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19 Article(s) on File
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A comparative encyclopedia of DNA elements in the mouse genome
Yue F,
Cheng Y,
Breschi A,
Vierstra J,
Wu W,
Ryba T,
Sandstrom R,
Ma Z,
Davis C,
Pope BD,
Shen Y,
Pervouchine DD,
Djebali S,
Thurman RE,
Kaul R,
Rynes E,
Kirilusha A,
Marinov GK,
Williams BA,
Trout D,
Amrhein H,
Fisher-Aylor K,
Antoshechkin I,
DeSalvo G,
See LH,
Fastuca M,
Drenkow J,
Zaleski C,
Dobin A,
Prieto P,
Lagarde J,
Bussotti G,
Tanzer A,
Denas O,
Li K,
Bender MA,
Zhang M,
Byron R,
Groudine MT,
McCleary D,
Pham L,
Ye Z,
Kuan S,
Edsall L,
Wu YC,
Rasmussen MD,
Bansal MS,
Kellis M,
Keller CA,
Morrissey CS,
Mishra T,
Jain D,
Dogan N,
Harris RS,
Cayting P,
Kawli T,
Boyle AP,
Euskirchen G,
Kundaje A,
Lin S,
Lin Y,
Jansen C,
Malladi VS,
Cline MS,
Erickson DT,
Kirkup VM,
Learned K,
Sloan CA,
Rosenbloom KR,
Lacerda de Sousa B,
Beal K,
Pignatelli M,
Flicek P,
Lian J,
Kahveci T,
Lee D,
Kent WJ,
Ramalho Santos M,
Herrero J,
Notredame C,
Johnson A,
Vong S,
Lee K,
Bates D,
Neri F,
Diegel M,
Canfield T,
Sabo PJ,
Wilken MS,
Reh TA,
Giste E,
Shafer A,
Kutyavin T,
Haugen E,
Dunn D,
Reynolds AP,
Neph S,
Humbert R,
Hansen RS,
De Bruijn M,
Selleri L,
Rudensky A,
Josefowicz S,
Samstein R,
Eichler EE,
Orkin SH,
Levasseur D,
Papayannopoulou T,
Chang KH,
Skoultchi A,
Gosh S,
Disteche C,
Treuting P,
Wang Y,
Weiss MJ,
Blobel GA,
Cao X,
Zhong S,
Wang T,
Good PJ,
Lowdon RF,
Adams LB,
Zhou XQ,
Pazin MJ,
Feingold EA,
Wold B,
Taylor J,
Mortazavi A,
Weissman SM,
Stamatoyannopoulos JA,
Snyder MP,
Guigo R,
Gingeras TR,
Gilbert DM,
Hardison RC,
Beer MA,
Ren B

Nature
  515 (7527): 355-64; Nov 20 2014   Nlm
[Abstract]
[DOI] [Full Text]

Distinct and predictive histone lysine acetylation patterns at promoters, enhancers, and gene bodies
Rajagopal N,
Ernst J,
Ray P,
Wu J,
Zhang M,
Kellis M,
Ren B

G3 (Bethesda)
  4 (11): 2051-63; Nov 1 2014   Nlm
[Abstract]
[DOI] [Full Text]

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease
Kellis M,
Wold B,
Snyder MP,
Bernstein BE,
Kundaje A,
Marinov GK,
Ward LD,
Birney E,
Crawford GE,
Dekker J,
Dunham I,
Elnitski LL,
Farnham PJ,
Feingold EA,
Gerstein M,
Giddings MC,
Gilbert DM,
Gingeras TR,
Green ED,
Guigo R,
Hubbard T,
Kent J,
Lieb JD,
Myers RM,
Pazin MJ,
Ren B,
Stamatoyannopoulos J,
Weng Z,
White KP,
Hardison RC

Proceedings of the National Academy of Sciences of the United States of America
  111 (33): E3366-E3366; Aug 19 2014   Elsevier
[DOI] [Full Text]

