Student Publications

McCorrison JM, Venepally P, Singh I, Fouts DE, Lasken RS, Methé BA. "NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly." BMC Bioinformatics. 2014;15:357. PubMed PMC DOI

Mollah SA, Dobrin JS, Feder RE, Tse SW, Matos IG, Cheong C, Steinman RM, Anandasabapathy N. "Flt3L dependence helps define an uncharacterized subset of murine cutaneous dendritic cells." J Invest Dermatol. 2014;134(5):1265-1275. PubMed PMC DOI

Morey R, Laurent LC. "Getting off the ground state: X chromosome inactivation knocks down barriers to differentiation." Cell Stem Cell. 2014;14(2):131-2. PubMed PMC DOI

Mukund K, Mathewson M, Minamoto V, Ward SR, Subramaniam S, Lieber RL. "Systems analysis of transcriptional data provides insights into muscle's biological response to botulinum toxin." Muscle Nerve. 2014;50(5):744-58. PubMed PMC DOI

Myers-Turnbull D, Bliven SE, Rose PW, Aziz ZK, Youkharibache P, Bourne PE, Prlić A. "Systematic detection of internal symmetry in proteins using CE-Symm." J Mol Biol. 2014;426(11):2255-68. PubMed PMC DOI

Neumann S, Campbell GE, Szpankowski L, Goldstein LS, Encalada SE. "Characterizing the composition of molecular motors on moving axonal cargo using 'cargo mapping' analysis." J Vis Exp. 2014(92):e52029. PubMed PMC DOI

O Cuív P, Klaassens ES, Smith WJ, Mondot S, Durkin AS, Harkins DM, Foster L, McCorrison J, Torralba M, Nelson KE, Morrison M. "Draft Genome Sequence of Enterococcus faecium PC4.1, a Clade B Strain Isolated from Human Feces." Genome Announc. 2014;2(1). PubMed PMC DOI

Ross MK, Wei W, Ohno-Machado L. "Big data and the electronic health record." Yearb Med Inform. 2014;9:97-104. PubMed PMC DOI

Sauls JT, Buescher JM. "Assimilating genome-scale metabolic reconstructions with modelBorgifier." Bioinformatics. 2014;30(7):1036-8. PubMed DOI

Skowronska-Krawczyk D, Ma Q, Schwartz M, Scully K, Li W, Liu Z, Taylor H, Tollkuhn J, Ohgi KA, Notani D, Kohwi Y, Kohwi-Shigematsu T, Rosenfeld MG. "Required enhancer-matrin-3 network interactions for a homeodomain transcription program." Nature. 2014;514(7521):257-61. PubMed PMC DOI

Stepanowsky P, Levy E, Kim J, Jiang X, Ohno-Machado L. "Prediction of MicroRNA Precursors Using Parsimonious Feature Sets." Cancer Inform. 2014;13(Suppl 1):95-102. PubMed PMC DOI

Thiagarajan RD, Morey R, Laurent LC. "The epigenome in pluripotency and differentiation." Epigenomics. 2014;6(1):121-37. PubMed DOI

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