Student Publications

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

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