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GENCODE: The reference human genome annotation for The ENCODE Project
41 auth.
J. Harrow,
A. Frankish,
J. Gonzalez,
Electra Tapanari,
M. Diekhans,
F. Kokocinski,
Bronwen L. Aken,
D. Barrell,
A. Zadissa,
S. Searle,
If H. A. Barnes,
A. Bignell,
Veronika Boychenko,
T. Hunt,
M. Kay,
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Gaurab Mukherjee,
J. Rajan,
Gloria Despacio-Reyes,
Gary I. Saunders,
C. Steward,
R. Harte,
Michael F. Lin,
C. Howald,
Andrea Tanzer,
T. Derrien,
Jacqueline Chrast,
Nathalie Walters,
S. Balasubramanian,
Baikang Pei,
M. Tress,
J. Rodríguez,
Iakes Ezkurdia,
Jeltje van Baren,
M. Brent,
D. Haussler,
Manolis Kellis,
A. Valencia,
A. Reymond,
M. Gerstein,
R. Guigó,
T. Hubbard
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12 |
2012 |
12
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GENCODE reference annotation for the human and mouse genomes
55 auth.
A. Frankish,
M. Diekhans,
Anne-Maud Ferreira,
Rory Johnson,
Irwin Jungreis,
J. Loveland,
Jonathan M. Mudge,
Cristina Sisu,
James C. Wright,
J. Armstrong,
If H. A. Barnes,
Andrew E. Berry,
A. Bignell,
S. C. Sala,
Jacqueline Chrast,
...
Fiona Cunningham,
T. Domenico,
S. Donaldson,
Ian T. Fiddes,
C. García-Girón,
J. Gonzalez,
Tiago Grego,
Matthew Hardy,
Thibaut Hourlier,
T. Hunt,
Osagie G. Izuogu,
Julien Lagarde,
Fergal J. Martin,
Laura Martínez,
Shamika Mohanan,
Paul Muir,
Fábio C. P. Navarro,
Anne Parker,
Baikang Pei,
F. Pozo,
Magali Ruffier,
Bianca M. Schmitt,
Eloise Stapleton,
M. Suner,
Irina Sycheva,
Barbara Uszczynska-Ratajczak,
Jinrui Xu,
Andrew D. Yates,
D. Zerbino,
Yan Zhang,
Bronwen L. Aken,
J. Choudhary,
M. Gerstein,
R. Guigó,
T. Hubbard,
Manolis Kellis,
B. Paten,
A. Reymond,
M. Tress,
Paul Flicek
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A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes
51 auth.
D. MacArthur,
S. Balasubramanian,
A. Frankish,
N. Huang,
James A. Morris,
Klaudia Walter,
L. Jostins,
L. Habegger,
Joseph K. Pickrell,
S. Montgomery,
C. A. Albers,
Zhengdong D. Zhang,
D. Conrad,
G. Lunter,
Hancheng Zheng,
...
Q. Ayub,
M. DePristo,
E. Banks,
Min Hu,
R. Handsaker,
J. Rosenfeld,
M. Fromer,
Mike Jin,
X. Mu,
Ekta Khurana,
K. Ye,
M. Kay,
Gary I. Saunders,
M. Suner,
T. Hunt,
If H. A. Barnes,
C. Amid,
D. Carvalho-Silva,
A. Bignell,
Catherine Snow,
Bryndís Yngvadóttir,
S. Bumpstead,
D. Cooper,
Yali Xue,
Irene Gallego Romero,
Jun Wang,
Yingrui Li,
R. Gibbs,
S. Mccarroll,
E. Dermitzakis,
J. Pritchard,
J. Barrett,
J. Harrow,
M. Hurles,
M. Gerstein,
C. Tyler-Smith
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10 |
2012 |
10
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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. Guigó,
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 Aït 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. O’Geen,
Xiaoqin Xu,
Kimberly R. Blahnik,
Alina R. Cao,
Sushma Iyengar,
R. Kaul,
R. Thurman,
Hao Wang,
P. Navas,
R. Sandstrom,
P. Sabo,
M. Weaver,
T. Canfield,
Kristen Lee,
Shane J. Neph,
Vaughan Roach,
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,
Yanbao Yu,
H. Gunawardena,
E. Feingold,
R. Lowdon,
Laura A. L. Dillon,
P. Good,
B. Risk
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10 |
2011 |
10
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GENCODE 2021
56 auth.
