ORTHOlogous MAmmalian Markers
Names
More detailed information about this field from each metasource.
ORTHOlogous MAmmalian Markers
metasource: Fairsharing.org
version: FAIRsharing.org: OrthoMaM ; ORTHOlogous MAmmalian Markers; DOI: https://doi.org/10.25504/FAIRsharing.2GMztk; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
OrthoMaM
metasource: Fairsharing.org
version: FAIRsharing.org: OrthoMaM ; ORTHOlogous MAmmalian Markers; DOI: https://doi.org/10.25504/FAIRsharing.2GMztk; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Names
More detailed information about this field from each metasource.
ORTHOlogous MAmmalian Markers
metasource: Fairsharing.orgversion: FAIRsharing.org: OrthoMaM ; ORTHOlogous MAmmalian Markers; DOI: https://doi.org/10.25504/FAIRsharing.2GMztk; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
OrthoMaM
metasource: Fairsharing.orgversion: FAIRsharing.org: OrthoMaM ; ORTHOlogous MAmmalian Markers; DOI: https://doi.org/10.25504/FAIRsharing.2GMztk; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Names
More detailed information about this field from each metasource.
ORTHOlogous MAmmalian Markers
metasource: Fairsharing.orgversion: FAIRsharing.org: OrthoMaM ; ORTHOlogous MAmmalian Markers; DOI: https://doi.org/10.25504/FAIRsharing.2GMztk; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
OrthoMaM
metasource: Fairsharing.orgversion: FAIRsharing.org: OrthoMaM ; ORTHOlogous MAmmalian Markers; DOI: https://doi.org/10.25504/FAIRsharing.2GMztk; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ORTHOlogous MAmmalian Markers database (OrthoMaM) describes the evolutionary dynamics of orthologous genes in mammalian genomes using a phylogenetic framework.
Description
More detailed information about this field from each metasource.
ORTHOlogous MAmmalian Markers database (OrthoMaM) describes the evolutionary dynamics of orthologous genes in mammalian genomes using a phylogenetic framework.
metasource: Fairsharing.orgversion: FAIRsharing.org: OrthoMaM ; ORTHOlogous MAmmalian Markers; DOI: https://doi.org/10.25504/FAIRsharing.2GMztk; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Webpage:
http://www.orthomam.univ-montp2.fr/orthomam/html/Webpage
More detailed information about this field from each metasource.
http://www.orthomam.univ-montp2.fr/orthomam/html/
metasource: Fairsharing.orgversion: FAIRsharing.org: OrthoMaM ; ORTHOlogous MAmmalian Markers; DOI: https://doi.org/10.25504/FAIRsharing.2GMztk; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics
PMID: 18053139
metasource: Fairsharing.org
version: FAIRsharing.org: OrthoMaM ; ORTHOlogous MAmmalian Markers; DOI: https://doi.org/10.25504/FAIRsharing.2GMztk; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals
PMID: 24723423
metasource: Fairsharing.org
version: FAIRsharing.org: OrthoMaM ; ORTHOlogous MAmmalian Markers; DOI: https://doi.org/10.25504/FAIRsharing.2GMztk; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications
More detailed information about this field from each metasource.
OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics
PMID: 18053139
metasource: Fairsharing.org
version: FAIRsharing.org: OrthoMaM ; ORTHOlogous MAmmalian Markers; DOI: https://doi.org/10.25504/FAIRsharing.2GMztk; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals
PMID: 24723423
metasource: Fairsharing.org
version: FAIRsharing.org: OrthoMaM ; ORTHOlogous MAmmalian Markers; DOI: https://doi.org/10.25504/FAIRsharing.2GMztk; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
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OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics
PubMed citations: 51.
