Orthologs, paralogs, and evolutionary genomics.

By Eugene V. Koonin. Annual Review of Genetics, 2005

792 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/561bedb4972ff60a011556a91640d8d3c13a5f4c

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Citations in the corpus

The Logic of Chance: The Nature and Origin of Biological Evolution (2011, background): “In other words, most of the genes evolve as orthologous lineages, with occasional duplications (Koonin, 2005).”
A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation (2014, background): “the same gene can be characterized as an ortholog or paralog to other genes depending on whether more strictly or more broadly defined taxonomic groups are considered [5].”
Phylogeny and Molecular Evolution of the Green Algae (2012, background): “Apart from vertical descent with modification, various other evolutionary events may affect gene histories, including gene duplication, gene loss, horizontal gene transfer and gene rearrangements (Koonin, 2005).”
Leveraging Logical Rules for Efficacious Representation of Large Orthology Datasets (2017, background): “Xenologs are homologous genes that are neither orthologs nor paralogs according to above definitions, but appear to be orthologous in genome comparisons [7].”
GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis (2013, background): “For this reason, orthologues are key elements in genome annotation and evolutionary studies (2, 3).”
OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs (2018, background): “Homologs with a reference to a specific phylogeny radiation, i.e. descendants from a single gene of the last common ancestor, are termed orthologs and referred to below as ortholog groups or OGs (1,2).”
TreeFam: a curated database of phylogenetic trees of animal gene families (2005, methodology): “Orthologs typically perform 65 equivalent functions, and paralogs sometimes have acquired new functions, but this is not always true (35).”
eggNOG: automated construction and annotation of orthologous groups of genes (2007, background): “These concepts have since been extended and reﬁned to include orthologous groups (2), in-paralogs and out-paralogs (3,4), but the identiﬁcation and classiﬁcation of homologous genes remains very diﬃcult.”
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences (2015, background): “However, due to the intricate evolution of most gene families, which often involves multiple nested duplications, genomic rearrangements and horizontal gene transfers, orthology prediction remains as a highly challenging task (4,5), both analytically and computationally.”