ArticleNucleic acids research2019
OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
70 citing papers in PubMed, 133 citations in OpenAlex.
- Dark matter matters: from noncoding RNA regulation to cancer immunity.Oncoimmunology · 2026Review
- Microproteins in Human Physiology and Pathology.Biochemistry · 2026Review
- Revisiting noncoding RNAs: emerging coding functions and their impact on skeletal muscle development.Experimental & molecular medicine · 2026Review
- Identification of Potentially Coding Small ORFs in Plant Transcriptomes.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Microproteins in Metabolic Biology: Emerging Functions and Potential Roles as Nutrient-Linked Biomarkers.International journal of molecular sciences · 2025Review
- Micropeptides in the oncological dark matter: decoding their roles in tumor progression and therapy resistance.Journal of translational medicine · 2025Review
- Chasing the Ghost Proteome in the Dark Matter.Molecular & cellular proteomics : MCP · 2025Review
- Identification of microprotein-coding intronic polyadenylation isoforms and function in genotoxic anticancer drug response.Genome biology · 2025Article
- Identification of Small Open Reading Frame-encoded Proteins in the Human Genome.Genomics, proteomics & bioinformatics · 2025Article
- Discovery of diverse chimeric peptides in a eukaryotic proteome sets the stage for experimental validation of the mosaic translation hypothesis.Computational and structural biotechnology journal · 2025Article
- ChiMSource improves the accuracy of studies on novel amino acid sequences by predicting alternative sources of mass spectrometry-derived peptides.Computational and structural biotechnology journal · 2025Article
- A universal pipeline MosaicProt enables large-scale modeling and detection of chimeric protein sequences for studies on programmed ribosomal frameshifting.Computational and structural biotechnology journal · 2025Article
- AthRiboNC: an Arabidopsis database for ncRNAs with coding potential revealed from ribosome profiling.Database : the journal of biological databases and curation · 2024Article
- Proteomics Can Rise to the Challenge of Pseudogenes' Coding Nature.Journal of proteome research · 2024Review
- Deciphering the ghost proteome in ovarian cancer cells by deep proteogenomic characterization.Cell death & disease · 2024Article
- HMPA: a pioneering framework for the noncanonical peptidome from discovery to functional insights.Briefings in bioinformatics · 2024Article
- Article
- Review
- SpliceProt 2.0: A Sequence Repository of Human, Mouse, and Rat Proteoforms.International journal of molecular sciences · 2024Article
- OpenProt 2.0 builds a path to the functional characterization of alternative proteins.Nucleic acids research · 2024Article
10 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
16 authors at 3 institutions in 2 countries.
Funding
Abstract
Advances in proteomics and sequencing have highlighted many non-annotated open reading frames (ORFs) in eukaryotic genomes. Genome annotations, cornerstones of today's research, mostly rely on protein prior knowledge and on ab initio prediction algorithms. Such algorithms notably enforce an arbitrary criterion of one coding sequence (CDS) per transcript, leading to a substantial underestimation of the coding potential of eukaryotes. Here, we present OpenProt, the first database fully endorsing a polycistronic model of eukaryotic genomes to date. OpenProt contains all possible ORFs longer than 30 codons across 10 species, and cumulates supporting evidence such as protein conservation, translation and expression. OpenProt annotates all known proteins (RefProts), novel predicted isoforms (Isoforms) and novel predicted proteins from alternative ORFs (AltProts). It incorporates cutting-edge algorithms to evaluate protein orthology and re-interrogate publicly available ribosome profiling and mass spectrometry datasets, supporting the annotation of thousands of predicted ORFs. The constantly growing database currently cumulates evidence from 87 ribosome profiling and 114 mass spectrometry studies from several species, tissues and cell lines. All data is freely available and downloadable from a web platform (www.openprot.org) supporting a genome browser and advanced queries for each species. Thus, OpenProt enables a more comprehensive landscape of eukaryotic genomes' coding potential.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.