Yannis Nevers
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whynevers.bsky.social
Yannis Nevers
@whynevers.bsky.social
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Reposted by Yannis Nevers
rosafernandez.bsky.social
The afternoon session of our workshop is dedicated to functional annotation & language models, with the great @amrojasm.bsky.social. She will guide us through the theory behind them and we'll talk about our recently-developed tool to explore the dark proteome: FANTASIA! ✨ @ibe-barcelona.bsky.social
May 7, 2025 at 12:21 PM
Reposted by Yannis Nevers
rosafernandez.bsky.social
The morning session of our workshop on genome annotation is dedicated to long reads, and we couldn't have better faculty! Many thanks
@anaconesa.bsky.social
and Pablo Atienza for guiding us through it! @ibe-barcelona.bsky.social
May 7, 2025 at 12:15 PM
Reposted by Yannis Nevers
rosafernandez.bsky.social
Second day of our workshop
@ibe-barcelona.bsky.social
learning about genome annotation with BRAKER, TSEBRA, GALBA, Tiberius & more with the one and only @katharinahoff.bsky.social! 🧬🧩🪱
May 6, 2025 at 1:19 PM
Reposted by Yannis Nevers
rosafernandez.bsky.social
The first day of our Workshop on Genome Annotation
@ibe-barcelona.bsky.social
was great! We had
@bombarelya.bsky.social
giving a primer on genome assembly to get started. Looking forward to zooming in into annotation itself tomorrow! 🪱🐦🧬🧩🌵☘️🌽
May 5, 2025 at 6:19 PM
Reposted by Yannis Nevers
katharinahoff.bsky.social
Annotation of 200 insect genomes. Work driven by @stepbystepsolution.bsky.social and Mario Stanke within @gevol.bsky.social : www.biorxiv.org/content/10.1...
Annotation of 200 Insect Genomes with BRAKER for Consistent Comparisons across Species
The annotation of genomes lags behind their sequencing and assembly. For example, of 5,092 insect species in GenBank, as one of the most widely used databases, only 375 currently have annotated genome...
www.biorxiv.org
April 21, 2025 at 5:37 AM
Reposted by Yannis Nevers
rmwaterhouse.bsky.social
Wow! CONSISTENT #genome annotations for 200 insect species from different families, including 85 species previously lacking annotations www.biorxiv.org/content/10.1...
Annotation of 200 Insect Genomes with BRAKER for Consistent Comparisons across Species
The annotation of genomes lags behind their sequencing and assembly. For example, of 5,092 insect species in GenBank, as one of the most widely used databases, only 375 currently have annotated genome...
www.biorxiv.org
April 21, 2025 at 12:55 PM
Reposted by Yannis Nevers
marcrr.bsky.social
Updated preprint by Agneesh Barua agneeshbarua.bsky.social on convergence and pleiotropy in teleost fish gene evolution, with lots of new results!
www.biorxiv.org/content/10.1...
Agneesh Barua (@agneeshbarua.bsky.social)
HFSP Long-Term fellow at the University of Lausanne. #Evolution #GeneExpression #Genetics
agneeshbarua.bsky.social
April 8, 2025 at 1:04 PM
Reposted by Yannis Nevers
sinamajidian.bsky.social
FastOMA is out now in Nature Methods 🎉: nature.com/articles/s41592-024-02552-8 A new orthology inference algorithm that scales linearly and is highly accurate. FastOMA can process all >2000 eukaryotic UniProt ref proteomes <24 hours 🚀. Try it out github.com/DessimozLab/fastoma @dessimoz.bsky.social
FastOMA retains OMA’s high precision accuracy and even improves upon it in terms of recall, positioning it on the Pareto frontier of orthology inference methods. FastOMA is not only fast but also accurate. a, QfO benchmar, agreement with SwissTree reference phylogeny covering manually curated gene trees. The error bars indicate 95% confidence intervals comparing FastOMA with EnsemblCompara, Domainoid, OrthoMCL, Ortholnspector, sonicparanoid, PANTHER, OrthoFinder, Hieranoid26 and the OMA family including OMA pairs, OMA groups and OMA GETHOGs (graph-based efficient technique for HOGs). c) A computation time comparison of FastOMA and state-of-the-art alternatives. https://www.nature.com/articles/s41592-024-02552-8
January 3, 2025 at 2:14 PM