A. Frankish,
M. Diekhans,
Irwin Jungreis,
Julien Lagarde,
J. Loveland,
Jonathan M. Mudge,
Cristina Sisu,
James C. Wright,
J. Armstrong,
If H. A. Barnes,
Andrew E. Berry,
A. Bignell,
C. Boix,
S. Carbonell Sala,
Fiona Cunningham,
...
Tomás Di Domenico,
S. Donaldson,
Ian T. Fiddes,
C. García Girón,
J. Gonzalez,
Tiago Grego,
Matthew Hardy,
Thibaut Hourlier,
K. Howe,
T. Hunt,
Osagie G. Izuogu,
Rory Johnson,
Fergal J. Martin,
Laura Martínez,
Shamika Mohanan,
Paul Muir,
Fábio C. P. Navarro,
Anne Parker,
Baikang Pei,
F. Pozo,
Ferriol Calvet Riera,
Magali Ruffier,
Bianca M. Schmitt,
Eloise Stapleton,
M. Suner,
Irina Sycheva,
Barbara Uszczynska-Ratajczak,
Maxim Y Wolf,
Jinuri Xu,
Yucheng T. Yang,
Andrew D. Yates,
D. Zerbino,
Yan Zhang,
J. Choudhary,
M. Gerstein,
R. Guigó,
T. Hubbard,
Manolis Kellis,
B. Paten,
M. Tress,
Paul Flicek
|
9 |
2020 |
9
🐜
|
|
🐜
|
Ensembl 2023
96 auth.
Fergal J. Martin,
M. Amode,
Alisha Aneja,
Olanrewaju Austine-Orimoloye,
A. G. Azov,
If H. A. Barnes,
Arne Becker,
Ruth Bennett,
Andrew E. Berry,
Jyothish Bhai,
Simarpreet Kaur Bhurji,
A. Bignell,
Sanjay Boddu,
Paulo R. B. Lins,
Lucy Brooks,
...
Shashank Budhanuru Ramaraju,
Mehrnaz Charkhchi,
Alexander Cockburn,
Luca Da Rin Fioretto,
C. Davidson,
K. Dodiya,
S. Donaldson,
Bilal El Houdaigui,
Tamara El Naboulsi,
Reham Fatima,
C. García-Girón,
T. Genez,
G. Ghattaoraya,
J. G. Martinez,
C. Guijarro,
Matthew Hardy,
Zoe Hollis,
Thibaut Hourlier,
T. Hunt,
M. Kay,
Vinay Kaykala,
Tuan Le,
Diana Lemos,
Diego Marques-Coelho,
José Carlos Marugán,
G. Merino,
Louisse Paola Mirabueno,
Aleena Mushtaq,
Syed Nakib Hossain,
Denye N. Ogeh,
M. P. Sakthivel,
Anne Parker,
Malcolm Perry,
Ivana Pilizota,
Irina Prosovetskaia,
J. Pérez-Silva,
A. I. A. Salam,
Nuno Saraiva-Agostinho,
Helen Schuilenburg,
Daniel Sheppard,
Swati Sinha,
Botond Sipos,
W. Stark,
E. Steed,
Ranjit Sukumaran,
Dulika Sumathipala,
M. Suner,
Likhitha Surapaneni,
Kyösti Sutinen,
M. Szpak,
Francesca Floriana Tricomi,
David Urbina-Gómez,
A. Veidenberg,
Thomas A. Walsh,
Brandon Walts,
Elizabeth Wass,
Natalie L. Willhoft,
Jamie Allen,
Jorge Álvarez,
Marc Chakiachvili,
Beth Flint,
Stefano Giorgetti,
Leanne Haggerty,
Garth R. Ilsley,
J. Loveland,
B. Moore,
Jonathan M. Mudge,
J. Tate,
David Thybert,
S. Trevanion,
Andrea Winterbottom,
A. Frankish,
S. Hunt,
Magali Ruffier,
Fiona Cunningham,
S. Dyer,
R. Finn,
K. Howe,
Peter W. Harrison,
Andrew D. Yates,
Paul Flicek
|
9 |
2022 |
9
🐜
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Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways.
38 auth.
N. Thomson,
Debra J Clayton,
D. Windhorst,
Georgios S. Vernikos,
Susanne Davidson,
C. Churcher,
M. Quail,
M. Stevens,
Michael A. Jones,
M. Watson,
Andrew J Barron,
Abigail N. Layton,
D. Pickard,
R. Kingsley,
A. Bignell,
...
