Student Publications

Loriaux PM, Tesler G, Hoffmann A. "Characterizing the relationship between steady state and response using analytical expressions for the steady states of mass action models." PLoS Comput Biol. 2013;9(2):e1002901. PubMed PMC DOI

Lovci MT, Ghanem D, Marr H, Arnold J, Gee S, Parra M, Liang TY, Stark TJ, Gehman LT, Hoon S, Massirer KB, Pratt GA, Black DL, Gray JW, Conboy JG, Yeo GW. "Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges." Nat Struct Mol Biol. 2013;20(12):1434-42. PubMed PMC DOI

Margeridon-Thermet S, Svarovskaia ES, Babrzadeh F, Martin R, Liu TF, Pacold M, Reuman EC, Holmes SP, Borroto-Esoda K, Shafer RW. "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. PubMed PMC DOI

Massanella M, Singhania A, Beliakova-Bethell N, Pier R, Lada SM, White CH, Pérez-Santiago J, Blanco J, Richman DD, Little SJ, Woelk CH. "Differential gene expression in HIV-infected individuals following ART." Antiviral Res. 2013;100(2):420-8. PubMed PMC DOI

Nagarajan H, Embree M, Rotaru AE, Shrestha PM, Feist AM, Palsson BØ, Lovley DR, Zengler K. "Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association." Nat Commun. 2013;4:2809. PubMed DOI

Nagarajan H, Sahin M, Nogales J, Latif H, Lovley DR, Ebrahim A, Zengler K. "Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii." Microb Cell Fact. 2013;12:118. PubMed PMC DOI

Nakatsuji T, Chiang HI, Jiang SB, Nagarajan H, Zengler K, Gallo RL. "The microbiome extends to subepidermal compartments of normal skin." Nat Commun. 2013;4:1431. PubMed PMC DOI

Nguyen DD, Wu CH, Moree WJ, Lamsa A, Medema MH, Zhao X, Gavilan RG, Aparicio M, Atencio L, Jackson C, Ballesteros J, Sanchez J, Watrous JD, Phelan VV, van de Wiel C, Kersten RD, Mehnaz S, De Mot R, Shank EA, Charusanti P, Nagarajan H, Duggan BM, Moore BS, Bandeira N, Palsson BØ, Pogliano K, Gutiérrez M, Dorrestein PC. "MS/MS networking guided analysis of molecule and gene cluster families." Proc Natl Acad Sci U S A. 2013;110(28):E2611-20. 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 faecalis PC1.1, a Candidate Probiotic Strain Isolated from Human Feces." Genome Announc. 2013;1(1). PubMed PMC DOI

O'Brien EJ, Lerman JA, Chang RL, Hyduke DR, Palsson BØ. "Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction." Mol Syst Biol. 2013;9:693. PubMed PMC DOI

Qiu Y, Nagarajan H, Embree M, Shieu W, Abate E, Juárez K, Cho BK, Elkins JG, Nevin KP, Barrett CL, Lovley DR, Palsson BO, Zengler K. "Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks." Nat Commun. 2013;4:1755. PubMed DOI

Ronen R, Udpa N, Halperin E, Bafna V. "Learning natural selection from the site frequency spectrum." Genetics. 2013;195(1):181-93. PubMed PMC DOI

Schmitz RJ, He Y, Valdés-López O, Khan SM, Joshi T, Urich MA, Nery JR, Diers B, Xu D, Stacey G, Ecker JR. "Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population." Genome Res. 2013;23(10):1663-74. PubMed PMC DOI

Schmitz RJ, Schultz MD, Urich MA, Nery JR, Pelizzola M, Libiger O, Alix A, McCosh RB, Chen H, Schork NJ, Ecker JR. "Patterns of population epigenomic diversity." Nature. 2013;495(7440):193-8. PubMed PMC DOI

Selvaraj S, R Dixon J, Bansal V, Ren B. "Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing." Nat Biotechnol. 2013;31(12):1111-8. PubMed PMC DOI

Shen L, Wu H, Diep D, Yamaguchi S, D'Alessio AC, Fung HL, Zhang K, Zhang Y. "Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics." Cell. 2013;153(3):692-706. PubMed PMC DOI

Shkoporov AN, Efimov BA, Khokhlova EV, Chaplin AV, Kafarskaya LI, Durkin AS, McCorrison J, Torralba M, Gillis M, Sutton G, Weibel DB, Nelson KE, Smeianov VV. "Draft Genome Sequences of Two Pairs of Human Intestinal Bifidobacterium longum subsp. longum Strains, 44B and 1-6B and 35B and 2-2B, Consecutively Isolated from Two Children after a 5-Year Time Period." Genome Announc. 2013;1(3). PubMed PMC DOI

Shokhirev MN, Hoffmann A. "FlowMax: A Computational Tool for Maximum Likelihood Deconvolution of CFSE Time Courses." PLoS One. 2013;8(6):e67620. PubMed PMC DOI

Varga JJ, Losada L, Zelazny AM, Kim M, McCorrison J, Brinkac L, Sampaio EP, Greenberg DE, Singh I, Heiner C, Ashby M, Nierman WC, Holland SM, Goldberg JB. "Draft Genome Sequences of Burkholderia cenocepacia ET12 Lineage Strains K56-2 and BC7." Genome Announc. 2013;1(5). PubMed PMC DOI

Vipond J, Kane J, Hatch G, McCorrison J, Nierman WC, Losada L. "Sequence Determination of Burkholderia pseudomallei Strain NCTC 13392 Colony Morphology Variants." Genome Announc. 2013;1(6). PubMed PMC DOI

Wagner GA, Pacold ME, Vigil E, Caballero G, Morris SR, Kosakovsky Pond SL, Little SJ, Richman DD, Gianella S, Smith DM. "Using ultradeep pyrosequencing to study HIV-1 coreceptor usage in primary and dual infection." J Infect Dis. 2013;208(2):271-4. PubMed PMC DOI

Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen CA, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung WY, Chi NC, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B. "Epigenomic analysis of multilineage differentiation of human embryonic stem cells." Cell. 2013;153(5):1134-48. PubMed PMC DOI

Zhou D, Udpa N, Ronen R, Stobdan T, Liang J, Appenzeller O, Zhao HW, Yin Y, Du Y, Guo L, Cao R, Wang Y, Jin X, Huang C, Jia W, Cao D, Guo G, Gamboa JL, Villafuerte F, Callacondo D, Xue J, Liu S, Frazer KA, Li Y, Bafna V, Haddad GG. "Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders." Am J Hum Genet. 2013;93(3):452-62. PubMed PMC DOI

Akiyama T, Tominaga M, Davoodi A, Nagamine M, Blansit K, Horwitz A, Carstens MI, Carstens E. "Cross-sensitization of histamine-independent itch in mouse primary sensory neurons." Neuroscience. 2012;226:305-12. PubMed PMC DOI

Bark SJ, Wegrzyn J, Taupenot L, Ziegler M, O'Connor DT, Ma Q, Smoot M, Ideker T, Hook V. "The protein architecture of human secretory vesicles reveals differential regulation of signaling molecule secretion by protein kinases." PLoS One. 2012;7(8):e41134. PubMed PMC DOI