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13 Article(s) on File
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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]

Diverse epigenetic strategies interact to control epidermal differentiation
Mulder KW,
Wang X,
Escriu C,
Ito Y,
Schwarz RF,
Gillis J,
Sirokmany G,
Donati G,
Uribe-Lewis S,
Pavlidis P,
Murrell A,
Markowetz F,
Watt FM

Nature Cell Biology
  14 (7): 753-763; Jul 2012  
[Abstract]
[DOI] [Full Text]

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
Roy S,
Ernst J,
Kharchenko PV,
Kheradpour P,
Negre N,
Eaton ML,
Landolin JM,
Bristow CA,
Ma LJ,
Lin MF,
Washietl S,
Arshinoff BI,
Ay F,
Meyer PE,
Robine N,
Washington NL,
Di Stefano L,
Berezikov E,
Brown CD,
Candeias R,
Carlson JW,
Carr A,
Jungreis I,
Marbach D,
Sealfon R,
Tolstorukov MY,
Will S,
Alekseyenko AA,
Artieri C,
Booth BW,
Brooks AN,
Dai Q,
Davis CA,
Duff MO,
Feng X,
Gorchakov AA,
Gu TT,
Henikoff JG,
Kapranov P,
Li RH,
MacAlpine HK,
Malone J,
Minoda A,
Nordman J,
Okamura K,
Perry M,
Powell SK,
Riddle NC,
Sakai A,
Samsonova A,
Sandler JE,
Schwartz YB,
Sher N,
Spokony R,
Sturgill D,
van Baren M,
Wan KH,
Yang L,
Yu C,
Feingold E,
Good P,
Guyer M,
Lowdon R,
Ahmad K,
Andrews J,
Berger B,
Brenner SE,
Brent MR,
Cherbas L,
Elgin SC,
Gingeras TR,
Grossman R,
Hoskins RA,
Kaufman TC,
Kent W,
Kuroda MI,
Orr-Weaver T,
Perrimon N,
Pirrotta V,
Posakony JW,
Ren B,
Russell S,
Cherbas P,
Graveley BR,
Lewis S,
Micklem G,
Oliver B,
Park PJ,
Celniker SE,
Henikoff S,
Karpen GH,
Lai EC,
MacAlpine DM,
Stein LD,
White KP,
Kellis M

Science
  330 (6012): 1787-1797; Dec 2010   PMC3192495
[Abstract]
[DOI] [Full Text] [PDF]

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project
Gerstein MB,
Lu ZJ,
Van Nostrand EL,
Cheng C,
Arshinoff BI,
Liu T,
Yip KY,
Robilotto R,
Rechtsteiner A,
Ikegami K,
Alves P,
Chateigner A,
Perry M,
Morris M,
Auerbach RK,
Feng X,
Leng J,
Vielle A,
Niu W,
Rhrissorrakrai K,
Agarwal A,
Alexander RP,
Barber G,
Brdlik CM,
Brennan J,
Brouillet JJ,
Carr A,
Cheung MS,
Clawson H,
Contrino S,
Dannenberg LO,
Dernburg AF,
Desai A,
Dick L,
Dose AC,
Du JA,
Egelhofer T,
Ercan S,
Euskirchen G,
Ewing B,
Feingold EA,
Gassmann R,
Good PJ,
Green P,
Gullier F,
Gutwein M,
Guyer MS,
Habegger L,
Han T,
Henikoff JG,
Henz SR,
Hinrichs A,
Holster H,
Hyman T,
Iniguez AL,
Janette J,
Jensen M,
Kato M,
Kent WJ,
Kephart E,
Khivansara V,
Khurana E,
Kim JK,
Kolasinska-Zwierz P,
Lai EC,
Latorre I,
Leahey A,
Lewis S,
Lloyd P,
Lochovsky L,
Lowdon RF,
Lubling Y,
Lyne R,
MacCoss M,
Mackowiak SD,
Mangone M,
McKay SJ,
Mecenas D,
Merrihew G,
Miller DM,
Muroyama A,
Murray JI,
Ooi SL,
Pham H,
Phippen T,
Preston EA,
Rajewsky N,
Ratsch G,
Rosenbaum H,
Rozowsky J,
Rutherford K,
Ruzanov P,
Sarov M,
Sasidharan R,
Sboner A,
Scheid P,
Segal E,
Shin HJ,
Shou C,
Slack FJ,
Slightam C,
Smith R,
Spencer WC,
Stinson EO,
Taing S,
Takasaki T,
Vafeados D,
Voronina K,
Wang GL,
Washington NL,
Whittle CM,
Wu BJ,
Yan KK,
Zeller G,
Zha Z,
Zhong M,
Zhou XL,
Ahringer J,
Strome S,
Gunsalus KC,
Micklem G,
Liu XS,
Reinke V,
Kim SK,
Hillier LW,
Henikoff S,
Piano F,
Snyder M,
Stein LD,
Lieb JD,
Waterston RH

