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The novel transcripts we keep rediscovering

delete2026-09-22
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PRE
AI
X
Xinchang Zheng
S
Sonia García-Ruiz
E
Emil K. Gustavsson
M
Mina Ryten
F
Fritz J. Sedlazeck *
DOI:10.1038/s41587-026-03321-ydelete
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Abstract

Abstract

En 中文
Interpreting transcript diversity requires moving beyond ‘known’ versus ‘novel’ and towards a multidimensional framework based on technical credibility, contextual prevalence, reproducibility, molecular consequence and phenotypic relevance.

Journal

Nature Biotechnology cover
Nature Biotechnology
IF:
41.7
Papers:
1.2W
Citations:
10.1W

Organization

B
baylor college of medicine
Scholars:
683
Papers: 220
Citations: 0
U
University of Cambridge
Scholars:
1.0K
Papers: 497
Citations: 0
Cited Papers

Cited Papers

Functional and dynamic profiling of transcript isoforms reveals essential roles of alternative splicing in interferon response
err2024-10-01
err0
errOAAI
errUeda, Mahoko Takahashi; Inamo, Jun; Miya, Fuyuki; Shimada, Mihoko; Yamaguchi, Kensuke; Kochi, Yuta
errShare
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CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise
err2018-11-28
err183
errOAAI
errPertea, Mihaela; Shumate, Alaina; Pertea, Geo; Varabyou, Ales; Breitwieser, Florian P.; Chang, Yu-Chi; Madugundu, Anil K.; Pandey, Akhilesh; Salzberg, Steven L.
errShare
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A joint NCBI and EMBL-EBI transcript set for clinical genomics and research
err2022-04-06
err0
errOAAI
errJoannella Morales; Shashikant Pujar; Jane E. Loveland; Alex Astashyn; Ruth Bennett; Andrew Berry; Eric Cox; Claire Davidson; Olga Ermolaeva; Catherine M. Farrell; Reham Fatima; Laurent Gil; Tamara Goldfarb; Jose M. Gonzalez; Diana Haddad; Matthew Hardy; Toby Hunt; John Jackson; Vinita S. Joardar; Michael Kay; Vamsi K. Kodali; Kelly M. McGarvey; Aoife McMahon; Jonathan M. Mudge; Daniel N. Murphy; Michael R. Murphy; Bhanu Rajput; Sanjida H. Rangwala; Lillian D. Riddick; Françoise Thibaud-Nissen; Glen Threadgold; Anjana R. Vatsan; Craig Wallin; David Webb; Paul Flicek; Ewan Birney; Kim D. Pruitt; Adam Frankish; Fiona Cunningham; Terence D. Murphy
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Transcriptomics in the era of long-read sequencing
err2025-03-28
err0
PREAI
errMonzo, Carolina; Liu, Tianyuan; Conesa, Ana
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The mutational constraint spectrum quantified from variation in 141,456 humans
err2020-05-27
err0
errOAAI
errKonrad J. Karczewski; Laurent C. Francioli; Grace Tiao; Beryl B. Cummings; Jessica Alföldi; Qingbo Wang; Ryan L. Collins; Kristen M. Laricchia; Andrea Ganna; Daniel P. Birnbaum; Laura D. Gauthier; Harrison Brand; Matthew Solomonson; Nicholas A. Watts; Daniel Rhodes; Moriel Singer-Berk; Eleina M. England; Eleanor G. Seaby; Jack A. Kosmicki; Raymond K. Walters; Katherine Tashman; Yossi Farjoun; Eric Banks; Timothy Poterba; Arcturus Wang; Cotton Seed; Nicola Whiffin; Jessica X. Chong; Kaitlin E. Samocha; Emma Pierce-Hoffman; Zachary Zappala; Anne H. O’Donnell-Luria; Eric Vallabh Minikel; Ben Weisburd; Monkol Lek; James S. Ware; Christopher Vittal; Irina M. Armean; Louis Bergelson; Kristian Cibulskis; Kristen M. Connolly; Miguel Covarrubias; Stacey Donnelly; Steven Ferriera; Stacey Gabriel; Jeff Gentry; Namrata