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9 Article(s) on File
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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]

The DNA60IFX contest
Schatz MC,
Taylor J,
Schelhorn SE

Genome Biol
  14 (6): 124; Jun 28 2013   NLM
[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,
Diekhans M,
Ezkurdia I,
Frankish A,
Gilbert J,
Gonzalez JM,
Griffiths E,
Harte R,
Hendrix DA,
Hunt T,
Jungreis I,
Kay M,
Khurana E,
Leng J,
Lin MF,
Loveland J,
Lu Z,
Manthravadi D,
Mariotti M,
Mudge J,
Mukherjee G,
Notredame C,
Pei BK,
Rodriguez JM,
Saunders G,
Sboner A,
Searle S,
Sisu C,
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,
Ebersol AK,
Frum T,
Garg K,
Gist E,
Hansen RS,
Boatman L,
Haugen E,
Humbert R,
Johnson AK,
Johnson EM,
Kutyavin TV,
Lee K,
Lotakis D,
Maurano MT,
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,
Stamatoyannopoulos G,
Beal K,
Brazma A,
Flicek P,
Johnson N,
Lukk M,
Luscombe NM,
Sobral D,
Vaquerizas JM,
Batzoglou S,
Sidow A,
Hussami N,
Kyriazopoulou-Panagi S,
Libbrecht MW,
Schaub MA,
Miller W,
Bickel PJ,
Banfai B,
Boley NP,
Huang HY,
Li JJ,
Noble WS,
Bilmes JA,
Buske OJ,
Sahu AD,
Kharchenko PV,
Park PJ,
Baker D,
Taylor J,
Lin XY,
Lochovsky L,
Min R,
Encode Project Conso

Nature
  489 (7414): 57-74; Sep 6 2012  
[Abstract]
[DOI] [Full Text]

An encyclopedia of mouse DNA elements (Mouse ENCODE)
Stamatoyannopoulos JA,
Snyder M,
Hardison R,
Ren B,
Gingeras T,
Gilbert DM,
Groudine M,
Bender M,
Kaul R,
Canfield T,
Giste E,
Johnson A,
Zhang M,
Balasundaram G,
Byron R,
Roach V,
Sabo PJ,
Sandstrom R,
Stehling AS,
Thurman RE,
Weissman SM,
Cayting P,
Hariharan M,
Lian J,
Cheng Y,
Landt SG,
Ma ZH,
Wold BJ,
Dekker J,
Crawford GE,
Keller CA,
Wu WS,
Morrissey C,
Kumar SA,
Mishra T,
Jain D,
Byrska-Bishop M,
Blankenberg D,
Lajoie BR,
Jain G,
Sanyal A,
Chen KB,
Denas O,
Taylor J,
Blobel GA,
Weiss MJ,
Pimkin M,
Deng WL,
Marinov GK,
Williams BA,
Fisher-Aylor KI,
Desalvo G,
Kiralusha A,
Trout D,
Amrhein H,
Mortazavi A,
Edsall L,
McCleary D,
Kuan S,
Shen Y,
Yue F,
Ye Z,
Davis CA,
Zaleski C,
Jha S,
Xue CH,
Dobin A,
Lin W,
Fastuca M,
Wang HI,
Guigo R,
Djebali S,
Lagarde J,
Ryba T,
Sasaki T,
Malladi VS,
Cline MS,
Kirkup VM,
Learned K,
Rosenbloom KR,
Kent WJ,
Feingold EA,
Good PJ,
Pazin M,
Lowdon RF,
Adams LB,
Mouse EC

Genome Biology
  13 (8): Aug 13 2012  
[Abstract]
[DOI] [Full Text]

