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31 Article(s) on File
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Comparative analysis of the transcriptome across distant species
Gerstein MB,
Rozowsky J,
Yan KK,
Wang D,
Cheng C,
Brown JB,
Davis CA,
Hillier L,
Sisu C,
Li JJ,
Pei B,
Harmanci AO,
Duff MO,
Djebali S,
Alexander RP,
Alver BH,
Auerbach R,
Bell K,
Bickel PJ,
Boeck ME,
Boley NP,
Booth BW,
Cherbas L,
Cherbas P,
Di C,
Dobin A,
Drenkow J,
Ewing B,
Fang G,
Fastuca M,
Feingold EA,
Frankish A,
Gao G,
Good PJ,
Guigo R,
Hammonds A,
Harrow J,
Hoskins RA,
Howald C,
Hu L,
Huang H,
Hubbard TJ,
Huynh C,
Jha S,
Kasper D,
Kato M,
Kaufman TC,
Kitchen RR,
Ladewig E,
Lagarde J,
Lai E,
Leng J,
Lu Z,
MacCoss M,
May G,
McWhirter R,
Merrihew G,
Miller DM,
Mortazavi A,
Murad R,
Oliver B,
Olson S,
Park PJ,
Pazin MJ,
Perrimon N,
Pervouchine D,
Reinke V,
Reymond A,
Robinson G,
Samsonova A,
Saunders GI,
Schlesinger F,
Sethi A,
Slack FJ,
Spencer WC,
Stoiber MH,
Strasbourger P,
Tanzer A,
Thompson OA,
Wan KH,
Wang G,
Wang H,
Watkins KL,
Wen J,
Wen K,
Xue C,
Yang L,
Yip K,
Zaleski C,
Zhang Y,
Zheng H,
Brenner SE,
Graveley BR,
Celniker SE,
Gingeras TR,
Waterston R

Nature
  512 (7515): 445-8; Aug 28 2014   Nlm
[Abstract]
[DOI] [Full Text]

High-coverage sequencing and annotated assemblies of the budgerigar genome
Ganapathy G,
Howard JT,
Ward JM,
Li J,
Li B,
Li Y,
Xiong Y,
Zhang Y,
Zhou S,
Schwartz DC,
Schatz M,
Aboukhalil R,
Fedrigo O,
Bukovnik L,
Wang T,
Wray G,
Rasolonjatovo I,
Winer R,
Knight JR,
Koren S,
Warren WC,
Zhang G,
Phillippy AM,
Jarvis ED

Gigascience
  3 (0): 11; Jul 8 2014   Nlm
[Abstract]
[DOI] [Full Text]

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]

Establishment of Highly Tumorigenic Human Colorectal Cancer Cell Line (CR4) with Properties of Putative Cancer Stem Cells
Rowehl RA,
Burke S,
Bialkowska AB,
Pettet DW,
Rowehl L,
Li E,
Antoniou E,
Zhang Y,
Bergamaschi R,
Shroyer KR,
Ojima I,
Botchkina GI

PLoS ONE
  9 (6): e99091; Jun 12 2014   NLM
[Abstract]
[DOI] [Full Text]

