ArticleNature methods2024
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.
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Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 199 papers, 1 of them a synthesis that pooled it.
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199citing papers in PubMed, 1 pooled it
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Who cites it
199 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Systematic review and meta-analysis of bulk RNAseq studies in human Alzheimer's disease brain tissue.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Pooled it
- Guidelines to Study Transcriptome Remodeling by Proteins Using Deep Sequencing (RNA-Seq).Methods in molecular biology (Clifton, N.J.) · 2027Article
- Cortical transcriptomic dysregulation in Autism spectrum disorder: A conceptual synthesis.IBRO neuroscience reports · 2026Review
- Epitranscriptomic profiling of VSMC phenotypes reveals uridine modifications linked to post-transcriptional regulation.Biochemistry and biophysics reports · 2026Article
- Review
- SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads.Nature methods · 2026Article
- Tumour-associated dsRNA accumulation and innate immune activation: mechanistic basis and therapeutic strategies.EBioMedicine · 2026Review
- LRP2: A proteogenomics pipeline for long-read informed protein isoform analysis and discovery.bioRxiv : the preprint server for biology · 2026Article
- Minigene-based characterization and classification of splice-associated variants in succinate dehydrogenase B.NPJ precision oncology · 2026Article
- Long-read transcriptome analysis using IsoRanker for identifying pathogenic variants in Mendelian conditions.American journal of human genetics · 2026Article
- Article
- IsoformSwitchAnalyzeR v2: analysis of functional isoform changes in long-read and single-cell sequencing data.NAR genomics and bioinformatics · 2026Article
- ONT-only genome assembly of a Korean male individual using a semen sample.Genes & genomics · 2026Article
- Toward the clinical application of long-read sequencing in repeat-expansion disorders.Nature genetics · 2026Review
- Validation of the International Weed Genomics Consortium genome annotation pipeline through reannotation of the model species Arabidopsis thaliana.The plant genome · 2026Article
- Spatial isoform sequencing at single-cell resolution reveals cell-type-specific spatial isoform variability in multiple brain cell types.Nature methods · 2026Article
- Handling biological replicates in long-read RNA sequencing data by joining or not joining.Nature communications · 2026Article
- A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq nanopore long reads data.NAR genomics and bioinformatics · 2026Article
- Advances in Poultry RNA-Omics Research: Technologies, RNA Information Layers, and Applications in Complex Traits.Animals : an open access journal from MDPI · 2026Review
- Leveraging long read RNA-seq to decipher neuronal regulation of alternative polyadenylation.Nature communications · 2026Article
139 more citing papers are in PubMed but not listed here.
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Authors and funding
87 authors.
Francisco J Pardo-Palacios *Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.ORCID http://orcid.org/0000-0002-3067-0166
Dingjie Wang *Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
Fairlie Reese *Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA.ORCID http://orcid.org/0000-0002-9240-0102
Mark Diekhans *UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.ORCID http://orcid.org/0000-0002-0430-0989
Sílvia Carbonell-Sala *Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.ORCID http://orcid.org/0000-0001-7956-6215
Brian Williams *Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.ORCID http://orcid.org/0000-0003-3253-611X
Jane E Loveland *European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK.ORCID http://orcid.org/0000-0002-7669-2934
Maite De María *Department of Physiological Sciences, College of Veterinary Medicine, Gainesville, FL, USA.ORCID http://orcid.org/0000-0002-5251-4869
Matthew S AdamsDepartment of Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.ORCID http://orcid.org/0000-0001-6793-6557
Gabriela Balderrama-GutierrezDepartment of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA.
Amit K BeheraDepartment of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.ORCID http://orcid.org/0000-0002-2087-7016
Jose M Gonzalez MartinezEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK.ORCID http://orcid.org/0000-0001-5569-0705
Toby HuntEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK.ORCID http://orcid.org/0000-0001-8377-0841
Julien LagardeCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
Cindy E LiangDepartment of Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.ORCID http://orcid.org/0000-0003-3763-2987
Haoran LiDepartment of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
Marcus Jerryd MeadeDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
David A Moraga AmadorInterdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA.
