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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
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The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity
45 auth.
Fairlie Reese,
B. Williams,
Gabriela Balderrama-Gutierrez,
D. Wyman,
M. H. Çelik,
Elisabeth Rebboah,
Narges Rezaie,
Diane Trout,
Milad Razavi-Mohseni,
Yunzhe Jiang,
Beatrice Borsari,
Samuel Morabito,
H. Liang,
Cassandra J. McGill,
Sorena Rahmanian,
...
Jasmine Sakr,
Shan Jiang,
Weihua Zeng,
Klebea Carvalho,
Annika K. Weimer,
Louise A. Dionne,
Ariel McShane,
Karan Bedi,
Shaimae I. Elhajjajy,
S. Upchurch,
Jennifer Jou,
Ingrid Youngworth,
I. Gabdank,
Paul Sud,
Otto Jolanki,
J. Strattan,
Meenakshi S. Kagda,
Michael P. Snyder,
B. Hitz,
Jill E. Moore,
Z. Weng,
David A. Bennett,
L. Reinholdt,
M. Ljungman,
Michael A. Beer,
M. Gerstein,
L. Pachter,
R. Guigó,
B. Wold,
A. Mortazavi
|
4 |
2023 |
4
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|
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Single-cell genomics and regulatory networks for 388 human brains
80 auth.
Prashant S. Emani,
Jason J. Liu,
Declan Clarke,
Matthew Jensen,
J. Warrell,
Chirag Gupta,
Ran Meng,
Cheyu Lee,
Siwei Xu,
Cagatay Dursun,
S. Lou,
Yuhang Chen,
Zhiyuan Chu,
Timur Galeev,
Aheyon Hwang,
...
Yunyang Li,
Pengyu Ni,
Xiao Zhou,
Trygve E Bakken,
J. Bendl,
Lucy K. Bicks,
Tanima Chatterjee,
Lijun Cheng,
Yuyan Cheng,
Yi Dai,
Ziheng Duan,
Mary Flaherty,
J. Fullard,
Michael Gancz,
D. Garrido-Martín,
Sophia C. Gaynor-Gillett,
Jennifer Grundman,
Natalie Hawken,
Ella Henry,
G. Hoffman,
Ao Huang,
Yunzhe Jiang,
Ting Jin,
Nikolas L. Jorstad,
R. Kawaguchi,
Saniya Khullar,
Jianyin Liu,
Junhao Liu,
Shuang Liu,
Shaojie Ma,
Michael Margolis,
Samantha Mazariegos,
Jill E. Moore,
Jennifer R. Moran,
Eric Nguyen,
Nishigandha Phalke,
M. Pjanic,
H. Pratt,
Diana Quintero,
Ananya S. Rajagopalan,
Tiernon R. Riesenmy,
Nicole Shedd,
Manman Shi,
Megan Spector,
Rosemarie Terwilliger,
K. Travaglini,
Brie Wamsley,
Gaoyuan Wang,
Yan Xia,
Shaohua Xiao,
Andrew C. Yang,
Suchen Zheng,
M. Gandal,
Donghoon Lee,
E. Lein,
P. Roussos,
Nenad Sestan,
Zhiping Weng,
Kevin P. White,
Hyejung Won,
M. Girgenti,
Jing Zhang,
Daifeng Wang,
Daniel H. Geschwind,
Marc H. Gerstein
|
4 |
2024 |
4
🐜
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|
🐜
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Single-cell genomics and regulatory networks for 388 human brains
81 auth.
Prashant S. Emani,
Jason J. Liu,
Declan Clarke,
Matthew Jensen,
J. Warrell,
Chirag Gupta,
Ran Meng,
Cheyu Lee,
Siwei Xu,
Cagatay Dursun,
S. Lou,
Yuhang Chen,
Zhiyuan Chu,
Timur Galeev,
Ahyeon Hwang,
...