Defining functional DNA elements in the human genome
Kellis M,
Wold B,
Snyder MP,
Bernstein BE,
Kundaje A,
Marinov GK,
Ward LD,
Birney E,
Crawford GE,
Dekker J,
Dunham I,
Elnitski LL,
Farnham PJ,
Feingold EA,
Gerstein M,
Giddings MC,
Gilbert DM,
Gingeras TR,
Green ED,
Guigo R,
Hubbard T,
Kent J,
Lieb JD,
Myers RM,
Pazin MJ,
Ren B,
Stamatoyannopoulos JA,
Weng ZP,
White KP,
Hardison RC

Proceedings of the National Academy of Sciences of the United States of America
  111 (17): 6131-6138; Apr 2014  
[Abstract]
[DOI] [Full Text]

An encyclopedia of mouse DNA elements (Mouse ENCODE)
Stamatoyannopoulos JA,
Snyder M,
Hardison R,
Ren B,
Gingeras T,
Gilbert DM,
Groudine M,
Bender M,
Kaul R,
Canfield T,
Giste E,
Johnson A,
Zhang M,
Balasundaram G,
Byron R,
Roach V,
Sabo PJ,
Sandstrom R,
Stehling AS,
Thurman RE,
Weissman SM,
Cayting P,
Hariharan M,
Lian J,
Cheng Y,
Landt SG,
Ma ZH,
Wold BJ,
Dekker J,
Crawford GE,
Keller CA,
Wu WS,
Morrissey C,
Kumar SA,
Mishra T,
Jain D,
Byrska-Bishop M,
Blankenberg D,
Lajoie BR,
Jain G,
Sanyal A,
Chen KB,
Denas O,
Taylor J,
Blobel GA,
Weiss MJ,
Pimkin M,
Deng WL,
Marinov GK,
Williams BA,
Fisher-Aylor KI,
Desalvo G,
Kiralusha A,
Trout D,
Amrhein H,
Mortazavi A,
Edsall L,
McCleary D,
Kuan S,
Shen Y,
Yue F,
Ye Z,
Davis CA,
Zaleski C,
Jha S,
Xue CH,
Dobin A,
Lin W,
Fastuca M,
Wang HI,
Guigo R,
Djebali S,
Lagarde J,
Ryba T,
Sasaki T,
Malladi VS,
Cline MS,
Kirkup VM,
Learned K,
Rosenbloom KR,
Kent WJ,
Feingold EA,
Good PJ,
Pazin M,
Lowdon RF,
Adams LB,
Mouse EC

Genome Biology
  13 (8): Aug 13 2012  
[Abstract]
[DOI] [Full Text]

Comparative functional genomics of the fission yeasts
Rhind N,
Chen Z,
Yassour M,
Thompson DA,
Haas BJ,
Habib N,
Wapinski I,
Roy S,
Lin MF,
Heiman DI,
Young SK,
Furuya K,
Guo Y,
Pidoux A,
Chen HM,
Robbertse B,
Goldberg JM,
Aoki K,
Bayne EH,
Berlin AM,
Desjardins CA,
Dobbs E,
Dukaj L,
Fan L,
FitzGerald MG,
French C,
Gujja S,
Hansen K,
Keifenheim D,
Levin JZ,
Mosher RA,
Muller CA,
Pfiffner J,
Priest M,
Russ C,
Smialowska A,
Swoboda P,
Sykes SM,
Vaughn M,
Vengrova S,
Yoder R,
Zeng Q,
Allshire R,
Baulcombe D,
Birren BW,
Brown W,
Ekwall K,
Kellis M,
Leatherwood J,
Levin H,
Margalit H,
Martienssen R,
Nieduszynski CA,
Spatafora JW,
Friedman N,
Dalgaard JZ,
Baumann P,
Niki H,
Regev A,
Nusbaum C

Science
  332 (6032): 930-6; May 20 2011  
[Abstract]
[DOI] [Full Text]

