|
π’
|
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Bo Li,
Colin N. Dewey
|
14 |
2011 |
14
π’
|
|
π
|
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
23 auth.
B. Haas,
A. Papanicolaou,
M. Yassour,
M. Grabherr,
Philip D. Blood,
Joshua C. Bowden,
M. B. Couger,
David A. Eccles,
Bo Li,
Matthias Lieber,
...
M. MacManes,
M. Ott,
Joshua Orvis,
N. Pochet,
F. Strozzi,
N. Weeks,
R. Westerman,
T. William,
Colin N. Dewey,
R. Henschel,
Richard D. LeDuc,
N. Friedman,
A. Regev
|
12 |
2013 |
12
π
|
|
π
|
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
310 auth.
E. Birney,
J. Stamatoyannopoulos,
A. Dutta,
R. GuigΓ³,
T. Gingeras,
E. Margulies,
Z. Weng,
M. Snyder,
E. Dermitzakis,
R. Thurman,
Michael S. Kuehn,
Christopher M. Taylor,
Shane J. Neph,
Christoph M. Koch,
S. Asthana,
...
A. Malhotra,
I. Adzhubei,
J. Greenbaum,
R. Andrews,
Paul Flicek,
Patrick J Boyle,
Hua Cao,
N. Carter,
Gayle K. Clelland,
S. Davis,
Nathan Day,
P. Dhami,
Shane C. Dillon,
M. Dorschner,
H. Fiegler,
P. Giresi,
J. Goldy,
M. Hawrylycz,
Andrew K. Haydock,
R. Humbert,
K. James,
Brett E. Johnson,
Ericka M. Johnson,
Tristan Frum,
Elizabeth R. Rosenzweig,
N. Karnani,
K. Lee,
Gregory Lefebvre,
P. Navas,
Fidencio V. Neri,
Stephen C. J. Parker,
P. Sabo,
R. Sandstrom,
A. Shafer,
D. Vetrie,
M. Weaver,
S. Wilcox,
Man Yu,
F. Collins,
J. Dekker,
J. Lieb,
T. Tullius,
G. Crawford,
S. Sunyaev,
W. S. Noble,
I. Dunham,
F. Denoeud,
A. Reymond,
P. Kapranov,
J. Rozowsky,
D. Zheng,
R. Castelo,
A. Frankish,
J. Harrow,
Srinka Ghosh,
A. Sandelin,
I. Hofacker,
R. Baertsch,
Damian Keefe,
S. Dike,
Jill Cheng,
H. Hirsch,
E. Sekinger,
Julien Lagarde,
J. F. Abril,
Atif Shahab,
Christoph Flamm,
C. Fried,
J. HackermΓΌller,
Jana Hertel,
Manja Lindemeyer,
Kristin Missal,
Andrea Tanzer,
Stefan Washietl,
J. Korbel,
O. Emanuelsson,
J. S. Pedersen,
N. Holroyd,
Ruth Taylor,
D. Swarbreck,
N. Matthews,
M. Dickson,
D. Thomas,
M. Weirauch,
J. Gilbert,
J. Drenkow,
I. Bell,
X. Zhao,
K. Srinivasan,
W. Sung,
H. Ooi,
K. Chiu,
S. Foissac,
T. Alioto,
M. Brent,
L. Pachter,
M. Tress,
A. Valencia,
S. Choo,
C. Choo,
C. Ucla,
C. Manzano,
Carine Wyss,
E. Cheung,
T. Clark,
James B. Brown,
M. Ganesh,
Sandeep Patel,
H. Tammana,
Jacqueline Chrast,
Charlotte N. Henrichsen,
C. Kai,
J. Kawai,
Ugrappa Nagalakshmi,
Jiaqian Wu,
Zheng Lian,
Jin Lian,
P. Newburger,
Xueqing Zhang,
P. Bickel,
J. Mattick,
Piero Carninci,
Y. Hayashizaki,
S. Weissman,
T. Hubbard,
R. M. Myers,
J. Rogers,
P. Stadler,
T. Lowe,
Chia-Lin Wei,
