Student Publications

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Pacold M, Soto P. "Retroviruses and opportunistic infections - 15th annual conference." IDrugs. 2008;11(4):233-5.
Raphael BJ, Volik S, Yu P, et al. "A sequence-based survey of the complex structural organization of tumor genomes." Genome Biol.. 2008;9(3):R59.
Chaisson MJ, Pevzner PA. "Short read fragment assembly of bacterial genomes." Genome Res.. 2008;18(2):324-30.
Kim S, Gupta N, Pevzner PA. "Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases." J. Proteome Res.. 2008;7(8):3354-63.
Rosen RF, Farberg AS, Gearing M, et al. "Tauopathy with paired helical filaments in an aged chimpanzee." J. Comp. Neurol.. 2008;509(3):259-70.
Walsh CT, Radeff-Huang J, Matteo R, et al. "Thrombin receptor and RhoA mediate cell proliferation through integrins and cysteine-rich protein 61." FASEB J.. 2008;22(11):4011-21.
Chang MW, Lindstrom W, Olson AJ, Belew RK. "Analysis of HIV wild-type and mutant structures via in silico docking against diverse ligand libraries." J Chem Inf Model. 2007;47(3):1258-62.
Zheng M, Barrera LO, Ren B, Wu Y. "ChIP-chip: data, model, and analysis." Biometrics. 2007;63(3):787-96.
Kim T H, 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.
Luban S, Kihara D. "Comparative genomics of small RNAs in bacterial genomes." OMICS. 2007;11(1):58-73.
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.
Lunyak VV, Prefontaine GG, Núñez E, et al. "Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis." Science. 2007;317(5835):248-51.
Ye C, Eskin E. "Discovering tightly regulated and differentially expressed gene sets in whole genome expression data." Bioinformatics. 2007;23(2):e84-90.
Zhang L, Rao F, Zhang K, et al. "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.
Heintzman ND, Stuart RK, Hon G, et al. "Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome." Nat. Genet.. 2007;39(3):311-8.
Berry RE, Shokhireva T K, Filippov I, Shokhirev MN, Zhang H, Walker AF. "Effect of the N-terminus on heme cavity structure, ligand equilibrium, rate constants, and reduction potentials of nitrophorin 2 from Rhodnius prolixus." Biochemistry. 2007;46(23):6830-43.
Yeung M, Thiele I, Palsson BO. "Estimation of the number of extreme pathways for metabolic networks." BMC Bioinformatics. 2007;8(1):363.
Bansal V, Bashir A, Bafna V. "Evidence for large inversion polymorphisms in the human genome from HapMap data." Genome Res.. 2007;17(2):219-30.
Feist AM, Henry CS, Reed JL, et al. "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol. Syst. Biol.. 2007;3:121.
Duarte NC, Becker SA, Jamshidi N, et al. "Global reconstruction of the human metabolic network based on genomic and bibliomic data." Proc. Natl. Acad. Sci. U.S.A.. 2007;104(6):1777-82.
Garcia-Bassets I, Kwon Y-S, Telese F, et al. "Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors." Cell. 2007;128(3):505-18.
O'Dea EL, Barken D, Peralta RQ, et al. "A homeostatic model of IkappaB metabolism to control constitutive NF-kappaB activity." Mol. Syst. Biol.. 2007;3:111.
Birney E, Stamatoyannopoulos JA, Dutta A, et al. "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project." Nature. 2007;447(7146):799-816.
Aktulga H M, Kontoyiannis I, Lyznik AL, Szpankowski L, Grama AY, Szpankowski W. "Identifying statistical dependence in genomic sequences via mutual information estimates." EURASIP J Bioinform Syst Biol. 2007:14741.
Tanner S, Shen Z, Ng J, et al. "Improving gene annotation using peptide mass spectrometry." Genome Res.. 2007;17(2):231-9.