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
Roy S,
Ernst J,
Kharchenko PV,
Kheradpour P,
Negre N,
Eaton ML,
Landolin JM,
Bristow CA,
Ma LJ,
Lin MF,
Washietl S,
Arshinoff BI,
Ay F,
Meyer PE,
Robine N,
Washington NL,
Di Stefano L,
Berezikov E,
Brown CD,
Candeias R,
Carlson JW,
Carr A,
Jungreis I,
Marbach D,
Sealfon R,
Tolstorukov MY,
Will S,
Alekseyenko AA,
Artieri C,
Booth BW,
Brooks AN,
Dai Q,
Davis CA,
Duff MO,
Feng X,
Gorchakov AA,
Gu TT,
Henikoff JG,
Kapranov P,
Li RH,
MacAlpine HK,
Malone J,
Minoda A,
Nordman J,
Okamura K,
Perry M,
Powell SK,
Riddle NC,
Sakai A,
Samsonova A,
Sandler JE,
Schwartz YB,
Sher N,
Spokony R,
Sturgill D,
van Baren M,
Wan KH,
Yang L,
Yu C,
Feingold E,
Good P,
Guyer M,
Lowdon R,
Ahmad K,
Andrews J,
Berger B,
Brenner SE,
Brent MR,
Cherbas L,
Elgin SC,
Gingeras TR,
Grossman R,
Hoskins RA,
Kaufman TC,
Kent W,
Kuroda MI,
Orr-Weaver T,
Perrimon N,
Pirrotta V,
Posakony JW,
Ren B,
Russell S,
Cherbas P,
Graveley BR,
Lewis S,
Micklem G,
Oliver B,
Park PJ,
Celniker SE,
Henikoff S,
Karpen GH,
Lai EC,
MacAlpine DM,
Stein LD,
White KP,
Kellis M

Science
  330 (6012): 1787-1797; Dec 2010   PMC3192495
[Abstract]
[DOI] [Full Text] [PDF]

p16INK4a-mediated suppression of telomerase in normal and malignant human breast cells
Bazarov AV,
van Sluis M,
Hines WC,
Bassett E,
Beliveau A,
Campeau E,
Mukhopadhyay R,
Lee WJ,
Melodyev S,
Zaslavsky Y,
Lee L,
Rodier F,
Chicas A,
Lowe SW,
Benhattar J,
Ren B,
Campisi J,
Yaswen P

Aging Cell
  9 (5): 736-746; Oct 2010   PMC2941554
[Abstract]
[DOI] [Full Text]

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
Harris RA,
Wang T,
Coarfa C,
Nagarajan RP,
Hong C,
Downey SL,
Johnson BE,
Fouse SD,
Delaney A,
Zhao Y,
Olshen A,
Ballinger T,
Zhou X,
Forsberg KJ,
Gu J,
Echipare L,
OGeen H,
Lister R,
Pelizzola M,
Xi Y,
Epstein CB,
Bernstein BE,
Hawkins RD,
Ren B,
Chung WY,
Gu H,
Bock C,
Gnirke A,
Zhang MQ,
Haussler D,
Ecker JR,
Li W,
Farnham PJ,
Waterland RA,
Meissner A,
Marra MA,
Hirst M,
Milosavljevic A,
Costello JF

Nature Biotechnology
  28 (10): 1097-1105; 2010   PMCID: PMC2955169
[Abstract]
[DOI] [Full Text] [PDF]

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
Johnson DS,
Li W,
Gordon DB,
Bhattacharjee A,
Curry B,
Ghosh J,
Brizuela L,
Carroll JS,
Brown M,
Flicek P,
Koch CM,
Dunham I,
Bieda M,
Xu X,
Farnham PJ,
Kapranov P,
Nix DA,
Gingeras TR,
Zhang X,
Holster H,
Jiang N,
Green RD,
Song JS,
McCuine SA,
Anton E,
Nguyen L,
Trinklein ND,
Ye Z,
Ching K,
Hawkins D,
Ren B,
Scacheri PC,
Rozowsky J,
Karpikov A,
Euskirchen G,
Weissman S,
Gerstein M,
Snyder M,
Yang A,
Moqtaderi Z,
Hirsch H,
Shulha HP,
Fu Y,
Weng Z,
Struhl K,
Myers RM,
Lieb JD,
Liu XS