Taking the Next Step: Building an Arabidopsis Information Portal
Baerenfaller K,
Bastow R,
Beynon J,
Brady S,
Brendel V,
Donaldson S,
Dooley R,
Forster M,
Friesner J,
Gifford D,
Grotewold E,
Gutierrez R,
Huala E,
Jaiswal P,
Joshi H,
Kersey P,
Liu L,
Loraine A,
Lyons E,
May S,
Mayer K,
MacLean D,
Meyers B,
Mueller L,
Muller R,
Muller HM,
Ouellette F,
Pires JC,
Provart N,
Staiger D,
Stanzione D,
Taylor J,
Taylor C,
Town C,
Toyoda T,
Vaughn M,
Walsh S,
Ware D,
Weckwerth W,
Int Arabidopsis I

Plant Cell
  24 (6): 2248-2256; Jun 2012  
[Abstract]
[DOI] [Full Text]

Manipulation of FASTQ data with Galaxy
Blankenberg D,
Gordon A,
Von Kuster G,
Coraor N,
Taylor J,
Nekrutenko A

Bioinformatics
  26 (14): 1783-1785; Jul 2010   PMCID: PMC2894519
[Abstract]
[DOI] [Full Text] [PDF]

Windshield splatter analysis with the Galaxy metagenomic pipeline
Pond SK,
Wadhawan S,
Chiaromonte F,
Ananda G,
Chung WY,
Taylor J,
Nekrutenko A

Genome Research
  19 (11): 2144-2153; Oct 9 2009   PMC2775585
[Abstract]
[DOI] [Full Text] [PDF]

Genome analysis of the platypus reveals unique signatures of evolution
Warren WC,
Hillier LW,
Marshall Graves JA,
Birney E,
Ponting CP,
Grutzner F,
Belov K,
Miller W,
Clarke L,
Chinwalla AT,
Yang SP,
Heger A,
Locke DP,
Miethke P,
Waters PD,
Veyrunes F,
Fulton L,
Fulton B,
Graves T,
Wallis J,
Puente XS,
Lopez-Otin C,
Ordonez GR,
Eichler EE,
Chen L,
Cheng Z,
Deakin JE,
Alsop A,
Thompson K,
Kirby P,
Papenfuss AT,
Wakefield MJ,
Olender T,
Lancet D,
Huttley GA,
Smit AF,
Pask A,
Temple-Smith P,
Batzer MA,
Walker JA,
Konkel MK,
Harris RS,
Whittington CM,
Wong ES,
Gemmell NJ,
Buschiazzo E,
Vargas Jentzsch IM,
Merkel A,
Schmitz J,
Zemann A,
Churakov G,
Kriegs JO,
Brosius J,
Murchison EP,
Sachidanandam R,
Smith C,
Hannon GJ,
Tsend-Ayush E,
McMillan D,
Attenborough R,
Rens W,
Ferguson-Smith M,
Lefevre CM,
Sharp JA,
Nicholas KR,
Ray DA,
Kube M,
Reinhardt R,
Pringle TH,
Taylor J,
Jones RC,
Nixon B,
Dacheux JL,
Niwa H,
Sekita Y,
Huang X,
Stark A,
Kheradpour P,
Kellis M,
Flicek P,
Chen Y,
Webber C,
Hardison R,
Nelson J,
Hallsworth-Pepin K,
Delehaunty K,
Markovic C,
Minx P,
Feng Y,
Kremitzki C,
Mitreva M,
Glasscock J,
Wylie T,
Wohldmann P,
Thiru P,
Nhan MN,
Pohl CS,
Smith SM,
Hou S,
Renfree MB,
Mardis ER,
Wilson RK

Nature
  453 (7192): 175-83; May 8 2008   PMC2803040
[Abstract]
[DOI] [Full Text] [PDF]

