorg. Med. Chem. Lett.. 2009;19(19):5665-9.
Liu W-T, Ng J, Meluzzi D, et al. "Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides." Anal. Chem.. 2009;81(11):4200-9.
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.
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.
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.
Kang H M, Zaitlen NA, Wade CM, et al. "Efficient control of population structure in model organism association mapping." Genetics. 2008;178(3):1709-23.
Shlomi T, Cabili MN, Herrgård MJ, Palsson BØ, Ruppin E. "Network-based prediction of human tissue-specific metabolism." Nat. Biotechnol.. 2008;26(9):1003-10.
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.
Dost B, Shlomi T, Gupta N, Ruppin E, Bafna V, Sharan R. "QNet: a tool for querying protein interaction networks." J. Comput. Biol.. 2008;15(7):913-25.
Zhi D, Keich U, Pevzner P, Heber S, Tang H. "Correcting base-assignment errors in repeat regions of shotgun assembly." IEEE/ACM Trans Comput Biol Bioinform. 2007;4(1):54-64.
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.
Zaitlen N, Kang H M, Eskin E, Halperin E. "Leveraging the HapMap correlation structure in association studies." Am. J. Hum. Genet.. 2007;80(4):683-91.
Becker SA, Feist AM, Mo ML, Hannum G, Palsson BØ, Herrgard MJ. "Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox." Nat Protoc. 2007;2(3):727-38.
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.
Harish N, Gupta R, Agarwal P, Scaria V, Pillai B. "DyNAVacS: an integrative tool for optimized DNA vaccine design." Nucleic Acids Res.. 2006;34(Web Server issue):W264-6.
Tanner S, Pevzner PA, Bafna V. "Unrestrictive identification of post-translational modifications through peptide mass spectrometry." Nat Protoc. 2006;1(1):67-72.
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.