ArticleMolecular biology and evolution2019
Advances and Applications in the Quest for Orthologs.
Article in Molecular biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
- Combining Annotation Software to Identify Orthologous Genes (CASIO) Provides a New Dataset of Orthologous Genes for Swallowtail Butterflies.Molecular ecology resources · 2026Article
- Unveiling Dynamic Defense Pathways: Transcriptome Analysis of Phenylpropanoids and (Iso)flavonoids in Cowpea Leaves Post-CABMV Inoculation.Biochemical genetics · 2026Article
- Quantifying Hierarchical Conflicts in Homology Statements.Journal of molecular evolution · 2025Article
- Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration.Journal of molecular evolution · 2025Review
- Review
- Annotation matters: the effect of structural gene annotation on orthology inference.Bioinformatics (Oxford, England) · 2025Article
- Whole genome sequencing and annotation of Pseudocercospora abelmoschi, a causal agent of black leaf mould of okra.World journal of microbiology & biotechnology · 2025Article
- Living on the Rocks: Genomic Analysis of Limestone Langurs Provides Novel Insights into the Adaptive Evolution in Extreme Karst Environments.Genomics, proteomics & bioinformatics · 2025Article
- Comprehensive analysis of orthologous genes reveals functional dynamics and energy metabolism in the rhizospheric microbiome of Moringa oleifera.Functional & integrative genomics · 2025Article
- Unveiling novel features and phylogenomic assessment of indigenousMicrobiology spectrum · 2025Article
- Orthology inference at scale with FastOMA.Nature methods · 2025Article
- UtilizingJournal of developmental biology · 2025Review
- PanBGC: a pangenome-inspired framework for comparative analysis of biosynthetic gene clusters.ISME communications · 2025Article
- How deep can we decipher protein evolution with deep learning models.Patterns (New York, N.Y.) · 2024Article
- Synthetic lethality and the minimal genome size problem.mSphere · 2024Article
- Bridge: A New Algorithm for Rooting Orthologous Genes in Large-Scale Evolutionary Analyses.Molecular biology and evolution · 2024Article
- OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem.Nucleic acids research · 2024Article
- Genome-wide expansion and reorganization during grass evolution: from 30 Mb chromosomes in rice and Brachypodium to 550 Mb in Avena.BMC plant biology · 2023Article
- Approaches to increase the validity of gene family identification using manual homology search tools.Genetica · 2023Review
- AlexandrusPS: A User-Friendly Pipeline for the Automated Detection of Orthologous Gene Clusters and Subsequent Positive Selection Analysis.Genome biology and evolution · 2023Article
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
Gene families evolve by the processes of speciation (creating orthologs), gene duplication (paralogs), and horizontal gene transfer (xenologs), in addition to sequence divergence and gene loss. Orthologs in particular play an essential role in comparative genomics and phylogenomic analyses. With the continued sequencing of organisms across the tree of life, the data are available to reconstruct the unique evolutionary histories of tens of thousands of gene families. Accurate reconstruction of these histories, however, is a challenging computational problem, and the focus of the Quest for Orthologs Consortium. We review the recent advances and outstanding challenges in this field, as revealed at a symposium and meeting held at the University of Southern California in 2017. Key advances have been made both at the level of orthology algorithm development and with respect to coordination across the community of algorithm developers and orthology end-users. Applications spanned a broad range, including gene function prediction, phylostratigraphy, genome evolution, and phylogenomics. The meetings highlighted the increasing use of meta-analyses integrating results from multiple different algorithms, and discussed ongoing challenges in orthology inference as well as the next steps toward improvement and integration of orthology resources.
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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.