Y. Ruan,
K. Struhl,
M. Gerstein,
S. Antonarakis,
Yutao Fu,
E. Green,
Ulas KaraΓΆz,
A. Siepel,
James Taylor,
L. Liefer,
K. Wetterstrand,
P. Good,
E. Feingold,
M. Guyer,
G. Cooper,
G. Asimenos,
Colin N. Dewey,
Minmei Hou,
S. Nikolaev,
J. Montoya-Burgos,
A. LΓΆytynoja,
S. Whelan,
F. Pardi,
Tim Massingham,
Haiyan Huang,
Na Zhang,
I. Holmes,
J. Mullikin,
A. Ureta-Vidal,
B. Paten,
Michael R. Seringhaus,
D. Church,
K. Rosenbloom,
W. Kent,
Eric A. Stone,
S. Batzoglou,
N. Goldman,
R. Hardison,
D. Haussler,
Webb Miller,
A. Sidow,
N. Trinklein,
Zhengdong D. Zhang,
Leah Barrera,
R. Stuart,
D. King,
A. Ameur,
Stefan Enroth,
M. Bieda,
Jonghwan Kim,
A. Bhinge,
N. Jiang,
Jun Liu,
Fei Yao,
V. Vega,
C. Lee,
A. Yang,
Z. Moqtaderi,
Zhou Zhu,
Xiaoqin Xu,
S. Squazzo,
M. Oberley,
David Inman,
Michael A. Singer,
T. Richmond,
Kyle J. Munn,
Γ. Rada-Iglesias,
O. Wallerman,
J. Komorowski,
J. Fowler,
Phillippe Couttet,
Alexander W. Bruce,
O. Dovey,
P. Ellis,
C. Langford,
D. Nix,
G. Euskirchen,
S. Hartman,
A. Urban,
P. Kraus,
Sara Van Calcar,
Nathaniel D. Heintzman,
Tae Hoon Kim,
Kun Wang,
Chunxu Qu,
G. Hon,
R. Luna,
C. Glass,
M. Rosenfeld,
S. F. Aldred,
S. Cooper,
Anason S. Halees,
J. M. Lin,
H. Shulha,
Xiaoling Zhang,
Mousheng Xu,
Jaafar N. Haidar,
Yon-Jong Yu,
V. Iyer,
Roland Green,
C. Wadelius,
P. Farnham,
B. Ren,
R. Harte,
A. Hinrichs,
Heather Trumbower,
H. Clawson,
Jennifer Hillman-Jackson,
A. Zweig,
Kayla E. Smith,
Archana Thakkapallayil,
G. Barber,
R. Kuhn,
D. Karolchik,
L. Armengol,
C. Bird,
P. D. de Bakker,
Andrew D. Kern,
N. LΓ³pez-Bigas,
Joel D Martin,
B. Stranger,
A. Woodroffe,
Eugene Davydov,
A. Dimas,
E. Eyras,
Ingileif B. HallgrΓmsdΓ³ttir,
J. Huppert,
M. Zody,
G. Abecasis,
X. Estivill,
G. Bouffard,
Xiaobin Guan,
Nancy F. Hansen,
J. Idol,
V. Maduro,
Baishali Maskeri,
Jennifer C Mcdowell,
Morgan Park,
Pamela J. Thomas,
Alice C. Young,
R. Blakesley,
D. Muzny,
E. Sodergren,
D. Wheeler,
K. Worley,
Huaiyang Jiang,
G. Weinstock,
R. Gibbs,
T. Graves,
R. Fulton,
E. Mardis,
R. Wilson,
M. Clamp,
James A. Cuff,
S. Gnerre,
D. Jaffe,
Jean L. Chang,
K. Lindblad-Toh,
E. Lander,
M. Koriabine,
M. Nefedov,
K. Osoegawa,
Y. Yoshinaga,
B. Zhu,
P. D. de Jong
|
12 |
2007 |
12
π
|
|
π
|
Initial sequencing and comparative analysis of the mouse genome.
222 auth.
R. Waterston,
K. Lindblad-Toh,
E. Birney,
J. Rogers,
J. F. Abril,
P. Agarwal,
R. Agarwala,
R. Ainscough,
M. Alexandersson,
Peter An,
S. Antonarakis,
J. Attwood,
R. Baertsch,
J. Bailey,
K. Barlow,
...
