ArticleMolecular biology and evolution2021
Ten Years of Collaborative Progress in the Quest for Orthologs.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability.Nature methods · 2026Article
- Genomica: linear mixed model based, multiple hypothesis testing corrected, ortholog functional enrichment analysis.BMC bioinformatics · 2026Article
- 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
- Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups.Journal of molecular evolution · 2025Review
- A Multi-level Perspective on the Evolution of Orthologs and Their Functions.Journal of molecular evolution · 2025Review
- Functional assays inGenome research · 2025Review
- Annotation matters: the effect of structural gene annotation on orthology inference.Bioinformatics (Oxford, England) · 2025Article
- Feature Architecture-Aware Ortholog Search With fDOG Reveals the Distribution of Plant Cell Wall-Degrading Enzymes Across Life.Molecular biology and evolution · 2025Article
- Orthology inference at scale with FastOMA.Nature methods · 2025Article
- Functional Annotation of Proteomes Using Protein Language Models: A High-Throughput Implementation of the ProtTrans Model.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Quest for Orthologs in the Era of Biodiversity Genomics.Genome biology and evolution · 2024Review
- Decoding functional proteome information in model organisms using protein language models.NAR genomics and bioinformatics · 2024Article
- The interkingdom horizontal gene transfer in 44 early diverging fungi boosted their metabolic, adaptive, and immune capabilities.Evolution letters · 2024Article
- Synthetic lethality and the minimal genome size problem.mSphere · 2024Article
- SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models.Genome biology · 2024Article
- Article
- Protein-Coding Gene Families in Prokaryote Genome Comparisons.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations.Biology direct · 2023Article
- ncOrtho: efficient and reliable identification of miRNA orthologs.Nucleic acids research · 2023Article
- OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes.Nucleic acids research · 2023Article
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14 authors.
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Abstract
Accurate determination of the evolutionary relationships between genes is a foundational challenge in biology. Homology-evolutionary relatedness-is in many cases readily determined based on sequence similarity analysis. By contrast, whether or not two genes directly descended from a common ancestor by a speciation event (orthologs) or duplication event (paralogs) is more challenging, yet provides critical information on the history of a gene. Since 2009, this task has been the focus of the Quest for Orthologs (QFO) Consortium. The sixth QFO meeting took place in Okazaki, Japan in conjunction with the 67th National Institute for Basic Biology conference. Here, we report recent advances, applications, and oncoming challenges that were discussed during the conference. Steady progress has been made toward standardization and scalability of new and existing tools. A feature of the conference was the presentation of a panel of accessible tools for phylogenetic profiling and several developments to bring orthology beyond the gene unit-from domains to networks. This meeting brought into light several challenges to come: leveraging orthology computations to get the most of the incoming avalanche of genomic data, integrating orthology from domain to biological network levels, building better gene models, and adapting orthology approaches to the broad evolutionary and genomic diversity recognized in different forms of life and viruses.
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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.