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19 Article(s) on File
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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]

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]

Chd5 orchestrates chromatin remodelling during sperm development
Li W,
Wu J,
Kim SY,
Zhao M,
Hearn SA,
Zhang MQ,
Meistrich ML,
Mills AA

Nat Commun
  5 (0): 3812; May 13 2014   Nlm
[Abstract]
[DOI] [Full Text]

Chd5 orchestrates chromatin remodelling during sperm development
Li W,
Wu J,
Kim SY,
Zhao M,
Hearn SA,
Zhang MQ,
Meistrich ML,
Mills AA

Nature Communications
  5 (0): May 13 2014   NLM
[DOI] [Full Text]

Mutant p53 Drives Pancreatic Cancer Metastasis through Cell-Autonomous PDGF Receptor beta Signaling
Weissmueller S,
Manchado E,
Saborowski M,
Morris JP,
Wagenblast E,
Davis CA,
Moon SH,
Pfister NT,
Tschaharganeh DF,
Kitzing T,
Aust D,
Markert EK,
Wu J,
Grimmond SM,
Pilarsky C,
Prives C,
Biankin AV,
Lowe SW

Cell
  157 (2): 382-94; Apr 10 2014   NLM
[Abstract]
[DOI] [Full Text]

Assessment of transcript reconstruction methods for RNA-seq
Steijger T,
Abril JF,
Engström PG,
Kokocinski F,
Akerman M,
Alioto T,
Ambrosini G,
Antonarakis SE,
Behr J,
Bertone P,
Bohnert R,
Bucher P,
Cloonan N,
Derrien T,
Djebali S,
Du J,
Dudoit S,
Gerstein M,
Gingeras TR,
Gonzalez D,
Grimmond SM,
Guigó R,
Habegger L,
Harrow J,
Hubbard TJ,
Iseli C,
Jean G,
Kahles A,
Lagarde J,
Leng J,
Lefebvre G,
Lewis S,
Mortazavi A,
Niermann P,
Rätsch G,
Reymond A,
Ribeca P,
Richard H,
Rougemont J,
Rozowsky J,
Sammeth M,
Sboner A,
Schulz MH,
Searle SM,
Solorzano ND,
Solovyev V,
Stanke M,
Stevenson BJ,
Stockinger H,
Valsesia A,
Weese D,
White S,
Wold BJ,
Wu J,
Wu TD,
Zeller G,
Zerbino D,
Zhang MQ

Nature Methods
  10 (12): 1177-1184; Nov 2013  
[Abstract]
[DOI] [Full Text]

OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds
Wu J,
Anczukow O,
Krainer AR,
Zhang MQ,
Zhang C

Nucleic Acids Res
  16 (6): 5149-5163; Apr 9 2013   NLM
[Abstract]
[DOI] [Full Text]

Improvement of the oryza sativa nipponbare reference genome using next generation sequence and optical map data
Kawahara Y,
de la Bastide M,
Cabal R,
Hamilton JP,
Kanamori H,
McCombie WR,
Ouyang S,
Schwartz DC,
Tanaka T,
Wu J,
Zhou S,
Childs KL,
Davidson RM,
Lin H,
Quesada-Ocampo L,
Vaillancourt B,
Sakai H,
Lee SS,
Kim J,
Numa H,
Itoh T,
Buell CR,
Matsumoto T

Rice
  6 (1): 1-10; Feb 6 2013   Springer
[Abstract]
[DOI] [Full Text]

Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)
Ming R,
VanBuren R,
Liu YL,
Yang M,
Han YP,
Li LT,
Zhang Q,
Kim MJ,
Schatz MC,
Campbell M,
Li JP,
Bowers JE,
Tang HB,
Lyons E,
Ferguson AA,
Narzisi G,
Nelson DR,
Blaby-Haas CE,
Gschwend AR,
Jiao YN,
Der JP,
Zeng FC,
Han J,
Min XJ,
Hudson KA,
Singh R,
Grennan AK,
Karpowicz SJ,
Watling JR,
Ito K,
Robinson SA,
Hudson ME,
Yu QY,
Mockler TC,
Carroll A,
Zheng Y,
Sunkar R,
Jia RZ,
Chen N,
Arro J,
Wai CM,
Wafula E,
Spence A,
Han YN,
Xu LM,
Zhang JS,
Peery R,
Haus MJ,
Xiong WW,
Walsh JA,
Wu J,
Wang ML,
Zhu YJ,
Paull RE,
Britt AB,
Du CG,
Downie SR,
Schuler MA,
Michael TP,
Long SP,
Ort DR,
Schopf JW,
Gang DR,
Jiang N,
Yandell M,
dePamphilis CW,
Merchant SS,
Paterson AH,
Buchanan BB,
Li SH,
Shen-Miller J

