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The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.

OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs

Kriventseva, Evgenia V, Kuznetsov, Dmitry, Tegenfeldt, Fredrik, Manni, Mosè, Dias, Renata, Simão, Felipe A, Zdobnov, Evgeny M·2019·Nucleic Acids Research
DOI 10.1093/nar/gky1053PMC PMC6323947
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  • Most orthology inference methods rely on sequence alignments and often incorporate a specific alignment overlap criterion as part of the orthology algorithm.

    “Most orthology inference methods rely on sequence alignments and often incorporate a specific alignment overlap criteria as part of the orthology algorithm [e.g. OMA (Train et al. 2017), OrthoDB (Kriventseva et al. 2019), PANTHER (Thomas et al. 2022)].”

    From Annotation matters: the effect of structural gene annotation on orthology inference (2025) · cites this paper as Kriventseva et al. 2019

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Research works printed but not linked: 24

  1. Fitch, 2000, Homology a personal view on some of the problems, Trends Genet., 16, 227, 10.1016/S0168-9525(00)02005-9 · DOI
  2. Koonin, 2005, Orthologs, paralogs, and evolutionary genomics, Annu. Rev. Genet., 39, 309, 10.1146/annurev.genet.39.073003.114725 · DOI · Paper page
  3. Tatusov, 1997, A genomic perspective on protein families, Science, 278, 631, 10.1126/science.278.5338.631 · DOI
  4. van der Heijden, 2007, Orthology prediction at scalable resolution by phylogenetic tree analysis, BMC Bioinformatics, 8, 83, 10.1186/1471-2105-8-83 · DOI
  5. Fischer, 2011, Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups, Curr. Protoc. Bioinform., 10.1002/0471250953.bi0612s35 · DOI
  6. Nakaya, 2013, KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters, Nucleic Acids Res., 41, D353, 10.1093/nar/gks1239 · DOI
  7. Huerta-Cepas, 2014, PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome, Nucleic Acids Res., 42, D897, 10.1093/nar/gkt1177 · DOI · Paper page
  8. Sonnhammer, 2015, InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic, Nucleic Acids Res., 43, D234, 10.1093/nar/gku1203 · DOI
  9. Uchiyama, 2015, MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data, Nucleic Acids Res., 43, D270, 10.1093/nar/gku1152 · DOI
  10. Huerta-Cepas, 2016, eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences, Nucleic Acids Res., 44, D286, 10.1093/nar/gkv1248 · DOI
  11. Galperin, 2017, Microbial genome analysis: the COG approach, Brief. Bioinform.
  12. Zdobnov, 2017, OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs, Nucleic Acids Res., 45, D744, 10.1093/nar/gkw1119 · DOI · Paper page
  13. Altenhoff, 2018, The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces, Nucleic Acids Res., 46, D477, 10.1093/nar/gkx1019 · DOI · Paper page
  14. Kriventseva, 2015, OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software, Nucleic Acids Res., 43, D250, 10.1093/nar/gku1220 · DOI
  15. Trachana, 2011, Orthology prediction methods: a quality assessment using curated protein families, Bioessays, 33, 769, 10.1002/bies.201100062 · DOI · Paper page
  16. Waterhouse, 2007, Evolutionary dynamics of immune-related genes and pathways in disease-vector mosquitoes, Science, 316, 1738, 10.1126/science.1139862 · DOI
  17. Hoy, 2016, Genome sequencing of the phytoseiid predatory mite metaseiulus occidentalis reveals completely atomized hox genes and superdynamic intron evolution, Genome Biol. Evol., 8, 1762, 10.1093/gbe/evw048 · DOI
  18. i, K.C., 2013, The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment, J. Hered., 104, 595, 10.1093/jhered/est050 · DOI
  19. Kriventseva, 2008, OrthoDB: the hierarchical catalog of eukaryotic orthologs, Nucleic Acids Res., 36, D271, 10.1093/nar/gkm845 · DOI
  20. Waterhouse, 2011, Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi, Genome Biol. Evol., 3, 75, 10.1093/gbe/evq083 · DOI
  21. Waterhouse, 2017, BUSCO applications from quality assessments to gene prediction and phylogenomics, Mol. Biol. Evol., 35, 543, 10.1093/molbev/msx319 · DOI · Paper page
  22. Ondov, 2016, Mash: fast genome and metagenome distance estimation using MinHash, Genome Biol., 17, 132, 10.1186/s13059-016-0997-x · DOI · Paper page
  23. Simao, 2015, BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics, 31, 3210, 10.1093/bioinformatics/btv351 · DOI · Paper page
  24. Steinegger, 2017, MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets, Nat. Biotechnol., 35, 1026, 10.1038/nbt.3988 · DOI · Paper page

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Metadata

Authors
Kriventseva, E. V., Kuznetsov, D., Tegenfeldt, F., Manni, M., Dias, R., Simão, F. A., & Zdobnov, E. M.
Affiliations
Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2018-11-05
Volume
47
Issue
D1
Pages
D807-D811
ISSN
  • 0305-1048
  • 1362-4962
DOI
10.1093/nar/gky1053
PMC
PMC6323947
Cited by
1,232
References
3
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (vor)
Funders
  • Swiss National Science Foundation (31003A_166483)
  • São Paulo Research Foundation (17/15195–2)

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