Database of Orthologous Groups
Names
More detailed information about this field from each metasource.
Database of Orthologous Groups
metasource: Fairsharing.org
version: FAIRsharing.org: OrthoDB; Database of Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.x989d5; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
OrthoDB
metasource: Fairsharing.org
version: FAIRsharing.org: OrthoDB; Database of Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.x989d5; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
orthodb
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
Names
More detailed information about this field from each metasource.
Database of Orthologous Groups
metasource: Fairsharing.orgversion: FAIRsharing.org: OrthoDB; Database of Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.x989d5; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
OrthoDB
metasource: Fairsharing.orgversion: FAIRsharing.org: OrthoDB; Database of Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.x989d5; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
orthodb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
Names
More detailed information about this field from each metasource.
Database of Orthologous Groups
metasource: Fairsharing.orgversion: FAIRsharing.org: OrthoDB; Database of Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.x989d5; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
OrthoDB
metasource: Fairsharing.orgversion: FAIRsharing.org: OrthoDB; Database of Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.x989d5; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
orthodb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny.
Description
More detailed information about this field from each metasource.
OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny.
metasource: Fairsharing.orgversion: FAIRsharing.org: OrthoDB; Database of Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.x989d5; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
OrthoDB is a comprehensive catalogue of orthologous, genes inherited by extant species from a single gene in their last common ancestor. In 2016 OrthoDB reached its 9th release, growing to over 22 million genes from over 5000 species, now adding plants, archaea and viruses. In this update we focused on usability of this fast-growing wealth of data: updating the user and programmatic interfaces to browse and query the data, and further enhancing the already extensive integration of available gene functional annotations. Collating functional annotations from over 100 resources, and enabled us to propose descriptive titles for 87% of ortholog groups. Additionally, OrthoDB continues to provide computed evolutionary annotations and to allow user queries by sequence homology. The OrthoDB resource now enables users to generate publication-quality comparative genomics charts, as well as to upload, analyze and interactively explore their own private data.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Catalog of eukaryotic orthologous protein-coding genes. OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. Available protein descriptors, together with Gene Ontology and InterPro attributes, serve to provide general descriptive annotations of the orthologous groups, and facilitate comprehensive database querying. Data sources include proteomes from arthropods, fungi, vertebrates and basal metazoans.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
Webpage:
http://orthodb.orgWebpage
More detailed information about this field from each metasource.
http://orthodb.org
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://www.orthodb.org/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
http://www.orthodb.org/v9/
metasource: Fairsharing.orgversion: FAIRsharing.org: OrthoDB; Database of Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.x989d5; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Licence:
Name: Creative Commons Attribution 4.0 International (CC BY 4.0)Licence name
More detailed information about this field from each metasource.
Creative Commons Attribution 4.0 International (CC BY 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: OrthoDB; Database of Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.x989d5; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Licence URL
More detailed information about this field from each metasource.
https://creativecommons.org/licenses/by/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: OrthoDB; Database of Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.x989d5; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software
PMID: 25428351
metasource: Fairsharing.org
version: FAIRsharing.org: OrthoDB; Database of Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.x989d5; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011
PMID: 20972218
metasource: Fairsharing.org
version: FAIRsharing.org: OrthoDB; Database of Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.x989d5; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
https://doi.org/10.1093/nar/gkaa1009
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1093/nar/gkw1119
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
Publications
More detailed information about this field from each metasource.
OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software
PMID: 25428351
metasource: Fairsharing.org
version: FAIRsharing.org: OrthoDB; Database of Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.x989d5; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011
PMID: 20972218
metasource: Fairsharing.org
version: FAIRsharing.org: OrthoDB; Database of Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.x989d5; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
https://doi.org/10.1093/nar/gkaa1009
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1093/nar/gkw1119
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
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OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software
PubMed citations: 156.
