ArticleNature biotechnology2025
Quality assessment of gene repertoire annotations with OMArk.
Article in Nature biotechnology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 134 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
134 citing papers in PubMed, 158 citations in OpenAlex.
- Combining Annotation Software to Identify Orthologous Genes (CASIO) Provides a New Dataset of Orthologous Genes for Swallowtail Butterflies.Molecular ecology resources · 2026Article
- Draft Genome Assembly and Annotation of a Male Mezayen Dromedary Camel of the Majaheem Type (Animals : an open access journal from MDPI · 2026Article
- Article
- De Novo Genome Sequence Assembly of the Algal Endosymbiont Micractinium conductrix Derived From Its Host Paramecium bursaria 186b.Genome biology and evolution · 2026Article
- Article
- Genome evolution and long-term demographic history in true crocodiles.G3 (Bethesda, Md.) · 2026Article
- From neuropeptides to toxins: illuminating the origins of venom complexity in cone snails.Molecular biology and evolution · 2026Article
- Genomic Identification and Comparative Characterization of Chemosensory Genes in Two Walnut Pests.Biology · 2026Article
- Expanding the triangle of U: comparative analysis of the Hirschfeldia incana genome provides insights into chromosomal evolution, phylogenomics and high photosynthesis-related traits.Annals of botany · 2026Article
- A chromosome-level genome assembly of Platycladus orientalis and comparative genomics reveal pivotal roles of transposable elements in gene duplication and pseudogenization across gymnosperm giga-genomes.Plant communications · 2026Article
- A T2T Genome of the Lobed-Lip Iguazu Joana (Crenicichla tuca) Reveals Intrachromosomal Rearrangements and Trans-species Polymorphism in Cichlid Fishes.Genome biology and evolution · 2026Article
- Telomere-to-telomere genome assembly of pumpkin (Horticulture research · 2026Article
- Dissecting flowering time and flower color in Carum carvi utilizing a long-read draft genome and a GBS-based QTL mapping.Scientific reports · 2026Article
- First Genome Assembly of the Critically Endangered Arabian Leopard (International journal of molecular sciences · 2026Article
- A Chromosome-Scale Genome Assembly and Annotation of the Antarctic Pearlwort Colobanthus quitensis (Caryophyllaceae).Genome biology and evolution · 2026Article
- De novo Genome Assembly, Annotation, and Comparative Analysis of the Lined Sole Achirus lineatus as a Resource for Evolutionary and Environmental Genomics.Marine biotechnology (New York, N.Y.) · 2026Article
- Wild tomato genome assemblies reveal structural variants and repeat content act as recombination barriers.Nature communications · 2026Article
- Gapless and phased genome assembly reveals post-allopolyploidization subgenomic diversification of tobacco centromeres.Genome biology · 2026Article
- Omics technologies in aquafeed: unlocking the black box towards systems biology.Functional & integrative genomics · 2026Review
- Article
74 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
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In the era of biodiversity genomics, it is crucial to ensure that annotations of protein-coding gene repertoires are accurate. State-of-the-art tools to assess genome annotations measure the completeness of a gene repertoire but are blind to other errors, such as gene overprediction or contamination. We introduce OMArk, a software package that relies on fast, alignment-free sequence comparisons between a query proteome and precomputed gene families across the tree of life. OMArk assesses not only the completeness but also the consistency of the gene repertoire as a whole relative to closely related species and reports likely contamination events. Analysis of 1,805 UniProt Eukaryotic Reference Proteomes with OMArk demonstrated strong evidence of contamination in 73 proteomes and identified error propagation in avian gene annotation resulting from the use of a fragmented zebra finch proteome as a reference. This study illustrates the importance of comparing and prioritizing proteomes based on their quality measures.
Indexed as
Identifiers
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.