Student Publications

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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.
Tan M, Luo H, Lee S, et al. "Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification." Cell. 2011;146(6):1016-28.
Ruiz S, Diep D, Gore A, et al. "Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells." Proc. Natl. Acad. Sci. U.S.A.. 2012;109(40):16196-201.
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.
Yost SE, Smith EN, Schwab RB, et al. "Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens." Nucleic Acids Res.. 2012;40(14):e107.
Roepcke S, Zhi D, Vingron M, Arndt PF. "Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters." Gene. 2006;365:48-56.
Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. "Identification of post-translational modifications by blind search of mass spectra." Nat. Biotechnol.. 2005;23(12):1562-7.
Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. "Identification of post-translational modifications via blind search of mass-spectra." Proc IEEE Comput Syst Bioinform Conf. 2005:157-66.
Li F, Thiele I, Jamshidi N, Palsson BØ. "Identification of potential pathway mediation targets in Toll-like receptor signaling." PLoS Comput. Biol.. 2009;5(2):e1000292.
Friedmann-Morvinski D, Bhargava V, Gupta S, Verma IM, Subramaniam S. "Identification of therapeutic targets for glioblastoma by network analysis." Oncogene. 2015.
Covert MW, Famili I, Palsson BO. "Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology?" Biotechnol. Bioeng.. 2003;84(7):763-72.
Zhi D, Raphael BJ, Price AL, Tang H, Pevzner PA. "Identifying repeat domains in large genomes." Genome Biol.. 2006;7(1):R7.
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.
Applebee KM, Herrgård MJ, Palsson BØ. "Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli." J. Bacteriol.. 2008;190(14):5087-94.
Tanner S, Shen Z, Ng J, et al. "Improving gene annotation using peptide mass spectrometry." Genome Res.. 2007;17(2):231-9.
Young JA, Johnson JR, Benner C, et al. "In silico discovery of transcription regulatory elements in Plasmodium falciparum." BMC Genomics. 2008;9:70.
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.
Lerman JA, Hyduke DR, Latif H, et al. "In silico method for modelling metabolism and gene product expression at genome scale." Nat Commun. 2012;3:929.
Wagner GA, Pacold ME, Kosakovsky Pond SL, et al. "Incidence and Prevalence of Intrasubtype HIV-1 Dual Infection in At-Risk Men in the United States." J. Infect. Dis.. 2013.
Hansen K D, Timp W, Bravo H C, et al. "Increased methylation variation in epigenetic domains across cancer types." Nat. Genet.. 2011;43(8):768-75.
Zaitlen NA, Kang H M, Feolo ML, Sherry ST, Halperin E, Eskin E. "Inference and analysis of haplotypes from combined genotyping studies deposited in dbSNP." Genome Res.. 2005;15(11):1594-600.
Lee E, Chuang H-Y, Kim J-W, Ideker T, Lee D. "Inferring pathway activity toward precise disease classification." PLoS Comput. Biol.. 2008;4(11):e1000217.
Tanner S, Shu H, Frank A, et al. "InsPecT: identification of posttranslationally modified peptides from tandem mass spectra." Anal. Chem.. 2005;77(14):4626-39.
Herrgård MJ, Lee B-S, 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.
Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. "Integrating high-throughput and computational data elucidates bacterial networks." Nature. 2004;429(6987):92-6.