Student Publications

DeBoever C, Reid EG, Smith EN, Wang X, Dumaop W, Harismendy O, Carson D, Richman D, Masliah E, Frazer KA. "Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas." PLoS One. 2013;8(9):e73956. PubMed PMC DOI

Depew J, Zhou B, McCorrison JM, Wentworth DE, Purushe J, Koroleva G, Fouts DE. "Sequencing viral genomes from a single isolated plaque." Virol J. 2013;10:181. PubMed PMC DOI

Ebrahim A, Lerman JA, Palsson BO, Hyduke DR. "COBRApy: COnstraints-Based Reconstruction and Analysis for Python." BMC Syst Biol. 2013;7:74. PubMed PMC DOI

Edwards RA, Haggerty JM, Cassman N, Busch JC, Aguinaldo K, Chinta S, Vaughn MH, Morey R, Harkins TT, Teiling C, Fredrikson K, Dinsdale EA. "Microbes, metagenomes and marine mammals: enabling the next generation of scientist to enter the genomic era." BMC Genomics. 2013;14:600. PubMed PMC DOI

Feldman KE, Loriaux PM, Saito M, Tuero I, Villaverde H, Siva T, Gotuzzo E, Gilman RH, Hoffmann A, Vinetz JM. "Ex vivo innate immune cytokine signature of enhanced risk of relapsing brucellosis." PLoS Negl Trop Dis. 2013;7(9):e2424. PubMed PMC DOI

Feupe SF, 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. PubMed PMC DOI

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. PubMed PMC DOI

Füllgrabe J, Lynch-Day MA, Heldring N, Li W, Struijk RB, Ma Q, Hermanson O, Rosenfeld MG, Klionsky DJ, Joseph B. "The histone H4 lysine 16 acetyltransferase hMOF regulates the outcome of autophagy." Nature. 2013;500(7463):468-71. PubMed PMC DOI

Heinz S, Romanoski CE, Benner C, Allison KA, Kaikkonen MU, Orozco LD, Glass CK. "Effect of natural genetic variation on enhancer selection and function." Nature. 2013;503(7477):487-92. PubMed PMC DOI

Hightower GK, May SJ, Pérez-Santiago J, Pacold ME, Wagner GA, Little SJ, Richman DD, Mehta SR, Smith DM, Pond SL. "HIV-1 clade B pol evolution following primary infection." PLoS One. 2013;8(6):e68188. PubMed PMC DOI

Hofree M, Shen JP, Carter H, Gross A, Ideker T. "Network-based stratification of tumor mutations." Nat Methods. 2013;10(11):1108-15. PubMed PMC DOI

Hu M, Deng K, Qin Z, Dixon J, Selvaraj S, Fang J, Ren B, Liu JS. "Bayesian inference of spatial organizations of chromosomes." PLoS Comput Biol. 2013;9(1):e1002893. PubMed PMC DOI

Hua Z, Pool JE, Schmitz RJ, Schultz MD, Shiu SH, Ecker JR, Vierstra RD. "Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis." Proc Natl Acad Sci U S A. 2013;110(42):16927-32. PubMed PMC DOI

Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen CA, Schmitt AD, Espinoza CA, Ren B. "A high-resolution map of the three-dimensional chromatin interactome in human cells." Nature. 2013;503(7475):290-4. PubMed PMC DOI

Jones JC, Sabatini K, Liao X, Tran HT, Lynch CL, Morey RE, Glenn-Pratola V, Boscolo FS, Yang Q, Parast MM, Liu Y, Peterson SE, Laurent LC, Loring JF, Wang YC. "Melanocytes derived from transgene-free human induced pluripotent stem cells." J Invest Dermatol. 2013;133(8):2104-8. PubMed PMC DOI

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. PubMed DOI

Kaikkonen MU, Spann NJ, Heinz S, Romanoski CE, Allison KA, Stender JD, Chun HB, Tough DF, Prinjha RK, Benner C, Glass CK. "Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription." Mol Cell. 2013;51(3):310-25. PubMed PMC DOI

Kim S, Jeong K, Bhutani K, Lee J, Patel A, Scott E, Nam H, Lee H, Gleeson JG, Bafna V. "Virmid: accurate detection of somatic mutations with sample impurity inference." Genome Biol. 2013;14(8):R90. PubMed PMC DOI

Latif H, Lerman JA, Portnoy VA, Tarasova Y, Nagarajan H, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Lee DH, Qiu Y, Zengler K. "The genome organization of Thermotoga maritima reflects its lifestyle." PLoS Genet. 2013;9(4):e1003485. PubMed PMC DOI

Lewis NE, Liu X, Li Y, Nagarajan H, Yerganian G, O'Brien E, Bordbar A, Roth AM, Rosenbloom J, Bian C, Xie M, Chen W, Li N, Baycin-Hizal D, Latif H, Forster J, Betenbaugh MJ, Famili I, Xu X, Wang J, Palsson BO. "Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome." Nat Biotechnol. 2013;31(8):759-65. PubMed DOI

Li W, Notani D, Ma Q, Tanasa B, Nunez E, Chen AY, Merkurjev D, Zhang J, Ohgi K, Song X, Oh S, Kim HS, Glass CK, Rosenfeld MG. "Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation." Nature. 2013;498(7455):516-20. PubMed PMC DOI

Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, Johnson ND, Lucero J, Huang Y, Dwork AJ, Schultz MD, Yu M, Tonti-Filippini J, Heyn H, Hu S, Wu JC, Rao A, Esteller M, He C, Haghighi FG, Sejnowski TJ, Behrens MM, Ecker JR. "Global epigenomic reconfiguration during mammalian brain development." Science. 2013;341(6146):1237905. PubMed PMC DOI

Liu W, Ma Q, Wong K, Li W, Ohgi K, Zhang J, Aggarwal A, Rosenfeld MG. "Brd4 and JMJD6-associated anti-pause enhancers in regulation of transcriptional pause release." Cell. 2013;155(7):1581-1595. PubMed PMC DOI

Lo JH, von Maltzahn G, Douglass J, Park JH, Sailor MJ, Ruoslahti E, Bhatia SN. "Nanoparticle amplification via photothermal unveiling of cryptic collagen binding sites." J Mater Chem B. 2013;1(39):5235-5240. PubMed PMC DOI

Loriaux PM, Hoffmann A. "A protein turnover signaling motif controls the stimulus-sensitivity of stress response pathways." PLoS Comput Biol. 2013;9(2):e1002932. PubMed PMC DOI