Guillaume GAUTREAU
@guigau.bsky.social
200 followers 440 following 27 posts
PhD in #CompBio. (Meta/Pan)genomics. Health Law. GDPR compliance. http://orcid.org/0000-0002-0970… INRAE scientist at MaIAGE.
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Reposted by Guillaume GAUTREAU
biorxiv-bioinfo.bsky.social
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
Reposted by Guillaume GAUTREAU
zaminiqbal.bsky.social
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...
Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology
LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.
www.nature.com
Reposted by Guillaume GAUTREAU
biorxiv-bioinfo.bsky.social
kSanity: A k-mer based application forprecision bacterial strain detection andquantification https://www.biorxiv.org/content/10.1101/2025.09.04.674052v1
Reposted by Guillaume GAUTREAU
jimshaw.bsky.social
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
biorxiv-bioinfo.bsky.social
High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
Reposted by Guillaume GAUTREAU
biorxiv-bioinfo.bsky.social
Clustering of plasmid genomes for genomic epidemiology by using rearrangement distances, with pling https://www.biorxiv.org/content/10.1101/2025.09.02.673752v1
Reposted by Guillaume GAUTREAU
biorxiv-bioinfo.bsky.social
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
Reposted by Guillaume GAUTREAU
biorxivpreprint.bsky.social
High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
Reposted by Guillaume GAUTREAU
biorxiv-bioinfo.bsky.social
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
Reposted by Guillaume GAUTREAU
biorxiv-bioinfo.bsky.social
AEMB: a computationally efficient abundance estimation method for metagenomic binning https://www.biorxiv.org/content/10.1101/2025.07.30.667338v1
Reposted by Guillaume GAUTREAU
biorxiv-bioinfo.bsky.social
Building pangenomes for domesticated and wild tree species: genomic complexity and strategies https://www.biorxiv.org/content/10.1101/2025.07.22.665893v1
Reposted by Guillaume GAUTREAU
biorxivpreprint.bsky.social
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
Reposted by Guillaume GAUTREAU
feargalr.bsky.social
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 🤣
TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases
Abstract. Microbial communities are essential regulators of ecosystem function, with their composition commonly assessed through DNA sequencing. Most curre
academic.oup.com
Reposted by Guillaume GAUTREAU
Reposted by Guillaume GAUTREAU
biorxiv-bioinfo.bsky.social
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
Reposted by Guillaume GAUTREAU
biorxiv-bioinfo.bsky.social
The MicrobeAtlas database: Global trends and insights into Earth's microbial ecosystems https://www.biorxiv.org/content/10.1101/2025.07.18.665519v1
Reposted by Guillaume GAUTREAU
inrae-maiage.bsky.social
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
Logo RITHMS
Reposted by Guillaume GAUTREAU
inrae-maiage.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.
Reposted by Guillaume GAUTREAU
bdegardins.bsky.social
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...
camillemrcht.bsky.social
@guigau.bsky.social Hanin Ali and @bdegardins.bsky.social discussing bacterial pangenome visualization
Reposted by Guillaume GAUTREAU
camillemrcht.bsky.social
Super proud that @bdegardins.bsky.social and Fiona Hak earned a Mini-symposium prize for the presentation and poster award at #JOBIM2025 🎉🏆
Reposted by Guillaume GAUTREAU
jobim2025.bsky.social
👏 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 ⤵️
Photo de groupe prise avec les participants et participantes à JOBIM 2025.
Reposted by Guillaume GAUTREAU
sfbi.fr
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
jebif.bsky.social
Une vraie réussite pour les premiers #jobFAIR organisés par @jebif.bsky.social et la @sfbi.fr dans le cadre de @jobim2025.bsky.social 🎯

Une occasion unique de rencontrer des professionnels de la #bioinformatique 🧬

Rdv demain !

#JOBIM2025
Reposted by Guillaume GAUTREAU
inrae-maiage.bsky.social
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
Logo Whooper