Yunyang Li,
Pengyu Ni,
Xiao Zhou,
PsychENCODE Consortium,
Trygve E Bakken,
J. Bendl,
Lucy K. Bicks,
Tanima Chatterjee,
Lijun Cheng,
Yuyan Cheng,
Yi Dai,
Ziheng Duan,
Mary Flaherty,
J. Fullard,
Michael Gancz,
Diego Garrido-Martín,
Sophie Gaynor-Gillett,
Jennifer Grundman,
Natalie Hawken,
Ella Henry,
G. Hoffman,
Ao Huang,
Yunzhe Jiang,
Ting Jin,
Nikolas L. Jorstad,
R. Kawaguchi,
Saniya Khullar,
Jianyin Liu,
Junhao Liu,
Shuang Liu,
Shaojie Ma,
Michael Margolis,
Samantha Mazariegos,
Jill E. Moore,
Jennifer R. Moran,
Eric Nguyen,
Nishigandha Phalke,
M. Pjanic,
H. Pratt,
Diana Quintero,
Ananya S. Rajagopalan,
Tiernon R. Riesenmy,
Nicole Shedd,
Manman Shi,
Megan Spector,
Rosemarie Terwilliger,
K. Travaglini,
Brie Wamsley,
Gaoyuan Wang,
Yan Xia,
Shaohua Xiao,
Andrew C. Yang,
Suchen Zheng,
Michael J. Gandal,
Donghoon Lee,
E. Lein,
P. Roussos,
Nenad Sestan,
Zhiping Weng,
Kevin P. White,
Hyejung Won,
Matthew J. Girgenti,
Jing Zhang,
Daifeng Wang,
Daniel H. Geschwind,
Marc H. Gerstein
|
3 |
2024 |
3
🐜
|
|
🐜
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Complex genetic variation in nearly complete human genomes
68 auth.
Glennis A. Logsdon,
Peter Ebert,
P. Audano,
Mark Loftus,
David Porubsky,
Jana Ebler,
F. Yilmaz,
P. Hallast,
Timofey Prodanov,
DongAhn Yoo,
Carolyn A. Paisie,
William T. Harvey,
Xuefang Zhao,
Gianni V. Martino,
Mir Henglin,
...
Katherine M. Munson,
Keon Rabbani,
Chen-Shan Chin,
Bida Gu,
Hufsah Ashraf,
Olanrewaju Austine-Orimoloye,
Parithi Balachandran,
M. Bonder,
Haoyu Cheng,
Zechen Chong,
J. Crabtree,
Mark B. Gerstein,
L. Guethlein,
Patrick Hasenfeld,
G. Hickey,
Kendra Hoekzema,
Sarah E Hunt,
Matthew Jensen,
Yunzhe Jiang,
S. Koren,
Youngjun Kwon,
Chong Li,
Heng Li,
Jiaqi Li,
Paul J. Norman,
Keisuke K. Oshima,
B. Paten,
A. Phillippy,
Nicholas R Pollock,
Tobias Rausch,
M. Rautiainen,
Stephan Scholz,
Yuwei Song,
Arda Söylev,
Arvis Sulovari,
Likhitha Surapaneni,
Vasiliki Tsapalou,
Weichen Zhou,
Ying Zhou,
Qihui Zhu,
Michael C Zody,
Ryan E. Mills,
S. Devine,
Xinghua Shi,
M. Talkowski,
Mark J. P. Chaisson,
Alexander T Dilthey,
Miriam K. Konkel,
J. Korbel,
Charles Lee,
Christine R. Beck,
E. Eichler,
T. Marschall
|
3 |
2024 |
3
🐜
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|
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GENCODE 2025: reference gene annotation for human and mouse
56 auth.
Jonathan M. Mudge,
Sílvia Carbonell-Sala,
M. Diekhans,
J. G. Martinez,
T. Hunt,
Irwin Jungreis,
J. Loveland,
Carme Arnan,
If H. A. Barnes,
Ruth Bennett,
Andrew E. Berry,
A. Bignell,
Daniel Cerdán-Vélez,
Kelly Cochran,
Lucas T Cortés,
...
C. Davidson,
S. Donaldson,
Cagatay Dursun,
Reham Fatima,
Matthew Hardy,
Prajna Hebbar,
Zoe Hollis,
Benjamin T. James,
Yunzhe Jiang,
Rory Johnson,
Gazaldeep Kaur,
M. Kay,
Riley J. Mangan,
Miguel Maquedano,
Laura Martínez Gómez,
Nourhen Mathlouthi,
Ryan Merritt,
Pengyu Ni,
Emilio Palumbo,
Tamara Perteghella,
F. Pozo,
Shriya Raj,
Cristina Sisu,
Emily Steed,
Dulika Sumathipala,
M. Suner,
Barbara Uszczynska-Ratajczak,
Elizabeth Wass,
Yucheng T. Yang,
Dingyao Zhang,
Robert D. Finn,
Marc H. Gerstein,
R. Guigó,
T. Hubbard,
M. Kellis,
A. Kundaje,
B. Paten,
M. Tress,
E. Birney,
Fergal J. Martin,
A. Frankish
|
3 |
2024 |
3
🐜
|
|
🐜
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Epitope-anchored contrastive transfer learning for paired CD8+ cell receptor-antigen recognition
9 auth.
Yumeng Zhang,
Zhikang Wang,
Yunzhe Jiang,
D. Littler,
Marc H. Gerstein,
Anthony W. Purcell,
...
Jamie Rossjohn,
Hong-Yu Ou,
Jiangning Song
|
1 |
2024 |
1
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