Genome Research
  18 (3): 393-403; 2008  
[Abstract]
[DOI] [Full Text]

Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs
Barrera LO,
Li Z,
Smith AD,
Arden KC,
Cavenee WK,
Zhang MQ,
Green RD,
Ren B

Genome Res
  18 (1): 46-59; Jan 2008   PMCID: PMC2134779
[Abstract]
[DOI] [Full Text] [PDF]

Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome
Kim TH,
Abdullaev ZK,
Smith AD,
Ching KA,
Loukinov DI,
Green RD,
Zhang MQ,
Lobanenkov VV,
Ren B

Cell
  128 (6): 1231-1245; Mar 2007  
[Abstract]
[DOI] [Full Text] [PDF]

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Birney E,
Stamatoyannopoulos JA,
Dutta A,
Guigó R,
Gingeras TR,
Margulies EH,
Weng Z,
Snyder M,
Dermitzakis ET,
Thurman RE,
Kuehn MS,
Taylor CM,
Neph S,
Koch CM,
Asthana S,
Malhotra A,
Adzhubei I,
Greenbaum JA,
Andrews RM,
Flicek P,
Boyle PJ,
Cao H,
Carter NP,
Clelland GK,
Davis S,
Day N,
Dhami P,
Dillon SC,
Dorschner MO,
Fiegler H,
Giresi PG,
Goldy J,
Hawrylycz M,
Haydock A,
Humbert R,
James KD,
Johnson BE,
Johnson EM,
Frum TT,
Rosenzweig ER,
Karnani N,
Lee K,
Lefebvre GC,
Navas PA,
Neri F,
Parker SC,
Sabo PJ,
Sandstrom R,
Shafer A,
Vetrie D,
Weaver M,
Wilcox S,
Yu M,
Collins FS,
Dekker J,
Lieb JD,
Tullius TD,
Crawford GE,
Sunyaev S,
Noble WS,
Dunham I,
Denoeud F,
Reymond A,
Kapranov P,
Rozowsky J,
Zheng D,
Castelo R,
Frankish A,
Harrow J,
Ghosh S,
Sandelin A,
Hofacker IL,
Baertsch R,
Keefe D,
Dike S,
Cheng J,
Hirsch HA,
Sekinger EA,
Lagarde J,
Abril JF,
Shahab A,
Flamm C,
Fried C,
Hackermüller J,
Hertel J,
Lindemeyer M,
Missal K,
Tanzer A,
Washietl S,
Korbel J,
Emanuelsson O,
Pedersen JS,
Holroyd N,
Taylor R,
Swarbreck D,
Matthews N,
Dickson MC,
Thomas DJ,
Weirauch MT,
Gilbert J,
Drenkow J,
Bell I,
Zhao X,
Srinivasan KG,
Sung WK,
Ooi HS,
Chiu KP,
Foissac S,
Alioto T,
Brent M,
Pachter L,
Tress ML,
Valencia A,
Choo SW,
Choo CY,
Ucla C,
Manzano C,
Wyss C,
Cheung E,
Clark TG,
Brown JB,
Ganesh M,
Patel S,
Tammana H,
Chrast J,
Henrichsen CN,
Kai C,
Kawai J,
Nagalakshmi U,
Wu J,
Lian Z,
Lian J,
