Student Publications

Joyce AR, Palsson BO. "Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach." Prog Drug Res. 2007;64:265, 267-309. PubMed

Kim TH, 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. PubMed DOI

Knipp M, Yang F, Berry RE, Zhang H, Shokhirev MN, Walker FA. "Spectroscopic and functional characterization of nitrophorin 7 from the blood-feeding insect Rhodnius prolixus reveals an important role of its isoform-specific N-terminus for proper protein function." Biochemistry. 2007;46(46):13254-68. PubMed PMC DOI

Kwon YS, Garcia-Bassets I, Hutt KR, Cheng CS, Jin M, Liu D, Benner C, Wang D, Ye Z, Bibikova M, Fan JB, Duan L, Glass CK, Rosenfeld MG, Fu XD. "Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters." Proc Natl Acad Sci U S A. 2007;104(12):4852-7. PubMed PMC DOI

Luban S, Kihara D. "Comparative genomics of small RNAs in bacterial genomes." OMICS. 2007;11(1):58-73. PubMed DOI

Lunyak VV, Prefontaine GG, Núñez E, Cramer T, Ju BG, Ohgi KA, Hutt K, Roy R, García-Díaz A, Zhu X, Yung Y, Montoliu L, Glass CK, Rosenfeld MG. "Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis." Science. 2007;317(5835):248-51. PubMed DOI

Maurya MR, Benner C, Pradervand S, Glass C, Subramaniam S. "Systems biology of macrophages." Adv Exp Med Biol. 2007;598:62-79. PubMed DOI

O'Dea EL, Barken D, Peralta RQ, Tran KT, Werner SL, Kearns JD, Levchenko A, Hoffmann A. "A homeostatic model of IkappaB metabolism to control constitutive NF-kappaB activity." Mol Syst Biol. 2007;3:111. PubMed PMC DOI

Parrish JR, Yu J, Liu G, Hines JA, Chan JE, Mangiola BA, Zhang H, Pacifico S, Fotouhi F, DiRita VJ, Ideker T, Andrews P, Finley RL Jr. "A proteome-wide protein interaction map for Campylobacter jejuni." Genome Biol. 2007;8(7):R130. PubMed PMC DOI

Rana BK, Insel PA, Payne SH, Abel K, Beutler E, Ziegler MG, Schork NJ, O'Connor DT. "Population-based sample reveals gene-gender interactions in blood pressure in White Americans." Hypertension. 2007;49(1):96-106. PubMed DOI

Rao F, Zhang L, Wessel J, Zhang K, Wen G, Kennedy BP, Rana BK, Das M, Rodriguez-Flores JL, Smith DW, Cadman PE, Salem RM, Mahata SK, Schork NJ, Taupenot L, Ziegler MG, O'Connor DT. "Tyrosine hydroxylase, the rate-limiting enzyme in catecholamine biosynthesis: discovery of common human genetic variants governing transcription, autonomic activity, and blood pressure in vivo." Circulation. 2007;116(9):993-1006. PubMed DOI

Sears DD, Hsiao A, Ofrecio JM, Chapman J, He W, Olefsky JM. "Selective modulation of promoter recruitment and transcriptional activity of PPARgamma." Biochem Biophys Res Commun. 2007;364(3):515-21. PubMed PMC DOI

Shlomi T, Herrgard M, Portnoy V, Naim E, Palsson BØ, Sharan R, Ruppin E. "Systematic condition-dependent annotation of metabolic genes." Genome Res. 2007;17(11):1626-33. PubMed PMC DOI

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