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29 Article(s) on File
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Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression
Pervouchine DD,
Djebali S,
Breschi A,
Davis CA,
Barja PP,
Dobin A,
Tanzer A,
Lagarde J,
Zaleski C,
See LH,
Fastuca M,
Drenkow J,
Wang H,
Bussotti G,
Pei B,
Balasubramanian S,
Monlong J,
Harmanci A,
Gerstein M,
Beer MA,
Notredame C,
Guigo R,
Gingeras TR

Nat Commun
  6 (0): 5903; Jan 13 2015   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]

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]

Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing
Le Thomas A,
Stuwe E,
Li S,
Du J,
Marinov G,
Rozhkov N,
Chen YC,
Luo Y,
Sachidanandam R,
Toth KF,
Patel D,
Aravin AA

Genes Development
  28 (15): 1667-80; Aug 1 2014   Nlm
[Abstract]
[DOI] [Full Text]

Large-Scale Identification and Analysis of Suppressive Drug Interactions
Cokol M,
Weinstein Z,
Yilancioglu K,
Tasan M,
Doak A,
Cansever D,
Mutlu B,
Li S,
Rodriguez-Esteban R,
Akhmedov M,
Guvenek A,
Cetiner S,
Giaever G,
Iossifov I,
Nislow C,
Shoichet B

Chemistry and Biology
  21 (4): 541-551; Apr 2 2014   NLM
[Abstract]
[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]

Systematic evaluation of spliced alignment programs for RNA-seq data
Engström PG,
Steijger T,
Sipos B,
Grant GR,
Kahles A,
Rätsch G,
Goldman N,
Hubbard TJ,
Harrow J,
Guigó R,
Bertone P,
Alioto T,
Behr J,
Bohnert R,
Campagna D,
Davis CA,
Dobin A,
Gingeras TR,
Jean G,
Kosarev P,
Li S,
Liu J,
Mason CE,
Molodtsov V,
Ning Z,
Ponstingl H,
Prins JF,
Ribeca P,
Seledtsov I,
Solovyev V,
Valle G,
Vitulo N,
Wang K,
Wu TD,
Zeller G

Nature Methods
  10 (12): 1185-1191; Dec 2013  
[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]

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]

Understanding transcriptional regulation by integrative analysis of transcription factor binding data
Cheng C,
Alexander R,
Min RQ,
Leng J,
Yip KY,
Rozowsky J,
Yan KK,
Dong XJ,
Djebali S,
Ruan YJ,
Davis CA,
Carninci P,
Lassman T,
Gingeras TR,
Guigo R,
Birney E,
Weng ZP,
Snyder M,
Gerstein M

Genome Research
  22 (9): 1658-1667; Sep 12 2012  
[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,
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Partridge EC,
Varley KE,
Gasper C,
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Jain P,
Amrhein H,
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Fisher-Aylor KI,
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Balasubramanian S,
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Eggleston T,
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Wong WH,
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Harte R,
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Khurana E,
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Manthravadi D,
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Mudge J,
Mukherjee G,
Notredame C,
Pei BK,
Rodriguez JM,
Saunders G,
Sboner A,
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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,
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Frum T,
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Haugen E,
Humbert R,
Johnson AK,
Johnson EM,
Kutyavin TV,
Lee K,
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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,
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