Newburger P,
Zhang X,
Bickel P,
Mattick JS,
Carninci P,
Hayashizaki Y,
Weissman S,
Hubbard T,
Myers RM,
Rogers J,
Stadler PF,
Lowe TM,
Wei CL,
Ruan Y,
Struhl K,
Gerstein M,
Antonarakis SE,
Fu Y,
Green ED,
Karaöz U,
Siepel A,
Taylor J,
Liefer LA,
Wetterstrand KA,
Good PJ,
Feingold EA,
Guyer MS,
Cooper GM,
Asimenos G,
Dewey CN,
Hou M,
Nikolaev S,
Montoya-Burgos JI,
Löytynoja A,
Whelan S,
Pardi F,
Massingham T,
Huang H,
Zhang NR,
Holmes I,
Mullikin JC,
Ureta-Vidal A,
Paten B,
Seringhaus M,
Church D,
Rosenbloom K,
Kent WJ,
Stone EA,
Batzoglou S,
Goldman N,
Hardison RC,
Haussler D,
Miller W,
Sidow A,
Trinklein ND,
Zhang ZD,
Barrera L,
Stuart R,
King DC,
Ameur A,
Enroth S,
Bieda MC,
Kim J,
Bhinge AA,
Jiang N,
Liu J,
Yao F,
Vega VB,
Lee CW,
Ng P,
Yang A,
Moqtaderi Z,
Zhu Z,
Xu X,
Squazzo S,
Oberley MJ,
Inman D,
Singer MA,
Richmond TA,
Munn KJ,
Rada-Iglesias A,
Wallerman O,
Komorowski J,
Fowler JC,
Couttet P,
Bruce AW,
Dovey OM,
Ellis PD,
Langford CF,
Nix DA,
Euskirchen G,
Hartman S,
Urban AE,
Kraus P,
Van Calcar S,
Heintzman N,
Hoon Kim T,
Wang K,
Qu C,
Hon G,
Luna R,
Glass CK,
Rosenfeld MG,
Aldred SF,
Cooper SJ,
Halees A,
Lin JM,
Shulha HP,
Xu M,
Haidar JN,
Yu Y,
Iyer VR,
Green RD,
Wadelius C,
Farnham PJ,
Ren B,
Harte RA,
Hinrichs AS,
Trumbower H,
Clawson H,
Hillman-Jackson J,
Zweig AS,
Smith K,
Thakkapallayil A,
Barber G,
Kuhn RM,
Karolchik D,
Armengol L,
Bird CP,
De Bakker PI,
Kern AD,
Lopez-Bigas N,
Martin JD,
Stranger BE,
Woodroffe A,
Davydov E,
Dimas A,
Eyras E,
Hallgrímsdóttir IB,
Huppert J,
Zody MC,
Abecasis GR,
Estivill X,
Bouffard GG,
Guan X,
Hansen NF,
Idol JR,
Maduro VV,
Maskeri B,
McDowell JC,
Park M,
Thomas PJ,
Young AC,
Blakesley RW,
Muzny DM,
Sodergren E,
Wheeler DA,
Worley KC,
Jiang H,
Weinstock GM,
Gibbs RA,
Graves T,
Fulton R,
Mardis ER,
Wilson RK,
Clamp M,
Cuff J,
Gnerre S,
Jaffe DB,
Chang JL,
Lindblad-Toh K,
Lander ES,
Koriabine M,
Nefedov M,
Osoegawa K,
Yoshinaga Y,
Zhu B,
De Jong PJ

Nature
  447 (7146): 799-816; 2007  
[Abstract]
[DOI] [Full Text]

