ArticleNature biotechnology2022
Standardized annotation of translated open reading frames.
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Article in Nature biotechnology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 174 papers.
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174citing papers in PubMed
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Who cites it
174 citing papers in PubMed.
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- Codon optimality predicts mRNA half-life but does not transfer to lncRNAs.Molecular genetics and genomics : MGG · 2026Article
- A novel mitochondrial microprotein reprograms cellular bioenergetics and protects against hepatic steatosis.iScience · 2026Article
- LRP2: A proteogenomics pipeline for long-read informed protein isoform analysis and discovery.bioRxiv : the preprint server for biology · 2026Article
- MetaTIS: a tool to predict cognate and near-cognate translation initiation sites in human.NAR genomics and bioinformatics · 2026Article
- A microprotein atlas of the human frontal cortex in Alzheimer's disease.Nature aging · 2026Article
- Subcellular localization of human long non-coding RNAs is an isoform-resolved property masked by gene-level analysis.Molecular genetics and genomics : MGG · 2026Article
- Ribo-ITP enables identification of translons from limited input samples.Nature communications · 2026Article
- Identification of unannotated microproteins involved in endothelial cell homeostasis, dysfunction, and vascular disease.Cardiovascular research · 2026Article
- A microprotein encoded by FERMT3 modulates endothelial cell protein catabolism and induces cell cycle arrest and senescence.Cell communication and signaling : CCS · 2026Article
- Annotating genomes at increased scale and resolution.Nature reviews. Genetics · 2026Review
- The long non-coding RNA landscape of endurance exercise training.Molecular metabolism · 2026Article
- Article
- A Proteogenomic Approach to Discover Novel lncRNA-Derived Microproteins and Their Potential Clinical Utility in Hepatocellular Carcinoma.Molecular & cellular proteomics : MCP · 2026Article
- Zero-shot de novo peptide sequencing with open posttranslational modification discovery.Nature biotechnology · 2026Article
- Human SRD5A1 as a case of gene expression indel-resistance in triple-coding region.Genome biology · 2026Article
- An Artificial Antibody-Based Toolbox Accelerates Validation of Hidden Microproteins Encoded by the Dark Genome.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Microproteins in Human Physiology and Pathology.Biochemistry · 2026Review
114 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
35 authors.
Jonathan M Mudge *European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK. jmudge@ebi.ac.uk.ORCID http://orcid.org/0000-0003-4789-7495
Jorge Ruiz-Orera *Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany. jorge.ruizorera@mdc-berlin.de.ORCID http://orcid.org/0000-0002-8317-0034
John R Prensner *Broad Institute of MIT and Harvard, Cambridge, MA, USA. prensner@broadinstitute.org.ORCID http://orcid.org/0000-0002-7024-636X
Marie A BrunetDepartment of Pediatrics, Medical Genetics Service, Université de Sherbrooke, Sherbrooke, Quebec, Canada.ORCID http://orcid.org/0000-0001-5973-3522
Ferriol CalvetEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID http://orcid.org/0000-0003-1841-9881
Irwin JungreisBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-3197-5367
Jose Manuel GonzalezEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID http://orcid.org/0000-0001-5569-0705
Michele MagraneEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID http://orcid.org/0000-0003-3544-996X
Thomas F MartinezClayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-4011-8164
Jana Felicitas SchulzCardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.ORCID http://orcid.org/0000-0002-8157-2224
Yucheng T YangProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-6873-5279
M Mar AlbàEvolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Research Institute (IMIM) and Universitat Pompeu Fabra (UPF), Barcelona, Spain.
Julie L AspdenSchool of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
Pavel V BaranovSchool of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.ORCID http://orcid.org/0000-0001-9017-0270
Ariel A BazziniStowers Institute for Medical Research, Kansas City, MO, USA.ORCID http://orcid.org/0000-0002-2251-5174
Elspeth BrufordEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID http://orcid.org/0000-0002-8380-5247
Maria Jesus MartinEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
Lorenzo CalvielloFunctional Genomics Centre, Human Technopole, Milan, Italy.
Anne-Ruxandra CarvunisDepartment of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.ORCID http://orcid.org/0000-0002-6474-6413
Jin ChenDepartment of Pharmacology and Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.ORCID http://orcid.org/0000-0002-6634-4397
Juan Pablo CousoCentro Andaluz de Biologia del Desarrollo, CSIC-UPO, Seville, Spain.ORCID http://orcid.org/0000-0002-8547-7312
Eric W DeutschInstitute for Systems Biology, Seattle, WA, USA.ORCID http://orcid.org/0000-0001-8732-0928
Paul FlicekEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID http://orcid.org/0000-0002-3897-7955
Adam FrankishEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
Mark GersteinProgram in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA.