156 articles citing: OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software
Taxonomy, comparative genomics and evolutionary insights of Penicillium ucsense: a novel species in series Oxalica. PMID:35678932
Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter. PMID:35545619
Natural variation and improved genome annotation of the emerging biofuel crop field pennycress (Thlaspi arvense). PMID:35416986
Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record. PMID:35315317
Long-distance dispersal of pigeons and doves generated new ecological opportunities for host-switching and adaptive radiation by their parasites. PMID:35259992
Convergent consequences of parthenogenesis on stick insect genomes. PMID:35196080
De Novo Reference Assembly of the Upriver Orange Mangrove (Bruguiera sexangula) Genome. PMID:35148390
A de novo reference assembly of the yellow mangrove Ceriops zippeliana genome. PMID:35106563
Genomic and transcriptomic analyses of the subterranean termite Reticulitermes speratus: Gene duplication facilitates social evolution. PMID:35042774
De novo Whole-Genome Assembly of Moringa oleifera Helps Identify Genes Regulating Drought Stress Tolerance. PMID:34970282
Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia. PMID:34963462
Unique roles of vaginal Megasphaera phylotypes in reproductive health. PMID:34898422
Functional Constraints on Insect Immune System Components Govern Their Evolutionary Trajectories. PMID:34893861
Evolutionary history and divergence times of Odonata (dragonflies and damselflies) revealed through transcriptomics. PMID:34805787
Novel ACE2 protein interactions relevant to COVID-19 predicted by evolutionary rate correlations. PMID:34616619
Neurogenomic divergence during speciation by reinforcement of mating behaviors in chorus frogs (Pseudacris). PMID:34600496
Drosophila female reproductive tract gene expression reveals coordinated mating responses and rapidly evolving tissue-specific genes. PMID:33890615
Inference of DNA methylation patterns in molluscs. PMID:33813896
The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control. PMID:33750380
Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics. PMID:33557827
PseudoBase: a genomic visualization and exploration resource for the Drosophila pseudoobscura subgroup. PMID:33319644
Dimeric Structure of the Pseudokinase IRAK3 Suggests an Allosteric Mechanism for Negative Regulation. PMID:33238146
OrthoDB in 2020: evolutionary and functional annotations of orthologs. PMID:33196836
Four myriapod relatives - but who are sisters? No end to debates on relationships among the four major myriapod subgroups. PMID:33148176
Cross-Species RNA-Seq Study Comparing Transcriptomes of Enriched Osteocyte Populations in the Tibia and Skull. PMID:33071985
Genome-enabled insights into the biology of thrips as crop pests. PMID:33070780
Genus-Wide Characterization of Bumblebee Genomes Provides Insights into Their Evolution and Variation in Ecological and Behavioral Traits. PMID:32946576
An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice. PMID:32899740
Adaptation of gene loci to heterochromatin in the course of Drosophila evolution is associated with insulator proteins. PMID:32681087
The genetic factors of bilaterian evolution. PMID:32672535
Survey for positively selected coding regions in the genome of the hematophagous tsetse fly Glossina morsitans identifies candidate genes associated with feeding habits and embryonic development. PMID:32555940
Protein signatures to identify the different genera within the Xanthomonadaceae family. PMID:32488841
Gene Expression Profiling Indicated Diverse Functions and Characteristics of Core Genes in Pea Aphid. PMID:32183501
Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites. PMID:32085510
Baby Genomics: Tracing the Evolutionary Changes That Gave Rise to Placentation. PMID:32053193
A transcriptomic and proteomic atlas of expression in the Nezara viridula (Heteroptera: Pentatomidae) midgut suggests the compartmentalization of xenobiotic metabolism and nutrient digestion. PMID:32028881