51 articles citing: OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics
Inferring Long-Term Effective Population Size with Mutation-Selection Models. PMID:34191010
Harnessing machine learning to guide phylogenetic-tree search algorithms. PMID:33790270
Evolutionarily conserved sequence motif analysis guides development of chemically defined hydrogels for therapeutic vascularization. PMID:32923589
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
Determinants of genetic variation across eco-evolutionary scales in pinnipeds. PMID:32514167
Is adaptation limited by mutation? A timescale-dependent effect of genetic diversity on the adaptive substitution rate in animals. PMID:32251427
STELAR: a statistically consistent coalescent-based species tree estimation method by maximizing triplet consistency. PMID:32039704
Divergent Evolution of TRC Genes in Mammalian Niche Adaptation. PMID:31068942
Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics. PMID:30783571
OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes. PMID:30698751
Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences. PMID:30634908
Influence of Recombination and GC-biased Gene Conversion on the Adaptive and Nonadaptive Substitution Rate in Mammals versus Birds. PMID:30590692
CAARS: comparative assembly and annotation of RNA-Seq data. PMID:30452539
Toward Reducing Phylostratigraphic Errors and Biases. PMID:30060201
Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat. PMID:29459707
Evolution of Digestive Enzymes and RNASE1 Provides Insights into Dietary Switch of Cetaceans. PMID:27651393
Evolutionary Genetics of Hypoxia Tolerance in Cetaceans during Diving. PMID:26912402
'Obesity' is healthy for cetaceans? Evidence from pervasive positive selection in genes related to triacylglycerol metabolism. PMID:26381091
Optimization of sequence alignments according to the number of sequences vs. number of sites trade-off. PMID:26055961
GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. PMID:25883146
Conservation of pro-longevity genes among mammals. PMID:25804384
Naked but not Hairless: the pitfalls of analyses of molecular adaptation based on few genome sequence comparisons. PMID:25714745
Indel reliability in indel-based phylogenetic inference. PMID:25409663
Phylostratigraphic bias creates spurious patterns of genome evolution. PMID:25312911
Monte Carlo algorithms for Brownian phylogenetic models. PMID:25053744
Assignment of Calibration Information to Deeper Phylogenetic Nodes is More Effective in Obtaining Precise and Accurate Divergence Time Estimates. PMID:24855333
Development of rapidly evolving intron markers to estimate multilocus species trees of rodents. PMID:24804779
Adaptive evolution of the osmoregulation-related genes in cetaceans during secondary aquatic adaptation. PMID:24015756
Genome-wide signatures of convergent evolution in echolocating mammals. PMID:24005325
Conventional simulation of biological sequences leads to a biased assessment of multi-Loci phylogenetic analysis. PMID:23997573
Evaluating phylogenetic informativeness as a predictor of phylogenetic signal for metazoan, fungal, and mammalian phylogenomic data sets. PMID:23878813
Bayesian selection of nucleotide substitution models and their site assignments. PMID:23233462
A method to find longevity-selected positions in the mammalian proteome. PMID:22701678
Impact of the partitioning scheme on divergence times inferred from Mammalian genomic data sets. PMID:22654486
Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping. PMID:22479459
Comprehensive primer design for analysis of population genetics in non-sequenced organisms. PMID:22393396
Testing synchrony in historical biogeography: the case of new world primates and hystricognathi rodents. PMID:22346342
Evolutionary and functional analyses of the interaction between the myeloid restriction factor SAMHD1 and the lentiviral Vpx protein. PMID:22305291
MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons. PMID:21949676
Model averaging and Bayes factor calculation of relaxed molecular clocks in Bayesian phylogenetics. PMID:21940644
Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the laurasiatherian mammals. PMID:21900649
PhyDesign: an online application for profiling phylogenetic informativeness. PMID:21627831
Protein structural modularity and robustness are associated with evolvability. PMID:21602570
Novel intron markers to study the phylogeny of closely related mammalian species. PMID:21118501
Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes. PMID:20530252
SuperTriplets: a triplet-based supertree approach to phylogenomics. PMID:20529895
Covariation of branch lengths in phylogenies of functionally related genes. PMID:20041191
The expansion of amino-acid repeats is not associated to adaptive evolution in mammalian genes. PMID:20021652
PhyloExplorer: a web server to validate, explore and query phylogenetic trees. PMID:19450253
IDEA: Interactive Display for Evolutionary Analyses. PMID:19061522
PhySIC_IST: cleaning source trees to infer more informative supertrees. PMID:18834542 -
OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals
PubMed citations: 34.
