Jean-Marc Aury
@jm-aury.bsky.social
- Bioinformatics, de novo sequencing and assembly, gene prediction
- Scientific coordinator of the SEQ-Sea project in the @atlasea.bsky.social program
Université Paris Saclay / CEA / Genoscope
www.genoscope.cns.fr/lbgb
- Scientific coordinator of the SEQ-Sea project in the @atlasea.bsky.social program
Université Paris Saclay / CEA / Genoscope
www.genoscope.cns.fr/lbgb
Reposted by Jean-Marc Aury
💼 ATLASea #recrute son nouveau chef de projet !
Mission : assurer la coordination du programme ATLASea à un niveau opérationnel et administratif et surveiller sa progression.
Lieu de travail : Paris 5ème
Expérience souhaitée : 1 à 4 années
Date limite : 04/11/25
emploi.cnrs.fr/Offres/CDD/U...
Mission : assurer la coordination du programme ATLASea à un niveau opérationnel et administratif et surveiller sa progression.
Lieu de travail : Paris 5ème
Expérience souhaitée : 1 à 4 années
Date limite : 04/11/25
emploi.cnrs.fr/Offres/CDD/U...
Portail Emploi CNRS - Offre d'emploi - H/F Chef de Projet dans le cadre du Programme ATLASea
emploi.cnrs.fr
October 20, 2025 at 11:09 AM
💼 ATLASea #recrute son nouveau chef de projet !
Mission : assurer la coordination du programme ATLASea à un niveau opérationnel et administratif et surveiller sa progression.
Lieu de travail : Paris 5ème
Expérience souhaitée : 1 à 4 années
Date limite : 04/11/25
emploi.cnrs.fr/Offres/CDD/U...
Mission : assurer la coordination du programme ATLASea à un niveau opérationnel et administratif et surveiller sa progression.
Lieu de travail : Paris 5ème
Expérience souhaitée : 1 à 4 années
Date limite : 04/11/25
emploi.cnrs.fr/Offres/CDD/U...
Reposted by Jean-Marc Aury
🎬 Advance screening of the documentary “ATLASea: In Pursuit of Marine Genomes” at Le Grand Action cinema!
On Oct 16, during the ATLASea General Assembly, members attended the advance screening of this inspiring film 🌊🔬
📺 Diffused on Ushuaïa TV, Sat Oct 18 at 8:30 p.m.: ushuaiatv.fr/programmes/a...
On Oct 16, during the ATLASea General Assembly, members attended the advance screening of this inspiring film 🌊🔬
📺 Diffused on Ushuaïa TV, Sat Oct 18 at 8:30 p.m.: ushuaiatv.fr/programmes/a...
October 20, 2025 at 11:07 AM
🎬 Advance screening of the documentary “ATLASea: In Pursuit of Marine Genomes” at Le Grand Action cinema!
On Oct 16, during the ATLASea General Assembly, members attended the advance screening of this inspiring film 🌊🔬
📺 Diffused on Ushuaïa TV, Sat Oct 18 at 8:30 p.m.: ushuaiatv.fr/programmes/a...
On Oct 16, during the ATLASea General Assembly, members attended the advance screening of this inspiring film 🌊🔬
📺 Diffused on Ushuaïa TV, Sat Oct 18 at 8:30 p.m.: ushuaiatv.fr/programmes/a...
Reposted by Jean-Marc Aury
🎉 The 100 ATLASea marine genomes milestone has been reached!
🔗 Explore the genomes of these 100 species on the ATLASea Data Portal: portal.atlasea.fr/home/
🔗 Read the latest ATLASea news on the CNRS Biologie website: www.insb.cnrs.fr/fr/cnrsinfo/...
#PEPR #France2030 #MarineGenomics #ATLASea
🔗 Explore the genomes of these 100 species on the ATLASea Data Portal: portal.atlasea.fr/home/
🔗 Read the latest ATLASea news on the CNRS Biologie website: www.insb.cnrs.fr/fr/cnrsinfo/...
#PEPR #France2030 #MarineGenomics #ATLASea
October 8, 2025 at 7:58 AM
🎉 The 100 ATLASea marine genomes milestone has been reached!