Gene content evolution in the arthropods. PMID:31969194
Comparative Genomics Identifies Putative Signatures of Sociality in Spiders. PMID:31960912
Enhanced genome assembly and a new official gene set for Tribolium castaneum. PMID:31937263
Whole Genome Sequencing and Assembly of the Asian Honey Bee Apis dorsata. PMID:31860080
Oxford Nanopore MinION Sequencing Enables Rapid Whole Genome Assembly of Rickettsia typhi in a Resource-Limited Setting. PMID:31820709
Systematic prediction of FFAT motifs across eukaryote proteomes identifies nucleolar and eisosome proteins with the predicted capacity to form bridges to the endoplasmic reticulum. PMID:31777772
Differential Expression of Candidate Salivary Effector Genes in Pea Aphid Biotypes With Distinct Host Plant Specificity. PMID:31695713
Patterns and Constraints in the Evolution of Sperm Individualization Genes in Insects, with an Emphasis on Beetles. PMID:31590243
Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance. PMID:31589316
Population Genomics of an Obligately Halophilic Basidiomycete Wallemia ichthyophaga. PMID:31551960
Assessing predictions on fitness effects of missense variants in calmodulin. PMID:31283071
RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification. PMID:31195970
Genomic Evidence of Recombination in the Basidiomycete Wallemia mellicola. PMID:31167502
Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles. PMID:31101123
YeasTSS: an integrative web database of yeast transcription start sites. PMID:31032841
Marker genes as predictors of shared genomic function. PMID:30947688
Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. PMID:30935422
Evolutionary and functional implications of 3' untranslated region length of mRNAs by comprehensive investigation among four taxonomically diverse metazoan species. PMID:30900191
AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution. PMID:30893420
A Phylogenomic Framework and Divergence History of Cephalochordata Amphioxus. PMID:30618839
De novo transcriptome assembly and its annotation for the black ant Formica fusca at the larval stage. PMID:30561435
De novo annotation of the transcriptome of the Northern Wheatear (Oenanthe oenanthe). PMID:30498627
The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water. PMID:30463532
OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs. PMID:30395283
Genetic and transcriptional variations in NRAMP-2 and OPAQUE1 genes are associated with salt stress response in wheat. PMID:30392081
Conservation Genomics of the Declining North American Bumblebee Bombus terricola Reveals Inbreeding and Selection on Immune Genes. PMID:30147708
Application of Transcriptomics to Compare the Carbohydrate Active Enzymes That Are Expressed by Diverse Genera of Anaerobic Fungi to Degrade Plant Cell Wall Carbohydrates. PMID:30061875
Cross-species systems analysis of evolutionary toolkits of neurogenomic response to social challenge. PMID:29968347
RegenDbase: a comparative database of noncoding RNA regulation of tissue regeneration circuits across multiple taxa. PMID:29872545
Fast Evolution and Lineage-Specific Gene Family Expansions of Aphid Salivary Effectors Driven by Interactions with Host-Plants. PMID:29788052
Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes. PMID:29764366
INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species. PMID:29746660
Signatures of DNA Methylation across Insects Suggest Reduced DNA Methylation Levels in Holometabola. PMID:29697817
ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements. PMID:29678129
Deciphering the mechanism of action of 089, a compound impairing the fungal cell cycle. PMID:29654251
A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals. PMID:29642853
Identifying potential maternal genes of Bombyx mori using digital gene expression profiling. PMID:29462160
A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). PMID:29386578
De Novo characterization of transcriptomes from two North American Papaipema stem-borers (Lepidoptera: Noctuidae). PMID:29364900
Cis-regulatory evolution integrated the Bric-à-brac transcription factors into a novel fruit fly gene regulatory network. PMID:29297463