The ENCODE (ENCyclopedia of DNA Elements) Project
Feingold EA,
Good PJ,
Guyer MS,
Kamholz S,
Liefer L,
Wetterstrand K,
Collins FS,
Gingeras TR,
Kampa D,
Sekinger EA,
Cheng J,
Hirsch H,
Ghosh S,
Zhu Z,
Patel S,
Piccolboni A,
Yang A,
Tammana H,
Bekiranov S,
Kapranov P,
Harrison R,
Church G,
Struhl K,
Ren B,
Kim TH,
Barrera LO,
Qu C,
van Calcar S,
Luna R,
Glass CK,
Rosenfeld MG,
Guigo R,
Antonarakis SE,
Birney E,
Brent M,
Pachter L,
Reymond A,
Dermitzakis ET,
Dewey C,
Keefe D,
Denoeud F,
Lagarde J,
Ashurst J,
Hubbard T,
Wesselink JJ,
Castelo R,
Eyras E,
Myers RM,
Sidow A,
Batzoglou S,
Trinklein ND,
Hartman SJ,
Aldred SF,
Anton E,
Schroeder DI,
Marticke SS,
Nguyen L,
Schmutz J,
Grimwood J,
Dickson M,
Cooper GM,
Stone EA,
Asimenos G,
Brudno M,
Dutta A,
Karnani N,
Taylor CM,
Kim HK,
Robins G,
Stamatoyannopoulos G,
Stamatoyannopoulos JA,
Dorschner M,
Sabo P,
Hawrylycz M,
Humbert R,
Wallace J,
Yu M,
Navas PA,
McArthur M,
Noble WS,
Dunham I,
Koch CM,
Andrews RM,
Clelland GK,
Wilcox S,
Fowler JC,
James KD,
Groth P,
Dovey OM,
Ellis PD,
Wraight VL,
Mungall AJ,
Dhami P,
Fiegler H,
Langford CF,
Carter NP,
Vetrie D,
Snyder M,
Euskirchen G,
Urban AE,
Nagalakshmi U,
Rinn J,
Popescu G,
Bertone P,
Hartman S,
Rozowsky J,
Emanuelsson O,
Royce T,
Chung S,
Gerstein M,
Lian Z,
Lian J,
Nakayama Y,
Weissman S,
Stolc V,
Tongprasit W,
Sethi H,
Jones S,
Marra M,
Shin H,
Schein J,
Clamp M,
Lindblad-Toh K,
Chang J,
Jaffe DB,
Kamal M,
Lander ES,
Mikkelsen TS,
Vinson J,
Zody MC,
de Jong PJ,
Osoegawa K,
Nefedov M,
Zhu B,
Baxevanis AD,
Wolfsberg TG,
Crawford GE,
Whittle J,
Holt IE,
Vasicek TJ,
Zhou D,
Luo S,
Green ED,
Bouffard GG,
Margulies EH,
Portnoy ME,
Hansen NF,
Thomas PJ,
McDowell JC,
Maskeri B,
Young AC,
Idol JR,
Blakesley RW,
Schuler G,
Miller W,
Hardison R,
Elnitski L,
Shah P,
Salzberg SL,
Pertea M,
Majoros WH,
Haussler D,
Thomas D,
Rosenbloom KR,
Clawson H,
Siepel A,
Kent WJ,
Weng Z,
Jin S,
Halees A,
Burden H,
Karaoz U,
Fu Y,
Yu Y,
Ding C,
Cantor CR,
Kingston RE,
Dennis J,
Green RD,
Singer MA,
Richmond TA,
Norton JE,
Farnham PJ,
Oberley MJ,
Inman DR,
McCormick MR,
Kim H,
Middle CL,
Pirrung MC,
Fu XD,
Kwon YS,
Ye Z,
Dekker J,
Tabuchi TM,
Gheldof N,
Dostie J,
Harvey SC

Science
  306 (5696): 636-640; 2004  
[Abstract]
[DOI] [Full Text]

The International HapMap Project
Gibbs RA,
Belmont JW,
Hardenbol P,
Willis TD,
Yu FL,
Yang HM,
Chang LY,
Huang W,
Liu B,
Shen Y,
Tam PK,
Tsui LC,
Waye MM,
Wong JT,
Zeng CQ,
Zhang QR,
Chee MS,
Galver LM,
Kruglyak S,
Murray SS,
Oliphant AR,
Montpetit A,
Hudson TJ,
Chagnon F,
Ferretti V,
Leboeuf M,
Phillips MS,
Verner A,
Kwok PY,
Duan SH,
Lind DL,
Miller RD,
Rice JP,
Saccone NL,
Taillon-Miller P,
Xiao M,
Nakamura Y,
Sekine A,
Sorimachi K,
Tanaka T,
Tanaka Y,
Tsunoda T,
Yoshino E,
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