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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 integrated encyclopedia of DNA elements in the human genome
Dunham I,
Kundaje A,
Aldred SF,
Collins PJ,
Davis C,
Doyle F,
Epstein CB,
Frietze S,
Harrow J,
Kaul R,
Khatun J,
Lajoie BR,
Landt SG,
Lee BK,
Pauli F,
Rosenbloom KR,
Sabo P,
Safi A,
Sanyal A,
Shoresh N,
Simon JM,
Song L,
Trinklein ND,
Altshuler RC,
Birney E,
Brown JB,
Cheng C,
Djebali S,
Dong XJ,
Ernst J,
Furey TS,
Gerstein M,
Giardine B,
Greven M,
Hardison RC,
Harris RS,
Herrero J,
Hoffman MM,
Iyer S,
Kellis M,
Kheradpour P,
Lassmann T,
Li QH,
Lin X,
Marinov GK,
Merkel A,
Mortazavi A,
Parker SC,
Reddy TE,
Rozowsky J,
Schlesinger F,
Thurman RE,
Wang J,
Ward LD,
Whitfield TW,
Wilder SP,
Wu W,
Xi HL,
Yip KY,
Zhuang JL,
Bernstein BE,
Green ED,
Gunter C,
Snyder M,
Pazin MJ,
Lowdon RF,
Dillon LA,
Adams LB,
Kelly CJ,
Zhang J,
Wexler JR,
Good PJ,
Feingold EA,
Crawford GE,
Dekker J,
Elnitski L,
Farnham PJ,
Giddings MC,
Gingeras TR,
Guigo R,
Hubbard TJ,
Kent WJ,
Lieb JD,
Margulies EH,
Myers RM,
Stamatoyannopoulos JA,
Tenenbaum SA,
Weng ZP,
White KP,
Wold B,
Yu Y,
Wrobel J,
Risk BA,
Gunawardena HP,
Kuiper HC,
Maier CW,
Xie L,
Chen X,
Mikkelsen TS,
Gillespie S,
Goren A,
Ram O,
Zhang XL,
Wang L,
Issner R,
Coyne MJ,
Durham T,
Ku M,
Truong T,
Eaton ML,
Davis CA,
Dobin A,
Tanzer A,
Lagarde J,
Lin W,
Xue CH,
Williams BA,
Zaleski C,
Roeder M,
Kokocinski F,
Abdelhamid RF,
Alioto T,
Antoshechkin I,
Baer MT,
Batut P,
Bell I,
Bell K,
Chakrabortty S,
Chrast J,
Curado J,
Derrien T,
Drenkow J,
Dumais E,
Dumais J,
Duttagupta R,
Fastuca M,
Fejes-Toth K,
Ferreira P,
Foissac S,
Fullwood MJ,
Gao H,
Gonzalez D,
Gordon A,
Howald C,
Jha S,
Johnson R,
Kapranov P,
King B,
Kingswood C,
Li GL,
Luo OJ,
Park E,
Preall JB,
Presaud K,
Ribeca P,
Robyr D,
Ruan XA,
Sammeth M,
Sandhu KS,
Schaeffer L,
See LH,
Shahab A,
Skancke J,
Suzuki AM,
Takahashi H,
Tilgner H,
Trout D,
Walters N,
Wang HE,
Yu YB,
Hayashizaki Y,
Reymond A,
Antonarakis SE,
Hannon GJ,
Ruan YJ,
Carninci P,
Sloan CA,
Learned K,
Malladi VS,
Wong MC,
Barber G,
Cline MS,
Dreszer TR,
Heitner SG,
Karolchik D,
Kirkup VM,
Meyer LR,
Long JC,
Maddren M,
Raney BJ,
Song LY,
Grasfeder LL,
Giresi PG,
Battenhouse A,
Sheffield NC,
Showers KA,
London D,
Bhinge AA,
Shestak C,
Schaner MR,
Kim SK,
Zhang ZZ,
Mieczkowski PA,
Mieczkowska JO,
Liu Z,
McDaniell RM,
Ni YY,
Rashid NU,
Kim MJ,
Adar S,
Zhang ZC,
Wang TY,
Winter D,
Keefe D,
Iyer VR,
Zheng MZ,
Wang P,
Gertz J,
Vielmetter J,
Partridge EC,