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
Brownstein CA,
Beggs AH,
Homer N,
Merriman B,
Yu TW,
Flannery KC,
Dechene ET,
Towne MC,
Savage SK,
Price EN,
Holm IA,
Luquette LJ,
Lyon E,
Majzoub J,
Neupert P,
McCallie D,
Szolovits P,
Willard HF,
Mendelsohn NJ,
Temme R,
Finkel RS,
Yum SW,
Medne L,
Sunyaev SR,
Adzhubey I,
Cassa CA,
de Bakker PI,
Duzkale H,
Dworzy Ski P,
Fairbrother W,
Francioli L,
Funke BH,
Giovanni MA,
Handsaker RE,
Lage K,
Lebo MS,
Lek M,
Leshchiner I,
Macarthur DG,
McLaughlin HM,
Murray MF,
Pers TH,
Polak PP,
Raychaudhuri S,
Rehm HL,
Soemedi R,
Stitziel NO,
Vestecka S,
Supper J,
Gugenmus C,
Klocke B,
Hahn A,
Schubach M,
Menzel M,
Biskup S,
Freisinger P,
Deng M,
Braun M,
Perner S,
Smith RJ,
Andorf JL,
Huang J,
Ryckman K,
Sheffield VC,
Stone EM,
Bair T,
Black-Ziegelbein EA,
Braun TA,
Darbro B,
Deluca AP,
Kolbe DL,
Scheetz TE,
Shearer AE,
Sompallae R,
Wang K,
Bassuk AG,
Edens E,
Mathews K,
Moore SA,
Shchelochkov OA,
Trapane P,
Bossler A,
Campbell CA,
Heusel JW,
Kwitek A,
Maga T,
Panzer K,
Wassink T,
Van Daele D,
Azaiez H,
Booth K,
Meyer N,
Segal MM,
Williams MS,
Tromp G,
White P,
Corsmeier D,
Fitzgerald-Butt S,
Herman G,
Lamb-Thrush D,
McBride KL,
Newsom D,
Pierson CR,
Rakowsky AT,
Maver A,
Lovre IL,
Palanda IA,
Peterlin B,
Torkamani A,
Wedell A,
Huss M,
Alexeyenko A,
Lindvall JM,
Magnusson M,
Nilsson D,
Stranneheim H,
Taylan F,
Gilissen C,
Hoischen A,
van Bon B,
Yntema H,
Nelen M,
Zhang W,
Sager J,
Zhang L,
Blair K,
Kural D,
Cariaso M,
Lennon GG,
Javed A,
Agrawal S,
Ng PC,
Sandhu KS,
Krishna S,
Veeramachaneni V,
Isakov O,
Halperin E,
Friedman E,
Shomron N,
Glusman G,
Roach JC,
Caballero J,
Cox HC,
Mauldin D,
Ament SA,
Rowen L,
Richards DR,
Lucas FA,
Gonzalez-Garay ML,
Caskey CT,
Bai Y,
Huang Y,
Fang F,
Zhang Y,
Wang Z,
Barrera J,
Garcia-Lobo JM,
Gonzalez-Lamuno D,
Llorca J,
Rodriguez MC,
Varela I,
Reese MG,
De La Vega FM,
Kiruluta E,
Cargill M,
Hart RK,
Sorenson JM,
Lyon GJ,
Stevenson DA,
Bray BE,
Moore BM,
Eilbeck K,
Yandell M,
Zhao H,
Hou L,
Chen X,
Yan X,
Chen M,
Li C,
Yang C,
Gunel M,
Li P,
Kong Y,
Alexander AC,
Albertyn ZI,
Boycott KM,
Bulman DE,
Gordon PM,
Innes AM,
Knoppers BM,
Majewski J,
Marshall CR,
Parboosingh JS,
Sawyer SL,
Samuels ME,
Schwartzentruber J,
Kohane IS,
Margulies DM

Genome Biology
  15 (3): R53; Mar 25 2014   NLM
[Abstract]
[DOI] [Full Text]

ZNF365 Promotes Stability of Fragile * Sites and Telomeres
Zhang Y,
Shin SJ,
Liu D,
Ivanova E,
Foerster F,
Ying H,
Zheng H,
Xiao Y,
Chen Z,
Protopopov A,
Depinho RA,
Paik JH

Cancer Discov
  3 (7): 798-811; Jul 2013   NLM
[Abstract]
[DOI] [Full Text]

Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets
Xu X,
Zhang Y,
Williams J,
Antoniou E,
McCombie WR,
Wu S,
Zhu W,
Davidson NO,
Denoya P,
Li E

BMC Bioinformatics
  14 Su (0): S1; Jun 28 2013   NLM
[Abstract]
[DOI] [Full Text]

A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor
Luo MC,
Gu YQ,
You FM,
Deal KR,
Ma Y,
Hu Y,
Huo N,
Wang Y,
Wang J,
Chen S,
Jorgensen CM,
Zhang Y,
McGuire PE,
Pasternak S,
Stein JC,
Ware D,
Kramer M,
McCombie WR,
Kianian SF,
Martis MM,
Mayer KF,
Sehgal SK,
Li W,
Gill BS,
Bevan MW,
Šimková H,
Doležel J,
Weining S,
Lazo GR,
Anderson OD,
Dvorak J

Proceedings of the National Academy of Sciences of the United States of America
  110 (19): 7940-7945; May 7 2013  
[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]

Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae)
McKain MR,
Wickett N,
Zhang Y,
Ayyampalayam S,
McCombie WR,
Chase MW,
Pires JC,
dePamphilis CW,
Leebens-Mack J

American Journal of Botany
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Genome Biology
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Genome Research
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Journal of Neurogenetics
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Nature
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Nature Genetics
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Journal of Biological Chemistry
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Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): Genome assembly and analysis
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Plos Biology
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Blood
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Genome Res
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J Biol Chem
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The miRNA-Processing Enzyme Dicer Is Essential for the Morphogenesis and Maintenance of Hair Follicles
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Current Biology
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Science
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Mol Cell Proteomics
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