Reposted by Pierre Nouhaud
Published online on Jan 2, 2025 and just appeared in the December 2025 issue!
A language model predicts the effects of genetic variants in the human genome go.nature.com/4gWppWg
rdcu.be/eUK6Z
rdcu.be/eUK6Z
A DNA language model based on multispecies alignment predicts the effects of genome-wide variants - Nature Biotechnology
A language model predicts the effects of genetic variants in the human genome.
go.nature.com
December 19, 2025 at 3:02 AM
Published online on Jan 2, 2025 and just appeared in the December 2025 issue!
Reposted by Pierre Nouhaud
GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Causal modelling of gene effects from regulators to programs to traits - Nature
Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.
www.nature.com
December 11, 2025 at 5:54 PM
GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Reposted by Pierre Nouhaud
How does population size shape the dynamics of structural variants across the genome?
Check out our new paper in @science.org www.science.org/doi/10.1126/...
Check out our new paper in @science.org www.science.org/doi/10.1126/...
December 11, 2025 at 7:48 PM
How does population size shape the dynamics of structural variants across the genome?
Check out our new paper in @science.org www.science.org/doi/10.1126/...
Check out our new paper in @science.org www.science.org/doi/10.1126/...
Reposted by Pierre Nouhaud
First paper from #TanguyMuller, PhD student in @cbgpmontpellier.bsky.social: Population genomics of incipient allochronic divergence in an infamous moth. #WGS #demography #inbreeding #mutation-load #genome-scan onlinelibrary.wiley.com/doi/10.1111/...
November 28, 2025 at 2:04 PM
First paper from #TanguyMuller, PhD student in @cbgpmontpellier.bsky.social: Population genomics of incipient allochronic divergence in an infamous moth. #WGS #demography #inbreeding #mutation-load #genome-scan onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Pierre Nouhaud
We set out to investigate polygenic footprints of altitude adaptation in a moth species, but instead we uncovered a major selective sweep at genes often associated with insecticide resistance @prrnhd.bsky.social @schifanoalexandre.bsky.social @mgda76.bsky.social @cbgpmontpellier.bsky.social
A major selective sweep likely linked to insecticide resistance identified along altitudinal gradients in the pine processionary moth https://www.biorxiv.org/content/10.1101/2025.11.24.690095v1
November 26, 2025 at 8:34 PM
We set out to investigate polygenic footprints of altitude adaptation in a moth species, but instead we uncovered a major selective sweep at genes often associated with insecticide resistance @prrnhd.bsky.social @schifanoalexandre.bsky.social @mgda76.bsky.social @cbgpmontpellier.bsky.social
Reposted by Pierre Nouhaud
Un poste d’IE en bioinformatique est actuellement ouvert au CEFE à Montpellier pour travailler dans le cadre de l'ERC RegEvol.
Détails ici:
emploi.cnrs.fr/Offres/CDD/U...
Début 01/01/2026 pour 18 mois potentiellement renouvelable.
candidature jusqu'au 29/11
N’hésitez pas à diffuser largement
Détails ici:
emploi.cnrs.fr/Offres/CDD/U...
Début 01/01/2026 pour 18 mois potentiellement renouvelable.
candidature jusqu'au 29/11
N’hésitez pas à diffuser largement
Portail Emploi CNRS - Offre d'emploi - Ingénieur d'études en bioinformatique (H/F)
emploi.cnrs.fr
November 18, 2025 at 3:09 PM
Un poste d’IE en bioinformatique est actuellement ouvert au CEFE à Montpellier pour travailler dans le cadre de l'ERC RegEvol.
Détails ici:
emploi.cnrs.fr/Offres/CDD/U...
Début 01/01/2026 pour 18 mois potentiellement renouvelable.
candidature jusqu'au 29/11
N’hésitez pas à diffuser largement
Détails ici:
emploi.cnrs.fr/Offres/CDD/U...
Début 01/01/2026 pour 18 mois potentiellement renouvelable.
candidature jusqu'au 29/11
N’hésitez pas à diffuser largement
Reposted by Pierre Nouhaud
Congrats Sarah, @mafnoor.bsky.social, and team on such a cool paper!
Transposable elements drive much of naturally occurring genetic lethality in Drosophila melanogaster
Recessive lethal mutations are widespread across studied species, with estimates suggesting that each individual carries at least one. Numerous lethal alleles persist in wild populations at higher fre...
www.biorxiv.org
October 22, 2025 at 11:06 PM
Congrats Sarah, @mafnoor.bsky.social, and team on such a cool paper!
Reposted by Pierre Nouhaud
In 2020, O Gaggiotti, J Goudet and I showed that Qst-Fst comparison was uncalibrated with high population structure.
During her PhD with us, Isa do O developed LogAV: a method that accounts for any population structure while testing for local adaptation :
journals.plos.org/plosgenetics...
During her PhD with us, Isa do O developed LogAV: a method that accounts for any population structure while testing for local adaptation :
journals.plos.org/plosgenetics...