S. Beck,
E. M. Berry,
B. Birren,
Toby Bloom,
P. Bork,
M. Botcherby,
Nicolas L. Bray,
M. Brent,
Daniel G. Brown,
Stephen Brown,
C. Bult,
J. Burton,
Jonathan Butler,
R. Campbell,
Piero Carninci,
S. Cawley,
Francesca Chiaromonte,
A. Chinwalla,
D. Church,
M. Clamp,
C. Clee,
F. Collins,
L. Cook,
R. Copley,
A. Coulson,
O. Couronne,
James A. Cuff,
V. Curwen,
T. Cutts,
M. Daly,
R. David,
J. Davies,
K. Delehaunty,
J. Deri,
E. Dermitzakis,
Colin N. Dewey,
N. Dickens,
M. Diekhans,
S. Dodge,
I. Dubchak,
D. Dunn,
S. Eddy,
L. Elnitski,
Richard D Emes,
P. Eswara,
E. Eyras,
A. Felsenfeld,
Ginger A. Fewell,
P. Flicek,
Karen Foley,
W. Frankel,
L. Fulton,
R. Fulton,
T. Furey,
D. Gage,
R. Gibbs,
GwΓͺnlyn Glusman,
S. Gnerre,
N. Goldman,
L. Goodstadt,
D. Grafham,
T. Graves,
E. Green,
S. Gregory,
R. GuigΓ³,
M. Guyer,
R. Hardison,
D. Haussler,
Y. Hayashizaki,
Deana W. LaHillier,
A. Hinrichs,
W. Hlavina,
T. Holzer,
F. Hsu,
A. Hua,
T. Hubbard,
A. Hunt,
I. Jackson,
D. Jaffe,
L. S. Johnson,
Matthew C. Jones,
T. A. Jones,
A. Joy,
Michael Kamal,
E. Karlsson,
D. Karolchik,
A. Kasprzyk,
J. Kawai,
Evan Keibler,
C. Kells,
W. Kent,
Andrew W. Kirby,
D. Kolbe,
I. Korf,
R. Kucherlapati,
E. Kulbokas,
D. Kulp,
Tom Landers,
J. Leger,
Steven Leonard,
Ivica Letunic,
R. Levine,
Jia Li,
Ming Li,
C. Lloyd,
S. Lucas,
Bin Ma,
D. Maglott,
E. Mardis,
L. Matthews,
E. Mauceli,
John Mayer,
M. McCarthy,
W. McCombie,
Stuart Mclaren,
K. McLay,
J. McPherson,
J. Meldrim,
B. Meredith,
J. Mesirov,
W. Miller,
T. Miner,
Emmanuel Mongin,
K. Montgomery,
M. Morgan,
R. Mott,
J. Mullikin,
D. Muzny,
W. Nash,
J. Nelson,
M. Nhan,
R. Nicol,
Z. Ning,
C. Nusbaum,
M. OβConnor,
Y. Okazaki,
K. Oliver,
E. Overton-Larty,
L. Pachter,
GenΓs Parra,
K. Pepin,
Jane L. Peterson,
P. Pevzner,
R. Plumb,
C. Pohl,
Alexander Poliakov,
Tracy C. Ponce,
C. Ponting,
Simon C. Potter,
M. Quail,
A. Reymond,
B. Roe,
K. Roskin,
E. Rubin,
A. Rust,
R. Santos,
V. Sapojnikov,
Brian Schultz,
J. Schultz,
M. Schwartz,
S. Schwartz,
C. Scott,
S. Seaman,
S. Searle,
Ted Sharpe,
A. Sheridan,
R. Shownkeen,
S. Sims,
J. Singer,
G. Slater,
A. Smit,
Douglas Smith,
B. Spencer,
Arne Stabenau,
N. Stange-thomann,
C. Sugnet,
M. Suyama,
G. Tesler,
J. Thompson,
D. Torrents,
E. Trevaskis,
J. Tromp,
C. Ucla,
A. Ureta-Vidal,
J. Vinson,
A. Niederhausern,
C. Wade,
M. Wall,
R. Weber,
R. Weiss,
M. Wendl,
A. West,
K. Wetterstrand,
R. Wheeler,
S. Whelan,
Jamey Wierzbowski,
D. Willey,
Sophie T. Williams,
R. Wilson,
E. Winter,
K. Worley,
D. Wyman,
Shan Yang,
Shiaw-Pyng Yang,
E. Zdobnov,
M. Zody,
E. Lander
|
12 |
2002 |
12
π
|
|
π
|
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
175 auth.
L. Hillier,
W. Miller,
E. Birney,
W. Warren,
R. Hardison,
C. Ponting,
P. Bork,
D. Burt,
M. Groenen,
M. Delany,
J. Dodgson,
A. Chinwalla,
P. Cliften,
S. Clifton,
K. Delehaunty,
...
