Student Publications

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Stepanowsky P, Levy E, Kim J, Jiang X, Ohno-Machado L. "Prediction of MicroRNA Precursors Using Parsimonious Feature Sets." Cancer Inform. 2014;13(Suppl 1):95-102.
Schmitz RJ, Schultz MD, Urich MA, et al. "Patterns of population epigenomic diversity." Nature. 2013;495(7440):193-8.
Doan S, Lin K-W, Conway M, et al. "PhenDisco: phenotype discovery system for the database of genotypes and phenotypes." J Am Med Inform Assoc. 2013.
Loriaux P M, Hoffmann A. "A protein turnover signaling motif controls the stimulus-sensitivity of stress response pathways." PLoS Comput. Biol.. 2013;9(2):e1002932.
Woo S, Cha S W, Merrihew G, et al. "Proteogenomic Database Construction Driven from Large Scale RNA-seq Data." J. Proteome Res.. 2013.
Baycin-Hizal D, Tabb DL, Chaerkady R, et al. "Proteomic analysis of Chinese hamster ovary cells." J. Proteome Res.. 2012;11(11):5265-76.
Cho B-K, Federowicz SA, Embree M, Park Y-S, Kim D, Palsson BØ. "The PurR regulon in Escherichia coli K-12 MG1655." Nucleic Acids Res.. 2011;39(15):6456-64.
Prlic A, Bliven S, Rose PW, et al. "Pre-calculated protein structure alignments at the RCSB PDB website." Bioinformatics. 2010;26(23):2983-5.
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.
DeBlasio D, Bruand J, Zhang S. "PMFastR: A New Approach to Multiple RNA Structure Alignment." In: Salzberg S, Warnow T, eds. Algorithms in Bioinformatics, 9th International Workshop, WABI 2009, Philadelphia, PA, USA, September 12-13, 2009. Proceedings. Springer; 2009.
Hon GC, Hawkins DR, Ren B. "Predictive chromatin signatures in the mammalian genome." Hum. Mol. Genet.. 2009;18(R2):R195-201.
Smith DM, May SJ, Tweeten S, et al. "A public health model for the molecular surveillance of HIV transmission in San Diego, California." AIDS. 2009;23(2):225-32.
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. "Predicting gene essentiality using genome-scale in silico models." Methods Mol. Biol.. 2008;416:433-57.
Lee K, Chuang H-Y, Beyer A, et al. "Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species." Nucleic Acids Res.. 2008;36(20):e136.
Rana BK, Insel PA, Payne SH, et al. "Population-based sample reveals gene-gender interactions in blood pressure in White Americans." Hypertension. 2007;49(1):96-106.
Parrish JR, Yu J, Liu G, et al. "A proteome-wide protein interaction map for Campylobacter jejuni." Genome Biol.. 2007;8(7):R130.
Fong SS, Joyce AR, Palsson BØ. "Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states." Genome Res.. 2005;15(10):1365-72.
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.
Suthram S, Sittler T, Ideker T. "The Plasmodium protein network diverges from those of other eukaryotes." Nature. 2005;438(7064):108-12.
Canet-Avilés RM, Wilson MA, Miller DW, et al. "The Parkinson's disease protein DJ-1 is neuroprotective due to cysteine-sulfinic acid-driven mitochondrial localization." Proc. Natl. Acad. Sci. U.S.A.. 2004;101(24):9103-8.