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154 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]

Comparison of the transcriptional landscapes between human and mouse tissues
Lin S,
Lin Y,
Nery JR,
Urich MA,
Breschi A,
Davis CA,
Dobin A,
Zaleski C,
Beer MA,
Chapman WC,
Gingeras TR,
Ecker JR,
Snyder MP

Proceedings of the National Academy of Sciences of the United States of America
  111 (48): 17224-17229; Nov 20 2014  
[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]

Diversity and dynamics of the Drosophila transcriptome
Brown JB,
Boley N,
Eisman R,
May GE,
Stoiber MH,
Duff MO,
Booth BW,
Wen J,
Park S,
Suzuki AM,
Wan KH,
Yu C,
Zhang D,
Carlson JW,
Cherbas L,
Eads BD,
Miller D,
Mockaitis K,
Roberts J,
Davis CA,
Frise E,
Hammonds AS,
Olson S,
Shenker S,
Sturgill D,
Samsonova AA,
Weiszmann R,
Robinson G,
Hernandez J,
Andrews J,
Bickel PJ,
Carninci P,
Cherbas P,
Gingeras TR,
Hoskins RA,
Kaufman TC,
Lai EC,
Oliver B,
Perrimon N,
Graveley BR,
Celniker SE

Nature
  512 (7515): 393; Aug 28 2014   NLM
[Abstract]
[DOI] [Full Text]

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease
Kellis M,
Wold B,
Snyder MP,
Bernstein BE,
Kundaje A,
Marinov GK,
Ward LD,
Birney E,
Crawford GE,
Dekker J,
Dunham I,
Elnitski LL,
Farnham PJ,
Feingold EA,
Gerstein M,
Giddings MC,
Gilbert DM,
Gingeras TR,
Green ED,
Guigo R,
Hubbard T,
Kent J,
Lieb JD,
Myers RM,
Pazin MJ,
Ren B,
Stamatoyannopoulos J,
Weng Z,
White KP,
Hardison RC

Proceedings of the National Academy of Sciences of the United States of America
  111 (33): E3366-E3366; Aug 19 2014   Elsevier
[DOI] [Full Text]

Considerations when investigating IncRNA function in vivo
Bassett AR,
Akhtar A,
Barlow DP,
Bird AP,
Brockdorff N,
Duboule D,
Ephrussi A,
Ferguson-Smith AC,
Gingeras TR,
Haerty W,
Higgs DR,
Miska EA,
Ponting CP

Elife
  3 (0): Aug 2014   NLM
[Abstract]
[DOI] [Full Text]

A Genome-Wide Survey of Sexually Dimorphic Expression of Drosophila miRNAs Identifies the Steroid Hormone-Induced miRNA let-7 as a Regulator of Sexual Identity
Fagegaltier D,
Konig A,
Gordon A,
Lai EC,
Gingeras TR,
Hannon GJ,
Shcherbata HR

Genetics
  198 (2): 647-668; Jul 31 2014   Nlm
[Abstract]
[DOI] [Full Text]

Multiplicity of 5 Cap Structures Present on Short RNAs
Abdelhamid RF,
Plessy C,
Yamauchi Y,
Taoka M,
de Hoon M,
Gingeras TR,
Isobe T,
Carninci P

PLoS One
  9 (7): e102895; Jul 31 2014   Nlm
[Abstract]
[DOI] [Full Text]

Conservation and novel functions of non-coding RNAs
Gingeras TR

Prion
  8 (0): 8-9; Apr-Jun 2014   Thomson Reuters


Defining functional DNA elements in the human genome
Kellis M,
Wold B,
Snyder MP,
Bernstein BE,
Kundaje A,
Marinov GK,
Ward LD,
Birney E,
Crawford GE,
Dekker J,
Dunham I,
Elnitski LL,
Farnham PJ,
Feingold EA,
Gerstein M,
Giddings MC,
Gilbert DM,
Gingeras TR,
Green ED,
Guigo R,
Hubbard T,
Kent J,
Lieb JD,
Myers RM,
Pazin MJ,
Ren B,
Stamatoyannopoulos JA,
Weng ZP,
White KP,
Hardison RC

Proceedings of the National Academy of Sciences of the United States of America
  111 (17): 6131-6138; Apr 2014  
[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]

RAMPAGE: Promoter activity profiling by paired-end sequencing of 5-complete cDNAs
Batut P,
Gingeras TR

Current Protocols in Molecular Biology
  (0): Unit 25B.11; Nov 11 2013   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]

Non-polyadenylated transcription in embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation
Livyatan I,
Harikumar A,
Nissim-Rafinia M,
Duttagupta R,
Gingeras TR,
Meshorer E

Nucleic Acids Res
  41 (12): 6300-6315; Jul 2013   Nlm
[Abstract]
[DOI] [Full Text]

De novo DNA demethylation and non-coding transcription define active intergenic regulatory elements
Schlesinger F,
Smith AD,
Gingeras TR,
Hannon GJ,
Hodges E

Genome Res
  23 (10): 1601-1614; Jun 28 2013   NLM
[Abstract]
[DOI] [Full Text]

STAR: ultrafast universal RNA-seq aligner
Dobin A,
Davis CA,
Schlesinger F,
Drenkow J,
Zaleski C,
Jha S,
Batut P,
Chaisson M,
Gingeras TR

Bioinformatics
  29 (1): 15-21; Jan 2013   NLM
[Abstract]
[DOI] [Full Text]

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression
Batut PJ,
Dobin A,
Plessy C,
Carninci P,
Gingeras TR

Genome Res
  23 (1): 169-180; Jan 2013   NLM
[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,
Vielmetter J,
Partridge EC,
Varley KE,
Gasper C,
Bansal A,
Pepke S,
Jain P,
Amrhein H,
Bowling KM,
Anaya M,
Cross MK,
Muratet MA,
Newberry KM,
McCue K,
Nesmith AS,
Fisher-Aylor KI,
Pusey B,
DeSalvo G,
Parker SL,
Balasubramanian S,
Davis NS,
Meadows SK,
Eggleston T,
Newberry JS,
Levy SE,
Absher DM,
Wong WH,
Blow MJ,
Visel A,
Pennachio LA,
Petrykowska HM,
Abyzov A,
Aken B,
Barrell D,
Barson G,
Berry A,
Bignell A,
Boychenko V,
Bussotti G,
Davidson C,
Despacio-Reyes G,
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