ArticlebioRxiv : the preprint server for biology2023
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.
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Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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83 authors.
Francisco J Pardo-PalaciosInstitute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.
Dingjie WangDepartment of Biomedical Informatics, The Ohio State University, Columbus, USA.
Fairlie ReeseDevelopmental and Cell Biology, University of California, Irvine, Irvine, USA.
Mark DiekhansUC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, USA.
Sílvia Carbonell-SalaCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.
Brian WilliamsDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA.
Jane E LovelandEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Maite De MaríaDepartment of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, USA.
Matthew S AdamsMolecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, USA.
Gabriela Balderrama-GutierrezDevelopmental and Cell Biology, University of California, Irvine, Irvine, USA.
Amit K BeheraDepartment of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA.
Jose M GonzalezEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Toby HuntEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Julien LagardeCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.
Cindy E LiangMolecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, USA.
Haoran LiDepartment of Biomedical Informatics, The Ohio State University, Columbus, USA.
Marcus Jerryd MeadeDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA.
David A Moraga AmadorInterdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA.
Andrey D PrjibelskiDepartment of Computer Science, University of Helsinki, Helsinki, Finland.
Inanc BirolCanada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada.
Hamed BostanBiostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA.
Ashley M BrooksBiostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA.
Muhammed Hasan ÇelikDevelopmental and Cell Biology, University of California, Irvine, Irvine, USA.
Ying ChenGenome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
Mei R M DuWalter and Eliza Hall Institute of Medical Research, Parkville, Australia.
Colette FeltonDepartment of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA.
Jonathan GökeGenome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
Saber HafezqoraniCanada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada.
Ralf HerwigDepartment Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany.
Hideya KawajiResearch Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.
Joseph LeeGenome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
Jian Liang LiBiostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA.
Matthias LienhardDepartment Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany.
Alla MikheenkoDepartment of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK.
Dennis MulliganDepartment of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA.
Ka Ming NipCanada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada.
Mihaela PerteaDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, USA.
Matthew E RitchieWalter and Eliza Hall Institute of Medical Research, Parkville, Australia.
Andre D SimGenome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
Alison D TangDepartment of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA.
Yuk Kei WanGenome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
Changqing WangWalter and Eliza Hall Institute of Medical Research, Parkville, Australia.
Brandon Y WongDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, USA.
Chen YangCanada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada.
If BarnesEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Andrew BerryEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Salvador CapellaBarcelona Supercomputing Cente, Barcelona, Spain.
Namrita DhillonDepartment of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA.
Jose M Fernandez-GonzalezBarcelona Supercomputing Cente, Barcelona, Spain.
Luis Ferrández-PeralInstitute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.
Natàlia Garcia-ReyeroEnvironmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, USA.
Stefan GoetzBiobam Bioinformatics SL, Valencia, Spain.
Carles Hernández-FerrerBarcelona Supercomputing Cente, Barcelona, Spain.
Liudmyla KondratovaGenetics Institute, University of Florida, Gainesville, USA.
Tianyuan LiuCardiff University, Cardiff, UK.
Alessandra Martinez-MartinInstitute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.
Carlos MenorBiobam Bioinformatics SL, Valencia, Spain.
Jorge Mestre-TomásInstitute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.
Jonathan M MudgeEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Nedka G PanayotovaInterdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA.
Alejandro PaniaguaInstitute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.
Dmitry RepchevskyBarcelona Supercomputing Cente, Barcelona, Spain.
Eric RouchkaDepartment of Biochemistry & Molecular Genetics, University of Louisville, Louisville, USA.
Brandon Saint-JohnDepartment of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA.
Enrique SapenaEuropean Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK, UK.
Leon SheynkmanDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA.
Melissa Laird SmithDepartment of Biochemistry & Molecular Genetics, University of Louisville, Louisville, USA.
Marie-Marthe SunerEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Hazuki TakahashiCenter for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan.
Ingrid Ashley YoungworthDepartment of Genetics, Stanford University, Palo Alto, USA.
Piero CarninciCenter for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan.
Nancy D DenslowDepartment of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, USA.
Roderic GuigóCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.
Margaret E HunterU.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, USA.
Hagen U TilgnerBrain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York City, USA.
Barbara J WoldDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA.
Christopher VollmersDepartment of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA.
Adam FrankishEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Kin Fai AuDepartment of Biomedical Informatics, The Ohio State University, Columbus, USA.
Gloria M SheynkmanDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA.
Ali MortazaviDevelopmental and Cell Biology, University of California, Irvine, Irvine, USA.
Ana ConesaInstitute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.
Angela N BrooksUC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, USA.
Funding
GENCODE Resource ProjectU41HG007234 · NHGRI · SANGER INSTITUTE · PI FLICEK, PAUL · 2013 to 2020
$20.3MGENCODE: comprehensive reference genome annotation for human and mouseU24HG007234 · NHGRI · EUROPEAN MOLECULAR BIOLOGY LABORATORY · PI Fergal James Martin · 2021 to 2026
$16.1MHigher Precision Human and Mouse TranscriptomesUM1HG009443 · NHGRI · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI MORTAZAVI, SEYED ALI, WOLD, BARBARA J · 2017 to 2021
$15.5MNovel approaches to improve comprehensive profiling of the epigenome and epitranscriptomeR35GM138122 · NIGMS · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI Angela Norie Brooks · 2020 to 2026
$2.8MQuantitative and function analysis platform for repetitive genes and gene isoforms in pluripotency regulation and differentiationsR01HG011469 · NHGRI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI AU, KIN FAI · 2021 to 2024
$2.6MUncovering the functional diversification mechanisms of transcription factor isoforms involved in stem cell differentiationR35GM142647 · NIGMS · UNIVERSITY OF VIRGINIA · PI SHEYNKMAN, GLORIA · 2021 to 2025
$2.1MBioinformatics platform for Hybrid-Seq transcriptome data analysisR01HG008759 · NHGRI · UNIVERSITY OF IOWA · PI AU, KIN FAI · 2016 to 2020
$1.9MExperimental and bioinformatics platform for epigenome analysis using nanopore sequencingR01GM136886 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI AU, KIN FAI · 2021 to 2024
$1.7MPlatform for transcriptome-wide RNA modification identification in long readsF31HG010999 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI TANG, ALISON · 2020 to 2022
$82kNHGRI NIH HHS F31 HG010999NHGRI NIH HHS R01 HG008759NHGRI NIH HHS R01 HG011469NHGRI NIH HHS U24 HG007234NHGRI NIH HHS U41 HG007234NHGRI NIH HHS UM1 HG009443NIGMS NIH HHS R01 GM136886NIGMS NIH HHS R35 GM138122NIGMS NIH HHS R35 GM142647Wellcome Trust
Abstract
The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as
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