Student Publications

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Friedmann-Morvinski D, Bhargava V, Gupta S, Verma IM, Subramaniam S. "Identification of therapeutic targets for glioblastoma by network analysis." Oncogene. 2015.
Appleton E, Tao J, Haddock T, Densmore D. "Interactive assembly algorithms for molecular cloning." Nat. Methods. 2014;11(6):657-62.
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.
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.
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.
Young JA, Johnson JR, Benner C, et al. "In silico discovery of transcription regulatory elements in Plasmodium falciparum." BMC Genomics. 2008;9:70.
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.
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.
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.
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.
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.
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.
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.
Zhi D, Raphael BJ, Price AL, Tang H, Pevzner PA. "Identifying repeat domains in large genomes." Genome Biol.. 2006;7(1):R7.
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.