scPRINT-2: Towards the next-generation of cell foundation models and benchmarks https://www.biorxiv.org/content/10.64898/2025.12.11.693702v1

scPRINT-2: Towards the next-generation of cell foundation models and benchmarks [new] Foundation model: ...evaluates features to enhance scRNA-seq analysis via pre-training on a vast, multi-organism dataset for diverse cell tasks.

Transformer-based Prediction of Microbial Growth Rates from Genomic Data doi.org/10.1145/3765...

Comparative metagenomics using pan-metagenomics graphs https://www.biorxiv.org/content/10.1101/2025.11.24.690211v1

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...

The level of this conference was outstanding for a student-led event. It truly matched the quality of established research conferences. Congratulations to the students who organized it and to the excellent speakers!

We are happy to share a new paper from our lab: The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals www.nature.com/articles/s42... which investigates environmental effects on microbiome interactions, using our previously published tool MANOCCA.

New publication🧬 𝐌𝐞𝐭𝐞𝐨𝐫𝟐 𝐢𝐬 𝐚𝐧 𝐨𝐩𝐞𝐧-𝐬𝐨𝐮𝐫𝐜𝐞 𝐭𝐨𝐨𝐥 𝐟𝐨𝐫 𝐭𝐚𝐱𝐨𝐧𝐨𝐦𝐢𝐜, 𝐟𝐮𝐧𝐜𝐭𝐢𝐨𝐧𝐚𝐥, 𝐚𝐧𝐝 𝐬𝐭𝐫𝐚𝐢𝐧-𝐥𝐞𝐯𝐞𝐥 𝐩𝐫𝐨𝐟𝐢𝐥𝐢𝐧𝐠 𝐨𝐟 𝐦𝐞𝐭𝐚𝐠𝐞𝐧𝐨𝐦𝐢𝐜 𝐬𝐚𝐦𝐩𝐥𝐞𝐬. 𝐟𝐨𝐫 𝐦𝐢𝐜𝐫𝐨𝐛𝐢𝐨𝐦𝐞 𝐫𝐞𝐬𝐞𝐚𝐫𝐜𝐡 microbiomejournal.biomedcentral.com/articles/10.... #metagenomic #science #data #lefrenchgut @inrae-france.bsky.social @institutpasteur.bsky.social

Seqwin: Ultrafast Identification of Signature Sequences in Microbial Genomes https://www.biorxiv.org/content/10.1101/2025.11.07.687294v1

I also talk about de-extinction in this paper & the need to have some name to call the organisms. Like many people, I know that the Colossal "Dire Wolves" are not the descendants of the extinct wolves they are named after. But they are *something*, so we need to have a name for them.

Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years. academic.oup.com/nar/advance-...

Predicting functions of uncharacterized gene products from microbial communities - @hutlab.bsky.social @hsph.harvard.edu @broadinstitute.org go.nature.com/435C4lp

Bravo !

Après six-ans (à mi-temps), bientôt plus #étudiant ! www.instagram.com/p/DP6FgQRitUJ/

Strainify: Strain-Level Microbiome Profiling for Low-Coverage Short-Read Metagenomic Datasets https://www.biorxiv.org/content/10.1101/2025.10.10.681738v1

Efficient and accurate search in petabase-scale sequence repositories www.nature.com/articles/s41... 🧬🖥️🧪 MetaGraph: metagraph.ethz.ch Code: github.com/ratschlab/me...

Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe https://www.biorxiv.org/content/10.1101/2025.09.29.678807v1

Sometimes you meet absolutely incredible bioinfo-magicians. It was a huge privilege when @shenwei356.bsky.social joined our group for a year on an @embl.org sabbatical. While here, he developed a new way of aligning to millions of bacteria, called LexicMap 1/n www.nature.com/articles/s41...

kSanity: A k-mer based application forprecision bacterial strain detection andquantification https://www.biorxiv.org/content/10.1101/2025.09.04.674052v1

For anyone who has used pling for comparing plasmids using rearrangement distances ("how many structural events apart are these plasmids"), here's how to tweak parameters, and integrate it with typing info, and the host phylogeny www.biorxiv.org/content/10.1... github.com/iqbal-lab-or...

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social 1 / N

Clustering of plasmid genomes for genomic epidemiology by using rearrangement distances, with pling https://www.biorxiv.org/content/10.1101/2025.09.02.673752v1

PhageAI: a new approach to predicting the lifestyle of bacteriophages using proteinBERT and convolutional neural networks https://www.biorxiv.org/content/10.1101/2025.09.02.673651v1

High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1

MiGenPro: A linked data workflow for phenotype-genotype prediction of microbial traits using machine learning. https://www.biorxiv.org/content/10.1101/2025.08.21.671437v1

AEMB: a computationally efficient abundance estimation method for metagenomic binning https://www.biorxiv.org/content/10.1101/2025.07.30.667338v1

Building pangenomes for domesticated and wild tree species: genomic complexity and strategies https://www.biorxiv.org/content/10.1101/2025.07.22.665893v1

SVPG: A pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples https://www.biorxiv.org/content/10.1101/2025.07.11.664486v1

