|
π
|
Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation
36 auth.
Guoliang Li,
Xiaoan Ruan,
Raymond K. Auerbach,
K. Sandhu,
Meizhen Zheng,
Ping Wang,
H. Poh,
Yufen Goh,
Joanne Lim,
Jingyao Zhang,
Hui Shan Sim,
Su Qin Peh,
F. Mulawadi,
C. T. Ong,
Y. Orlov,
...
Shuzhen Hong,
Zhizhuo Zhang,
S. Landt,
D. Raha,
G. Euskirchen,
Chia-Lin Wei,
W. Ge,
Huaien Wang,
Carrie A. Davis,
Katherine I. Fisher-Aylor,
A. Mortazavi,
M. Gerstein,
T. Gingeras,
B. Wold,
Y. Sun,
M. Fullwood,
E. Cheung,
E. Liu,
W. Sung,
M. Snyder,
Y. Ruan
|
10 |
2012 |
10
π
|
|
π
|
A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
314 auth.
R. Myers,
J. Stamatoyannopoulos,
M. Snyder,
I. Dunham,
R. Hardison,
B. Bernstein,
T. Gingeras,
W. Kent,
E. Birney,
B. Wold,
G. Crawford,
C. Epstein,
N. Shoresh,
J. Ernst,
T. Mikkelsen,
...
Pouya Kheradpour,
Xiaolan Zhang,
Li Wang,
Robbyn Issner,
Michael J. Coyne,
Timothy J. Durham,
Manching Ku,
Thanh Truong,
L. D. Ward,
Robert C. Altshuler,
Michael F. Lin,
Manolis Kellis,
Carrie A. Davis,
P. Kapranov,
A. Dobin,
C. Zaleski,
F. Schlesinger,
P. Batut,
S. Chakrabortty,
Sonali Jha,
Wei Lin,
J. Drenkow,
Huaien Wang,
K. Bell,
I. Bell,
Hui Gao,
E. Dumais,
Jacqueline Dumais,
S. Antonarakis,
C. Ucla,
C. Borel,
R. GuigΓ³,
S. Djebali,
Julien Lagarde,
C. Kingswood,
Paolo Ribeca,
M. Sammeth,
T. Alioto,
A. Merkel,
Hagen U. Tilgner,
Piero Carninci,
Y. Hayashizaki,
T. Lassmann,
Hazuki Takahashi,
Rehab F Abdelhamid,
G. Hannon,
Katalin Fejes,
Jonathan Preall,
Assaf Gordon,
V. Sotirova,
A. Reymond,
C. Howald,
Emilie AΓ―t Yahya Graison,
Jacqueline Chrast,
Y. Ruan,
Xiaoan Ruan,
Atif Shahab,
W. Poh,
Chia-Lin Wei,
T. Furey,
A. Boyle,
Nathan C. Sheffield,
Lingyun Song,
Yoichiro Shibata,
T. Vales,
D. Winter,
Zhancheng Zhang,
D. London,
Tian-yuan Wang,
Damian Keefe,
V. Iyer,
Bum-Kyu Lee,
Ryan McDaniell,
Zheng Liu,
Anna M. Battenhouse,
A. Bhinge,
J. Lieb,
L. Grasfeder,
Kimberly A. Showers,
P. Giresi,
Seul K.C. Kim,
Christopher Shestak,
Florencia Pauli,
Timothy E. Reddy,
Jason Gertz,
E. Partridge,
Preti Jain,
Rebekka O. Sprouse,
A. Bansal,
Barbara N. Pusey,
M. Muratet,
K. Varley,
K. Bowling,
Kimberly M. Newberry,
Amy S. Nesmith,
Jason A. Dilocker,
S. Parker,
L. Waite,
Krista S. Thibeault,
Kevin Roberts,
D. Absher,
A. Mortazavi,
B. Williams,
G. Marinov,
Diane Trout,
Brandon King,
Kenneth McCue,
Anthony Kirilusha,
Gilberto Desalvo,
Katherine Fisher,
Henry Amrhein,
S. Pepke,
J. Vielmetter,
G. Sherlock,
A. Sidow,
S. Batzoglou,
Rami Rauch,
A. Kundaje,
Maxwell W. Libbrecht,
E. Margulies,
Stephen C. J. Parker,
L. Elnitski,
E. Green,
T. Hubbard,
J. Harrow,
S. Searle,
F. Kokocinski,
B. Aken,
A. Frankish,
T. Hunt,
Gloria Despacio-Reyes,
M. Kay,
Gaurab Mukherjee,
A. Bignell,
Gary Saunders,
Veronika Boychenko,
M. Brent,
M. Baren,
Randall H. Brown,
M. Gerstein,
Ekta Khurana,
S. Balasubramanian,
Hugo Y. K. Lam,
Philip Cayting,
R. Robilotto,
Z. Lu,
T. Derrien,
Andrea Tanzer,
David G. Knowles,
M. Mariotti,
D. Haussler,
R. Harte,
M. Diekhans,
A. Valencia,
M. Tress,
S. Landt,
D. Raha,
Minyi Shi,
G. Euskirchen,
Fabian Grubert,
Maya Kasowski,
Jin Lian,
P. Lacroute,
Youhan Xu,
Hannah Monahan,
Dorrelyn Patacsil,
T. Slifer,
Xinqiong Yang,
Alexandra E. Charos,
Brian D. Reed,
Linfeng Wu,
Raymond K. Auerbach,
L. Habegger,
M. Hariharan,
J. Rozowsky,
A. Abyzov,
S. Weissman,
K. Struhl,
Nathan Lamarre-Vincent,
Marianne Lindahl-Allen,
B. Miotto,
Z. Moqtaderi,
J. D. Fleming,
P. Newburger,
P. Farnham,
S. Frietze,
H. OβGeen,