Science
  330 (6012): 1775-1787; Dec 2010   PMC3142569
[Abstract]
[DOI] [Full Text] [PDF]

Reactome knowledgebase of human biological pathways and processes
Matthews L,
Gopinath G,
Gillespie M,
Caudy M,
Croft D,
de Bono B,
Garapati P,
Hemish J,
Hermjakob H,
Jassal B,
Kanapin A,
Lewis S,
Mahajan S,
May B,
Schmidt E,
Vastrik I,
Wu G,
Birney E,
Stein LD,
DEustachio P

Nucleic Acids Res
  37 (0): D619-22; Jan 2009   PMCID: PMC2686536
[Abstract]
[DOI] [Full Text] [PDF]

Reactome: a knowledge base of biologic pathways and processes
Vastrik I,
DEustachio P,
Schmidt E,
Joshi-Tope G,
Gopinath G,
Croft D,
de Bono B,
Gillespie M,
Jassal B,
Lewis S,
Matthews L,
Wu G,
Birney E,
Stein LD

Genome Biol
  8 (3): R39; 2007  
[Abstract]
[DOI] [Full Text] [PDF]

EGASP: the human ENCODE Genome Annotation Assessment Project
Guigó R,
Flicek P,
Abril JF,
Reymond A,
Lagarde J,
Denoeud F,
Antonarakis S,
Ashburner M,
Bajic VB,
Birney E,
Castelo R,
Eyras E,
Ucla C,
Gingeras TR,
Harrow J,
Hubbard T,
Lewis SE,
Reese MG

Genome Biology
  7 Sup (0): S2.1-31; 2006  
[Abstract]
[Full Text]

Reactome: a knowledgebase of biological pathways
Joshi-Tope G,
Gillespie M,
Vastrik I,
DEustachio P,
Schmidt E,
de Bono B,
Jassal B,
Gopinath GR,
Wu GR,
Matthews L,
Lewis S,
Birney E,
Stein LD

Nucleic Acids Res
  33 (0): D428-32; Jan 1 2005  
[Abstract]
[DOI] [Full Text]

The Sequence Ontology: a tool for the unification of genome annotations
Eilbeck K,
Lewis SE,
Mungall CJ,
Yandell M,
Stein L,
Durbin R,
Ashburner M

Genome Biology
  6 (5): 2005  
[Abstract]
[DOI] [Full Text]

The genome knowledgebase: A resource for biologists and bioinformaticists
Joshi-Tope G,
Vastrik I,
Gopinath GR,
Matthews L,
Schmidt E,
Gillespie M,
DEustachio P,
Jassal B,
Lewis S,
Wu G,
Birney E,
Stein L

Cold Spring Harbor Symposia on Quantitative Biology LXVIII: The genome of Homo Sapiens
  68 237-243; 2003  
[DOI]

The Generic Genome Browser: A building block for a model organism system database
Stein LD,
Mungall C,
Shu SQ,
Caudy M,
Mangone M,
Day A,
Nickerson E,
Stajich JE,
Harris TW,
Arva A,
Lewis S

Genome Research
  12 (10): 1599-1610; Oct 2002  
[Abstract]
[Full Text]

Arabidopsis genes essential for seedling viability: isolation of insertional mutants and molecular cloning
Budziszewski GJ,
Lewis SP,
Glover LW,
Reineke J,
Jones G,
Ziemnik LS,
Lonowski J,
Nyfeler B,
Aux G,
Zhou Q,
McElver J,
Patton DA,
Martienssen R,
Grossniklaus U,
Ma H,
Law M,
Levin JZ

Genetics
  159 (4): 1765-78; Dec 2001  
[Abstract]
[Full Text]

A high-resolution radiation hybrid map of the human genome draft sequence
Olivier M,
Aggarwal A,
Allen J,
Almendras AA,
Bajorek ES,
Beasley EM,
Brady SD,
Bushard JM,
Bustos VI,
Chu A,
Chung TR,
De Witte A,
Denys ME,
Dominguez R,
Fang NY,
Foster BD,
Freudenberg RW,
Hadley D,
Hamilton LR,
Jeffrey TJ,
Kelly L,
Lazzeroni L,
Levy MR,
Lewis SC,
Liu X,
Lopez FJ,
Louie B,
Marquis JP,
Martinez RA,
Matsuura MK,
Misherghi NS,
Norton JA,
Olshen A,
Perkins SM,
Perou AJ,
Piercy C,
Piercy M,
Qin F,
Reif T,
Sheppard K,
Shokoohi V,
Smick GA,
Sun WL,
Stewart EA,
Tejeda JF,
Tran NM,
Trejo T,
Vo NT,
Yan SC,
Zierten DL,
Zhao SY,
Sachidanandam R,
Trask BJ,
Myers RM,
Cox DR

Science
  291 (5507): 1298-+; Feb 2001  
[Abstract]
[Full Text]


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