Tomorrow at 9:40am I’ll be speaking at #ISMBECCB2025 about how we can speed up microbiome data interpretation using taxon sets Paper: academic.oup.com/bib/article/... R package on #Bioconductor: TaxSEA #RStats #Microbiome Come say hi, I flew from Australia for this 🤣

Today at 2 PM at 3DSIG #ISMBECCB2025, @nbordin.bsky.social presents our joint work on metagenomic-scale clustering and novel domain discovery in predicted structures! 📄 www.biorxiv.org/content/10.1... Also check out poster: B-50 lolalign Sensitive structural alignments by Lasse B-123 BFVD by Rachel

New online! Lactobacilli biology, applications and host interactions

Leviathan: A fast, memory-efficient, and scalable taxonomic and pathway profiler for next generation sequencing (pan)genome-resolved metagenomics and metatranscriptomics https://www.biorxiv.org/content/10.1101/2025.07.14.664802v1

The MicrobeAtlas database: Global trends and insights into Earth's microbial ecosystems https://www.biorxiv.org/content/10.1101/2025.07.18.665519v1

Solène Pety will present at #JOBIM2025 on 11 July at 10:10 am in Amphi D, discussing RITHMS: An advanced stochastic framework for simulating transgenerational hologenomic data. #holobiont #genotype #microbiota #simulationframework @mahendram.bsky.social

We are thrilled to be involved in the Robustness Assessment of LLM by designing evaluation metrics and by LLM experiments #project. A great #collaboration with Huazhong Agricultural University (HZAU), China. More information at maiage.inrae.fr/node/3331. Image designed by Freepik.

And many thanks to @guigau.bsky.social and Hanin Ali for using and promoting our methods in bacterial gene family analysis. Check their work ! bsky.app/profile/cami...

Super proud that @bdegardins.bsky.social and Fiona Hak earned a Mini-symposium prize for the presentation and poster award at #JOBIM2025 🎉🏆

👏 Ca y est, #JOBIM2025 est officiellement fini ! Au nom de toute l'équipe, merci pour votre participation, et pour toutes ces discussions scientifiques intenses et stimulantes. Merci aussi pour votre enthousiasme, votre bienveillance et tous ces rires échangés pendant la conférence. 1/2 ⤵️

Vu l'enthousiasme autour de ce 1er #JobFair, probablement un #evenement à pérenniser pour les prochains #JOBIM. 📍Ne loupez pas la 2ème session au déjeuner du 10 juillet

Meet Sylvain Marthey on July 8th at #JOBIM2025 for a demonstration about WHOOPER Web application for Hands-On identification of proteins co-Occurrence among Phyla, focused on user ERgonomics (Amphi D at 6 pm) #webapplication #proteins #evolution #datavisualization #userergonomics

Meet Hajar Bouamout on July 8th at #JOBIM2025 at the poster session to talk about HoloOligoDB: an open platform for the exploration of milk oligosaccharides in mammalian species #database #webinterface #oligosaccharide @sandraderozier.bsky.social @vloux.bsky.social @inrae-migale.bsky.social

Meet Anne-Laure Abraham on July 8th at #JOBIM2025 at the poster session to talk about Bacterial transfers in dairy systems under changing farming practices #INRAE #MaIAGE #UMRF #Holoflux

Meet Christelle Hennequet-Antier on July 8th at #JOBIM2025 at the poster session to talk about StatOmique: sharing experience on statistical analysis of omics data statomique.github.io #GDRBIMMM #Statistique #Omiquedata

L'unité MaIAGE via la plateforme #bioinformatique @inrae-migale.bsky.social participera au #JobFair de #JOBIM2025 Pensez à vous #inscrire via forms.gle/rFPD8aGKRSrW... pour participer aux #echanges❗

Meet Erwan Le Floch on July 9th at #JOBIM2025 at the poster session to talk about Data stewardship strategy of the Ferments du Futur grand challenge #fermentsdufutur @vloux.bsky.social @sophieschbath.bsky.social @inrae-migale.bsky.social

Meet Agnès Barnabé on July 9th at #JOBIM2025 at the poster session to talk about SIDURI: from an integrative information system to a user-friendly portal for data analysis #fermentsdufutur @vloux.bsky.social @sophieschbath.bsky.social @inrae-migale.bsky.social

On day 2, posters : 122 Large Language Models-driven Reconstruction of Sequence Read Archive Metadata for Cancer Research by Fiona Hak 120 Bridging gene-level and sequence-level pangenome graph to explore microbial diversity by Hanin Ali

Meet Hanin Ali on July 9th at #JOBIM2025 at the poster session to talk about Bridging gene-level and sequence-level pangenome graph to explore microbial diversity #INRAE #MaIAGE @guigau.bsky.social #UniversiteLille #CRIStAL @camillemrcht.bsky.social

@guigau.bsky.social Hanin Ali and @bdegardins.bsky.social discussing bacterial pangenome visualization

La @sfbi.fr arrive doucement mais sûrement à #bordeaux pour @jobim2025.bsky.social 🥰