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Sushma Iyengar,
R. Kaul,
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Hao Wang,
P. Navas,
R. Sandstrom,
P. Sabo,
M. Weaver,
T. Canfield,
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Alex P. Reynolds,
Audra K. Johnson,
Eric Rynes,
Erika Giste,
Shinny Vong,
Jun Neri,
Tristan Frum,
Eric D Nguyen,
Abigail K. Ebersol,
Minerva E. Sanchez,
Hadar H. Sheffer,
D. Lotakis,
E. Haugen,
R. Humbert,
T. Kutyavin,
Tony Shafer,
William Stafford Noble,
J. Dekker,
B. Lajoie,
Amartya Sanyal,
K. Rosenbloom,
T. Dreszer,
B. Raney,
G. Barber,
L. Meyer,
C. A. Sloan,
V. Malladi,
M. Cline,
K. Learned,
Vanessa Swing,
A. Zweig,
B. Rhead,
P. Fujita,
K. Roskin,
D. Karolchik,
R. Kuhn,
S. Wilder,
D. Sobral,
Javier Herrero,
Kathryn M Beal,
M. Lukk,
A. Brazma,
Juan M. Vaquerizas,
N. Luscombe,
P. Bickel,
Nathan Boley,
James B. Brown,
Qunhua Li,
Haiyan Huang,
A. Sboner,
Kevin Y. Yip,
Chao Cheng,
Koon-Kiu Yan,
N. Bhardwaj,
Jing Wang,
L. Lochovsky,
J. Jee,
Theodore Gibson,
Jing Leng,
Jiang Du,
Robert S. Harris,
Giltae Song,
W. Miller,
Bernard B. Suh,
B. Paten,
M. M. Hoffman,
Orion J. Buske,
Z. Weng,
Xianjun Dong,
Jie Wang,
H. Xi,
S. Tenenbaum,
F. Doyle,
S. Chittur,
L. O. Penalva,
T. Tullius,
K. White,
S. Karmakar,
Alec Victorsen,
Nader Jameel,
N. Bild,
R. Grossman,
P. Collins,
N. Trinklein,
Morgan C. Giddings,
Jainab Khatun,
Christopher W. Maier,
Ting Wang,
T. Whitfield,
Xian Chen,
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H. Gunawardena,
E. Feingold,
R. Lowdon,
Laura A. L. Dillon,
P. Good,
B. Risk
|
10 |
2011 |
10
π
|
|
π
|
Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project
131 auth.
M. Gerstein,
Z. Lu,
Eric L. Van Nostrand,
Chao Cheng,
Bradley I. Arshinoff,
Tao Liu,
Kevin Y. Yip,
R. Robilotto,
A. Rechtsteiner,
Kohta Ikegami,
P. Alves,
A. Chateigner,
M. Perry,
M. Morris,
Raymond K. Auerbach,
...
Xin Feng,
Jing Leng,
A. Vielle,
W. Niu,
Kahn Rhrissorrakrai,
A. Agarwal,
Roger P. Alexander,
G. Barber,
Cathleen Brdlik,
J. Brennan,
J. Brouillet,
Adrian Carr,
Ming-Sin Cheung,
H. Clawson,
S. Contrino,
Luke O Dannenberg,
A. Dernburg,
A. Desai,
L. Dick,
A. DoseΜ,
Jiang Du,
Thea A. Egelhofer,
Sevinç Ercan,
G. Euskirchen,
B. Ewing,
E. Feingold,
R. Gassmann,
P. Good,
P. Green,
F. Gullier,
M. Gutwein,
M. Guyer,
L. Habegger,
Ting Han,
J. Henikoff,
Stefan R. Henz,
A. Hinrichs,
H. Holster,
T. Hyman,
A. Iniguez,
J. Janette,
M. Jensen,
Masaomi Kato,
W. Kent,
E. Kephart,
Vishal Khivansara,
Ekta Khurana,
John K. Kim,
P. Kolasinska-Zwierz,
E. Lai,
I. Latorre,
A. Leahey,
S. Lewis,
P. Lloyd,
L. Lochovsky,
R. Lowdon,
Yaniv Lubling,
R. Lyne,
M. MacCoss,
Sebastian D. Mackowiak,
Marco Mangone,
S. McKay,
D. Mecenas,
Gennifer E. Merrihew,
David M. Miller,
A. Muroyama,
J. Murray,
S. Ooi,
Hoang N. Pham,
T. Phippen,
E. Preston,
N. Rajewsky,
Gunnar RΓ€tsch,
Heidi Rosenbaum,
J. Rozowsky,
Kim M Rutherford,
P. Ruzanov,
M. Sarov,
Rajkumar Sasidharan,
A. Sboner,
P. Scheid,
E. Segal,
Hyunjin Shin,
C. Shou,
F. Slack,
C. Slightam,
Richard Smith,
W. C. Spencer,
E. Stinson,
S. Taing,
T. Takasaki,
D. Vafeados,
K. Voronina,
Guilin Wang,
N. Washington,
Christina M. Whittle,
Beijing Wu,
Koon-Kiu Yan,
G. Zeller,
Z. Zha,
Mei Zhong,
Xingliang Zhou,
J. Ahringer,
S. Strome,
K. Gunsalus,
G. Micklem,
X. Liu,
V. Reinke,
Stuart K. Kim,
L. Hillier,
S. Henikoff,
F. Piano,
M. Snyder,
L. Stein,
J. Lieb,
R. Waterston
|
9 |
2010 |
9
π
|
|
π
|
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
9 auth.
