Publications

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Students, please keep the Graduate Program Coordinator appraised of your new publications and any inaccuracies or omissions on this list. Most articles are indexed in PubMed; please provide the PubMed ID numbers (PMID) for your articles if available, to expedite the maintenance of this list. Please remember to acknowledge your grants in your papers, including the training grant if you were a recipient; see here for sample wording.

2011

Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D, Briem E, Zhang K, Irizarry RA, Feinberg AP. "Increased methylation variation in epigenetic domains across cancer types." Nat Genet. 2011;43(8):768-75. PubMed PMC DOI
Hawkins RD, Hon GC, Yang C, Antosiewicz-Bourget JE, Lee LK, Ngo QM, Klugman S, Ching KA, Edsall LE, Ye Z, Kuan S, Yu P, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Ren B. "Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency." Cell Res. 2011;21(10):1393-409. PubMed PMC DOI
Johnson DB, Xu J, Shen Z, Takimoto JK, Schultz MD, Schmitz RJ, Xiang Z, Ecker JR, Briggs SP, Wang L. "RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites." Nat Chem Biol. 2011;7(11):779-86. PubMed PMC DOI
Laurent LC, Ulitsky I, Slavin I, Tran H, Schork A, Morey R, Lynch C, Harness JV, Lee S, Barrero MJ, Ku S, Martynova M, Semechkin R, Galat V, Gottesfeld J, Izpisua Belmonte JC, Murry C, Keirstead HS, Park HS, Schmidt U, Laslett AL, Muller FJ, Nievergelt CM, Shamir R, Loring JF. "Dynamic changes in the copy number of pluripotency and cell proliferation genes in human ESCs and iPSCs during reprogramming and time in culture." Cell Stem Cell. 2011;8(1):106-18. PubMed PMC DOI
Liu GH, Barkho BZ, Ruiz S, Diep D, Qu J, Yang SL, Panopoulos AD, Suzuki K, Kurian L, Walsh C, Thompson J, Boue S, Fung HL, Sancho-Martinez I, Zhang K, Yates J 3rd, Izpisua Belmonte JC. "Recapitulation of premature ageing with iPSCs from Hutchinson-Gilford progeria syndrome." Nature. 2011;472(7342):221-5. PubMed PMC DOI
Narayanan T, Gersten M, Subramaniam S, Grama A. "Modularity detection in protein-protein interaction networks." BMC Res Notes. 2011;4:569. PubMed PMC DOI
Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist AM, Palsson BØ. "A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011." Mol Syst Biol. 2011;7:535. PubMed PMC DOI
Polymenidou M, Lagier-Tourenne C, Hutt KR, Huelga SC, Moran J, Liang TY, Ling SC, Sun E, Wancewicz E, Mazur C, Kordasiewicz H, Sedaghat Y, Donohue JP, Shiue L, Bennett CF, Yeo GW, Cleveland DW. "Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43." Nat Neurosci. 2011;14(4):459-68. PubMed PMC DOI
Prindle A, Samayoa P, Razinkov I, Danino T, Tsimring LS, Hasty J. "A sensing array of radically coupled genetic 'biopixels'." Nature. 2011;481(7379):39-44. PubMed PMC DOI
Schmitz RJ, Schultz MD, Lewsey MG, O'Malley RC, Urich MA, Libiger O, Schork NJ, Ecker JR. "Transgenerational epigenetic instability is a source of novel methylation variants." Science. 2011;334(6054):369-73. PubMed PMC DOI
Tan M, Luo H, Lee S, Jin F, Yang JS, Montellier E, Buchou T, Cheng Z, Rousseaux S, Rajagopal N, Lu Z, Ye Z, Zhu Q, Wysocka J, Ye Y, Khochbin S, Ren B, Zhao Y. "Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification." Cell. 2011;146(6):1016-28. PubMed PMC DOI
Udpa N, Zhou D, Haddad GG, Bafna V. "Tests of selection in pooled case-control data: an empirical study." Front Genet. 2011;2:83. PubMed PMC DOI
Xu X, Nagarajan H, Lewis NE, Pan S, Cai Z, Liu X, Chen W, Xie M, Wang W, Hammond S, Andersen MR, Neff N, Passarelli B, Koh W, Fan HC, Wang J, Gui Y, Lee KH, Betenbaugh MJ, Quake SR, Famili I, Palsson BO, Wang J. "The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line." Nat Biotechnol. 2011;29(8):735-41. PubMed PMC DOI
Young ND, Debellé F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H, Van de Peer Y, Proost S, Cook DR, Meyers BC, Spannagl M, Cheung F, De Mita S, Krishnakumar V, Gundlach H, Zhou S, Mudge J, Bharti AK, Murray JD, Naoumkina MA, Rosen B, Silverstein KA, Tang H, Rombauts S, Zhao PX, Zhou P, Barbe V, Bardou P, Bechner M, Bellec A, Berger A, Bergès H, Bidwell S, Bisseling T, Choisne N, Couloux A, Denny R, Deshpande S, Dai X, Doyle JJ, Dudez AM, Farmer AD, Fouteau S, Franken C, Gibelin C, Gish J, Goldstein S, González AJ, Green PJ, Hallab A, Hartog M, Hua A, Humphray SJ, Jeong DH, Jing Y, Jöcker A, Kenton SM, Kim DJ, Klee K, Lai H, Lang C, Lin S, Macmil SL, Magdelenat G, Matthews L, McCorrison J, Monaghan EL, Mun JH, Najar FZ, Nicholson C, Noirot C, O'Bleness M, Paule CR, Poulain J, Prion F, Qin B, Qu C, Retzel EF, Riddle C, Sallet E, Samain S, Samson N, Sanders I, Saurat O, Scarpelli C, Schiex T, Segurens B, Severin AJ, Sherrier DJ, Shi R, Sims S, Singer SR, Sinharoy S, Sterck L, Viollet A, Wang BB, Wang K, Wang M, Wang X, Warfsmann J, Weissenbach J, White DD, White JD, Wiley GB, Wincker P, Xing Y, Yang L, Yao Z, Ying F, Zhai J, Zhou L, Zuber A, Dénarié J, Dixon RA, May GD, Schwartz DC, Rogers J, Quétier F, Town CD, Roe BA. "The Medicago genome provides insight into the evolution of rhizobial symbioses." Nature. 2011;480(7378):520-4. PubMed PMC DOI
Zhou D, Udpa N, Gersten M, Visk DW, Bashir A, Xue J, Frazer KA, Posakony JW, Subramaniam S, Bafna V, Haddad GG. "Experimental selection of hypoxia-tolerant Drosophila melanogaster." Proc Natl Acad Sci U S A. 2011;108(6):2349-54. PubMed PMC DOI