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,
Day N,
Dhami P,
Dillon SC,
Dorschner MO,
Fiegler H,
Giresi PG,
Goldy J,
Hawrylycz M,
Haydock A,
Humbert R,
James KD,
Johnson BE,
Johnson EM,
Frum TT,
Rosenzweig ER,
Karnani N,
Lee K,
Lefebvre GC,
Navas PA,
Neri F,
Parker SC,
Sabo PJ,
Sandstrom R,
Shafer A,
Vetrie D,
Weaver M,
Wilcox S,
Yu M,
Collins FS,
Dekker J,
Lieb JD,
Tullius TD,
Crawford GE,
Sunyaev S,
Noble WS,
Dunham I,
Denoeud F,
Reymond A,
Kapranov P,
Rozowsky J,
Zheng D,
Castelo R,
Frankish A,
Harrow J,
Ghosh S,
Sandelin A,
Hofacker IL,
Baertsch R,
Keefe D,
Dike S,
Cheng J,
Hirsch HA,
Sekinger EA,
Lagarde J,
Abril JF,
Shahab A,
Flamm C,
Fried C,
Hackermüller J,
Hertel J,
Lindemeyer M,
Missal K,
Tanzer A,
Washietl S,
Korbel J,
Emanuelsson O,
Pedersen JS,
Holroyd N,
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Swarbreck D,
Matthews N,
Dickson MC,
Thomas DJ,
Weirauch MT,
Gilbert J,
Drenkow J,
Bell I,
Zhao X,
Srinivasan KG,
Sung WK,
Ooi HS,
Chiu KP,
Foissac S,
Alioto T,
Brent M,
Pachter L,
Tress ML,
Valencia A,
Choo SW,
Choo CY,
Ucla C,
Manzano C,
Wyss C,
Cheung E,
Clark TG,
Brown JB,
Ganesh M,
Patel S,
Tammana H,
Chrast J,
Henrichsen CN,
Kai C,
Kawai J,
Nagalakshmi U,
Wu J,
Lian Z,
Lian J,
Newburger P,
Zhang X,
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Miller W,
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Kim J,
Bhinge AA,
Jiang N,
Liu J,
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Vega VB,
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Yang A,
Moqtaderi Z,
Zhu Z,
Xu X,
Squazzo S,
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Inman D,
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Rada-Iglesias A,
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Langford CF,
Nix DA,
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Hartman S,
Urban AE,
Kraus P,
Van Calcar S,
Heintzman N,
Hoon Kim T,
Wang K,
Qu C,
Hon G,
Luna R,
Glass CK,
Rosenfeld MG,
Aldred SF,
Cooper SJ,
Halees A,
Lin JM,
Shulha HP,
Xu M,
Haidar JN,
Yu Y,
Iyer VR,
Green RD,
Wadelius C,
Farnham PJ,
Ren B,
Harte RA,
Hinrichs AS,
Trumbower H,
Clawson H,
Hillman-Jackson J,
Zweig AS,
Smith K,
Thakkapallayil A,
Barber G,
Kuhn RM,
Karolchik D,
Armengol L,
Bird CP,
De Bakker PI,
Kern AD,
Lopez-Bigas N,
Martin JD,
Stranger BE,
Woodroffe A,
Davydov E,
Dimas A,
Eyras E,
Hallgrímsdóttir IB,
Huppert J,
Zody MC,
Abecasis GR,
Estivill X,
Bouffard GG,
Guan X,
Hansen NF,
Idol JR,
Maduro VV,
Maskeri B,
McDowell JC,
Park M,
Thomas PJ,
Young AC,
Blakesley RW,
Muzny DM,
Sodergren E,
Wheeler DA,
Worley KC,
Jiang H,
Weinstock GM,
Gibbs RA,
Graves T,
Fulton R,
Mardis ER,
Wilson RK,
Clamp M,
Cuff J,
Gnerre S,
Jaffe DB,
Chang JL,
Lindblad-Toh K,
Lander ES,
Koriabine M,
Nefedov M,
Osoegawa K,
Yoshinaga Y,
Zhu B,
De Jong PJ

Nature
  447 (7146): 799-816; 2007  
[Abstract]
[DOI] [Full Text]


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