Student Publications

Tanner S, Shen Z, Ng J, Florea L, Guigó R, Briggs SP, Bafna V. "Improving gene annotation using peptide mass spectrometry." Genome Res. 2007;17(2):231-9. PubMed PMC DOI

Xie L, Wang J, Bourne PE. "In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators." PLoS Comput Biol. 2007;3(11):e217. PubMed PMC DOI

Ye C, Eskin E. "Discovering tightly regulated and differentially expressed gene sets in whole genome expression data." Bioinformatics. 2007;23(2):e84-90. PubMed DOI

Yeung M, Thiele I, Palsson BO. "Estimation of the number of extreme pathways for metabolic networks." BMC Bioinformatics. 2007;8(1):363. PubMed PMC DOI

Zaitlen N, Kang HM, Eskin E, Halperin E. "Leveraging the HapMap correlation structure in association studies." Am J Hum Genet. 2007;80(4):683-91. PubMed PMC DOI

Zhang H, Liu AY, Loriaux P, Wollscheid B, Zhou Y, Watts JD, Aebersold R. "Mass spectrometric detection of tissue proteins in plasma." Mol Cell Proteomics. 2007;6(1):64-71. PubMed DOI

Zhang L, Rao F, Zhang K, Khandrika S, Das M, Vaingankar SM, Bao X, Rana BK, Smith DW, Wessel J, Salem RM, Rodriguez-Flores JL, Mahata SK, Schork NJ, Ziegler MG, O'Connor DT. "Discovery of common human genetic variants of GTP cyclohydrolase 1 (GCH1) governing nitric oxide, autonomic activity, and cardiovascular risk." J Clin Invest. 2007;117(9):2658-71. PubMed PMC DOI

Zheng M, Barrera LO, Ren B, Wu YN. "ChIP-chip: data, model, and analysis." Biometrics. 2007;63(3):787-96. PubMed DOI

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. PubMed DOI

Allen TE, Price ND, Joyce AR, Palsson BØ. "Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization." PLoS Comput Biol. 2006;2(1):e2. PubMed PMC DOI

Bandyopadhyay S, Kelley R, Ideker T. "Discovering regulated networks during HIV-1 latency and reactivation." Pac Symp Biocomput. 2006:354-66. PubMed PMC

Bandyopadhyay S, Sharan R, Ideker T. "Systematic identification of functional orthologs based on protein network comparison." Genome Res. 2006;16(3):428-35. PubMed PMC DOI

Barrera LO, Ren B. "The transcriptional regulatory code of eukaryotic cells--insights from genome-wide analysis of chromatin organization and transcription factor binding." Curr Opin Cell Biol. 2006;18(3):291-8. PubMed DOI

Chaisson MJ, Raphael BJ, Pevzner PA. "Microinversions in mammalian evolution." Proc Natl Acad Sci U S A. 2006;103(52):19824-9. PubMed PMC DOI

Gianchandani EP, Brautigan DL, Papin JA. "Systems analyses characterize integrated functions of biochemical networks." Trends Biochem Sci. 2006;31(5):284-91. PubMed DOI

Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BO. "Matrix formalism to describe functional states of transcriptional regulatory systems." PLoS Comput Biol. 2006;2(8):e101. PubMed PMC DOI

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. PubMed PMC DOI

Hawkins T, Luban S, Kihara D. "Enhanced automated function prediction using distantly related sequences and contextual association by PFP." Protein Sci. 2006;15(6):1550-6. PubMed PMC DOI

Herrgård MJ, Fong SS, Palsson BØ. "Identification of genome-scale metabolic network models using experimentally measured flux profiles." PLoS Comput Biol. 2006;2(7):e72. PubMed PMC DOI

Herrgård MJ, Lee BS, Portnoy V, Palsson BØ. "Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae." Genome Res. 2006;16(5):627-35. PubMed PMC DOI

Herring CD, Raghunathan A, Honisch C, Patel T, Applebee MK, Joyce AR, Albert TJ, Blattner FR, van den Boom D, Cantor CR, Palsson BØ. "Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale." Nat Genet. 2006;38(12):1406-12. PubMed DOI

Hirose S, Payne SH, Loomis WF. "cis-Acting site controlling bidirectional transcription at the growth-differentiation transition in Dictyostelium discoideum." Eukaryot Cell. 2006;5(7):1104-10. PubMed PMC DOI

Hua Q, Joyce AR, Fong SS, Palsson BØ. "Metabolic analysis of adaptive evolution for in silico-designed lactate-producing strains." Biotechnol Bioeng. 2006;95(5):992-1002. PubMed DOI

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. PubMed PMC DOI

Joyce AR, Palsson BØ. "The model organism as a system: integrating 'omics' data sets." Nat Rev Mol Cell Biol. 2006;7(3):198-210. PubMed DOI