J. Rozowsky,
G. Euskirchen,
Raymond K. Auerbach,
Zhengdong D. Zhang,
Theodore Gibson,
R. Bjornson,
...
N. Carriero,
M. Snyder,
M. Gerstein
|
9 |
2009 |
9
π
|
|
π¬
|
The real cost of sequencing: higher than you think!
A. Sboner,
X. Mu,
D. Greenbaum,
Raymond K. Auerbach,
M. Gerstein
|
8 |
2011 |
8
π¬
|
|
π
|
Diverse Roles and Interactions of the SWI/SNF Chromatin Remodeling Complex Revealed Using Global Approaches
9 auth.
G. Euskirchen,
Raymond K. Auerbach,
E. Davidov,
T. Gianoulis,
Guoneng Zhong,
J. Rozowsky,
...
N. Bhardwaj,
M. Gerstein,
M. Snyder
|
7 |
2011 |
7
π
|
|
π¦
|
Mapping accessible chromatin regions using Sono-Seq
9 auth.
Raymond K. Auerbach,
G. Euskirchen,
J. Rozowsky,
Nathan Lamarre-Vincent,
Z. Moqtaderi,
P. Lefrançois,
...
K. Struhl,
M. Gerstein,
M. Snyder
|
7 |
2009 |
7
π¦
|
|
π
|
Phylogeography of Francisella tularensis: Global Expansion of a Highly Fit Clone
18 auth.
Amy J. Vogler,
D. Birdsell,
L. Price,
J. Bowers,
S. Beckstrom-Sternberg,
Raymond K. Auerbach,
James S. Beckstrom-Sternberg,
A. Johansson,
A. Clare,
Jordan L. Buchhagen,
...
J. Petersen,
Talima R. Pearson,
J. Vaissaire,
M. Dempsey,
P. Foxall,
D. Engelthaler,
D. Wagner,
P. Keim
|
7 |
2009 |
7
π
|
|
π
|
Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer
27 auth.
Talima R. Pearson,
P. Giffard,
S. Beckstrom-Sternberg,
Raymond K. Auerbach,
Heidie M. Hornstra,
A. Tuanyok,
E. Price,
M. Glass,
B. Leadem,
James S. Beckstrom-Sternberg,
G. Allan,
J. Foster,
D. Wagner,
R. Okinaka,
S. Sim,
...
O. Pearson,
Zaining Wu,
Jean Chang,
R. Kaul,
A. Hoffmaster,
T. Brettin,
R. Robison,
M. Mayo,
J. Gee,
Patrick Tan,
B. Currie,
P. Keim
|
7 |
2009 |
7
π
|
|
π
|
Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response
22 auth.
Mei Zhong,
W. Niu,
Z. Lu,
M. Sarov,
J. Murray,
J. Janette,
D. Raha,
Karyn L. Sheaffer,
Hugo Y. K. Lam,
E. Preston,
...
C. Slightham,
L. Hillier,
Trisha J. Brock,
A. Agarwal,
Raymond K. Auerbach,
A. Hyman,
M. Gerstein,
S. Mango,
Stuart K. Kim,
R. Waterston,
V. Reinke,
M. Snyder
|
7 |
2010 |
7
π
|
|
π¬
|
SWI/SNF Chromatin-remodeling Factors: Multiscale Analyses and Diverse Functions*
G. Euskirchen,
Raymond K. Auerbach,
M. Snyder
|
7 |
2012 |
7
π¬
|
|
π
|
Genomic islands from five strains of Burkholderia pseudomallei
13 auth.
A. Tuanyok,
B. Leadem,
Raymond K. Auerbach,
S. Beckstrom-Sternberg,
James S. Beckstrom-Sternberg,
M. Mayo,
V. Wuthiekanun,
Thomas Brettin,
W. Nierman,
Sharon J. Peacock,
...
Bart J Currie,
David M. Wagner,
Paul Keim
|
6 |
2008 |
6
π
|