2010

Brinza D, Schultz M, Tesler G, Bafna V. "RAPID detection of gene-gene interactions in genome-wide association studies." Bioinformatics. 2010;26(22):2856-62. PubMed PMC DOI
Chang RL, Luo F, Johnson S, Scheuermann RH. "Deterministic graph-theoretic algorithm for detecting modules in biological interaction networks." Int J Bioinform Res Appl. 2010;6(2):101-19. PubMed DOI
Chang RL, Xie L, Xie L, Bourne PE, Palsson BØ. "Drug off-target effects predicted using structural analysis in the context of a metabolic network model." PLoS Comput Biol. 2010;6(9):e1000938. PubMed PMC DOI
Cohen T, Whitfield GK, Schvaneveldt RW, Mukund K, Rindflesch T. "EpiphaNet: An Interactive Tool to Support Biomedical Discoveries." J Biomed Discov Collab. 2010;5:21-49. PubMed PMC
Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P, Nazarenko I, Nilsen GB, Yeung G, Dahl F, Fernandez A, Staker B, Pant KP, Baccash J, Borcherding AP, Brownley A, Cedeno R, Chen L, Chernikoff D, Cheung A, Chirita R, Curson B, Ebert JC, Hacker CR, Hartlage R, Hauser B, Huang S, Jiang Y, Karpinchyk V, Koenig M, Kong C, Landers T, Le C, Liu J, McBride CE, Morenzoni M, Morey RE, Mutch K, Perazich H, Perry K, Peters BA, Peterson J, Pethiyagoda CL, Pothuraju K, Richter C, Rosenbaum AM, Roy S, Shafto J, Sharanhovich U, Shannon KW, Sheppy CG, Sun M, Thakuria JV, Tran A, Vu D, Zaranek AW, Wu X, Drmanac S, Oliphant AR, Banyai WC, Martin B, Ballinger DG, Church GM, Reid CA. "Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays." Science. 2010;327(5961):78-81. PubMed DOI
Feist AM, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, Palsson BØ. "Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli." Metab Eng. 2010;12(3):173-86. PubMed PMC DOI
Gay SC, Shah MB, Talakad JC, Maekawa K, Roberts AG, Wilderman PR, Sun L, Yang JY, Huelga SC, Hong WX, Zhang Q, Stout CD, Halpert JR. "Crystal structure of a cytochrome P450 2B6 genetic variant in complex with the inhibitor 4-(4-chlorophenyl)imidazole at 2.0-A resolution." Mol Pharmacol. 2010;77(4):529-38. PubMed PMC DOI
Grubisic I, Shokhirev MN, Orzechowski M, Miyashita O, Tama F. "Biased coarse-grained molecular dynamics simulation approach for flexible fitting of X-ray structure into cryo electron microscopy maps." J Struct Biol. 2010;169(1):95-105. PubMed DOI
Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S, Antosiewicz-Bourget J, Ye Z, Espinoza C, Agarwahl S, Shen L, Ruotti V, Wang W, Stewart R, Thomson JA, Ecker JR, Ren B. "Distinct epigenomic landscapes of pluripotent and lineage-committed human cells." Cell Stem Cell. 2010;6(5):479-91. PubMed PMC DOI
Hughey JJ, Lee TK, Covert MW. "Computational modeling of mammalian signaling networks." Wiley Interdiscip Rev Syst Biol Med. 2010;2(2):194-209. PubMed PMC DOI

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