Andrey D PrjibelskiDepartment of Computer Science, University of Helsinki, Helsinki, Finland.ORCID http://orcid.org/0000-0003-2816-4608
Inanc BirolCanada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.ORCID http://orcid.org/0000-0003-0950-7839
Hamed BostanBiostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA.ORCID http://orcid.org/0000-0003-4102-807X
Ashley M BrooksBiostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA.ORCID http://orcid.org/0000-0003-2242-5942
Muhammed Hasan ÇelikDepartment of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA.ORCID http://orcid.org/0000-0001-7185-3711
Ying ChenGenome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.ORCID http://orcid.org/0000-0001-7876-4877
Mei R M DuWalter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.ORCID http://orcid.org/0000-0001-6915-6765
Colette FeltonDepartment of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.ORCID http://orcid.org/0000-0003-0810-0084
Jonathan GökeGenome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.ORCID http://orcid.org/0000-0002-0825-4991
Saber HafezqoraniCanada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.ORCID http://orcid.org/0000-0003-0553-9227
Ralf HerwigDepartment Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany.ORCID http://orcid.org/0000-0002-9335-1760
Hideya KawajiResearch Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.ORCID http://orcid.org/0000-0002-0575-0308
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, NC, USA.ORCID http://orcid.org/0000-0002-6487-081X
Matthias LienhardDepartment Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany.ORCID http://orcid.org/0000-0002-2549-3142
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, CA, USA.
Ka Ming NipCanada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.ORCID http://orcid.org/0000-0002-1574-3363
Mihaela PerteaDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.ORCID http://orcid.org/0000-0003-0762-8637
Matthew E RitchieWalter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.ORCID http://orcid.org/0000-0002-7383-0609
Andre D SimGenome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.ORCID http://orcid.org/0000-0002-4062-469X
Alison D TangDepartment of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
Yuk Kei WanGenome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.ORCID http://orcid.org/0000-0003-1774-261X
Changqing WangWalter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.ORCID http://orcid.org/0000-0001-7868-3882
Brandon Y WongDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.ORCID http://orcid.org/0000-0002-7644-1916
Chen YangCanada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.
If BarnesEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK.
Andrew E BerryEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK.ORCID http://orcid.org/0000-0001-5096-7701
Salvador Capella-GutierrezBarcelona Supercomputing Center, Barcelona, Spain.ORCID http://orcid.org/0000-0002-0309-604X
Alyssa CousineauProgram in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA.
Namrita DhillonDepartment of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
Jose M Fernandez-GonzalezBarcelona Supercomputing Center, Barcelona, Spain.ORCID http://orcid.org/0000-0002-4806-5140
Luis Ferrández-PeralInstitute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.ORCID http://orcid.org/0000-0003-0338-0603
Natàlia Garcia-ReyeroEnergy, Installations & Environment, Office of the Assistant Secretary of Defense, Washington, DC, USA.ORCID http://orcid.org/0000-0002-1667-5294
Stefan GötzBiobam Bioinformatics, Valencia, Spain.ORCID http://orcid.org/0000-0001-5777-3520
Carles Hernández-FerrerBarcelona Supercomputing Center, Barcelona, Spain.ORCID http://orcid.org/0000-0002-8029-7160
Liudmyla KondratovaGenetics Institute, University of Florida, Gainesville, FL, USA.ORCID http://orcid.org/0000-0002-7427-0164
Tianyuan LiuCardiff University, Cardiff, UK.ORCID http://orcid.org/0000-0002-8561-6239
Alessandra Martinez-MartinInstitute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.
Carlos MenorBiobam Bioinformatics, Valencia, Spain.ORCID http://orcid.org/0009-0000-6433-4585
Jorge Mestre-TomásInstitute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.ORCID http://orcid.org/0000-0002-8983-3417
Jonathan M MudgeEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK.ORCID http://orcid.org/0000-0003-4789-7495
Nedka G PanayotovaInterdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA.
Alejandro PaniaguaInstitute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.
Dmitry RepchevskyBarcelona Supercomputing Center, Barcelona, Spain.ORCID http://orcid.org/0000-0001-6415-0532
Xingjie RenInstitute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-2348-4162
Eric RouchkaDepartment of Biochemistry & Molecular Genetics, University of Louisville, Louisville, KY, USA.ORCID http://orcid.org/0000-0003-3487-6572
Brandon Saint-JohnDepartment of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
Enrique SapenaEuropean Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID http://orcid.org/0000-0003-4554-9040
Leon SheynkmanDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
Melissa Laird SmithDepartment of Biochemistry & Molecular Genetics, University of Louisville, Louisville, KY, USA.ORCID http://orcid.org/0000-0001-7151-3207
Marie-Marthe SunerEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK.ORCID http://orcid.org/0000-0002-0380-7171
Hazuki TakahashiCenter for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan.ORCID http://orcid.org/0000-0001-7315-7349
Ingrid A YoungworthDepartment of Genetics, Stanford University, Palo Alto, CA, USA.