A method for identifying local adaptation in structured populations
Species occupy diverse, heterogeneous environments, which expose populations to spatially varied selective pressures. Populations in different environments can diverge due to local adaptation. However...
journals.plos.org
September 24, 2025 at 7:23 AM
In 2020, O Gaggiotti, J Goudet and I showed that Qst-Fst comparison was uncalibrated with high population structure.
During her PhD with us, Isa do O developed LogAV: a method that accounts for any population structure while testing for local adaptation :
journals.plos.org/plosgenetics...
During her PhD with us, Isa do O developed LogAV: a method that accounts for any population structure while testing for local adaptation :
journals.plos.org/plosgenetics...
Reposted by Pierre Nouhaud
Hybridization and introgression are major evolutionary processes. Since the 1940s, the prevailing view has been that they shape plants far more than animals. In our new study (www.science.org/doi/10.1126/...
), we find the opposite: animals exchange genes more, and for longer, than plants
), we find the opposite: animals exchange genes more, and for longer, than plants
September 12, 2025 at 7:55 AM
Hybridization and introgression are major evolutionary processes. Since the 1940s, the prevailing view has been that they shape plants far more than animals. In our new study (www.science.org/doi/10.1126/...
), we find the opposite: animals exchange genes more, and for longer, than plants
), we find the opposite: animals exchange genes more, and for longer, than plants
Reposted by Pierre Nouhaud
Still possible to apply to this #post-doc position at CESAB #Montpellier.
Application closing date: September 15th 2025 (12:00 PM CET)
How taking intraspecific diversity and evolutionary processes into account in translocation-based programs.
Please share widely #PopGen #NbS #Biodiversity
Application closing date: September 15th 2025 (12:00 PM CET)
How taking intraspecific diversity and evolutionary processes into account in translocation-based programs.
Please share widely #PopGen #NbS #Biodiversity
3-year #postdoc position at Centre de synthèse et d'analyse de la biodiversité (CESAB) in Montpellier to work on how taking intraspecific diversity and evolutionary processes into account in translocation-based programs. Please share widely #PopGen #NbS
[📢 Postdoc offer in Montpellier] Work on intraspecific diversity & translocation in Nature-based Solutions 🌿
Join the EVOLUTION Knowledge-Hub at the #FRB-CESAB
🔗 More informations: bit.ly/43uRz6Z
@cnrs.fr @inrae-france.bsky.social @umontpellier.bsky.social
Join the EVOLUTION Knowledge-Hub at the #FRB-CESAB
🔗 More informations: bit.ly/43uRz6Z
@cnrs.fr @inrae-france.bsky.social @umontpellier.bsky.social
September 2, 2025 at 2:28 PM
Still possible to apply to this #post-doc position at CESAB #Montpellier.
Application closing date: September 15th 2025 (12:00 PM CET)
How taking intraspecific diversity and evolutionary processes into account in translocation-based programs.
Please share widely #PopGen #NbS #Biodiversity
Application closing date: September 15th 2025 (12:00 PM CET)
How taking intraspecific diversity and evolutionary processes into account in translocation-based programs.
Please share widely #PopGen #NbS #Biodiversity
Reposted by Pierre Nouhaud
For those interested: 🚀 BayPass v3.1 released!
🔹 Improved MCMC adaptive phase
🔹 Computation reduced >6X with default (recommended) options, while keeping similar accuracy
🔹 Plus other minor edits
📖 Details in the manual / changelog
🔗 Repo: forge.inrae.fr/mathieu.gaut...
🔹 Improved MCMC adaptive phase
🔹 Computation reduced >6X with default (recommended) options, while keeping similar accuracy
🔹 Plus other minor edits
📖 Details in the manual / changelog
🔗 Repo: forge.inrae.fr/mathieu.gaut...
GAUTIER Mathieu / baypass public · GitLab
GitLab Community Edition
forge.inrae.fr
August 26, 2025 at 2:48 PM
For those interested: 🚀 BayPass v3.1 released!
🔹 Improved MCMC adaptive phase
🔹 Computation reduced >6X with default (recommended) options, while keeping similar accuracy
🔹 Plus other minor edits
📖 Details in the manual / changelog
🔗 Repo: forge.inrae.fr/mathieu.gaut...
🔹 Improved MCMC adaptive phase
🔹 Computation reduced >6X with default (recommended) options, while keeping similar accuracy
🔹 Plus other minor edits
📖 Details in the manual / changelog
🔗 Repo: forge.inrae.fr/mathieu.gaut...
Reposted by Pierre Nouhaud
Two papers in today's issue of @nature.com : 1) we assemble 65 genomes to near completion, including centromeres and the MHC. tinyurl.com/3huhax6w. 2) we sequence 1,019 genomes from the 1kGP with long reads, revealing SVs down to low allele frequencies tinyurl.com/wbx3we9x.
Complex genetic variation in nearly complete human genomes - Nature
Using sequencing and haplotype-resolved assembly of 65 diverse human genomes, complex regions including the major histocompatibility complex and centromeres are analysed.
tinyurl.com
July 23, 2025 at 3:12 PM
Two papers in today's issue of @nature.com : 1) we assemble 65 genomes to near completion, including centromeres and the MHC. tinyurl.com/3huhax6w. 2) we sequence 1,019 genomes from the 1kGP with long reads, revealing SVs down to low allele frequencies tinyurl.com/wbx3we9x.