Norbert HubnerCardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.ORCID http://orcid.org/0000-0002-1218-6223
Nicholas T IngoliaDepartment of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-3395-1545
Manolis KellisBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-7113-9630
Gerben MenschaertBiobix, Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium.
Robert L MoritzInstitute for Systems Biology, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-3216-9447
Uwe OhlerBerlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.ORCID http://orcid.org/0000-0002-0881-3116
Xavier RoucouDepartment of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada.ORCID http://orcid.org/0000-0001-9370-5584
Alan SaghatelianClayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-0427-563X
Jonathan S WeissmanDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0003-2445-670X
Sebastiaan van Heesch *Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands. S.vanHeesch@prinsesmaximacentrum.nl.ORCID http://orcid.org/0000-0001-9593-1980
Funding
Systems BiologyU19AG023122 · NIA · TRANSLATIONAL GENOMICS RESEARCH INST · PI NICHOLAS Joseph SCHORK · 2004 to 2026
$102.6MViral Vector Core (VVC)P30CA014195 · NCI · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI TONY R. HUNTER · 1985 to 2026
$82.8MUniProt - Text Mining and Large Language models to Enhance Functional Annotation in UniProt of Protein Variants Associated with Alzheimer's DiseaseU24HG007822 · NHGRI · GEORGETOWN UNIVERSITY · PI Alex Bateman, Alan James Bridge · 2018 to 2026
$53.0MGENCODE Resource ProjectU41HG007234 · NHGRI · SANGER INSTITUTE · PI FLICEK, PAUL · 2013 to 2020
$20.3MTraining Program in Nervous System TumorsK12CA090354 · NCI · MASSACHUSETTS GENERAL HOSPITAL · PI PLOTKIN, SCOTT R · 2001 to 2025
$16.3MGENCODE: comprehensive reference genome annotation for human and mouseU24HG007234 · NHGRI · EUROPEAN MOLECULAR BIOLOGY LABORATORY · PI Fergal James Martin · 2021 to 2026
$16.1MShortening the development cycle time of Trans Proteomic Pipeline tools with high performance computingR01GM087221 · NIGMS · INSTITUTE FOR SYSTEMS BIOLOGY · PI DEUTSCH, ERIC, MORITZ, ROBERT L · 2010 to 2021
$6.0MRegulatory Morif Discovery in the Human Genome Using Comparative GenomicsR01HG004037 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI KELLIS, MANOLIS · 2007 to 2015
$3.9MThe Nomenclature of Human and Vertebrate GenesU24HG003345 · NHGRI · UNIVERSITY OF CAMBRIDGE · PI Elspeth Bruford · 2018 to 2026
$3.9MFrom non-coding to coding: uncovering the hidden coding potential of non-coding sequences and its role in de novo gene evolutionDP2GM137422 · NIGMS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI CARVUNIS, ANNE-RUXANDRA · 2019 to 2019
$2.3MSmall translated ORFs in the 3'UTR enhance translation in vertebratesR01GM136849 · NIGMS · STOWERS INSTITUTE FOR MEDICAL RESEARCH · PI BAZZINI, ARIEL · 2021 to 2025
$2.0MFunctional genomics of the dynamic molecular network controlling mRNA translation and decayR01GM130996 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI INGOLIA, NICHOLAS T · 2019 to 2022
$1.2MBiotechnology and Biological Sciences Research Council BB/S007407/1Howard Hughes Medical InstituteMedical Research Council MR/N000471/1NCI NIH HHS K12 CA090354NHGRI NIH HHS R01 HG004037NHGRI NIH HHS U24 HG003345NHGRI NIH HHS U24 HG007234NHGRI NIH HHS U24 HG007822NHGRI NIH HHS U41 HG007234NIA NIH HHS U19 AG023122NIGMS NIH HHS DP2 GM137422NIGMS NIH HHS F32 GM123685NIGMS NIH HHS R00 GM134154NIGMS NIH HHS R01 GM087221NIGMS NIH HHS R01 GM130996NIGMS NIH HHS R01 GM136849NIGMS NIH HHS R24 GM127667NIH HHS S10 OD026936Wellcome TrustWellcome Trust 108749/Z/15/ZWellcome Trust 208349/Z/17/ZWellcome Trust 210692/Z/18/Z
Abstract
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Indexed as
Protein BiosynthesisRibosomesMolecular Sequence AnnotationOpen Reading Frames
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