ArticleScience (New York, N.Y.)2023
Integrating gene annotation with orthology inference at scale.
Article in Science (New York, N.Y.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 153 papers.
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Who cites it
153 citing papers in PubMed, 186 citations in OpenAlex.
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- Comparative Genomics Reveals Convergent Evolution Between Avivorous Bats (Ia io and Nyctalus aviator).Integrative zoology · 2026Article
- Advances in genomics-driven genetic decoding and genomic design breeding in tomato.Horticulture research · 2026Article
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- Convergent latitudinal erosion of circadian systems in a rapidly diversifying order of fishes.PLoS genetics · 2026Article
- CroCoNet: a framework for the quantitative comparison of gene regulatory networks across species.Genome biology · 2026Article
- The howler monkey genome provides new insights into the distinctive howling and folivorous adaptations of New World monkeys.Genome biology · 2026Article
- Adaptation across an extreme elevational gradient in Andean leaf-eared mice, the world's highest-dwelling mammal.Science (New York, N.Y.) · 2026Article
- Molecular dynamics simulations of intrinsically disordered protein regions enable biophysical interpretation of variant-effect predictors.HGG advances · 2026Article
- Phylogenomic analysis of vocal fold length evolution reveals links between vocal and auditory systems in terrestrial mammals.Molecular biology and evolution · 2026Article
- Tutorial: annotation of animal genomes.Nature protocols · 2026Review
- Stepwise emergence of recombination suppression precedes fissiparous asexuality in the planarian Schmidtea mediterranea.Nature communications · 2026Article
- Quantifying the Influence of Genetic Context on Duplicated Mammalian Genes.Molecular biology and evolution · 2026Article
- DupyliCate: mining, classifying, and characterizing gene duplications.Scientific reports · 2026Article
- Elevated retrocopy burden and sloth-specific expansions illuminate mammalian genome evolution.BMC biology · 2026Article
- The Paipu framework enables creation of a large-scale mammalian cancer transcriptomics atlas.bioRxiv : the preprint server for biology · 2026Article
- The genomic basis of independent marine transitions in turtles: convergent episodic adaptation and demographic shifts.Molecular biology and evolution · 2026Article
93 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
14 authors at 3 institutions in 3 countries.
Funding
Abstract
Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method that integrates structural gene annotation and orthology inference. TOGA implements a different paradigm to infer orthologous loci, improves ortholog detection and annotation of conserved genes compared with state-of-the-art methods, and handles even highly fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 501 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. TOGA is a powerful and scalable method to annotate and compare genes in the genomic era.
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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.