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229 Article(s) on File
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An Arabidopsis gene regulatory network for secondary cell wall synthesis
Taylor-Teeples M,
Lin L,
de Lucas M,
Turco G,
Toal TW,
Gaudinier A,
Young NF,
Trabucco GM,
Veling MT,
Lamothe R,
Handakumbura PP,
Xiong G,
Wang C,
Corwin J,
Tsoukalas A,
Zhang L,
Ware D,
Pauly M,
Kliebenstein DJ,
Dehesh K,
Tagkopoulos I,
Breton G,
Pruneda-Paz JL,
Ahnert SE,
Kay SA,
Hazen SP,
Brady SM

Nature
  (0): Dec 24 2014   Nlm
[Abstract]
[DOI] [Full Text]

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]

Brain stem cell division and maintenance studied using multi-isotope imaging mass spectrometry (MIMS)
Enikolopov G,
Guillermier C,
Wang M,
Trakimas L,
Steinhauser ML,
Lechene C

Surface and Interface Analysis
  46 (0): 140-143; Nov 1 2014   Elsevier
[Abstract]
[DOI] [Full Text]

Dephosphorylation of Tyrosine 393 in Argonaute 2 by Protein Tyrosine Phosphatase 1B Regulates Gene Silencing in Oncogenic RAS-Induced Senescence
Yang M,
Haase AD,
Huang FK,
Coulis G,
Rivera KD,
Dickinson BC,
Chang CJ,
Pappin DJ,
Neubert TA,
Hannon GJ,
Boivin B,
Tonks NK

Molecular Cell
  55 (5): 782-790; Aug 27 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]

Synaptic modifications in the medial prefrontal cortex in susceptibility and resilience to stress
Wang M,
Perova Z,
Arenkiel BR,
Li B

J Neurosci
  34 (22): 7485-92; May 28 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

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]