Genome Biology
  14 (5): 2013  
[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]

The lncRNA Malat1 Is Dispensable for Mouse Development but Its Transcription Plays a cis-Regulatory Role in the Adult
Zhang B,
Arun G,
Mao Y,
Lazar Z,
Hung G,
Bhattacharjee G,
Xiao X,
Booth C,
Wu J,
Zhang C,
Spector D

Cell Reports
  2 (1): 111-123; Jul 26 2012  
[Abstract]
[DOI] [Full Text]

Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression
Shen ML,
Eyras E,
Wu J,
Khanna A,
Josiah S,
Rederstorff M,
Zhang MQ,
Stamm S

Nucleic Acids Research
  39 (22): 9720-9730; Dec 2011  
[Abstract]
[DOI] [Full Text]

SpliceTrap: a method to quantify alternative splicing under single cellular conditions
Wu J,
Akerman M,
Sun S,
McCombie WR,
Krainer AR,
Zhang MQ

Bioinformatics
  27 (21): 3010-3016 ; Nov 2011   PMC3198574
[Abstract]
[DOI]

The rice annotation project database (RAP-DB): 2008 update
Tanaka T,
Antonio BA,
Kikuchi S,
Matsumoto T,
Nagamura Y,
Numa H,
Sakai H,
Wu J,
Itoh T,
Sasaki T,
Aono R,
Fujii Y,
Habara T,
Harada E,
Kanno M,
Kawahara Y,
Kawashima H,
Kubooka H,
Matsuya A,
Nakaoka H,
Saichi N,
Sanbonmatsu R,
Sato Y,
Shinso Y,
Suzuki M,
Takeda JI,
Tanino M,
Todokoro F,
Yamaguchi K,
Yamamoto N,
Yamasaki C,
Imanishi T,
Okido T,
Tada M,
Ikeo K,
Tateno Y,
Gojobori T,
Lin YC,
Wei FJ,
Hsing YI,
Zhao Q,
Han B,
Kramer MR,
McCombie RW,
Lonsdale D,
ODonovan CC,
Whitfield EJ,
Apweiler R,
Koyanagi KO,
Khurana JP,
Raghuvanshi S,
Singh NK,
Tyagi AK,
Haberer G,
Fujisawa M,
Hosokawa S,
Ito Y,
Ikawa H,
Shibata M,
Yamamoto M,
Bruskiewich RM,
Hoen DR,
Bureau TE,
Namiki N,
Ohyanagi H,
Sakai Y,
Nobushima S,
Sakata K,
Barrero RA,
Souvorov A,
Smith-White B,
Tatusova T,
An S,
An G,
Oota S,
Fuks G,
Messing J,
Christie KR,
Lieberherr D,
Kim H,
Zuccolo A,
Wing RA,
Nobuta K,
Green PJ,
Lu C,
Meyers BC,
Chaparro C,
Piegu B,
Panaud O

Nucleic Acids Research
  36 (0): D1028-D1033; Jan 2008   PMCID: PMC2238920
[Abstract]
[DOI] [Full Text] [PDF]

The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci
Rozowsky JS,
Newburger D,
Sayward F,
Wu J,
Jordan G,
Korbel JO,
Nagalakshmi U,
Yang J,
Zheng D,
Guigó R,
Gingeras TR,
Weissman S,
Miller P,
Snyder M,
Gerstein MB

Genome Research
  17 (6): 732-745; 2007  
[Abstract]
[DOI] [Full Text]

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,
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