34 articles citing: OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals
ExTraMapper: Exon- and Transcript-level mappings for orthologous gene pairs. PMID:34014317
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
Is adaptation limited by mutation? A timescale-dependent effect of genetic diversity on the adaptive substitution rate in animals. PMID:32251427
STELAR: a statistically consistent coalescent-based species tree estimation method by maximizing triplet consistency. PMID:32039704
Amino acid exchangeabilities vary across the tree of life. PMID:31840062
Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements. PMID:31710677
The Estimated Pacemaker for Great Apes Supports the Hominoid Slowdown Hypothesis. PMID:31223232
Comparative genomics provides new insights into the remarkable adaptations of the African wild dog (Lycaon pictus). PMID:31171819
Detecting adaptive convergent amino acid evolution. PMID:31154974
Pervasive hybridizations in the history of wheat relatives. PMID:31049399
Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics. PMID:30783571
OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes. PMID:30698751
Influence of Recombination and GC-biased Gene Conversion on the Adaptive and Nonadaptive Substitution Rate in Mammals versus Birds. PMID:30590692
MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons. PMID:30165589
In Cold Blood: Compositional Bias and Positive Selection Drive the High Evolutionary Rate of Vampire Bats Mitochondrial Genomes. PMID:29931241
Lipidome Evolution in Mammalian Tissues. PMID:29762743
Alignment Modulates Ancestral Sequence Reconstruction Accuracy. PMID:29618097
Delimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets. PMID:29495400
Human C-to-U Coding RNA Editing Is Largely Nonadaptive. PMID:29385526
Phylogenomic Resolution of the Phylogeny of Laurasiatherian Mammals: Exploring Phylogenetic Signals within Coding and Noncoding Sequences. PMID:28830116
SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm. PMID:28460062
Gene Tree Discordance Does Not Explain Away the Temporal Decline of Convergence in Mammalian Protein Sequence Evolution. PMID:28379570
LINEs between Species: Evolutionary Dynamics of LINE-1 Retrotransposons across the Eukaryotic Tree of Life. PMID:27702814
Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates. PMID:27532052
Fast and accurate branch lengths estimation for phylogenomic trees. PMID:26744021
Inferring Indel Parameters using a Simulation-based Approach. PMID:26537226
Neurodevelopmental LincRNA Microsyteny Conservation and Mammalian Brain Size Evolution. PMID:26134977
Optimization of sequence alignments according to the number of sequences vs. number of sites trade-off. PMID:26055961
Are Convergent and Parallel Amino Acid Substitutions in Protein Evolution More Prevalent Than Neutral Expectations? PMID:25862140
Assessing associations between the AURKA-HMMR-TPX2-TUBG1 functional module and breast cancer risk in BRCA1/2 mutation carriers. PMID:25830658
Gene expression, chromosome heterogeneity and the fast-X effect in mammals. PMID:25716091
Naked but not Hairless: the pitfalls of analyses of molecular adaptation based on few genome sequence comparisons. PMID:25714745
A new method for estimating species age supports the coexistence of malaria parasites and their Mammalian hosts. PMID:25589738
Open source libraries and frameworks for biological data visualisation: a guide for developers. PMID:25475079
Tags:
Tags
More detailed information about this field from each metasource.
genome
metasource: Fairsharing.org
version: FAIRsharing.org: OrthoMaM ; ORTHOlogous MAmmalian Markers; DOI: https://doi.org/10.25504/FAIRsharing.2GMztk; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
orthologous
metasource: Fairsharing.org
version: FAIRsharing.org: OrthoMaM ; ORTHOlogous MAmmalian Markers; DOI: https://doi.org/10.25504/FAIRsharing.2GMztk; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Tags
More detailed information about this field from each metasource.
genome
metasource: Fairsharing.orgversion: FAIRsharing.org: OrthoMaM ; ORTHOlogous MAmmalian Markers; DOI: https://doi.org/10.25504/FAIRsharing.2GMztk; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
orthologous
metasource: Fairsharing.orgversion: FAIRsharing.org: OrthoMaM ; ORTHOlogous MAmmalian Markers; DOI: https://doi.org/10.25504/FAIRsharing.2GMztk; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
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