C. Fronick,
R. Fulton,
T. Graves,
Colin L. Kremitzki,
Daniel Layman,
V. Magrini,
J. McPherson,
T. Miner,
P. Minx,
W. Nash,
M. Nhan,
J. Nelson,
Lachlan Oddy,
C. Pohl,
Jennifer Randall-Maher,
Scott M. Smith,
J. Wallis,
Shiaw-Pyng Yang,
Michael N Romanov,
C. Rondelli,
Bob Paton,
Jacqueline Smith,
D. Morrice,
Laura M. Daniels,
H. Tempest,
L. Robertson,
J. Masabanda,
D. Griffin,
A. Vignal,
V. Fillon,
L. Jacobbson,
S. Kerje,
L. Andersson,
R. Crooijmans,
J. Aerts,
J. J. Poel,
H. Ellegren,
R. B. Caldwell,
S. Hubbard,
D. Grafham,
A. Kierzek,
Stuart Mclaren,
I. Overton,
H. Arakawa,
K. Beattie,
Yuri Bezzubov,
Paul E. Boardman,
J. Bonfield,
M. Croning,
R. Davies,
M. Francis,
S. Humphray,
C. Scott,
Ruth Taylor,
C. Tickle,
W. Brown,
J. Rogers,
J. Buerstedde,
Stuart A. Wilson,
L. Stubbs,
I. Ovcharenko,
L. Gordon,
S. Lucas,
Marcia M. Miller,
H. Inoko,
T. Shiina,
J. Kaufman,
J. Salomonsen,
K. Skjoedt,
G. Wong,
Jun Wang,
Bin Liu,
Jian Wang,
Jun Yu,
Huanming Yang,
M. Nefedov,
M. Koriabine,
P. Dejong,
L. Goodstadt,
C. Webber,
N. Dickens,
Ivica Letunic,
M. Suyama,
D. Torrents,
C. V. Mering,
E. Zdobnov,
K. Makova,
A. Nekrutenko,
L. Elnitski,
P. Eswara,
D. King,
Shan Yang,
S. Tyekucheva,
Anusha Radakrishnan,
Robert S. Harris,
Francesca Chiaromonte,
James Taylor,
Jianbin He,
M. Rijnkels,
S. Griffiths-Jones,
A. Ureta-Vidal,
M. M. Hoffman,
Jessica Severin,
S. Searle,
A. Law,
D. Speed,
D. Waddington,
Ze Cheng,
Eray TΓΌzΓΌn,
E. Eichler,
Z. Bao,
P. Flicek,
David D. Shteynberg,
M. Brent,
J. Bye,
E. Huckle,
Sourav Chatterji,
Colin N. Dewey,
L. Pachter,
A. Kouranov,
Z. Mourelatos,
A. Hatzigeorgiou,
A. Paterson,
R. Ivarie,
Mikael BrandstrΓΆm,
Erik Axelsson,
N. BackstrΓΆm,
S. Berlin,
M. Webster,
O. PourquiΓ©,
A. Reymond,
C. Ucla,
S. Antonarakis,
M. Long,
J. Emerson,
E. BetrΓ‘n,
I. Dupanloup,
H. Kaessmann,
A. Hinrichs,
G. Bejerano,
T. Furey,
R. Harte,
B. Raney,
A. Siepel,
W. Kent,
D. Haussler,
E. Eyras,
R. Castelo,
J. F. Abril,
S. Castellano,
F. Camara,
GenΓs Parra,
R. GuigΓ³,
G. Bourque,
G. Tesler,
P. Pevzner,
A. Smit,
L. Fulton,
E. Mardis,
R. Wilson
|
11 |
2004 |
11
π
|
|
π
|
The ENCODE (ENCyclopedia Of DNA Elements) Project
197 auth.
E. Feingold,
P. Good,
M. Guyer,
S. Kamholz,
L. Liefer,
K. Wetterstrand,
F. Collins,
T. Gingeras,
D. Kampa,
E. Sekinger,
Jill Cheng,
H. Hirsch,
Srinka Ghosh,
Z. Zhu,
Sandeep Patel,
...