🔗 Explore the genomes of these 100 species on the ATLASea Data Portal: portal.atlasea.fr/home/
🔗 Read the latest ATLASea news on the CNRS Biologie website: www.insb.cnrs.fr/fr/cnrsinfo/...
#PEPR #France2030 #MarineGenomics #ATLASea
🔗 Explore the genomes of these 100 species on the ATLASea Data Portal: portal.atlasea.fr/home/
🔗 Read the latest ATLASea news on the CNRS Biologie website: www.insb.cnrs.fr/fr/cnrsinfo/...
#PEPR #France2030 #MarineGenomics #ATLASea
Reposted by Jean-Marc Aury
Thrilled to announce new @biogeneurope.bsky.social @ergabiodiv.bsky.social genomes reports! The irresistible Hanak's bat (Pipistrellus hanaki) open-research-europe.ec.europa.eu/articles/5-298 & the lovely sea cucumber Holothuria (Platyperona) sanctori open-research-europe.ec.europa.eu/articles/5-297
October 9, 2025 at 3:11 PM
Thrilled to announce new @biogeneurope.bsky.social @ergabiodiv.bsky.social genomes reports! The irresistible Hanak's bat (Pipistrellus hanaki) open-research-europe.ec.europa.eu/articles/5-298 & the lovely sea cucumber Holothuria (Platyperona) sanctori open-research-europe.ec.europa.eu/articles/5-297
Reposted by Jean-Marc Aury
#Institutionnel 🧬 | En septembre 2025, le programme de recherche ATLASea a franchi la barre des 100 génomes marins séquencés !
#PEPR #France2030
▶️
#PEPR #France2030
▶️
ATLASea : déjà 100 génomes marins séquencés !
En septembre 2025, le programme de recherche ATLASea a franchi la barre des 100 génomes marins séquencés.
buff.ly
October 3, 2025 at 5:00 AM
#Institutionnel 🧬 | En septembre 2025, le programme de recherche ATLASea a franchi la barre des 100 génomes marins séquencés !
#PEPR #France2030
▶️
#PEPR #France2030
▶️
Reposted by Jean-Marc Aury
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:40 AM
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
Reposted by Jean-Marc Aury
🌊 Exploring the Ocean’s Genetic Secrets! Guided by @jm-aury.bsky.social and France Denoeud, @lafucarmen.bsky.social Doctoral Candidate at Genoscope - Centre National de Séquençage, shares how she's using long-reads on marine samples from the Tara Oceans expedition to explore genetic novelty.
July 13, 2025 at 8:37 AM
🌊 Exploring the Ocean’s Genetic Secrets! Guided by @jm-aury.bsky.social and France Denoeud, @lafucarmen.bsky.social Doctoral Candidate at Genoscope - Centre National de Séquençage, shares how she's using long-reads on marine samples from the Tara Oceans expedition to explore genetic novelty.
Reposted by Jean-Marc Aury
ATLASea Mission – Day 6
In the dissection room, the final sampling steps are underway
🔬 Tissue fragments are collected, labeled, weighed, and logged into a data sheet for full traceability
❄️ Samples are flash-frozen in liquid nitrogen at -196°C to preserve DNA quality for sequencing at Genoscope
In the dissection room, the final sampling steps are underway
🔬 Tissue fragments are collected, labeled, weighed, and logged into a data sheet for full traceability
❄️ Samples are flash-frozen in liquid nitrogen at -196°C to preserve DNA quality for sequencing at Genoscope
June 21, 2025 at 8:41 AM
ATLASea Mission – Day 6
In the dissection room, the final sampling steps are underway
🔬 Tissue fragments are collected, labeled, weighed, and logged into a data sheet for full traceability
❄️ Samples are flash-frozen in liquid nitrogen at -196°C to preserve DNA quality for sequencing at Genoscope
In the dissection room, the final sampling steps are underway
🔬 Tissue fragments are collected, labeled, weighed, and logged into a data sheet for full traceability
❄️ Samples are flash-frozen in liquid nitrogen at -196°C to preserve DNA quality for sequencing at Genoscope
Reposted by Jean-Marc Aury
📸 ATLASea Mission – Day 4 - photography
Each selected specimen is individually photographed in the photo room by 3 dedicated teams.