Functional and evolutionary analysis of Korean bob-tailed native dog using whole-genome sequencing data. PMID:29230066
IsoPlot: a database for comparison of mRNA isoforms in fruit fly and mosquitoes. PMID:29220459
ECOdrug: a database connecting drugs and conservation of their targets across species. PMID:29140522
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces. PMID:29106550
TFClass: expanding the classification of human transcription factors to their mammalian orthologs. PMID:29087517
Expanded and updated data and a query pipeline for iBeetle-Base. PMID:29069517
Identification of cis-regulatory sequences reveals potential participation of lola and Deaf1 transcription factors in Anopheles gambiae innate immune response. PMID:29028826
Gearing up to handle the mosaic nature of life in the quest for orthologs. PMID:28968857
Microbial genome analysis: the COG approach. PMID:28968633
Autoantibody Repertoire in APECED Patients Targets Two Distinct Subgroups of Proteins. PMID:28861084
Gene expression analysis of whole blood RNA from pigs infected with low and high pathogenic African swine fever viruses. PMID:28860602
Orthonome - a new pipeline for predicting high quality orthologue gene sets applicable to complete and draft genomes. PMID:28859620
Variation in DNA Methylation Is Not Consistently Reflected by Sociality in Hymenoptera. PMID:28854636
Deep evolutionary conservation of autism-related genes. PMID:28760967
Rapid evolution of female-biased genes among four species of Anopheles malaria mosquitoes. PMID:28747381
Tick Haller's Organ, a New Paradigm for Arthropod Olfaction: How Ticks Differ from Insects. PMID:28718821
OrthoReD: a rapid and accurate orthology prediction tool with low computational requirement. PMID:28633662
Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes. PMID:28609292
TC003132 is essential for the follicle stem cell lineage in telotrophic Tribolium oogenesis. PMID:28533810
Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals. PMID:28403820
High GC content causes orphan proteins to be intrinsically disordered. PMID:28355220
Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius. PMID:28327943
Risk alleles of genes with monoallelic expression are enriched in gain-of-function variants and depleted in loss-of-function variants for neurodevelopmental disorders. PMID:28265118
Unity in defence: honeybee workers exhibit conserved molecular responses to diverse pathogens. PMID:28249569
Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes. PMID:28209129
Draft genome sequence of Sugiyamaella xylanicola UFMG-CM-Y1884T, a xylan-degrading yeast species isolated from rotting wood samples in Brazil. PMID:28180086
Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes. PMID:28168115
Genomic Features of the Damselfly Calopteryx splendens Representing a Sister Clade to Most Insect Orders. PMID:28137743
Symbiont-induced odorant binding proteins mediate insect host hematopoiesis. PMID:28079523
Reading the Evolution of Compartmentalization in the Ribosome Assembly Toolbox: The YRG Protein Family. PMID:28072865
Phylogenetic Origin and Diversification of RNAi Pathway Genes in Insects. PMID:28062756
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes. PMID:28003436
Increased complexity of circRNA expression during species evolution. PMID:27982734
Functional Genomics Identifies Tis21-Dependent Mechanisms and Putative Cancer Drug Targets Underlying Medulloblastoma Shh-Type Development. PMID:27965576
Exploring FlyBase Data Using QuickSearch. PMID:27930807
FlyRNAi.org-the database of the Drosophila RNAi screening center and transgenic RNAi project: 2017 update. PMID:27924039
Identification of critical paralog groups with indispensable roles in the regulation of signaling flow. PMID:27922122
OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs. PMID:27899580
A scored human protein-protein interaction network to catalyze genomic interpretation. PMID:27892958
The retardant effect of 2-Tridecanone, mediated by Cytochrome P450, on the Development of Cotton bollworm, Helicoverpa armigera. PMID:27875986