A. Piccolboni,
A. Yang,
H. Tammana,
S. Bekiranov,
P. Kapranov,
R. Harrison,
G. Church,
K. Struhl,
B. Ren,
Tae Hoon Kim,
Leah Barrera,
Chunxu Qu,
S. V. Calcar,
R. Luna,
C. Glass,
M. Rosenfeld,
R. GuigΓ³,
S. Antonarakis,
E. Birney,
M. Brent,
L. Pachter,
A. Reymond,
E. Dermitzakis,
Colin N. Dewey,
Damian Keefe,
F. Denoeud,
Julien Lagarde,
J. Ashurst,
T. Hubbard,
J. Wesselink,
R. Castelo,
E. Eyras,
R. Myers,
A. Sidow,
S. Batzoglou,
N. Trinklein,
S. Hartman,
S. F. Aldred,
Elizabeth Anton,
D. I. Schroeder,
S. Marticke,
Leann Nguyen,
J. Schmutz,
J. Grimwood,
M. Dickson,
G. Cooper,
Eric A. Stone,
G. Asimenos,
M. Brudno,
Anindya Dutta,
N. Karnani,
Christopher M. Taylor,
H. K. Kim,
G. Robins,
G. Stamatoyannopoulos,
J. Stamatoyannopoulos,
M. Dorschner,
P. Sabo,
M. Hawrylycz,
R. Humbert,
J. Wallace,
Min Yu,
P. Navas,
M. McArthur,
William Stafford Noble,
I. Dunham,
Christof Koch,
R. Andrews,
Gayle K. Clelland,
S. Wilcox,
J. Fowler,
K. James,
Paul T. Groth,
O. Dovey,
P. Ellis,
Vicki L. Wraight,
A. Mungall,
P. Dhami,
H. Fiegler,
C. Langford,
N. Carter,
D. Vetrie,
M. Snyder,
G. Euskirchen,
A. Urban,
Ugrappa Nagalakshmi,
J. Rinn,
George V. Popescu,
Paul Bertone,
S. Hartman,
J. Rozowsky,
O. Emanuelsson,
Thomas E. Royce,
Sambath Chung,
M. Gerstein,
Zheng Lian,
Jin Lian,
Y. Nakayama,
S. Weissman,
V. Ε tolc,
W. Tongprasit,
H. Sethi,
Steven J. M. Jones,
M. Marra,
H. Shin,
J. Schein,
M. Clamp,
K. Lindblad-Toh,
Jean L. Chang,
D. Jaffe,
Michael Kamal,
E. Lander,
T. Mikkelsen,
J. Vinson,
M. Zody,
P. Jong,
K. Osoegawa,
M. Nefedov,
B. Zhu,
A. D. Baxevanis,
T. Wolfsberg,
G. Crawford,
J. Whittle,
I. Holt,
T. Vasicek,
D. Zhou,
S. Luo,
E. Green,
G. Bouffard,
E. Margulies,
M. Portnoy,
Nancy F. Hansen,
Pamela J. Thomas,
Jennifer C Mcdowell,
Baishali Maskeri,
Alice C. Young,
J. Idol,
R. Blakesley,
G. Schuler,
W. Miller,
R. Hardison,
L. Elnitski,
P. Shah,
S. Salzberg,
M. PerΘea,
William H. Majoros,
D. Haussler,
D. Thomas,
K. Rosenbloom,
H. Clawson,
A. Siepel,
W. Kent,
Z. Weng,
S. Jin,
Anason S. Halees,
H. Burden,
U. Karaoz,
Yutao Fu,
Yong Yu,
Chunming Ding,
C. Cantor,
R. Kingston,
J. Dennis,
Roland Green,
Michael A. Singer,
T. Richmond,
J. Norton,
P. Farnham,
M. Oberley,
D. Inman,
M. McCormick,
H. Kim,
C. Middle,
M. Pirrung,
Xiang-Dong Fu,
Y. S. Kwon,
Z. Ye,
J. Dekker,
T. Tabuchi,
N. Gheldof,
J. Dostie,
S. Harvey
|
11 |
2004 |
11
π
|
|
π
|
Genome sequence of the Brown Norway rat yields insights into mammalian evolution
228 auth.
R. Gibbs,
G. Weinstock,
M. Metzker,
D. Muzny,
E. Sodergren,
S. Scherer,
Graham Scott,
David L. Steffen,
K. Worley,
P. Burch,
Geoffrey Okwuonu,
S. Hines,
L. Lewis,
Christine DeRamo,
O. Delgado,
...