🗂️ Images are paired with species sheets + unique ATLASea & MNHN labels to ensure full data traceability.
Next stop: the dissection room!
#MarineGenomics #Biodiversity
Each selected specimen is individually photographed in the photo room by 3 dedicated teams.
🗂️ Images are paired with species sheets + unique ATLASea & MNHN labels to ensure full data traceability.
Next stop: the dissection room!
#MarineGenomics #Biodiversity
June 19, 2025 at 1:58 PM
📸 ATLASea Mission – Day 4 - photography
Each selected specimen is individually photographed in the photo room by 3 dedicated teams.
🗂️ Images are paired with species sheets + unique ATLASea & MNHN labels to ensure full data traceability.
Next stop: the dissection room!
#MarineGenomics #Biodiversity
Each selected specimen is individually photographed in the photo room by 3 dedicated teams.
🗂️ Images are paired with species sheets + unique ATLASea & MNHN labels to ensure full data traceability.
Next stop: the dissection room!
#MarineGenomics #Biodiversity
Reposted by Jean-Marc Aury
ATLASea has just launched a new sampling campaign in one of the most iconic sites of marine biodiversity.
For the next 10 days, our team of researchers will be working around the #Endoume_Marine_Station in Marseille to collect samples of marine species from the surrounding area.
For the next 10 days, our team of researchers will be working around the #Endoume_Marine_Station in Marseille to collect samples of marine species from the surrounding area.
June 16, 2025 at 8:32 AM
ATLASea has just launched a new sampling campaign in one of the most iconic sites of marine biodiversity.
For the next 10 days, our team of researchers will be working around the #Endoume_Marine_Station in Marseille to collect samples of marine species from the surrounding area.
For the next 10 days, our team of researchers will be working around the #Endoume_Marine_Station in Marseille to collect samples of marine species from the surrounding area.
Reposted by Jean-Marc Aury
🔍 ATLASea Mission – Day 3
Taxonomic experts examine each specimen, compare it to reference catalogs, and confirm ID - sometimes with help from global colleagues!
If the species is new to sequencing efforts, it’s selected (GO)
If not, it’s returned to the sea (NO GO)
#MarineBiodiversity #Fieldwork
Taxonomic experts examine each specimen, compare it to reference catalogs, and confirm ID - sometimes with help from global colleagues!
If the species is new to sequencing efforts, it’s selected (GO)
If not, it’s returned to the sea (NO GO)
#MarineBiodiversity #Fieldwork
June 18, 2025 at 10:29 AM
🔍 ATLASea Mission – Day 3
Taxonomic experts examine each specimen, compare it to reference catalogs, and confirm ID - sometimes with help from global colleagues!
If the species is new to sequencing efforts, it’s selected (GO)
If not, it’s returned to the sea (NO GO)
#MarineBiodiversity #Fieldwork
Taxonomic experts examine each specimen, compare it to reference catalogs, and confirm ID - sometimes with help from global colleagues!
If the species is new to sequencing efforts, it’s selected (GO)
If not, it’s returned to the sea (NO GO)
#MarineBiodiversity #Fieldwork
Reposted by Jean-Marc Aury
@atlasea.bsky.social Sampling Day 2
Samples from the sea head straight to the wet lab for taxonomic grouping.
Dragged sediments are sieved and size-fractioned - revealing hidden benthic diversity.
Uncertain samples go into aquaria, then safely back to the sea if not selected.
#MarineBiodiversity
Samples from the sea head straight to the wet lab for taxonomic grouping.
Dragged sediments are sieved and size-fractioned - revealing hidden benthic diversity.
Uncertain samples go into aquaria, then safely back to the sea if not selected.
#MarineBiodiversity
June 17, 2025 at 9:40 AM
@atlasea.bsky.social Sampling Day 2
Samples from the sea head straight to the wet lab for taxonomic grouping.
Dragged sediments are sieved and size-fractioned - revealing hidden benthic diversity.
Uncertain samples go into aquaria, then safely back to the sea if not selected.
#MarineBiodiversity
Samples from the sea head straight to the wet lab for taxonomic grouping.
Dragged sediments are sieved and size-fractioned - revealing hidden benthic diversity.
