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Jean-Marc Aury

@jm-aury.bsky.social
136 followers 116 following 6 posts

- 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

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Reposted by Jean-Marc Aury
Carmen Lafuente Sanz @lafucarmen.bsky.social · 22/09/2026
Excited to share my first paper out in Scientific Data: We generated long-read metagenomic and metatranscriptomic datasets from four marine plankton samples from the Tara Pacific expedition. www.nature.com/articles/s41...
nature.com
Long-read metagenomic and metatranscriptomic datasets from marine plankton - Scientific Data
Scientific Data - Long-read metagenomic and metatranscriptomic datasets from marine plankton
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Yann Dussert @yanndussert.bsky.social · 11/09/2026
The LBGB team at @genoscopeumr.bsky.social, led by @jm-aury.bsky.social, recently released Hobrac, a tool to investigate synteny between genomes! Can be used for assembly validation or comparative genomics. doi.org/10.64898/202... github.com/Genoscope-LB... See below for what Hobrac can do:
Figure showing some outputs of the Hobrac tool (e.g. ribbon plots & oxford plots), here illutrating synteny between bivalve genomes.
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Bertrand Bed'Hom @bedhom.bsky.social · 14/04/2026
Après Roscoff, une nouvelle mission #DIVE-Sea par @mnhn.fr avec #MIO @univ-amu.fr cible cette fois les espèces gélatineuses pélagiques, étranges et mal connues ! Ex: le siphonophore (hydrozoaire) Rhizophysa filiformis ou la salpe (tunicier pélagique) Doliolum denticulatum @atlasea.bsky.social
Siphonophore (hydrozoaire) Rhizophysa filiformisSalpe (tunicier pélagique) Doliolum denticulatum
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Rob Waterhouse @rmwaterhouse.bsky.social · 29/11/2025
Species sequenced by Project Psyche also contribute to the aims of other projects including ERGA and EBP www.cell.com/trends/ecolo...
cell.com
Project Psyche: reference genomes for all Lepidoptera in Europe
Project Psyche is a transnational initiative to generate and study chromosome-level reference genomes of all ~11 000 species of Lepidoptera (butterflies and moths) found in Europe. Here, we describe t...
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ATLASea @atlasea.bsky.social · 20/10/2025
💼 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...
emploi.cnrs.fr
Portail Emploi CNRS - Offre d'emploi - H/F Chef de Projet dans le cadre du Programme ATLASea
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ATLASea @atlasea.bsky.social · 20/10/2025
🎬 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...
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ATLASea @atlasea.bsky.social · 08/10/2025
🎉 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
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Biodiversity Genomics Europe plus (BGE+) @biogeneurope.bsky.social · 09/10/2025
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
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CNRS Biologie @cnrsbiologie.bsky.social · 03/10/2025
#Institutionnel 🧬 | En septembre 2025, le programme de recherche ATLASea a franchi la barre des 100 génomes marins séquencés ! #PEPR #France2030 ▶️
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ATLASea : déjà 100 génomes marins séquencés !
En septembre 2025, le programme de recherche ATLASea a franchi la barre des 100 génomes marins séquencés.
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James Bonfield @jbonfield.bsky.social · 15/09/2025
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
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LongTREC @longtrec.bsky.social · 13/07/2025
🌊 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.
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ATLASea @atlasea.bsky.social · 21/06/2025
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
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ATLASea @atlasea.bsky.social · 19/06/2025
📸 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
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ATLASea @atlasea.bsky.social · 16/06/2025
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.
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ATLASea @atlasea.bsky.social · 18/06/2025
🔍 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
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ATLASea @atlasea.bsky.social · 17/06/2025
@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
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ATLASea @atlasea.bsky.social · 20/06/2025
🐚 𝑳𝒊𝒎𝒂𝒓𝒊𝒂 Leads the Way — ATLASea Hits 1500 with a Mollusc That Claps! 🎉🎉 The #DIVE-Sea team has sampled the 1500th species for #ATLASea this week in Marseille! 𝑳𝒊𝒎𝒂𝒓𝒊𝒂 𝒕𝒖𝒃𝒆𝒓𝒄𝒖𝒍𝒂𝒕𝒂, a gorgeous bivalve mollusc of the family 𝐿𝑖𝑚𝑖𝑑𝑎𝑒, first described in 1792 by Giuseppe Olivi.
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Tom Mathers @tom-mathers.bsky.social · 16/05/2025
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
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Camille Marchet ⚡ @camillemrcht.bsky.social · 23/04/2025
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.
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ATLASea @atlasea.bsky.social · 02/04/2025
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
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Roscoff Culture Collection @roscoff-collection.bsky.social · 28/03/2025
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
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 ...
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Carolina Monzó @carolinamonzo.bsky.social · 28/03/2025
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 😀
rdcu.be
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UMR Génomique Métabolique @genoscopeumr.bsky.social · 18/03/2025
📢 #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
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Björn Usadel @usadellab.bsky.social · 14/03/2025
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...
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Francis M. Martin @fmartin54.bsky.social · 06/03/2025
Genus-wide plant pangenome could inform next-generation crop design www.nature.com/articles/d41...
nature.com
Genus-wide plant pangenome could inform next-generation crop design
A pangenome for the genus Solanum.
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CNRS Biologie @cnrsbiologie.bsky.social · 13/02/2025
🌊🔬 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
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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.
