Student Publications

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

Baycin-Hizal D, Tabb DL, Chaerkady R, Chen L, Lewis NE, Nagarajan H, Sarkaria V, Kumar A, Wolozny D, Colao J, Jacobson E, Tian Y, O'Meally RN, Krag SS, Cole RN, Palsson BO, Zhang H, Betenbaugh M. "Proteomic analysis of Chinese hamster ovary cells." J Proteome Res. 2012;11(11):5265-76. PubMed PMC DOI

Bean GJ, Ideker T. "Differential analysis of high-throughput quantitative genetic interaction data." Genome Biol. 2012;13(12):R123. PubMed PMC DOI

Bernard A, Lubbers LS, Tanis KQ, Luo R, Podtelezhnikov AA, Finney EM, McWhorter MM, Serikawa K, Lemon T, Morgan R, Copeland C, Smith K, Cullen V, Davis-Turak J, Lee CK, Sunkin SM, Loboda AP, Levine DM, Stone DJ, Hawrylycz MJ, Roberts CJ, Jones AR, Geschwind DH, Lein ES. "Transcriptional architecture of the primate neocortex." Neuron. 2012;73(6):1083-99. PubMed PMC DOI

Bliven S, Prlić A. "Circular permutation in proteins." PLoS Comput Biol. 2012;8(3):e1002445. PubMed PMC DOI

Chaisson MJ, Tesler G. "Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory." BMC Bioinformatics. 2012;13:238. PubMed PMC DOI

Chan JE, Kolodner RD. "Rapid analysis of Saccharomyces cerevisiae genome rearrangements by multiplex ligation-dependent probe amplification." PLoS Genet. 2012;8(3):e1002539. PubMed PMC DOI

Charusanti P, Fong NL, Nagarajan H, Pereira AR, Li HJ, Abate EA, Su Y, Gerwick WH, Palsson BO. "Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction." PLoS One. 2012;7(3):e33727. PubMed PMC DOI

Diep D, Plongthongkum N, Gore A, Fung HL, Shoemaker R, Zhang K. "Library-free methylation sequencing with bisulfite padlock probes." Nat Methods. 2012;9(3):270-2. PubMed PMC DOI

Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. "Topological domains in mammalian genomes identified by analysis of chromatin interactions." Nature. 2012;485(7398):376-80. PubMed PMC DOI

Dixon-Salazar TJ, Silhavy JL, Udpa N, Schroth J, Bielas S, Schaffer AE, Olvera J, Bafna V, Zaki MS, Abdel-Salam GH, Mansour LA, Selim L, Abdel-Hadi S, Marzouki N, Ben-Omran T, Al-Saana NA, Sonmez FM, Celep F, Azam M, Hill KJ, Collazo A, Fenstermaker AG, Novarino G, Akizu N, Garimella KV, Sougnez C, Russ C, Gabriel SB, Gleeson JG. "Exome sequencing can improve diagnosis and alter patient management." Sci Transl Med. 2012;4(138):138ra78. PubMed PMC DOI

Gendron JM, Pruneda-Paz JL, Doherty CJ, Gross AM, Kang SE, Kay SA. "Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor." Proc Natl Acad Sci U S A. 2012;109(8):3167-72. PubMed PMC DOI

He Y, Zhang Y, Zheng G, Wei C. "CTF: a CRF-based transcription factor binding sites finding system." BMC Genomics. 2012;13 Suppl 8:S18. PubMed PMC DOI