Genetic and mechanistic diversity of piRNA 3'-end formation. PMID:27851737
Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface. PMID:27832824
Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse). PMID:27812417
Transcriptomic data from panarthropods shed new light on the evolution of insulator binding proteins in insects : Insect insulator proteins. PMID:27809783
FlyBase at 25: looking to the future. PMID:27799470
A computational interactome and functional annotation for the human proteome. PMID:27770567
Chromosomal inversions and ecotypic differentiation in Anopheles gambiae: the perspective from whole-genome sequencing. PMID:27759895
Genome-Wide Identification and Functional Classification of Tomato (Solanum lycopersicum) Aldehyde Dehydrogenase (ALDH) Gene Superfamily. PMID:27755582
HieranoiDB: a database of orthologs inferred by Hieranoid. PMID:27742821
Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life. PMID:27733110
Using FlyBase, a Database of Drosophila Genes and Genomes. PMID:27730573
LINEs between Species: Evolutionary Dynamics of LINE-1 Retrotransposons across the Eukaryotic Tree of Life. PMID:27702814
Divergence of cuticular hydrocarbons in two sympatric grasshopper species and the evolution of fatty acid synthases and elongases across insects. PMID:27677406
Genomic Mining of Phylogenetically Informative Nuclear Markers in Bark and Ambrosia Beetles. PMID:27668729
Evolutionary Analyses of Hanwoo (Korean Cattle)-Specific Single-Nucleotide Polymorphisms and Genes Using Whole-Genome Resequencing Data of a Hanwoo Population. PMID:27640093
OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis. PMID:27561358
Testis-Specific Bb8 Is Essential in the Development of Spermatid Mitochondria. PMID:27529784
Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta. PMID:27522922
Transcriptomic and functional resources for the small hive beetle Aethina tumida, a worldwide parasite of honey bees. PMID:27453819
Genome engineering uncovers 54 evolutionarily conserved and testis-enriched genes that are not required for male fertility in mice. PMID:27357688
How cells kill a "killer" messenger. PMID:27120800
Heterogeneous molecular processes among the causes of how sequence similarity scores can fail to recapitulate phylogeny. PMID:27103098
The Genome and Methylome of a Subsocial Small Carpenter Bee, Ceratina calcarata. PMID:27048475
Two Bacterial Genera, Sodalis and Rickettsia, Associated with the Seal Louse Proechinophthirus fluctus (Phthiraptera: Anoplura). PMID:26994086
Genome Sequencing of the Phytoseiid Predatory Mite Metaseiulus occidentalis Reveals Completely Atomized Hox Genes and Superdynamic Intron Evolution. PMID:26951779
Functional Evolution in Orthologous Cell-encoded RNA-dependent RNA Polymerases. PMID:26907693
Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes. PMID:26793234
Novel insights into human respiratory syncytial virus-host factor interactions through integrated proteomics and transcriptomics analysis. PMID:26760927
The neurotranscriptome of the Aedes aegypti mosquito. PMID:26738925
orthoFind Facilitates the Discovery of Homologous and Orthologous Proteins. PMID:26624019
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. PMID:26582926
Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine. PMID:26578564
Bovine Genome Database: new tools for gleaning function from the Bos taurus genome. PMID:26481361
SwissPalm: Protein Palmitoylation database. PMID:26339475
Drosophila and Caenorhabditis elegans as Discovery Platforms for Genes Involved in Human Alcohol Use Disorder. PMID:26173477
Natural Loss of eyeless/Pax6 Expression in Eyes of Bicyclus anynana Adult Butterflies Likely Leads to Exponential Decrease of Eye Fluorescence in Transgenics. PMID:26173066
Databases for Microbiologists. PMID:26013493
OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species. PMID:25964301
The 2015 Nucleic Acids Research Database Issue and molecular biology database collection. PMID:25593347 -
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011
PubMed citations: 78.