L. Clark,
B. Harris,
D. Ormond,
Zahra Abdellah,
K. Brooks,
Inna Cherevach,
T. Chillingworth,
J. Woodward,
Halina Norberczak,
Angela Lord,
C. Arrowsmith,
K. Jagels,
S. Moule,
K. Mungall,
M. Sanders,
S. Whitehead,
J. Chabalgoity,
D. Maskell,
T. Humphrey,
M. Roberts,
P. Barrow,
G. Dougan,
J. Parkhill
|
8 |
2008 |
8
🐜
|
|
🐜
|
Ensembl 2022
95 auth.
Fiona Cunningham,
James E. Allen,
James E. Allen,
Jorge Álvarez,
M. Amode,
Irina M. Armean,
Olanrewaju Austine-Orimoloye,
A. G. Azov,
If H. A. Barnes,
Ruth Bennett,
Andrew E. Berry,
Jyothish Bhai,
A. Bignell,
Konstantinos Billis,
Sanjay Boddu,
...
Lucy Brooks,
Mehrnaz Charkhchi,
Carla A. Cummins,
Luca Da Rin Fioretto,
C. Davidson,
K. Dodiya,
S. Donaldson,
Bilal El Houdaigui,
Tamara El Naboulsi,
Reham Fatima,
C. García-Girón,
T. Genez,
J. G. Martinez,
Cristina Guijarro-Clarke,
A. Gymer,
Matthew Hardy,
Zoe Hollis,
Thibaut Hourlier,
T. Hunt,
Thomas Juettemann,
V. Kaikala,
M. Kay,
Ilias Lavidas,
Tuan Le,
Diana Lemos,
José Carlos Marugán,
Shamika Mohanan,
Aleena Mushtaq,
Marc Naven,
Denye N. Oheh,
Anne Parker,
Andrew Parton,
Malcolm Perry,
Ivana Pilizota,
Irina Prosovetskaia,
M. P. Sakthivel,
A. I. A. Salam,
Bianca M. Schmitt,
Helen Schuilenburg,
Daniel Sheppard,
J. Pérez-Silva,
W. Stark,
E. Steed,
Kyösti Sutinen,
Ranjit Sukumaran,
Dulika Sumathipala,
M. Suner,
M. Szpak,
A. Thormann,
Francesca Floriana Tricomi,
David Urbina-Gómez,
A. Veidenberg,
Thomas A. Walsh,
Brandon Walts,
N. Willhoft,
Andrea Winterbottom,
Elizabeth Wass,
Marc Chakiachvili,
Beth Flint,
A. Frankish,
Stefano Giorgetti,
Leanne Haggerty,
S. Hunt,
Garth IIsley,
J. Loveland,
Fergal J. Martin,
B. Moore,
Jonathan M. Mudge,
Matthieu Muffato,
Emily Perry,
Magali Ruffier,
J. Tate,
David Thybert,
S. Trevanion,
S. Dyer,
P. W. Harrison,
K. Howe,
Andrew D. Yates,
D. Zerbino,
P. Flicek
|
8 |
2021 |
8
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|
🐜
|
Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa.
19 auth.
C. Winstanley,
M. Langille,
J. Fothergill,
I. Kukavica-Ibrulj,
Catherine Paradis-Bleau,
F. Sanschagrin,
N. Thomson,
G. Winsor,
M. Quail,
Nicola J Lennard,
...
A. Bignell,
L. Clarke,
K. Seeger,
D. Saunders,
D. Harris,
J. Parkhill,
R. Hancock,
F. Brinkman,
R. Lévesque
|
8 |
2008 |
8
🐜
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|
🐜
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GENCODE: reference annotation for the human and mouse genomes in 2023
62 auth.
A. Frankish,
S. C. Sala,
M. Diekhans,
Irwin Jungreis,
J. Loveland,
Jonathan M. Mudge,
Cristina Sisu,
James C. Wright,
Carme Arnan,
If H. A. Barnes,
Abhimanyu Banerjee,
Ruth Bennett,
Andrew E. Berry,
A. Bignell,
C. Boix,
...