S. Dugan-Rocha,
George R. Miner,
M. Morgan,
A. Hawes,
Rachel B. Gill,
Celera,
R. Holt,
M. Adams,
P. Amanatides,
Holly Baden-Tillson,
Mary Barnstead,
Soo H. Chin,
C. Evans,
S. Ferriera,
C. Fosler,
A. Glodek,
Z. Gu,
Donald Jennings,
C. Kraft,
T. Nguyen,
C. Pfannkoch,
Cynthia D. Sitter,
G. Sutton,
J. Venter,
T. Woodage,
Douglas R. Smith,
H. Lee,
E. Gustafson,
P. Cahill,
A. Kana,
L. Doucette-Stamm,
K. Weinstock,
K. Fechtel,
R. Weiss,
D. Dunn,
E. Green,
R. Blakesley,
G. Bouffard,
P. D. de Jong,
K. Osoegawa,
B. Zhu,
M. Marra,
J. Schein,
I. Bosdet,
C. Fjell,
Steven P. Jones,
M. Krzywinski,
Carrie A. Mathewson,
A. Siddiqui,
N. Wye,
J. McPherson,
Shaying Zhao,
C. Fraser,
Jyoti Shetty,
S. Shatsman,
Keita Geer,
Yixin Chen,
Sofyia Abramzon,
W. Nierman,
P. Havlak,
Rui Chen,
K. Durbin,
Amy Egan,
Yanru Ren,
Xing-Zhi Song,
Bingshan Li,
Yue Liu,
X. Qin,
S. Cawley,
A. Cooney,
Lisa M. D'Souza,
Kirt A. Martin,
Jia Qian Wu,
M. Gonzalez-Garay,
Andrew R. Jackson,
Ken J Kalafus,
M. P. McLeod,
A. Milosavljevic,
D. Virk,
A. Volkov,
D. Wheeler,
Zhengdong D. Zhang,
J. Bailey,
E. Eichler,
Eray Tuzun,
E. Birney,
Emmanuel Mongin,
A. Ureta-Vidal,
Cara Woodwark,
E. Zdobnov,
P. Bork,
M. Suyama,
D. Torrents,
M. Alexandersson,
B. Trask,
Janet M. Young,
Hui Huang,
Huajun Wang,
Heming Xing,
Sue Daniels,
D. Gietzen,
Jeanette Schmidt,
Kristian Stevens,
U. Vitt,
J. Wingrove,
F. Camara,
M. Mar AlbΓ ,
J. F. Abril,
R. GuigΓ³,
A. Smit,
I. Dubchak,
E. Rubin,
O. Couronne,
Alexander Poliakov,
N. HΓΌbner,
D. Ganten,
Claudia Goesele,
O. Hummel,
T. Kreitler,
Young-Ae Lee,
J. Monti,
H. Schulz,
H. Zimdahl,
H. Himmelbauer,
H. Lehrach,
H. Jacob,
Susan Bromberg,
J. Gullings-Handley,
M. Jensen-Seaman,
A. Kwitek,
Jozef Lazar,
D. Pasko,
P. Tonellato,
S. Twigger,
C. Ponting,
JosΓ© M Duarte,
S. Rice,
L. Goodstadt,
S. Beatson,
Richard D Emes,
E. Winter,
C. Webber,
P. Brandt,
G. Nyakatura,
Margaret Adetobi,
Francesca Chiaromonte,
L. Elnitski,
P. Eswara,
R. Hardison,
Minmei Hou,
D. Kolbe,
K. Makova,
W. Miller,
A. Nekrutenko,
C. Riemer,
S. Schwartz,
James Taylor,
Shan Yang,
Yi Zhang,
K. Lindpaintner,
T. Andrews,
M. CΓ‘ccamo,
M. Clamp,
Laura Clarke,
V. Curwen,
R. Durbin,
E. Eyras,
S. Searle,
G. Cooper,
S. Batzoglou,
M. Brudno,
A. Sidow,
Eric A. Stone,
B. Payseur,
G. Bourque,
C. LΓ³pez-OtΓn,
X. Puente,
Kushal Chakrabarti,
Sourav Chatterji,
Colin N. Dewey,
L. Pachter,
Nicolas L. Bray,
Von Bing Yap,
A. Caspi,
G. Tesler,
P. Pevzner,
D. Haussler,
K. Roskin,
R. Baertsch,
H. Clawson,
T. Furey,
A. Hinrichs,
D. Karolchik,
W. Kent,
K. Rosenbloom,
Heather Trumbower,
M. Weirauch,
D. Cooper,
P. Stenson,
Bin Ma,
M. Brent,
Manimozhiyan Arumugam,
David D. Shteynberg,
R. Copley,
Martin S. Taylor,
H. Riethman,
U. Mudunuri,
Jane L. Peterson,
M. Guyer,
A. Felsenfeld,
S. Old,
Stephen Mockrin,
F. Collins
|
11 |
2004 |
11
π
|
|
π’
|
RNA-Seq gene expression estimation with read mapping uncertainty
Bo Li,
Victor Ruotti,
R. Stewart,
J. Thomson,
Colin N. Dewey
|
10 |
2009 |
10
π’
|
|
π
|
Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans
13 auth.
