#ortholog — Public Fediverse posts

Nice new paper of the Quest for Orthologs consortium, addressing 5 timely challenges:
• Ortholog Search Across Tens of Thousands of Genomes
• Tracking Functional Changes of Orthologs
• Orthology Inference off the Beaten Track
• Integrating Orthology With Protein Structure
• Making Orthology Inferences FAIR
with @dessimoz and many others #ortholog #orthology #bioinformatics
https://academic.oup.com/gbe/article/16/10/evae224/7822254

Nice new paper of the Quest for Orthologs consortium, addressing 5 timely challenges:
• Ortholog Search Across Tens of Thousands of Genomes
• Tracking Functional Changes of Orthologs
• Orthology Inference off the Beaten Track
• Integrating Orthology With Protein Structure
• Making Orthology Inferences FAIR
with @dessimoz and many others #ortholog #orthology #bioinformatics
https://academic.oup.com/gbe/article/16/10/evae224/7822254

Very nice preprint on most-diverged vs. less-diverged ortholog among paralog pairs: https://www.biorxiv.org/content/10.1101/2024.10.29.620890v1 @dessimoz #ortholog #paralog #MolecularEvolution

Very nice preprint on most-diverged vs. less-diverged ortholog among paralog pairs: https://www.biorxiv.org/content/10.1101/2024.10.29.620890v1 @dessimoz #ortholog #paralog #MolecularEvolution

Updated preprint of work by Tina Begum et al showing that paralogs from small-scale duplications have jumps in expression phenotype, much more than orthologs or whole genome duplication paralogs
https://www.biorxiv.org/content/10.1101/2023.12.29.571877v2 #ortholog #paralog #phylogenetics #GeneExpression #MolecularEvolution #FishEvolution

Updated preprint of work by Tina Begum et al showing that paralogs from small-scale duplications have jumps in expression phenotype, much more than orthologs or whole genome duplication paralogs
https://www.biorxiv.org/content/10.1101/2023.12.29.571877v2 #ortholog #paralog #phylogenetics #GeneExpression #MolecularEvolution #FishEvolution

Registrations open to our @SIB course for PhD students in Lausanne 🇨🇭 with @rmwaterhouse and @dessimoz :
Biodiversity bioinformatics: from large-scale phylogenomics to gene families and functions
with @bgeedb, OMA and BUSCO inside
https://www.sib.swiss/training/course/20240828_COMGE #BiodiversityGenomics #MolecularEvolution #ortholog #paralog #bioinformatics

Registrations open to our @SIB course for PhD students in Lausanne 🇨🇭 with @rmwaterhouse and @dessimoz :
Biodiversity bioinformatics: from large-scale phylogenomics to gene families and functions
with @bgeedb, OMA and BUSCO inside
https://www.sib.swiss/training/course/20240828_COMGE #BiodiversityGenomics #MolecularEvolution #ortholog #paralog #bioinformatics

We posted this cool preprint between Xmas and new year, now time for a thread about the results: Begum et al "Phylogenetic modeling provides evidence for sudden shifts in expression after small-scale duplication in vertebrates and strong support for the ortholog conjecture"
https://www.biorxiv.org/content/10.1101/2023.12.29.571877v1
#paralog #ortholog #GeneDuplication #GenomeDuplication #MolecularEvolution #phylogeny #ohnolog

We posted this cool preprint between Xmas and new year, now time for a thread about the results: Begum et al "Phylogenetic modeling provides evidence for sudden shifts in expression after small-scale duplication in vertebrates and strong support for the ortholog conjecture"
https://www.biorxiv.org/content/10.1101/2023.12.29.571877v1
#paralog #ortholog #GeneDuplication #GenomeDuplication #MolecularEvolution #phylogeny #ohnolog

First mention of the word #ortholog at #SMBE2023 during first keynote (well it's on a slide). Also first mention of #bayesian statistics.

First mention of the word #ortholog at #SMBE2023 during first keynote (well it's on a slide). Also first mention of #bayesian statistics.