Varley KE,
Gasper C,
Bansal A,
Pepke S,
Jain P,
Amrhein H,
Bowling KM,
Anaya M,
Cross MK,
Muratet MA,
Newberry KM,
McCue K,
Nesmith AS,
Fisher-Aylor KI,
Pusey B,
DeSalvo G,
Parker SL,
Balasubramanian S,
Davis NS,
Meadows SK,
Eggleston T,
Newberry JS,
Levy SE,
Absher DM,
Wong WH,
Blow MJ,
Visel A,
Pennachio LA,
Petrykowska HM,
Abyzov A,
Aken B,
Barrell D,
Barson G,
Berry A,
Bignell A,
Boychenko V,
Bussotti G,
Davidson C,
Despacio-Reyes G,
Diekhans M,
Ezkurdia I,
Frankish A,
Gilbert J,
Gonzalez JM,
Griffiths E,
Harte R,
Hendrix DA,
Hunt T,
Jungreis I,
Kay M,
Khurana E,
Leng J,
Lin MF,
Loveland J,
Lu Z,
Manthravadi D,
Mariotti M,
Mudge J,
Mukherjee G,
Notredame C,
Pei BK,
Rodriguez JM,
Saunders G,
Sboner A,
Searle S,
Sisu C,
Snow C,
Steward C,
Tapanari E,
Tress ML,
van Baren MJ,
Washietl S,
Wilming L,
Zadissa A,
Zhang ZD,
Brent M,
Haussler D,
Valencia A,
Addleman N,
Alexander RP,
Auerbach RK,
Bettinger K,
Bhardwaj N,
Boyle AP,
Cao AR,
Cayting P,
Charos A,
Cheng Y,
Eastman C,
Euskirchen G,
Fleming JD,
Grubert F,
Habegger L,
Hariharan M,
Harmanci A,
Iyengar S,
Jin VX,
Karczewski KJ,
Kasowski M,
Lacroute P,
Lam H,
Lamarre-Vincent N,
Lian J,
Lindahl-Allen M,
Min RQ,
Miotto B,
Monahan H,
Moqtaderi Z,
Mu XM,
OGeen H,
Ouyang ZQ,
Patacsil D,
Raha D,
Ramirez L,
Reed B,
Shi MY,
Slifer T,
Witt H,
Wu LF,
Xu XQ,
Yan KK,
Yang XQ,
Struhl K,
Weissman SM,
Penalva LO,
Karmakar S,
Bhanvadia RR,
Choudhury A,
Domanus M,
Ma LJ,
Moran J,
Victorsen A,
Auer T,
Centanin L,
Eichenlaub M,
Gruhl F,
Heermann S,
Hoeckendorf B,
Inoue D,
Kellner T,
Kirchmaier S,
Mueller C,
Reinhardt R,
Schertel L,
Schneider S,
Sinn R,
Wittbrodt B,
Wittbrodt J,
Jain G,
Balasundaram G,
Bates DL,
Byron R,
Canfield TK,
Diegel MJ,
Dunn D,
Ebersol AK,
Frum T,
Garg K,
Gist E,
Hansen RS,
Boatman L,
Haugen E,
Humbert R,
Johnson AK,
Johnson EM,
Kutyavin TV,
Lee K,
Lotakis D,
Maurano MT,
Neph SJ,
Neri FV,
Nguyen ED,
Qu HZ,
Reynolds AP,
Roach V,
Rynes E,
Sanchez ME,
Sandstrom RS,
Shafer AO,
Stergachis AB,
Thomas S,
Vernot B,
Vierstra J,
Vong S,
Wang H,
Weaver MA,
Yan YQ,
Zhang MH,
Akey JM,
Bender M,
Dorschner MO,
Groudine M,
MacCoss MJ,
Navas P,
Stamatoyannopoulos G,
Beal K,
Brazma A,
Flicek P,
Johnson N,
Lukk M,
Luscombe NM,
Sobral D,
Vaquerizas JM,
Batzoglou S,
Sidow A,
Hussami N,
Kyriazopoulou-Panagi S,
Libbrecht MW,
Schaub MA,
Miller W,
Bickel PJ,
Banfai B,
Boley NP,
Huang HY,
Li JJ,
Noble WS,
Bilmes JA,
Buske OJ,
Sahu AD,
Kharchenko PV,
Park PJ,
Baker D,
Taylor J,
Lin XY,
Lochovsky L,
Min R,
Encode Project Conso

