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Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel
Delaneau O,
Marchini J,
McVeanh GA,
Donnelly P,
Lunter G,
Marchini JL,
Myers S,
Gupta-Hinch A,
Iqbal Z,
Mathieson I,
Rimmer A,
Xifara DK,
Kerasidou A,
Churchhouse C,
Altshuler DM,
Gabriel SB,
Lander ES,
Gupta N,
Daly MJ,
DePristo MA,
Banks E,
Bhatia G,
Carneiro MO,
Del Angel G,
Genovese G,
Handsaker RE,
Hartl C,
McCarroll SA,
Nemesh JC,
Poplin RE,
Schaffner SF,
Shakir K,
Sabeti PC,
Grossman SR,
Tabrizi S,
Tariyal R,
Li H,
Reich D,
Durbin RM,
Hurles ME,
Balasubramaniam S,
Burton J,
Danecek P,
Keane TM,
Kolb-Kokocinski A,
McCarthy S,
Stalker J,
Quail M,
Ayub Q,
Chen Y,
Coffey AJ,
Colonna V,
Huang N,
Jostins L,
Scally A,
Walter K,
Xue Y,
Zhang Y,
Blackburne B,
Lindsay SJ,
Ning Z,
Frankish A,
Harrow J,
Chris TS,
Abecasis GR,
Kang HM,
Anderson P,
Blackwell T,
Busonero F,
Fuchsberger C,
Jun G,
Maschio A,
Porcu E,
Sidore C,
Tan A,
Trost MK,
Bentley DR,
Grocock R,
Humphray S,
James T,
Kingsbury Z,
Bauer M,
Cheetham RK,
Cox T,
Eberle M,
Murray L,
Shaw R,
Chakravarti A,
Clark AG,
Keinan A,
Rodriguez-Flores JL,
De LaVega FM,
Degenhardt J,
Eichler EE,
Flicek P,
Clarke L,
Leinonen R,
Smith RE,
Zheng-Bradley X,
Beal K,
Cunningham F,
Herrero J,
McLaren WM,
Ritchie GR,
Barker J,
Kelman G,
Kulesha E,
Radhakrishnan R,
Roa A,
Smirnov D,
Streeter I,
Toneva I,
Gibbs RA,
Dinh H,
Kovar C,
Lee S,
Lewis L,
Muzny D,
Reid J,
Wang M,
Yu F,
Bainbridge M,
Challis D,
Evani US,
Lu J,
Nagaswamy U,
Sabo A,
Wang Y,
Yu J,
Fowler G,
Hale W,
Kalra D,
Green ED,
Knoppers BM,
Korbel JO,
Rausch T,
Sttz AM,
Lee C,
Griffin L,
Hsieh CH,
Mills RE,
Von Grotthuss M,
Zhang C,
Shi X,
Lehrach H,
Sudbrak R,
Amstislavskiy VS,
Lienhard M,
Mertes F,
Sultan M,
Timmermann B,
Yaspo ML,
Herwig SR,
Mardis ER,
Wilson RK,
Fulton L,
Fulton R,
Weinstock GM,
Chinwalla A,
Ding L,
Dooling D,
Koboldt DC,
McLellan MD,
Wallis JW,
Wendl MC,
Zhang Q,
Marth GT,
Garrison EP,
Kural D,
Lee WP,
Leong WF,
Ward AN,
Wu J,
Zhang M,
Nickerson DA,
Alkan C,
Hormozdiari F,
Ko A,
Sudmant PH,
Schmidt JP,
Davies CJ,
Gollub J,
Webster T,
Wong B,
Zhan Y,
Sherry ST,
Xiao C,
Church D,
Ananiev V,
Belaia Z,
Beloslyudtsev D,
Bouk N,
Chen C,
Cohen R,
Cook C,
Garner J,
Hefferon T,
Kimelman M,
Liu C,
Lopez J,
Meric P,
Ostapchuk Y,
Phan L,
Ponomarov S,
Schneider V,
Shekhtman E,
Sirotkin K,
Slotta D,
Zhang H,
Wang J,
Fang X,
Guo X,
Jian M,
Jiang H,
Jin X,
Li G,
Li J,
Li Y,
Liu X,
Lu Y,
Ma X,
Tai S,
Tang M,
Wang B,
Wang G,
Wu H,
Wu R,
Yin Y,
Zhang W,
Zhao J,
Zhao M,
Zheng X,
Lachlan H,
Fang L,
Li Q,
Li Z,
Lin H,
Liu B,
Luo R,
Shao H,
Xie Y,
Ye C,
Yu C,
Zheng H,
Zhu H,
Cai H,
Cao H,
Su Y,
Tian Z,
Yang H,
Yang L,
Zhu J,
Cai Z,
Albrecht MW,
Borodina TA,
Auton A,
Yoon SC,
Lihm J,
Makarov V,
Jin H,
Kim W,
Kim KC,
Gottipati S,
Jones D,
Cooper DN,
Ball EV,
Stenson PD,
Barnes B,
Kahn S,
Ye K,
Batzer MA,
Konkel MK,
Walker JA,
MacArthur DG,
Lek M,
Shriver MD,
Bustamante CD,
Gravel S,
Kenny EE,
Kidd JM,
Lacroute P,
Maples BK,
Moreno-Estrada A,
Zakharia F,
Henn B,
Sandoval K,
Byrnes JK,
Halperin E,
Baran Y,
Craig DW,
Christoforides A,
Izatt T,
Kurdoglu AA,
Sinari SA,
Homer N,
Squire K,
Sebat J,
Bafna V,
Burchard EG,
Hernandez RD,
Gignoux CR,
Haussler D,
Katzman SJ,
Kent WJ,
Howie B,
Ruiz-Linares A,
Dermitzakis ET,
Lappalainen T,
Devine SE,
Maroo A,
Tallon LJ,
Rosenfeld JA,
Michelson LP,
Angius A,
Cucca F,
Sanna S,
Bigham A,
Jones C,
Reinier F,
Lyons R,
Schlessinger D,
Awadalla P,
Hodgkinson A,
Oleksyk TK,
Martinez-Cruzado JC,
Fu Y,
Xiong M,
Jorde L,
Witherspoon D,
Xing J,
Browning BL,
Hajirasouliha I,
Chen K,
Albers CA,
Gerstein MB,
Abyzov A,
Chen J,
Habegger L,
Harmanci AO,
Mu XJ,
Sisu C,
Balasubramanian S,
Jin M,
Khurana E,
Clarke D,
Michaelson JJ,
Osullivan C,
Barnes KC,
Gharani N,
Toji LH,
Gerry N,
Kaye JS,
Kent A,
Mathias R,
Ossorio PN,
Parker M,
Rotimi CN,
Royal CD,
Tishkoff S,
Via M,
Bodmer W,
Bedoya G,
Yang G,
You CJ,
Garcia-Montero A,
Orfao A,
Dutil J,
Brooks LD,
Felsenfeld AL