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 14/02/2025
Coral venom and toxins as protection against crown-of-thorns sea star attack www.biorxiv.org/content/10.1101/202…
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Jean-Marc Aury @jm-aury.bsky.social · 14/02/2025
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...
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KamilSJaron.bsky.social @kamilsjaron.bsky.social · 31/01/2025
🚨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!
https://coursesandconferences.wellcomeconnectingscience.org/event/k-mer-workshop-for-biodiversity-genomics-20250601/
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ATLASea @atlasea.bsky.social · 30/01/2025
From 17/01 to 8/02, the International Bottom Trawl Survey 🚢 (IBTS) Mission 🌊 🎣 is underway, to assess commercial fish stocks in the North Sea 🔎 #DIVE-Sea team from ATLASea, coordinated by Elio Raphalen #Ifremer, is joining the mission for the first 3 days to collect new marine specimens in this area
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Ensembl @ensembl.org · 20/01/2025
Did you know our colleagues have been working tirelessly on a new #Ensembl genome browser? 🥳 Join us at this @ebi.embl.org webinar to learn more about the new browser and how to navigate it 🧬 💻 Registration is free but essential 📆 Wed, 29 Jan 2025 🕞 15:30 – 16:30 GMT 📍 Virtual ℹ bit.ly/EnsBeta
Webinar advertisement.
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Conesa Lab @conesalab.bsky.social · 14/01/2025
Attention people of Bluesky! Today, we had a double celebration. Alejandro has gotten his paper published #ConesaLab 🧑‍🔬 genome.cshlp.org/content/earl...
genome.cshlp.org
Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
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Nicolas Robine 🇪🇺🇫🇷🇺🇸 @nicorobine.bsky.social · 12/01/2025
[fr] Vincent Colot, héraut de l’épigénétique des plantes www.lemonde.fr/sciences/art...
lemonde.fr
Vincent Colot, héraut de l’épigénétique des plantes
Le généticien des plantes, directeur de recherche au CNRS, explore le rôle de l’épigénétique à travers le monde végétal depuis plus de vingt-cinq ans. A l’orée de la retraite, il continue de chercher ...
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Yann Dussert @yanndussert.bsky.social · 10/01/2025
Richard Cordeaux (EGCE lab, Gif sur Yvette, France) is offering an 18-month postdoc position in evolutionary genomics to study sex determination and resistance to vertical transmission of feminizing Wolbachia endosymbionts in an isopod. #SymbioSky #Wolbachia filesender.renater.fr?s=download&t...
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Arnau Sebé-Pedrós @arnausebe.bsky.social · 08/01/2025
Monod Conference "Origin of metazoans": fossils, genomes, cell biology, gene regulation, development, and more. Join us in Roscoff for an exceptional speaker line-up and stunning venue! 🗓️Abstract deadline: March 4. Register and share! www.insb.cnrs.fr/fr/origin-me...
insb.cnrs.fr
Origin of metazoans
Roscoff (Bretagne), France, June 16-20, 2025Deadline for application: March 4, 2025
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Elodie Laine @laineelodie.bsky.social · 07/01/2025
Curious about alternative splicing? Kick off the year with our latest review in COSB! authors.elsevier.com/sd/article/S...
authors.elsevier.com
ScienceDirect.com | Science, health and medical journals, full text articles and books.
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Vikram Shivakumar @vikramshivakumar.bsky.social · 06/01/2025
Excited to share a preprint for (w/ @benlangmead.bsky.social) our new tool, Mumemto, on biorxiv! Mumemto finds multi-MUMs across pangenomes (i.e. mummer but for pangenomes). It can rapidly visualize synteny, identify misassemblies, and accelerate core genome and multiple alignment, highlighting SVs.
biorxiv.org
Mumemto: efficient maximal matching across pangenomes
Aligning genomes into common coordinates is central to pangenome analysis and construction, but it is also computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) are guideposts ...
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Ana Conesa @anaconesa.bsky.social · 06/01/2025
@conesalab.bsky.social @i2sysbio.bsky.social presents their tool PaintOmics4. It is a web-based tool for the integrative analysis and interpretation of multiomics data. Follow the online seminar at us06web.zoom.us/j/88518061453on January 15th at 11:00 CET
us06web.zoom.us
Join our Cloud HD Video Meeting
Zoom is the leader in modern enterprise video communications, with an easy, reliable cloud platform for video and audio conferencing, chat, and webinars across mobile, desktop, and room systems. Zoom ...
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Jean-Marc Aury @jm-aury.bsky.social · 20/12/2024
Happy to be part of this long journey in the world of brown algae: Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems www.cell.com/cell/fulltex... @fr-genomics.bsky.social @sbroscoff.bsky.social @cnrsbiologie.bsky.social
cell.com
Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems
Comparative genomics charts the evolutionary history of the brown algal lineage, identifying an early period of accelerated genome evolution followed by diversification of the major orders, and a major impact of continuous, widespread viral genome integration.
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Genome Research @genomeresearch.bsky.social · 20/11/2024
SPECIAL ISSUE! This month Genome Research publishes a diverse collection of research and review articles in a special issue highlighting advances in long-read sequencing applications in biology and medicine. Full issue links here: tinyurl.com/Genome-Res-3....
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ATLASea @atlasea.bsky.social · 21/11/2024
🎉 ATLASea Milestone✅ We’re thrilled to announce that ATLASea has already collected over 1️⃣0️⃣0️⃣0️⃣ species across 5 sampling expeditions to the Mediterranean, Caribbean, South Pacific with #MHNH, English Channel with @ifremer.bsky.social and Dinard in Brittany with all partners!
Coryphopterus venezuelae: the 1000th species sampled by ATLASea
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ATLASea @atlasea.bsky.social · 13/12/2024
🌟 “Small steps lead to big results!” The first 20 genomes sequenced by ATLASea and sampled in Leucate, Roscoff & Marseille are now published and available on our data portal. A milestone in our journey to explore marine biodiversity! Explore the data: portal.atlasea.fr/home/ #Genomics #Biodiversity
portal.atlasea.fr
ATLASeaexplorer: home
ATLASea
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