Gupta; Thibault Jeandet; Diane Kaplan; Christopher Llanwarne; Ruchi Munshi; Sam Novod; Nikelle Petrillo; David Roazen; Valentin Ruano-Rubio; Andrea Saltzman; Molly Schleicher; Jose Soto; Kathleen Tibbetts; Charlotte Tolonen; Gordon Wade; Michael E. Talkowski; Carlos A. Aguilar Salinas; Tariq Ahmad; Christine M. Albert; Diego Ardissino; Gil Atzmon; John Barnard; Laurent Beaugerie; Emelia J. Benjamin; Michael Boehnke; Lori L. Bonnycastle; Erwin P. Bottinger; Donald W. Bowden; Matthew J. Bown; John C. Chambers; Juliana C. Chan; Daniel Chasman; Judy Cho; Mina K. Chung; Bruce Cohen; Adolfo Correa; Dana Dabelea; Mark J. Daly; Dawood Darbar; Ravindranath Duggirala; Josée Dupuis; Patrick T. Ellinor; Roberto Elosua; Jeanette Erdmann; Tõnu Esko; Martti Färkkilä; Jose Florez; Andre Franke; Gad Getz; Benjamin Glaser; Stephen J. Glatt; David Goldstein; Clicerio Gonzalez; Leif Groop; Christopher Haiman; Craig Hanis; Matthew Harms; Mikko Hiltunen; Matti M. Holi; Christina M. Hultman; Mikko Kallela; Jaakko Kaprio; Sekar Kathiresan; Bong-Jo Kim; Young Jin Kim; George Kirov; Jaspal Kooner; Seppo Koskinen; Harlan M. Krumholz; Subra Kugathasan; Soo Heon Kwak; Markku Laakso; Terho Lehtimäki; Ruth J. F. Loos; Steven A. Lubitz; Ronald C. W. Ma; Daniel G. MacArthur; Jaume Marrugat; Kari M. Mattila; Steven McCarroll; Mark I. McCarthy; Dermot McGovern; Ruth McPherson; James B. Meigs; Olle Melander; Andres Metspalu; Benjamin M. Neale; Peter M. Nilsson; Michael C. O’Donovan; Dost Ongur; Lorena Orozco; Michael J. Owen; Colin N. A. Palmer; Aarno Palotie; Kyong Soo Park; Carlos Pato; Ann E. Pulver; Nazneen Rahman; Anne M. Remes; John D. Rioux; Samuli Ripatti; Dan M. Roden; Danish Saleheen; Veikko Salomaa; Nilesh J. Samani; Jeremiah Scharf; Heribert Schunkert; Moore B. Shoemaker; Pamela Sklar; Hilkka Soininen; Harry Sokol; Tim Spector; Patrick F. Sullivan; Jaana Suvisaari; E. Shyong Tai; Yik Ying Teo; Tuomi Tiinamaija; Ming Tsuang; Dan Turner; Teresa Tusie-Luna; Erkki Vartiainen; Marquis P. Vawter; James S. Ware; Hugh Watkins; Rinse K. Weersma; Maija Wessman; James G. Wilson; Ramnik J. Xavier; Benjamin M. Neale; Mark J. Daly; Daniel G. MacArthur
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SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms
err2024-03-20
err16
errOAAI
errPardo-Palacios, Francisco J.; Arzalluz-Luque, Angeles; Kondratova, Liudmyla; Salguero, Pedro; Mestre-Tomas, Jorge; Amorin, Rocio; Estevan-Morio, Eva; Liu, Tianyuan; Nanni, Adalena; Mcintyre, Lauren; Tseng, Elizabeth; Conesa, Ana
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Enhanced protein isoform characterization through long-read proteogenomics
err2022-03-03
err42
errOAAI
errMiller, Rachel M.; Jordan, Ben T.; Mehlferber, Madison M.; Jeffery, Erin D.; Chatzipantsiou, Christina; Kaur, Simi; Millikin, Robert J.; Dai, Yunxiang; Tiberi, Simone; Castaldi, Peter J.; Shortreed, Michael R.; Luckey, Chance John; Conesa, Ana; Smith, Lloyd M.; Mays, Anne Deslattes; Sheynkman, Gloria M.
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Long-read transcriptomics of a diverse human cohort reveals ancestry bias in gene annotation
err2025-12-03
err0
errOAAI
errPau Clavell-Revelles; Fairlie Reese; Sílvia Carbonell-Sala; Fabien Degalez; Carme Arnan; Winona Oliveros; Emilio Palumbo; Tamara Perteghella; Roderic Guigó; Marta Melé
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A comprehensive long-read isoform analysis platform and sequencing resource for breast cancer