Nature Communications
  5 (0): Jun 13 2014   Elsevier
[Abstract]
[DOI] [Full Text]

An integrated map of genetic variation from 1,092 human genomes
Altshuler DM,
Durbin RM,
Abecasis GR,
Bentley DR,
Chakravarti A,
Clark AG,
Donnelly P,
Eichler EE,
Flicek P,
Gabriel SB,
Gibbs RA,
Green ED,
Hurles ME,
Knoppers BM,
Korbel JO,
Lander ES,
Lee C,
Lehrach H,
Mardis ER,
Marth GT,
McVean GA,
Nickerson DA,
Schmidt JP,
Sherry ST,
Wang J,
Wilson RK,
Dinh H,
Kovar C,
Lee S,
Lewis L,
Muzny D,
Reid J,
Wang M,
Fang XD,
Guo XS,
Jian M,
Jiang H,
Jin X,
Li GQ,
Li JX,
Li YR,
Li Z,
Liu X,
Lu Y,
Ma XD,
Su Z,
Tai SS,
Tang MF,
Wang B,
Wang GB,
Wu HL,
Wu RH,
Yin Y,
Zhang WW,
Zhao J,
Zhao MR,
Zheng XL,
Zhou Y,
Gupta N,
Clarke L,
Leinonen R,
Smith RE,
Zheng-Bradley X,
Grocock R,
Humphray S,
James T,
Kingsbury Z,
Sudbrak R,
Albrecht MW,
Amstislavskiy VS,
Borodina TA,
Lienhard M,
Mertes F,
Sultan M,
Timmermann B,
Yaspo ML,
Fulton L,
Fulton R,
Weinstock GM,
Balasubramaniam S,
Burton J,
Danecek P,
Keane TM,
Kolb-Kokocinski A,
McCarthy S,
Stalker J,
Quail M,
Davies CJ,
Gollub J,
Webster T,
Wong B,
Zhan YP,
Auton A,
Yu F,
Bainbridge M,
Challis D,
Evani US,
Lu J,
Nagaswamy U,
Sabo A,
Wang Y,
Yu J,
Coin LJ,
Fang L,
Li QB,
Li ZY,
Lin HX,
Liu BH,
Luo RB,
Qin N,
Shao HJ,
Wang BQ,
Xie YL,
Ye C,
Yu C,
Zhang F,
Zheng HC,
Zhu HM,
Garrison EP,
Kural D,
Lee WP,
Leong WF,
Ward AN,
Wu JT,
Zhang MY,
Griffin L,
Hsieh CH,
Mills RE,
Shi XH,
von Grotthuss M,
Zhang CS,
Daly MJ,
DePristo MA,
Banks E,
Bhatia G,
Carneiro MO,
del Angel G,
Genovese G,
Handsaker RE,
Hartl C,
McCarroll SA,
Nemesh JC,
Poplin RE,
Schaffner SF,
Shakir K,
Yoon SC,
Lihm J,
Makarov V,
Jin HJ,
Kim W,
Kim KC,
Rausch T,
Beal K,
Cunningham F,
Herrero J,
McLaren WM,
Ritchie GR,
Gottipati S,
Keinan A,
Rodriguez-Flores JL,
Sabeti PC,
Grossman SR,
Tabrizi S,
Tariyal R,
Cooper DN,
Ball EV,
Stenson PD,
Barnes B,
Bauer M,
Cheetham RK,
Cox T,
Eberle M,
Kahn S,
Murray L,
Peden J,
Shaw R,
Ye K,
Batzer MA,
Konkel MK,
Walker JA,
MacArthur DG,
Lek M,
Herwig R,
Shriver MD,
Bustamante CD,
Byrnes JK,
De la Vega FM,
Gravel S,
Kenny EE,
Kidd JM,
Lacroute P,
Maples BK,
Moreno-Estrada A,
Zakharia F,