Reposted by Pierre Nouhaud
📢 next CBGP seminar, Tue. 29th, 11AM (Fr. time).
"(Pan-)genomic variation in the Anopheles gambiae species complex, and genomic insights into the evolution of extreme specialisation in one of its member, A. bwambae.
by #Michael_Fontaine, CNRS-Mivegec"
Zoom: tinyurl.com/94srdfm4
Pwd: MF@cbgp!29
"(Pan-)genomic variation in the Anopheles gambiae species complex, and genomic insights into the evolution of extreme specialisation in one of its member, A. bwambae.
by #Michael_Fontaine, CNRS-Mivegec"
Zoom: tinyurl.com/94srdfm4
Pwd: MF@cbgp!29
April 23, 2025 at 6:27 AM
📢 next CBGP seminar, Tue. 29th, 11AM (Fr. time).
"(Pan-)genomic variation in the Anopheles gambiae species complex, and genomic insights into the evolution of extreme specialisation in one of its member, A. bwambae.
by #Michael_Fontaine, CNRS-Mivegec"
Zoom: tinyurl.com/94srdfm4
Pwd: MF@cbgp!29
"(Pan-)genomic variation in the Anopheles gambiae species complex, and genomic insights into the evolution of extreme specialisation in one of its member, A. bwambae.
by #Michael_Fontaine, CNRS-Mivegec"
Zoom: tinyurl.com/94srdfm4
Pwd: MF@cbgp!29
Reposted by Pierre Nouhaud
Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...
Efficient near telomere-to-telomere assembly of Nanopore Simplex reads
Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads w...
www.biorxiv.org
April 18, 2025 at 9:54 PM
Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...
Reposted by Pierre Nouhaud
A PhD position in plant evolutionary genomics is available at Univ.Vienna 🇦🇹. Focus: genomic drivers underlying the diversification of Tillandsia 😍. Funded by a project between France & Austria (ANR-FWF project RadiaSpe).
Come join the team!
More information: thibaultleroyfr.github.io/pdf/Univie_R...
Come join the team!
More information: thibaultleroyfr.github.io/pdf/Univie_R...
thibaultleroyfr.github.io
April 18, 2025 at 4:40 AM
A PhD position in plant evolutionary genomics is available at Univ.Vienna 🇦🇹. Focus: genomic drivers underlying the diversification of Tillandsia 😍. Funded by a project between France & Austria (ANR-FWF project RadiaSpe).
Come join the team!
More information: thibaultleroyfr.github.io/pdf/Univie_R...
Come join the team!
More information: thibaultleroyfr.github.io/pdf/Univie_R...
Reposted by Pierre Nouhaud
🚀 A new version of BayPass (v3.0) is now available for GEA/pGWAS analyses. This update brings support for Genotype-Likelihood data, hybrid datasets (allele counts and/or Pool-Seq and/or GL), or local-score computation (see updated manual).
🔗 forgemia.inra.fr/mathieu.gaut...
#BayPass #popgen
🔗 forgemia.inra.fr/mathieu.gaut...
#BayPass #popgen
GAUTIER Mathieu / baypass public · GitLab
ForgeMia
forgemia.inra.fr
April 7, 2025 at 1:38 PM
🚀 A new version of BayPass (v3.0) is now available for GEA/pGWAS analyses. This update brings support for Genotype-Likelihood data, hybrid datasets (allele counts and/or Pool-Seq and/or GL), or local-score computation (see updated manual).
🔗 forgemia.inra.fr/mathieu.gaut...
#BayPass #popgen
🔗 forgemia.inra.fr/mathieu.gaut...
#BayPass #popgen
Reposted by Pierre Nouhaud
🚨 Postdoc Opportunity in Quantitative & Population Genetics!
We’re hiring a 2-year postdoc at CBGP (INRAE, Montpellier, France) to work on quantitative and population genetics applied to Drosophila biarmipes.
📍 More details: umr-cbgp.fr/rejoindre-le...
#Postdoc #Genetics #Drosophila
We’re hiring a 2-year postdoc at CBGP (INRAE, Montpellier, France) to work on quantitative and population genetics applied to Drosophila biarmipes.
📍 More details: umr-cbgp.fr/rejoindre-le...
#Postdoc #Genetics #Drosophila
April 2, 2025 at 2:32 PM
🚨 Postdoc Opportunity in Quantitative & Population Genetics!
We’re hiring a 2-year postdoc at CBGP (INRAE, Montpellier, France) to work on quantitative and population genetics applied to Drosophila biarmipes.
📍 More details: umr-cbgp.fr/rejoindre-le...
#Postdoc #Genetics #Drosophila
We’re hiring a 2-year postdoc at CBGP (INRAE, Montpellier, France) to work on quantitative and population genetics applied to Drosophila biarmipes.
📍 More details: umr-cbgp.fr/rejoindre-le...
#Postdoc #Genetics #Drosophila