D. Begun,
A. K. Holloway,
Kristian Stevens,
L. Hillier,
Yu-Ping Poh,
Matthew W. Hahn,
Phil Nista,
Corbin D. Jones,
Andrew D. Kern,
Colin N. Dewey,
...
L. Pachter,
E. Myers,
C. Langley
|
9 |
2007 |
9
π
|
|
π
|
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
44 auth.
A. Stark,
Michael F. Lin,
Pouya Kheradpour,
J. S. Pedersen,
L. Parts,
J. Carlson,
M. Crosby,
Matthew D. Rasmussen,
Sushmita Roy,
Ameya N. Deoras,
J. Ruby,
J. Brennecke,
E. Hodges,
A. Hinrichs,
A. Caspi,
...
B. Paten,
SeungβWon Park,
Mira V. Han,
Morgan L. Maeder,
Benjamin J. Polansky,
Bryanne E. Robson,
S. Aerts,
J. Helden,
Bassem A. Hassan,
D. Gilbert,
Deborah Eastman,
Michael Rice,
M. Weir,
Matthew W. Hahn,
Yongkyu Park,
Colin N. Dewey,
L. Pachter,
W. Kent,
D. Haussler,
E. Lai,
D. Bartel,
G. Hannon,
T. Kaufman,
M. Eisen,
A. Clark,
Douglas R. Smith,
S. Celniker,
W. Gelbart,
Manolis Kellis
|
9 |
2007 |
9
π
|
|
π
|
A Genome-Wide Map of Conserved MicroRNA Targets in C. elegans
15 auth.
S. Lall,
Dominic GrΓΌn,
A. Krek,
Kevin C. Chen,
Yi-Lu Wang,
Colin N. Dewey,
Pranidhi Sood,
T. Colombo,
Nicolas L. Bray,
P. MacMenamin,
...
Huey-Ling Kao,
K. Gunsalus,
L. Pachter,
F. Piano,
N. Rajewsky
|
8 |
2006 |
8
π
|
|
π¬
|
BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis
B. Larget,
Satish K. Kotha,
Colin N. Dewey,
C. AnΓ©
|
8 |
2010 |
8
π¬
|
|
π
|
De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity
22 auth.
B. Haas,
A. Papanicolaou,
M. Yassour,
M. Grabherr,
Philip D. Blood,
Joshua C. Bowden,
M. B. Couger,
David A. Eccles,
Matthias Lieber,
M. MacManes,
...
M. Ott,
Joshua Orvis,
N. Pochet,
F. Strozzi,
N. Weeks,
R. Westerman,
T. William,
Colin N. Dewey,
R. Henschel,
Richard D. LeDuc,
N. Friedman,
A. Regev
|
8 |
2013 |
8
π
|
|
π
|
Fast Statistical Alignment
8 auth.
R. Bradley,
Adam Roberts,
M. Smoot,
Sudeep Juvekar,
Jaeyoung Do,
Colin N. Dewey,
...
I. Holmes,
L. Pachter
|
8 |
2009 |
8
π
|
|
π
|
Genomic Variation in Natural Populations of Drosophila melanogaster
18 auth.
C. Langley,
Kristian Stevens,
Charis M. CardeΓ±o,
Y. C. G. Lee,
Daniel R. Schrider,
J. Pool,
Sasha A. Langley,
Charlyn Suarez,
Russell B. Corbett-Detig,
Bryan D. Kolaczkowski,
...
Shu Fang,
Phil Nista,
A. K. Holloway,
A. Kern,
Colin N. Dewey,
Yun S. Song,
Matthew W. Hahn,
D. Begun
|
8 |
2012 |
8
π
|