Halperin E,
Baran Y,
Craig DW,
Christoforides A,
Homer N,
Izatt T,
Kurdoglu AA,
Sinari SA,
Squire K,
Xiao CL,
Sebat J,
Bafna V,
Burchard EG,
Hernandez RD,
Gignoux CR,
Haussler D,
Katzman SJ,
Kent WJ,
Howie B,
Ruiz-Linares A,
Dermitzakis ET,
Lappalainen T,
Devine SE,
Liu XY,
Maroo A,
Tallon LJ,
Rosenfeld JA,
Michelson LP,
Kang HM,
Anderson P,
Angius A,
Bigham A,
Blackwell T,
Busonero F,
Cucca F,
Fuchsberger C,
Jones C,
Jun G,
Li Y,
Lyons R,
Maschio A,
Porcu E,
Reinier F,
Sanna S,
Schlessinger D,
Sidore C,
Tan A,
Trost MK,
Awadalla P,
Hodgkinson A,
Lunter G,
Marchini JL,
Myers S,
Churchhouse C,
Delaneau O,
Gupta-Hinch A,
Iqbal Z,
Mathieson I,
Rimmer A,
Xifara DK,
Oleksyk TK,
Fu YX,
Liu XM,
Xiong MM,
Jorde L,
Witherspoon D,
Xing JC,
Browning BL,
Alkan C,
Hajirasouliha I,
Hormozdiari F,
Ko A,
Sudmant PH,
Chen K,
Chinwalla A,
Ding L,
Dooling D,
Koboldt DC,
McLellan MD,
Wallis JW,
Wendl MC,
Zhang QY,
Tyler-Smith C,
Albers CA,
Ayub Q,
Chen Y,
Coffey AJ,
Colonna V,
Huang N,
Jostins L,
Li H,
Scally A,
Walter K,
Xue YL,
Zhang YJ,
Gerstein MB,
Abyzov A,
Balasubramanian S,
Chen JM,
Clarke D,
Fu Y,
Habegger L,
Harmanci AO,
Jin MK,
Khurana E,
Mu XJ,
Sisu C,
Degenhardt J,
Stutz AM,
Church D,
Michaelson JJ,
Ben B,
Lindsay SJ,
Ning ZM,
Yu FL,
Frankish A,
Harrow J,
Fowler G,
Hale W,
Kalra D,
Guo X,
Li G,
Zheng X,
Barker J,
Kelman G,
Kulesha E,
Radhakrishnan R,
Roa A,
Smirnov D,
Streeter I,
Toneva I,
Vaughan B,
Ananiev V,
Belaia Z,
Beloslyudtsev D,
Bouk N,
Chen C,
Cohen R,
Cook C,
Garner J,
Hefferon T,
Kimelman M,
Liu C,
Lopez J,
Meric P,
OSullivan C,
Ostapchuk Y,
Phan L,
Ponomarov S,
Schneider V,
Shekhtman E,
Sirotkin K,
Slotta D,
Zhang H,
Barnes KC,
Beiswanger C,
Cai HY,
Cao HZ,
Gharani N,
Henn B,
Jones D,
Kaye JS,
Kent A,
Kerasidou A,
Mathias R,
Ossorio PN,
Parker M,
Reich D,
Rotimi CN,
Royal CD,
Sandoval K,
Su YY,
Tian ZM,
Tishkoff S,
Toji LH,
Via M,
Wang YH,
Yang HM,
Yang L,
Zhu JY,
Bodmer W,
Bedoya G,
Ming CZ,
Yang G,
You CJ,
Peltonen L,
Garcia-Montero A,
Orfao A,
Dutil J,
Martinez-Cruzado JC,
Brooks LD,
Felsenfeld AL,
McEwen JE,
Clemm NC,
Duncanson A,
Dunn M,
Guyer MS,
Peterson JL,
Genomes Project C