78 articles citing: OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011
Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus). PMID:34534224
Phylogenomic analysis sheds light on the evolutionary pathways towards acoustic communication in Orthoptera. PMID:33009390
Gene content evolution in the arthropods. PMID:31969194
Su(var)2-10 and the SUMO Pathway Link piRNA-Guided Target Recognition to Chromatin Silencing. PMID:31901446
Genomic changes associated with adaptation to arid environments in cactophilic Drosophila species. PMID:30651071
Efficient inference of homologs in large eukaryotic pan-proteomes. PMID:30257640
phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R. PMID:29874797
Phylogenomic analysis of Apoidea sheds new light on the sister group of bees. PMID:29776336
The molecular evolutionary dynamics of oxidative phosphorylation (OXPHOS) genes in Hymenoptera. PMID:29281964
Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community. PMID:29220441
Severe Fertility Effects of sheepish Sperm Caused by Failure To Enter Female Sperm Storage Organs in Drosophila melanogaster. PMID:29158336
Assembling large genomes: analysis of the stick insect (Clitarchus hookeri) genome reveals a high repeat content and sex-biased genes associated with reproduction. PMID:29145825
Orthonome - a new pipeline for predicting high quality orthologue gene sets applicable to complete and draft genomes. PMID:28859620
Rapid evolution of female-biased genes among four species of Anopheles malaria mosquitoes. PMID:28747381
Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes. PMID:28209129
The caste- and sex-specific DNA methylome of the termite Zootermopsis nevadensis. PMID:27848993
Comparative Genomic Analyses Provide New Insights into the Evolutionary Dynamics of Heterochromatin in Drosophila. PMID:27513559
Comparative performance of transcriptome assembly methods for non-model organisms. PMID:27464550
Holding it together: rapid evolution and positive selection in the synaptonemal complex of Drosophila. PMID:27150275
Comparative transcriptomics reveals the conserved building blocks involved in parallel evolution of diverse phenotypic traits in ants. PMID:26951146
Genomic insights into the Ixodes scapularis tick vector of Lyme disease. PMID:26856261
Effects of DNA Methylation and Chromatin State on Rates of Molecular Evolution in Insects. PMID:26637432
Evolutionary divergence of core and post-translational circadian clock genes in the pitcher-plant mosquito, Wyeomyia smithii. PMID:26444857
A depauperate immune repertoire precedes evolution of sociality in bees. PMID:25908406
Global transcriptional dynamics of diapause induction in non-blood-fed and blood-fed Aedes albopictus. PMID:25897664
aTRAM - automated target restricted assembly method: a fast method for assembling loci across divergent taxa from next-generation sequencing data. PMID:25887972
Orthology and paralogy constraints: satisfiability and consistency. PMID:25572629
Identifying gene clusters by discovering common intervals in indeterminate strings. PMID:25571793
Bidirectional promoters of insects: genome-wide comparison, evolutionary implication and influence on gene expression. PMID:25463441
On the evolution of Yeti, a Drosophila melanogaster heterochromatin gene. PMID:25405891
A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation. PMID:25369365
The Chironomus tentans genome sequence and the organization of the Balbiani ring genes. PMID:25261295
Natural selection canalizes expression variation of environmentally induced plasticity-enabling genes. PMID:25158801
The Fog signaling pathway: insights into signaling in morphogenesis. PMID:25127992
Discovering non-coding RNA elements in Drosophila 3' untranslated regions. PMID:24989864
Evaluating synteny for improved comparative studies. PMID:24932010
Epigenetic inheritance and genome regulation: is DNA methylation linked to ploidy in haplodiploid insects? PMID:24789901
Patterns of positive selection in seven ant genomes. PMID:24782441
Molecular evolution of the Yap/Yorkie proto-oncogene and elucidation of its core transcriptional program. PMID:24509725
Insights into the preservation of the homomorphic sex-determining chromosome of Aedes aegypti from the discovery of a male-biased gene tightly linked to the M-locus. PMID:24398378
Phylogenetic investigation of Peptide hormone and growth factor receptors in five dipteran genomes. PMID:24379806
Inducible defenses stay up late: temporal patterns of immune gene expression in Tenebrio molitor. PMID:24318927
CpGislandEVO: a database and genome browser for comparative evolutionary genomics of CpG islands. PMID:24205506
The basis for evolution of DNA-binding specificity of the Aft1 transcription factor in yeasts. PMID:24172132
Immune response of the Caribbean sea fan, Gorgonia ventalina, exposed to an Aplanochytrium parasite as revealed by transcriptome sequencing. PMID:23898300
Evolution of three parent genes and their retrogene copies in Drosophila species. PMID:23841016
Transcriptome sequencing as a platform to elucidate molecular components of the diapause response in the Asian tiger mosquito, Aedes albopictus. PMID:23833391
A burst of ABC genes in the genome of the polyphagous spider mite Tetranychus urticae. PMID:23663308