err2022-01-21
err30
errOAAI
errVeiga, Diogo F. T.; Nesta, Alex; Zhao, Yuqi; Mays, Anne Deslattes; Huynh, Richie; Rossi, Robert; Wu, Te-Chia; Palucka, Karolina; Anczukow, Olga; Beck, Christine R.; Banchereau, Jacques
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Transcript expression-aware annotation improves rare variant interpretation
err2020-05-27
err0
errOAAI
errBeryl B. Cummings; Konrad J. Karczewski; Jack A. Kosmicki; Eleanor G. Seaby; Nicholas A. Watts; Moriel Singer-Berk; Jonathan M. Mudge; Juha Karjalainen; F. Kyle Satterstrom; Anne H. O’Donnell-Luria; Timothy Poterba; Cotton Seed; Matthew Solomonson; Jessica Alföldi; Jessica Alföldi; Irina M. Armean; Eric Banks; Louis Bergelson; Kristian Cibulskis; Ryan L. Collins; Kristen M. Connolly; Miguel Covarrubias; Beryl B. Cummings; Mark J. Daly; Stacey Donnelly; Yossi Farjoun; Steven Ferriera; Laurent Francioli; Stacey Gabriel; Laura D. Gauthier; Jeff Gentry; Namrata Gupta; Thibault Jeandet; Diane Kaplan; Konrad J. Karczewski; Kristen M. Laricchia; Christopher Llanwarne; Eric V. Minikel; Ruchi Munshi; Benjamin M. Neale; Sam Novod; Anne H. O’Donnell-Luria; Nikelle Petrillo; Timothy Poterba; David Roazen; Valentin Ruano-Rubio; Andrea Saltzman; Kaitlin E. Samocha; Molly Schleicher; Cotton Seed; Matthew Solomonson; Jose Soto; Grace Tiao; Kathleen Tibbetts; Charlotte Tolonen; Christopher Vittal; Gordon Wade; Arcturus Wang; Qingbo Wang; James S. Ware; Nicholas A. Watts; Ben Weisburd; Nicola Whiffin; Carlos A. Aguilar Salinas; Tariq Ahmad; Christine M. Albert; Diego Ardissino; Gil Atzmon; John Barnard; Laurent Beaugerie; Emelia J. Benjamin; Michael Boehnke; Lori L. Bonnycastle; Erwin P. Bottinger; Donald W. Bowden; Matthew J. Bown; John C. Chambers; Juliana C. Chan; Daniel Chasman; Judy Cho; Mina K. Chung; Bruce Cohen; Adolfo Correa; Dana Dabelea; Mark J. Daly; Dawood Darbar; Ravindranath Duggirala; Josée Dupuis; Patrick T. Ellinor; Roberto Elosua; Jeanette Erdmann; Tõnu Esko; Martti Färkkilä; Jose Florez; Andre Franke; Gad Getz; Benjamin Glaser; Stephen J. Glatt; David Goldstein; Clicerio Gonzalez; Leif Groop; Christopher Haiman; Craig Hanis; Matthew Harms; Mikko Hiltunen; Matti M. Holi; Christina M. Hultman; Mikko Kallela; Jaakko Kaprio; Sekar Kathiresan; Bong-Jo Kim; Young Jin Kim; George Kirov; Jaspal Kooner; Seppo Koskinen; Harlan M. Krumholz; Subra Kugathasan; Soo Heon Kwak; Markku Laakso; Terho Lehtimäki; Ruth J. F. Loos; Steven A. Lubitz; Ronald C. W. Ma; Daniel G. MacArthur; Jaume Marrugat; Kari M. Mattila; Steven McCarroll; Mark I. McCarthy; Dermot McGovern; Ruth McPherson; James B. Meigs; Olle Melander; Andres Metspalu; Benjamin M. Neale; Peter M. Nilsson; Michael C. O’Donovan; Dost Ongur; Lorena Orozco; Michael J. Owen; Colin N. A. Palmer; Aarno Palotie; Kyong Soo Park; Carlos Pato; Ann E. Pulver; Nazneen Rahman; Anne M. Remes; John D. Rioux; Samuli Ripatti; Dan M. Roden; Danish Saleheen; Veikko Salomaa; Nilesh J. Samani; Jeremiah Scharf; Heribert Schunkert; Moore B. Shoemaker; Pamela Sklar; Hilkka Soininen; Harry Sokol; Tim Spector; Patrick F. Sullivan; Jaana Suvisaari; E. Shyong Tai; Yik Ying Teo; Tuomi Tiinamaija; Ming Tsuang; Dan Turner; Teresa Tusie-Luna; Erkki Vartiainen; Marquis P. Vawter; James S. Ware; Hugh Watkins; Rinse K. Weersma; Maija Wessman; James G. Wilson; Ramnik J. Xavier; Mark J. Daly; Daniel G. MacArthur
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