Nature
  491 (7422): 56-65; Nov 1 2012  
[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]

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project
Gerstein MB,
Lu ZJ,
Van Nostrand EL,
Cheng C,
Arshinoff BI,
Liu T,
Yip KY,
Robilotto R,
Rechtsteiner A,
Ikegami K,
Alves P,
Chateigner A,
Perry M,
Morris M,
Auerbach RK,
Feng X,
Leng J,
Vielle A,
Niu W,
Rhrissorrakrai K,
Agarwal A,
Alexander RP,
Barber G,
Brdlik CM,
Brennan J,
Brouillet JJ,
Carr A,
Cheung MS,
Clawson H,
Contrino S,
Dannenberg LO,
Dernburg AF,
Desai A,
Dick L,
Dose AC,
Du JA,
Egelhofer T,
Ercan S,
Euskirchen G,
Ewing B,
Feingold EA,
Gassmann R,
Good PJ,
Green P,
Gullier F,
Gutwein M,
Guyer MS,
Habegger L,
Han T,
Henikoff JG,
Henz SR,
Hinrichs A,
Holster H,
Hyman T,
Iniguez AL,
Janette J,
Jensen M,
Kato M,
Kent WJ,
Kephart E,
Khivansara V,
Khurana E,
Kim JK,
Kolasinska-Zwierz P,
Lai EC,
Latorre I,
Leahey A,
Lewis S,
Lloyd P,
Lochovsky L,
Lowdon RF,
Lubling Y,
Lyne R,
MacCoss M,
Mackowiak SD,
Mangone M,
McKay SJ,
Mecenas D,
Merrihew G,
Miller DM,
Muroyama A,
Murray JI,
Ooi SL,
Pham H,
Phippen T,
Preston EA,
Rajewsky N,
Ratsch G,
Rosenbaum H,
Rozowsky J,
Rutherford K,
Ruzanov P,
Sarov M,
Sasidharan R,
Sboner A,
Scheid P,
Segal E,
Shin HJ,
Shou C,
Slack FJ,
Slightam C,
Smith R,
Spencer WC,
Stinson EO,
Taing S,
Takasaki T,
Vafeados D,
Voronina K,
Wang GL,
Washington NL,
Whittle CM,
Wu BJ,
Yan KK,
Zeller G,
Zha Z,
Zhong M,
Zhou XL,
Ahringer J,
Strome S,
Gunsalus KC,
Micklem G,
Liu XS,
Reinke V,
Kim SK,
Hillier LW,
Henikoff S,
Piano F,
Snyder M,
Stein LD,
Lieb JD,
Waterston RH

Science
  330 (6012): 1775-1787; Dec 2010   PMC3142569
[Abstract]
[DOI] [Full Text] [PDF]

Completing the map of human genetic variation
Eichler EE,
Nickerson DA,
Altshuler D,
Bowcock AM,
Brooks LD,
Carter NP,
Church DM,
Felsenfeld A,
Guyer M,
Lee C,
Lupski JR,
Mullikin JC,
Pritchard JK,
Sebat J,
Sherry ST,
Smith D,
Valle D,
Waterston RH

Nature
  447 (7141): 161-165; May 2007  
[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,
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[Abstract]
[DOI] [Full Text]

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