Uncertain samples go into aquaria, then safely back to the sea if not selected.
#MarineBiodiversity
Reposted by Jean-Marc Aury
Reposted by Jean-Marc Aury
Struggling to find the tiny microchromosomes in draft bird genome assemblies?
Our new #preprint introducing MicroFinder can help: www.biorxiv.org/content/10.1...
🧵 below
(1/n)
@sangerinstitute.bsky.social
Our new #preprint introducing MicroFinder can help: www.biorxiv.org/content/10.1...
🧵 below
(1/n)
@sangerinstitute.bsky.social
May 16, 2025 at 10:07 AM
Struggling to find the tiny microchromosomes in draft bird genome assemblies?
Our new #preprint introducing MicroFinder can help: www.biorxiv.org/content/10.1...
🧵 below
(1/n)
@sangerinstitute.bsky.social
Our new #preprint introducing MicroFinder can help: www.biorxiv.org/content/10.1...
🧵 below
(1/n)
@sangerinstitute.bsky.social
Reposted by Jean-Marc Aury
1/ We made a tool called Vizitig to explore sequencing datasets visually, interactively, and with metadata.
It uses a colored de Bruijn graph under the hood.
It uses a colored de Bruijn graph under the hood.
Vizitig: context-rich exploration of sequencing datasets https://www.biorxiv.org/content/10.1101/2025.04.19.649656v1
April 23, 2025 at 9:43 AM
1/ We made a tool called Vizitig to explore sequencing datasets visually, interactively, and with metadata.
It uses a colored de Bruijn graph under the hood.
It uses a colored de Bruijn graph under the hood.
Reposted by Jean-Marc Aury
This week, ATLASea is in the Endoume marine station from @univ-amu.fr for a new sampling expedition focused on fish and some additional species! The team has already collected 30 new species.
In the lab, our colleagues Caroline, Janaina and Morgane sampling tissues from a coral.
#MarineBiodiversity
In the lab, our colleagues Caroline, Janaina and Morgane sampling tissues from a coral.
#MarineBiodiversity
April 2, 2025 at 1:51 PM
This week, ATLASea is in the Endoume marine station from @univ-amu.fr for a new sampling expedition focused on fish and some additional species! The team has already collected 30 new species.
In the lab, our colleagues Caroline, Janaina and Morgane sampling tissues from a coral.
#MarineBiodiversity
In the lab, our colleagues Caroline, Janaina and Morgane sampling tissues from a coral.
#MarineBiodiversity
Reposted by Jean-Marc Aury
New paper using 2 RCC Pelagomonas strains, co-authored by 2 members of the RCC, Pris and Ian.
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
Transcriptomic response of the picoalga Pelagomonas calceolata to nitrogen availability: new insights into cyanate lyase function | Microbiology Spectrum
Vast oceanic regions are nutrient-poor, yet several microalgae thrive in these environments. While various acclimation strategies to these conditions have been discovered in a limited number of model microalgae, many important lineages remain ...
journals.asm.org
March 28, 2025 at 4:57 PM
New paper using 2 RCC Pelagomonas strains, co-authored by 2 members of the RCC, Pris and Ian.
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
Reposted by Jean-Marc Aury
It's finally out!!!! Our review on long-reads transcriptomics was published in @natrevgenet.bsky.social!! You can have a look at the paper here rdcu.be/efugl! We hope you like it 😀
March 28, 2025 at 11:25 AM
It's finally out!!!! Our review on long-reads transcriptomics was published in @natrevgenet.bsky.social!! You can have a look at the paper here rdcu.be/efugl! We hope you like it 😀
Reposted by Jean-Marc Aury
📢 #PhD and #postdoctoral positions available in Pedro Oliveira lab. We seek candidates for Microbial Genomic and Epigenetic teams to work on #epigenomics of #bacteria and #microbiomes. Start: Fall 2025.
Please RT!
@cea.fr @univparissaclay.bsky.social @genopole.bsky.social @upcite.bsky.social
Please RT!
