Student Publications

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Margeridon-Thermet S, Svarovskaia ES, Babrzadeh F, et al. "Low-level persistence of drug resistance mutations in hepatitis B virus-infected subjects with a past history of Lamivudine treatment." Antimicrob. Agents Chemother.. 2013;57(1):343-9.
Nakatsuji T, Chiang H-I, Jiang SB, Nagarajan H, Zengler K, Gallo RL. "The microbiome extends to subepidermal compartments of normal skin." Nat Commun. 2013;4:1431.
Nguyen D D, Wu C-H, Moree WJ, et al. "MS/MS networking guided analysis of molecule and gene cluster families." Proc. Natl. Acad. Sci. U.S.A.. 2013;110(28):E2611-20.
Hofree M, Shen JP, Carter H, Gross A, Ideker T. "Network-based stratification of tumor mutations." Nat. Methods. 2013;10(11):1108-15.
Feupe S F, Frias PF, Mednick SC, McDevitt EA, Heintzman ND. "Nocturnal continuous glucose and sleep stage data in adults with type 1 diabetes in real-world conditions." J Diabetes Sci Technol. 2013;7(5):1337-45.
Schmitz RJ, Schultz MD, Urich MA, et al. "Patterns of population epigenomic diversity." Nature. 2013;495(7440):193-8.
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.
Loriaux P M, Hoffmann A. "A protein turnover signaling motif controls the stimulus-sensitivity of stress response pathways." PLoS Comput. Biol.. 2013;9(2):e1002932.
Woo S, Cha S W, Merrihew G, et al. "Proteogenomic Database Construction Driven from Large Scale RNA-seq Data." J. Proteome Res.. 2013.
Bhargava V, Ko P, Willems E, Mercola M, Subramaniam S. "Quantitative transcriptomics using designed primer-based amplification." Sci Rep. 2013;3:1740.
Lovci MT, Ghanem D, Marr H, et al. "Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges." Nat. Struct. Mol. Biol.. 2013;20(12):1434-42.
Fong NL, Lerman JA, Lam I, Palsson BO, Charusanti P. "Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant." FEMS Microbiol. Lett.. 2013;342(1):62-9.
Kaikkonen MU, Spann NJ, Heinz S, et al. "Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription." Mol. Cell. 2013;51(3):310-25.
Embree M, Nagarajan H, Movahedi N, Chitsaz H, Zengler K. "Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community." ISME J. 2013.
Chang RL, Andrews K, Kim D, Li Z, Godzik A, Palsson BO. "Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli." Science. 2013;340(6137):1220-3.
Jung H, Bleazard T, Lee J, Hong D. "Systematic investigation of cancer-associated somatic point mutations in SNP databases." Nat. Biotechnol.. 2013;31(9):787-9.
Wagner GA, Pacold ME, Vigil E, et al. "Using ultradeep pyrosequencing to study HIV-1 coreceptor usage in primary and dual infection." J. Infect. Dis.. 2013;208(2):271-4.
Allison KA, Kaikkonen MU, Gaasterland T, Glass CK. "Vespucci: a system for building annotated databases of nascent transcripts." Nucleic Acids Res.. 2013.
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.
Selvaraj S, Dixon JR, Bansal V, Ren B. "Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing." Nat. Biotechnol.. 2013.
Zhou D, Udpa N, Ronen R, et al. "Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders." Am. J. Hum. Genet.. 2013;93(3):452-62.
Gendron JM, Pruneda-Paz JL, Doherty CJ, Gross AM, S Kang E, Kay SA. "Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor." Proc. Natl. Acad. Sci. U.S.A.. 2012;109(8):3167-72.
Prlić A, Yates A, Bliven SE, et al. "BioJava: an open-source framework for bioinformatics in 2012." Bioinformatics. 2012;28(20):2693-5.
Bliven S, Prlić A. "Circular permutation in proteins." PLoS Comput. Biol.. 2012;8(3):e1002445.
Pacold ME, Pond S KL, Wagner GA, et al. "Clinical, virologic, and immunologic correlates of HIV-1 intraclade B dual infection among men who have sex with men." AIDS. 2012;26(2):157-65.