Ferriol Calvet Riera,
Daniel Cerdán-Vélez,
Fiona Cunningham,
C. Davidson,
S. Donaldson,
Cagatay Dursun,
Reham Fatima,
Stefano Giorgetti,
C. García-Girón,
J. Gonzalez,
Matthew Hardy,
Peter W. Harrison,
Thibaut Hourlier,
Zoe Hollis,
T. Hunt,
Benjamin T. James,
Yunzhe Jiang,
Rory Johnson,
M. Kay,
Julien Lagarde,
Fergal J. Martin,
Laura Martínez Gómez,
Surag Nair,
Pengyu Ni,
F. Pozo,
Vivekanandan Ramalingam,
Magali Ruffier,
Bianca M. Schmitt,
J. Schreiber,
E. Steed,
M. Suner,
Dulika Sumathipala,
Irina Sycheva,
Barbara Uszczynska-Ratajczak,
Elizabeth Wass,
Yucheng T. Yang,
Andrew D. Yates,
Zahoor Zafrulla,
J. Choudhary,
M. Gerstein,
R. Guigó,
Tim J. P. Hubbard,
M. Kellis,
A. Kundaje,
B. Paten,
M. Tress,
Paul Flicek
|
7 |
2022 |
7
🐜
|
|
🐜
|
Perspectives on ENCODE
501 auth.
F. Abascal,
Reyes Acosta,
Nicholas J. Addleman,
Jessika Adrian,
Veena Afzal,
Bronwen L. Aken,
Rizi Ai,
J. Akiyama,
O. A. Jammal,
Henry Amrhein,
S. Anderson,
Gregory Andrews,
I. Antoshechkin,
K. Ardlie,
J. Armstrong,
...
Matthew Astley,
Budhaditya Banerjee,
Amira A. Barkal,
If H. A. Barnes,
I. Barozzi,
D. Barrell,
Gemma Barson,
Daniel Bates,
Ulugbek K. Baymuradov,
C. Bazile,
Michael A. Beer,
Samantha P. Beik,
M. Bender,
Ruth Bennett,
L. Bouvrette,
Bradley E. Bernstein,
Andrew E. Berry,
A. Bhaskar,
A. Bignell,
S. Blue,
D. Bodine,
C. Boix,
Nathan Boley,
Tyler Borrman,
Beatrice Borsari,
A. Boyle,
Laurel A. Brandsmeier,
A. Breschi,
E. Bresnick,
Jason A. Brooks,
Michael Buckley,
C. Burge,
Rachel Byron,
Eileen W. Cahill,
Lingling Cai,
Lulu Cao,
Mark Carty,
R. Castanon,
Andres Castillo,
H. Chaib,
Esther T. Chan,
Daniel R. Chee,
Sora Chee,
Huaming Chen,
Jia-Yu Chen,
Songjie Chen,
J. M. Cherry,
S. Chhetri,
J. Choudhary,
Jacqueline Chrast,
Dongjun Chung,
Declan Clarke,
Neal A. L. Cody,
Candice J. Coppola,
J. Coursen,
A. D'Ippolito,
S. Dalton,
Cassidy Danyko,
C. Davidson,
J. Dávila-Velderrain,
Carrie A. Davis,
J. Dekker,
A. Deran,
Gilberto Desalvo,
Gloria Despacio-Reyes,
Colin N. Dewey,
D. Dickel,
Morgan Diegel,
M. Diekhans,
V. Dileep,
Bo Ding,
S. Djebali,
A. Dobin,
Daniel Dominguez,
S. Donaldson,
J. Drenkow,
T. Dreszer,
Y. Drier,
M. Duff,
D. Dunn,
Catharine L. Eastman,
J. Ecker,
Matthew D. Edwards,
Nicole C. El-Ali,
Shaimae I. Elhajjajy,
Keri Elkins,
A. Emili,
C. Epstein,
Rachel C. Evans,
Iakes Ezkurdia,
K. Fan,
P. Farnham,
Nina P. Farrell,
E. Feingold,
Anne-Maud Ferreira,
Katherine I. Fisher-Aylor,
Stephen Fitzgerald,
Paul Flicek,
Chuan-Sheng Foo,
K. Fortier,
A. Frankish,
Peter Freese,
Shaliu Fu,
Xiang-Dong Fu,
Yu Fu,
Yoko Fukuda-Yuzawa,
M. Fulciniti,
Alister P. W. Funnell,
I. Gabdank,
Timur Galeev,
M. Gao,
C. G. Girón,
Tyler H. Garvin,
C. Gelboin-Burkhart,
G. Georgolopoulos,
M. Gerstein,
B. Giardine,
D. Gifford,
D. Gilbert,
Daniel A. Gilchrist,
Shawn M. Gillespie,
T. Gingeras,
Peng Gong,
Alvaro J. González,
J. Gonzalez,
P. Good,
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David U. Gorkin,
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