Student Publications

Troll CJ, Adhikary S, Cueff M, Mitra I, Eichman BF, Camps M. "Interplay between base excision repair activity and toxicity of 3-methyladenine DNA glycosylases in an E. coli complementation system." Mutat Res. 2014;763-764:64-73. PubMed PMC DOI

Udpa N, Ronen R, Zhou D, Liang J, Stobdan T, Appenzeller O, Yin Y, Du Y, Guo L, Cao R, Wang Y, Jin X, Huang C, Jia W, Cao D, Guo G, Claydon VE, Hainsworth R, Gamboa JL, Zibenigus M, Zenebe G, Xue J, Liu S, Frazer KA, Li Y, Bafna V, Haddad GG. "Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes." Genome Biol. 2014;15(2):R36. PubMed PMC DOI

Wagner GA, Pacold ME, Kosakovsky Pond SL, Caballero G, Chaillon A, Rudolph AE, Morris SR, Little SJ, Richman DD, Smith DM. "Incidence and prevalence of intrasubtype HIV-1 dual infection in at-risk men in the United States." J Infect Dis. 2014;209(7):1032-8. PubMed PMC DOI

Wang CC, Bajikar SS, Jamal L, Atkins KA, Janes KA. "A time- and matrix-dependent TGFBR3-JUND-KRT5 regulatory circuit in single breast epithelial cells and basal-like premalignancies." Nat Cell Biol. 2014;16(4):345-56. PubMed PMC DOI

Woo S, Cha SW, Merrihew G, He Y, Castellana N, Guest C, MacCoss M, Bafna V. "Proteogenomic database construction driven from large scale RNA-seq data." J Proteome Res. 2014;13(1):21-8. PubMed PMC DOI

Akiyama T, Tominaga M, Davoodi A, Nagamine M, Blansit K, Horwitz A, Carstens MI, Carstens E. "Roles for substance P and gastrin-releasing peptide as neurotransmitters released by primary afferent pruriceptors." J Neurophysiol. 2013;109(3):742-8. PubMed PMC DOI

Arnold ES, Ling SC, Huelga SC, Lagier-Tourenne C, Polymenidou M, Ditsworth D, Kordasiewicz HB, McAlonis-Downes M, Platoshyn O, Parone PA, Da Cruz S, Clutario KM, Swing D, Tessarollo L, Marsala M, Shaw CE, Yeo GW, Cleveland DW. "ALS-linked TDP-43 mutations produce aberrant RNA splicing and adult-onset motor neuron disease without aggregation or loss of nuclear TDP-43." Proc Natl Acad Sci U S A. 2013;110(8):E736-45. PubMed PMC DOI

Babrzadeh F, Varghese V, Pacold M, Liu TF, Nyrén P, Schiffer C, Fessel WJ, Shafer RW. "Collinearity of protease mutations in HIV-1 samples with high-level protease inhibitor class resistance." J Antimicrob Chemother. 2013;68(2):414-8. PubMed PMC DOI

Behar M, Barken D, Werner SL, Hoffmann A. "The dynamics of signaling as a pharmacological target." Cell. 2013;155(2):448-61. PubMed PMC DOI

Bhargava V, Ko P, Willems E, Mercola M, Subramaniam S. "Quantitative transcriptomics using designed primer-based amplification." Sci Rep. 2013;3:1740. PubMed PMC DOI

Chaillon A, Wagner GA, Hepler NL, Little SJ, Kosakovsky Pond SL, Caballero G, Pacold ME, Phung P, Wrin T, Richman DD, Wertheim JO, Smith DM. "Dynamics of viral evolution and neutralizing antibody response after HIV-1 superinfection." J Virol. 2013;87(23):12737-44. PubMed PMC DOI

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. PubMed PMC DOI

Chang RL, Xie L, Bourne PE, Palsson BO. "Antibacterial mechanisms identified through structural systems pharmacology." BMC Syst Biol. 2013;7:102. PubMed PMC DOI

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