Networks of bZIP protein-protein interactions diversified over a billion years of evolution. PMID:23661758
InterMOD: integrated data and tools for the unification of model organism research. PMID:23652793
Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality. PMID:23636946
An automated graphics tool for comparative genomics: the Coulson plot generator. PMID:23621955
Deep sequencing reveals complex mechanisms of diapause preparation in the invasive mosquito, Aedes albopictus. PMID:23516243
Patterning and regulatory associations of DNA methylation are mirrored by histone modifications in insects. PMID:23458712
Bioinformatics analysis reveals biophysical and evolutionary insights into the 3-nitrotyrosine post-translational modification in the human proteome. PMID:23389939
Inferring hierarchical orthologous groups from orthologous gene pairs. PMID:23342000
Widespread horizontal transfer of retrotransposons. PMID:23277587
HAMAP in 2013, new developments in the protein family classification and annotation system. PMID:23193261
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. PMID:23180791
Computational workflow for analysis of gain and loss of genes in distantly related genomes. PMID:23046496
Satellite DNA-like elements associated with genes within euchromatin of the beetle Tribolium castaneum. PMID:22908042
Identification of critical host mitochondrion-associated genes during Ehrlichia chaffeensis infections. PMID:22851751
De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system. PMID:22776250
QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence. PMID:22726705
Conservation of the RNA Transport Machineries and Their Coupling to Translation Control across Eukaryotes. PMID:22666086
BRCT domains: A little more than kin, and less than kind. PMID:22584059
PaxDb, a database of protein abundance averages across all three domains of life. PMID:22535208
The multiple facets of dermcidin in cell survival and host defense. PMID:22455996
Revealing mammalian evolutionary relationships by comparative analysis of gene clusters. PMID:22454131
A vector space model approach to identify genetically related diseases. PMID:22227640
Gene discovery in the threatened elkhorn coral: 454 sequencing of the Acropora palmata transcriptome. PMID:22216101
Evidence for intron length conservation in a set of mammalian genes associated with embryonic development. PMID:22151910
A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits. PMID:22098672
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. PMID:22096231
Orthology prediction methods: a quality assessment using curated protein families. PMID:21853451
Proteome of human perilymph. PMID:21740021
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. PMID:21737420
Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi. PMID:21148284 - https://doi.org/10.1093/nar/gkaa1009
- http://dx.doi.org/10.1093/nar/gkw1119
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More detailed information about this field from each metasource.
deoxyribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: OrthoDB; Database of Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.x989d5; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
orthologous
metasource: Fairsharing.org
version: FAIRsharing.org: OrthoDB; Database of Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.x989d5; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: OrthoDB; Database of Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.x989d5; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
protein domain databases; protein classification
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
evolutionary biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
function analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
phylogeny
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
model organisms
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
gene and protein families
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
Tags
More detailed information about this field from each metasource.
deoxyribonucleic acid
metasource: Fairsharing.orgversion: FAIRsharing.org: OrthoDB; Database of Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.x989d5; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
orthologous
metasource: Fairsharing.orgversion: FAIRsharing.org: OrthoDB; Database of Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.x989d5; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: OrthoDB; Database of Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.x989d5; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein domain databases; protein classification
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
evolutionary biology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
function analysis
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
genomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
phylogeny
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
model organisms
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
gene and protein families
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
dna orthology protein protein sequence protein domains and classification evolutionary biology function analysis genomics phylogeny model organisms gene and protein families
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