Student Publications

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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.
Appleton E, Tao J, Haddock T, Densmore D. "Interactive assembly algorithms for molecular cloning." Nat. Methods. 2014;11(6):657-62.
Beyer A, Bandyopadhyay S, Ideker T. "Integrating physical and genetic maps: from genomes to interaction networks." Nat. Rev. Genet.. 2007;8(9):699-710.
Cline MS, Smoot M, Cerami E, et al. "Integration of biological networks and gene expression data using Cytoscape." Nat Protoc. 2007;2(10):2366-82.
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.
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.
Covert MW, Xiao N, Chen TJ, Karr JR. "Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli." Bioinformatics. 2008;24(18):2044-50.
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.
Friedmann-Morvinski D, Bhargava V, Gupta S, Verma IM, Subramaniam S. "Identification of therapeutic targets for glioblastoma by network analysis." Oncogene. 2015.
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.
Haugen AC, Kelley R, Collins JB, et al. "Integrating phenotypic and expression profiles to map arsenic-response networks." Genome Biol.. 2004;5(12):R95.
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.
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.
Huelga SC, Vu AQ, Arnold JD, et al. "Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins." Cell Rep. 2012;1(2):167-178.
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.
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.
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.
Liu W-T, Ng J, Meluzzi D, et al. "Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides." Anal. Chem.. 2009;81(11):4200-9.
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.
Tanner S, Shen Z, Ng J, et al. "Improving gene annotation using peptide mass spectrometry." Genome Res.. 2007;17(2):231-9.
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.
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.