A promoter-level mammalian expression atlas
Forest AR,
Kawaji H,
Rehli M,
Baillie JK,
De Hoon MJ,
Haberle V,
Lassmann T,
Kulakovskiy IV,
Lizio M,
Itoh M,
Andersson R,
Mungall CJ,
Meehan TF,
Schmeier S,
Bertin N,
Jørgensen M,
Dimont E,
Arner E,
Schmidl C,
Schaefer U,
Medvedeva YA,
Plessy C,
Vitezic M,
Severin J,
Semple CA,
Ishizu Y,
Young RS,
Francescatto M,
Altschuler IA,
Albanese D,
Altschule GM,
Arakawa T,
Archer JA,
Arner P,
Babina M,
Rennie S,
Balwierz PJ,
Beckhouse AG,
Pradhan-Bhatt S,
Blake JA,
Blumenthal A,
Bodega B,
Bonetti A,
Briggs J,
Brombacher F,
Burroughs AM,
Califano A,
Cannistraci CV,
Carbajo D,
Chen Y,
Chierici M,
Ciani Y,
Clevers HC,
Dalla E,
Davis CA,
Detmar M,
Diehl AD,
Dohi T,
Drabløs F,
Edge AS,
Edinger M,
Ekwall K,
Endoh M,
Enomoto H,
Fagiolini M,
Fairbairn L,
Fang H,
Farach-Carson MC,
Faulkner GJ,
Favorov AV,
Fisher ME,
Frith MC,
Fujita R,
Fukuda S,
Furlanello C,
Furuno M,
Furusawa JI,
Geijtenbeek TB,
Gibson AP,
Gingeras T,
Goldowitz D,
Gough J,
Guhl S,
Guler R,
Gustincich S,
Ha TJ,
Hamaguchi M,
Hara M,
Harbers M,
Harshbarger J,
Hasegawa A,
Hasegawa Y,
Hashimoto T,
Herlyn M,
Hitchens KJ,
Sui SJ,
Hofmann OM,
Hoof I,
Hori F,
Huminiecki L,
Iida K,
Ikawa T,
Jankovic BR,
Jia H,
Joshi A,
Jurman G,
Kaczkowski B,
Kai C,
Kaida K,
Kaiho A,
Kajiyama K,
Kanamori-Katayama M,
Kasianov AS,
Kasukawa T,
Katayama S,
Kato S,
Kawaguchi S,
Kawamoto H,
Kawamura YI,
Kawashima T,
Kempfle JS,
Kenna TJ,
Kere J,
Khachigian LM,
Kitamura T,
Klinken SP,
Knox AJ,
Kojima M,
Kojima S,
Kondo N,
Koseki H,
Koyasu S,
Krampitz S,
Kubosaki A,
Kwon AT,
Laros JF,
Lee W,
Lennartsson A,
Li K,
Lilje B,
Lipovich L,
Mackay-sim A,
Manabe RI,
Mar JC,
Marchand B,
Mathelier A,
Mejhert N,
Meynert A,
Mizuno Y,
De Morais DA,
Morikawa H,
Morimoto M,
Moro K,
Motakis E,
Motohashi H,
Mummery CL,
Murata M,
Nagao-Sato S,
Nakachi Y,
Nakahara F,
Nakamura T,
Nakamura Y,
Nakazato K,
Van Nimwegen E,
Ninomiya N,
Nishiyori H,
Noma S,
Nozaki T,
Ogishima S,
Ohkura N,
Ohmiya H,
Ohno H,
Ohshima M,
Okada-Hatakeyama M,
Okazaki Y,
Orlando V,
Ovchinnikov DA,
Pain A,
Passier R,
Patrikakis M,
Persson H,
Piazza S,
Prendergast JG,
Rackham OJ,
Ramilowski JA,
Rashid M,
Ravasi T,
Rizzu P,
Roncador M,
Roy S,
Rye MB,
Saijyo E,
Sajantila A,
Saka A,
Sakaguchi S,
Sakai M,
Sato H,
Satoh H,
Savvi S,
Saxena A,
Schneider C,
Schultes EA,
Schulze-Tanzil GG,
Schwegmann A,
Sengstag T,
Sheng G,
Shimoji H,
Shimoni Y,
Shin JW,
Simon C,
Sugiyama D,
Sugiyama T,
Suzuki M,
Suzuki N,
Swoboda RK,
T Hoen PA,
Tagami M,
Tagami NT,
Takai J,
Tanaka H,
Tatsukawa H,
Tatum Z,
Thompson M,
Toyoda H,
Toyoda T,
Valen E,
Van De Wetering M,
Van Den Berg LM,
Verardo R,
Vijayan D,
Vorontsov IE,
Wasserman WW,
Watanabe S,
Wells CA,
Winteringham LN,
Wolvetang E,
Wood EJ,
Yamaguchi Y,
Yamamoto M,
Yoneda M,
Yonekura Y,
Yoshida S,
Zabierowski SE,
Zhang PG,
Zhao X,
Zucchelli S,
Summers KM,
Suzuki H,
Daub CO,
Kawai J,
Heutink P,
Hide W,
Freeman TC,
Lenhard B,
Bajic LV,
Taylor MS,
Makeev VJ,
Sandelin A,
Hume DA,
Carninci P,
Hayashizaki Y

Nature
  507 (7493): 462-470; Mar 27 2014   NLM
[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]

Interchangeable punishments during aversive conditioning in Drosophila
Robinson BG,
Khurana S,
Nguyen A,
Chuang T,
Young M,
Yu J,
Hooten J,
Atkinson NS

Current Science
  105 (9): 1254-1261; Nov 10 2013   Elsevier
[Abstract]
[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]

The transcription factor Foxo1 controls central-memory CD8+ T cell responses to infection
Kim MV,
Ouyang W,
Liao W,
Zhang MQ,
Li MO

Immunity
  39 (2): 286-97; Aug 22 2013   Nlm
[Abstract]
[DOI] [Full Text]

The effects of carbon dioxide and temperature on microRNA expression in Arabidopsis development
May P,
Liao W,
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