Student Publications

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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.
Duarte NC, Herrgård MJ, Palsson BØ. "Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model." Genome Res.. 2004;14(7):1298-309.
Dost B, Shlomi T, Gupta N, Ruppin E, Bafna V, Sharan R. "QNet: a tool for querying protein interaction networks." J. Comput. Biol.. 2008;15(7):913-25.
Doan S, Lin K-W, Conway M, et al. "PhenDisco: phenotype discovery system for the database of genotypes and phenotypes." J Am Med Inform Assoc. 2013.
Dixon-Salazar TJ, Silhavy JL, Udpa N, et al. "Exome sequencing can improve diagnosis and alter patient management." Sci Transl Med. 2012;4(138):138ra78.
Dixon JR, Selvaraj S, Yue F, et al. "Topological domains in mammalian genomes identified by analysis of chromatin interactions." Nature. 2012;485(7398):376-80.
Diep D, Plongthongkum N, Gore A, Fung H-L, Shoemaker R, Zhang K. "Library-free methylation sequencing with bisulfite padlock probes." Nat. Methods. 2012;9(3):270-2.
Diep D, Zhang K. "Genome-wide mapping of the sixth base." Genome Biol.. 2011;12(6):116.
Devaraj NK, Miller GP, Ebina W, et al. "Chemoselective covalent coupling of oligonucleotide probes to self-assembled monolayers." J. Am. Chem. Soc.. 2005;127(24):8600-1.
DeBoever C, Reid EG, Smith EN, et al. "Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas." PLoS ONE. 2013;8(9):e73956.
DeBoever C, Ghia EM, Shepard PJ, et al. "Transcriptome sequencing reveals potential mechanism of cryptic 3' splice site selection in SF3B1-mutated cancers." PLoS Comput. Biol.. 2015;11(3):e1004105.
DeBlasio D, Bruand J, Zhang S. "PMFastR: A New Approach to Multiple RNA Structure Alignment." In: Salzberg S, Warnow T, eds. Algorithms in Bioinformatics, 9th International Workshop, WABI 2009, Philadelphia, PA, USA, September 12-13, 2009. Proceedings. Springer; 2009.