Announcing #SIB Comparative genomics course, taught by Christophe Dessimoz, Natasha Glover, @rmwaterhouse and myself, 30 August - 01 September in Lausanne #UNIL
• Introduction to molecular evolution & phylogenetics
• Orthology-focused arthropod comparative genomics
• Duplication of genes and genomes, expression
with #SIB resources #OMA, #Orthodb #BUSCO and @bgeedb #ortholog #orthologs #paralog #duplication #MolecularEvolution #Genomics #bioinformatics #training @P_Palagi https://www.sib.swiss/training/course/20230830_COMGE

Announcing #SIB Comparative genomics course, taught by Christophe Dessimoz, Natasha Glover, @rmwaterhouse and myself, 30 August - 01 September in Lausanne #UNIL
• Introduction to molecular evolution & phylogenetics
• Orthology-focused arthropod comparative genomics
• Duplication of genes and genomes, expression
with #SIB resources #OMA, #Orthodb #BUSCO and @bgeedb #ortholog #orthologs #paralog #duplication #MolecularEvolution #Genomics #bioinformatics #training @P_Palagi https://www.sib.swiss/training/course/20230830_COMGE

These observations of conserved homologous expression are easy to reproduce! Go to a gene page, click "orthologs", and chose a taxonomic level, here Theria:
TLK1 https://bgee.org/gene/ENSG00000198586/#orthologs -> https://bgee.org/analysis/expr-comparison?data=4a7fc4f9fba1b1e63c458881a6ca8f5b61367fd2
HAT1 https://bgee.org/analysis/expr-comparison?data=d9510c624d21931605aa16a7c378f8ede9ce4fe6
#bioinformatics #biocuration #evodevo #ortholog #homology

These observations of conserved homologous expression are easy to reproduce! Go to a gene page, click "orthologs", and chose a taxonomic level, here Theria:
TLK1 https://bgee.org/gene/ENSG00000198586/#orthologs -> https://bgee.org/analysis/expr-comparison?data=4a7fc4f9fba1b1e63c458881a6ca8f5b61367fd2
HAT1 https://bgee.org/analysis/expr-comparison?data=d9510c624d21931605aa16a7c378f8ede9ce4fe6
#bioinformatics #biocuration #evodevo #ortholog #homology

Marc Feuermann: PAN-GO phylogenetic annotation of @go, implicitly relying on the #ortholog conjecture for annotation, mapping the changes in function to duplication nodes (my interpretation) #biocuration2023

Marc Feuermann: PAN-GO phylogenetic annotation of @go, implicitly relying on the #ortholog conjecture for annotation, mapping the changes in function to duplication nodes (my interpretation) #biocuration2023

Bgee used to support the identification of the target gene for depletion experiment in zebrafish: https://elifesciences.org/articles/83652
#zebrafish #cytoskeleton #ortholog #paralog #GeneExpression #SIB @dee_unil @marcrr

Bgee used to support the identification of the target gene for depletion experiment in zebrafish: https://elifesciences.org/articles/83652
#zebrafish #cytoskeleton #ortholog #paralog #GeneExpression #SIB @dee_unil @marcrr

Will be fun to remember this later if #ScienceMastodon takes off: right now my posts seem to be the only hits for #ortholog and #paralog.

Will be fun to remember this later if #ScienceMastodon takes off: right now my posts seem to be the only hits for #ortholog and #paralog.

Orthologs, lots of #orthologs!

#OrthoDB: 17 551 bacteria, 607 archea, 1935 eukaryotes https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac998/6814468

#EggNOG: 10 756 bacteria, 457 archaea, 1322 eukaryotes https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1022/6833261

#bioinformatics #ortholog #databases

Orthologs, lots of #orthologs!

#OrthoDB: 17 551 bacteria, 607 archea, 1935 eukaryotes https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac998/6814468

#EggNOG: 10 756 bacteria, 457 archaea, 1322 eukaryotes https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1022/6833261

#bioinformatics #ortholog #databases

Now published in its final form: Parallel evolution of amphioxus and vertebrate small-scale gene duplications by Brasó-Vives et al
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02808-6
#EvoDevo #EvolutionaryBiology #Genomics #Amphioxus #Chordate #ortholog #paralog #GeneDuplication

Now published in its final form: Parallel evolution of amphioxus and vertebrate small-scale gene duplications by Brasó-Vives et al
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02808-6
#EvoDevo #EvolutionaryBiology #Genomics #Amphioxus #Chordate #ortholog #paralog #GeneDuplication

Very exciting preprint led by Manu Irimia on evolution of tissue-specificity of expression in vertebrates and insects, providing great data, evidence for "low conservation of tissue-specific expression profiles", and tissue-specific gains associated with duplications and with the emergence of unique phenotypes
https://www.biorxiv.org/content/10.1101/2022.11.14.516384v1
#geneexpression #EvolutionaryBiology #TissueSpecifity #ortholog #paralog #DeneDuplication

Very exciting preprint led by Manu Irimia on evolution of tissue-specificity of expression in vertebrates and insects, providing great data, evidence for "low conservation of tissue-specific expression profiles", and tissue-specific gains associated with duplications and with the emergence of unique phenotypes
https://www.biorxiv.org/content/10.1101/2022.11.14.516384v1
#geneexpression #EvolutionaryBiology #TissueSpecifity #ortholog #paralog #DeneDuplication