Nature
  489 (7414): 57-74; Sep 6 2012  
[Abstract]
[DOI] [Full Text]

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay
Melnikov A,
Murugan A,
Zhang X,
Tesileanu T,
Wang L,
Rogov P,
Feizi S,
Gnirke A,
Callan Jr CG,
Kinney JB,
Kellis M,
Lander ES,
Mikkelsen TS

Nature Biotechnology
  30 (3): 271-277; Mar 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]

A Users Guide to the Encyclopedia of DNA Elements (ENCODE)
Myers RM,
Stamatoyannopoulos J,
Snyder M,
Dunham I,
Hardison RC,
Bernstein BE,
Gingeras TR,
Kent WJ,
Birney E,
Wold B,
Crawford GE,
Epstein CB,
Shoresh N,
Ernst J,
Mikkelsen TS,
Kheradpour P,
Zhang XL,
Wang L,
Issner R,
Coyne MJ,
Durham T,
Ku MC,
Truong T,
Ward LD,
Altshuler RC,
Lin MF,
Kellis M,
Davis CA,
Kapranov P,
Dobin A,
Zaleski C,
Schlesinger F,
Batut P,
Chakrabortty S,
Jha S,
Lin W,
Drenkow J,
Wang HE,
Bell KG,
Gao H,
Bell I,
Dumais E,
Dumais J,
Antonarakis SE,
Ucla C,
Borel C,
Guigo R,
Djebali S,
Lagarde J,
Kingswood C,
Ribeca P,
Sammeth M,
Alioto T,
Merkel A,
Tilgner H,
Carninci P,
Hayashizaki Y,
Lassmann T,
Takahashi H,
Abdelhamid RF,
Hannon G,
Fejes-Toth K,
Preall J,
Gordon A,
Sotirova V,
Reymond A,
Howald C,
Graison EA,
Chrast J,
Ruan YJ,
Ruan XA,
Shahab A,
Poh WT,
Wei CL,
Furey TS,
Boyle AP,
Sheffield NC,
Song LY,
Shibata Y,
Vales T,
Winter D,
Zhang ZC,
London D,
Wang TY,
Keefe D,
Iyer VR,
Lee BK,
McDaniell RM,
Liu Z,
Battenhouse A,
Bhinge AA,
Lieb JD,
Grasfeder LL,
Showers KA,
Giresi PG,
Kim SK,
Shestak C,
Pauli F,
Reddy TE,
Gertz J,
Partridge EC,
Jain P,
Sprouse RO,
Bansal A,
Pusey B,
Muratet MA,
Varley KE,
Bowling KM,
Newberry KM,
Nesmith AS,
Dilocker JA,
Parker SL,
Waite LL,
Thibeault K,
Roberts K,
Absher DM,
Mortazavi A,
Williams B,
Marinov G,
Trout D,
Pepke S,
King B,
McCue K,
Kirilusha A,
DeSalvo G,
Fisher-Aylor K,
Amrhein H,
Vielmetter J,
Sherlock G,
Sidow A,
Batzoglou S,
Rauch R,
Kundaje A,
Libbrecht M,
Margulies EH,
Parker SC,
Elnitski L,
Green ED,
Hubbard T,
Harrow J,
Searle S,
Kokocinski F,
Aken B,
Frankish A,
Hunt T,
Despacio-Reyes G,
Kay M,
Mukherjee G,
Bignell A,
Saunders G,
Boychenko V,
Brent M,
Van Baren MJ,
Brown RH,
Gerstein M,
Khurana E,
Balasubramanian S,
Zhang ZD,
Lam H,
Cayting P,
Robilotto R,
Lu Z,
Derrien T,
Tanzer A,
Knowles DG,
Mariotti M,
Haussler D,
Harte R,
Diekhans M,
Lin M,
Valencia A,
Tress M,
Rodriguez JM,
Landt SG,
Raha D,
Shi MY,
Euskirchen G,
Grubert F,
Kasowski M,
Lian J,
Lacroute P,
Xu YH,
Monahan H,
Patacsil D,
Slifer T,
Yang XQ,
Charos A,
Reed B,
Wu LF,
Auerbach RK,
Habegger L,
Hariharan M,
Rozowsky J,
Abyzov A,
Weissman SM,
Struhl K,
Lamarre-Vincent N,
Lindahl-Allen M,
Miotto B,
Moqtaderi Z,
Fleming JD,
Newburger P,
Farnham PJ,
Frietze S,
OGeen H,
Xu XQ,
Blahnik KR,
Cao AR,
Iyengar S,
Stamatoyannopoulos JA,
Kaul R,
Thurman RE,
Wang H,
Navas PA,
Sandstrom R,
Sabo PJ,
Weaver M,
Canfield T,
Lee K,
Neph S,
Roach V,
Reynolds A,
Johnson A,
Rynes E,
Giste E,
Vong S,
Neri J,
Frum T,
Johnson EM,
Nguyen ED,
Ebersol AK,
Sanchez ME,
Sheffer HH,
Lotakis D,
Haugen E,
Humbert R,
Kutyavin T,
Shafer T,
Dekker J,
Lajoie BR,
Sanyal A,
Rosenbloom KR,
Dreszer TR,
Raney BJ,
Barber GP,
Meyer LR,
Sloan CA,
Malladi VS,
Cline MS,
Learned K,
Swing VK,
Zweig AS,
Rhead B,
Fujita PA,
Roskin K,
Karolchik D,
Kuhn RM,
Wilder SP,
Sobral D,
Herrero J,
Beal K,
Lukk M,
Brazma A,
Vaquerizas JM,
Luscombe NM,
Bickel PJ,
Boley N,
Brown JB,
Li QH,
Huang HY,
Sboner A,
Yip KY,
Cheng C,
Yan KK,
Bhardwaj N,
Wang J,
Lochovsky L,
Jee J,
Gibson T,
Leng J,
Du J,
Harris RS,
Song G,
Miller W,
Suh B,
Wang T,
Paten B,
Noble WS,
Hoffman MM,
Buske OJ,
Weng ZP,
Dong XJ,
Xi HL,
Tenenbaum SA,
Doyle F,
Penalva LO,
Chittur S,
Tullius TD,
White KP,
Karmakar S,
Victorsen A,
Jameel N,
Bild N,
Grossman RL,
Whitfield TW,
Collins PJ,
Trinklein ND,
Giddings MC,
Chen X,
Khatun J,
Maier C,
Yu YB,
Gunawardena H,
Risk B,
Feingold EA,
Lowdon RF,
Dillon LA,
Good PJ,
Encode Project Conso

Plos Biology
  9 (4): Apr 2011   PMCID: PMC3079585
[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,