Piero CarninciCenter for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan.ORCID http://orcid.org/0000-0001-7202-7243
Nancy D DenslowDepartment of Physiological Sciences, College of Veterinary Medicine, Gainesville, FL, USA.ORCID http://orcid.org/0000-0002-3946-3112
Roderic GuigóCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.ORCID http://orcid.org/0000-0002-5738-4477
Margaret E HunterUS Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, USA.ORCID http://orcid.org/0000-0002-4760-9302
Rene MaehrProgram in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA.ORCID http://orcid.org/0000-0002-9520-3382
Yin ShenInstitute for Human Genetics, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0001-9901-5613
Hagen U TilgnerBrain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York City, NY, USA.
Barbara J WoldDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.ORCID http://orcid.org/0000-0003-3235-8130
Christopher VollmersDepartment of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA. vollmers@ucsc.edu.ORCID http://orcid.org/0000-0002-7626-6222
Adam FrankishEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK. frankish@ebi.ac.uk.ORCID http://orcid.org/0000-0002-4333-628X
Kin Fai AuDepartment of Biomedical Informatics, The Ohio State University, Columbus, OH, USA. kinfai@med.umich.edu.ORCID http://orcid.org/0000-0002-9222-4241
Gloria M SheynkmanDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA. gs9yr@virginia.edu.ORCID http://orcid.org/0000-0002-4223-9947
Ali MortazaviDepartment of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA. ali.mortazavi@uci.edu.ORCID http://orcid.org/0000-0002-4259-6362
Ana ConesaInstitute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain. ana.conesa@csic.es.ORCID http://orcid.org/0000-0001-9597-311X
Angela N BrooksUC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA. anbrooks@ucsc.edu.ORCID http://orcid.org/0000-0002-7898-3073
Funding
GENCODE Resource ProjectU41HG007234 · NHGRI · SANGER INSTITUTE · PI FLICEK, PAUL · 2013 to 2020
$20.3MHigher Precision Human and Mouse TranscriptomesUM1HG009443 · NHGRI · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI MORTAZAVI, SEYED ALI, WOLD, BARBARA J · 2017 to 2021
$15.5MIntegrative BioinformaticsZICES103371 · NIEHS · NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES · PI LI, JIAN-LIANG · 2022 to 2025
$11.5MUniversity of Louisville Center for Integrative Environmental Health SciencesP30ES030283 · NIEHS · UNIVERSITY OF LOUISVILLE · PI Juw Won Park · 2020 to 2026
$10.0MHigh throughput CRISPR-mediated functional validation of regulatory elementsUM1HG009402 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI REN, BING, SHEN, YIN · 2017 to 2021
$8.4MRealizing the potential of long-read sequencing technologyR35GM133569 · NIGMS · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI Christopher Vollmers · 2019 to 2026
$3.4MNovel 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
$2.1MDe Novo Assembly Tools: Research with Unbiased Engines - Renewal (DNA-TRUER)R01HG007182 · NHGRI · PROVINCIAL HEALTH SERVICES AUTHORITY · PI BIROL, INANC · 2014 to 2022
$1.9MBioinformatics 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
$1.7MNHGRI NIH HHS F31 HG010999NHGRI NIH HHS R01 HG007182NHGRI NIH HHS R01 HG008759NHGRI NIH HHS R01 HG011469NHGRI NIH HHS R21 HG011280NHGRI NIH HHS U41 HG007234NHGRI NIH HHS UM1 HG009402NHGRI NIH HHS UM1 HG009443NIEHS NIH HHS P30 ES030283NIGMS NIH HHS R01 GM136886NIGMS NIH HHS R35 GM133569NIGMS NIH HHS R35 GM138122NIGMS NIH HHS R35 GM142647Saint Petersburg State University (St. Petersburg State University) 73023672U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) F31HG010999U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) R01GM136886U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) R01HG008759U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) R01HG011469U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) U41HG007234U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R35GM138122U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R35GM14264Wellcome TrustWellcome Trust (Wellcome) WT108749/Z/15/Z
Abstract
The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the consortium generated over 427 million long-read sequences from complementary DNA and direct RNA datasets, encompassing human, mouse and manatee species. Developers utilized these data to address challenges in transcript isoform detection, quantification and de novo transcript detection. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. Incorporating additional orthogonal data and replicate samples is advised when aiming to detect rare and novel transcripts or using reference-free approaches. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.
Indexed as
Gene Expression ProfilingRNA-SeqAnimalsHumansMiceMolecular Sequence AnnotationSequence Analysis, RNATranscriptome
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