@cea.fr @univparissaclay.bsky.social @genopole.bsky.social @upcite.bsky.social
March 18, 2025 at 8:58 PM
📢 #PhD and #postdoctoral positions available in Pedro Oliveira lab. We seek candidates for Microbial Genomic and Epigenetic teams to work on #epigenomics of #bacteria and #microbiomes. Start: Fall 2025.
Please RT!
@cea.fr @univparissaclay.bsky.social @genopole.bsky.social @upcite.bsky.social
Please RT!
@cea.fr @univparissaclay.bsky.social @genopole.bsky.social @upcite.bsky.social
Reposted by Jean-Marc Aury
If you are looking for published plant genomes www.plabipd.de/pubplant_mai... might be useful where Rainer is tracking species with genomes for almost 10 years now... time flies. As he has added new useful views, we thought it is time to summarize this. www.biorxiv.org/content/10.1...
March 14, 2025 at 9:08 AM
If you are looking for published plant genomes www.plabipd.de/pubplant_mai... might be useful where Rainer is tracking species with genomes for almost 10 years now... time flies. As he has added new useful views, we thought it is time to summarize this. www.biorxiv.org/content/10.1...
Reposted by Jean-Marc Aury
Reposted by Jean-Marc Aury
🌊🔬 ATLASea : bilan exceptionnel en 2024 !
Plus de 1000 espèces marines collectées lors des campagnes océanographiques du PEPR ATLASea en Nouvelle-Calédonie, à Dinard, dans la Manche et en Guadeloupe ! 🐠🦑
🤝 @atlasea.bsky.social @cea.fr
➡️ Plongez dans cette aventure scientifique
Plus de 1000 espèces marines collectées lors des campagnes océanographiques du PEPR ATLASea en Nouvelle-Calédonie, à Dinard, dans la Manche et en Guadeloupe ! 🐠🦑
🤝 @atlasea.bsky.social @cea.fr
➡️ Plongez dans cette aventure scientifique
ATLASea : plus de 1000 espèces marines collectées en 2024 !
Un an après son lancement, le programme ATLASea, progresse vers son objectif de séquencer les génomes d’espèces marines.
buff.ly
February 13, 2025 at 7:00 AM
🌊🔬 ATLASea : bilan exceptionnel en 2024 !
Plus de 1000 espèces marines collectées lors des campagnes océanographiques du PEPR ATLASea en Nouvelle-Calédonie, à Dinard, dans la Manche et en Guadeloupe ! 🐠🦑
🤝 @atlasea.bsky.social @cea.fr
➡️ Plongez dans cette aventure scientifique
Plus de 1000 espèces marines collectées lors des campagnes océanographiques du PEPR ATLASea en Nouvelle-Calédonie, à Dinard, dans la Manche et en Guadeloupe ! 🐠🦑
🤝 @atlasea.bsky.social @cea.fr
➡️ Plongez dans cette aventure scientifique
Reposted by Jean-Marc Aury
Coral venom and toxins as protection against crown-of-thorns sea star attack https://www.biorxiv.org/content/10.1101/2025.02.10.637440v1
February 14, 2025 at 4:47 PM
Coral venom and toxins as protection against crown-of-thorns sea star attack https://www.biorxiv.org/content/10.1101/2025.02.10.637440v1
For those working with Hi-C data and the Arima workflow, we have rewritten the Arima tools using htslib to speed up the process. Any feedback is welcome: github.com/Genoscope-LB...
February 14, 2025 at 4:24 PM
For those working with Hi-C data and the Arima workflow, we have rewritten the Arima tools using htslib to speed up the process. Any feedback is welcome: github.com/Genoscope-LB...
Reposted by Jean-Marc Aury
🚨Registration open🚨 1st - 6th of June, me, Katie Jenike, @rayanchikhi.bsky.social and Gene Myers will run a week long workshop on k-mers for biodiversity genomics organised by @connectingscience.bsky.social at @sangerinstitute.bsky.social. Join us & get equipped to wrestle large genomic datasets!
January 31, 2025 at 3:17 PM
🚨Registration open🚨 1st - 6th of June, me, Katie Jenike, @rayanchikhi.bsky.social and Gene Myers will run a week long workshop on k-mers for biodiversity genomics organised by @connectingscience.bsky.social at @sangerinstitute.bsky.social. Join us & get equipped to wrestle large genomic datasets!