Guillaume GAUTREAU
guigau.bsky.social
Guillaume GAUTREAU
@guigau.bsky.social
PhD in #CompBio. (Meta/Pan)genomics. Health Law. GDPR compliance.
http://orcid.org/0000-0002-0970…
INRAE scientist at MaIAGE.
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!
JC2B 2025 - Junior Conference of Computational Biology - 13 novembre 2025
JC2B 2025 - Junior Conference of Computational Biology - 13 novembre 2025
The students of the Computational Biology M.Sc. of Paris-Saclay (AMI2B) are delighted to organize and invite you to the Junior Conference on Computational Biology (JC2B) that will be held on November 13, 2025 at I2BC CNRS, Gif-sur-Yvette.   Paris-Saclay Junior Conference on Computational Biology Round 2025: AI and predictive models in bioinformatics November 13, 2025 — 9am to 5pm I2BC, CNRS : 91190 Gif-sur-Yvette — Auditorium Bat. 21   The Junior Conference aims to bring together the community of computational biology (Master students, PhD students, PostDocs, senior researchers, and industry professionals) from different institutions.   Selected participants will present research conducted in two main fields: Structures and Evolution and Genomics and Health. The conference also fosters discussions between participants, encourages idea sharing, and promotes collaborations. Additionally, a roundtable session will be organized for those seeking internships, traineeships, or information about Master programs.   On the program, two keynote speakers on AI and predictive models in bioinformatics: Morning session: AI applications in Structure and Evolution: Laurent Jacob (Laboratory of Computational and Quantitative Biology — CNRS, Sorbonne Université) Afternoon session: Predictive Modeling in Genomics and Health: Magali Richard (Laboratory of Translational Research and Innovation in Medicine and Complexity — CNRS, Université Grenoble Alpes)   More selected abstract presentations from participants are to be announced.   Registrations to participate are now open until October 20, 2025.   Please note that registration is mandatory whether you are presenting an abstract or attending as a participant. For more information about the full program, check the JC2B webpage.
sco.lt
November 13, 2025 at 7:30 PM
Reposted by Guillaume GAUTREAU
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.
The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals - Communications Biology
Co-abundance analysis of 938 healthy individuals uncovers how host factors shape gut microbiome interactions, highlighting a core set of 200 impacted genera and additional factor-specific interactions...
www.nature.com
November 10, 2025 at 5:00 PM
Reposted by Guillaume GAUTREAU
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
Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2 - Microbiome
Background The characterization of complex microbial communities is a critical challenge in microbiome research, as it is essential for understanding the intricate relationships between microorganisms...
microbiomejournal.biomedcentral.com
November 6, 2025 at 4:38 PM
Reposted by Guillaume GAUTREAU
Seqwin: Ultrafast Identification of Signature Sequences in Microbial Genomes https://www.biorxiv.org/content/10.1101/2025.11.07.687294v1
November 10, 2025 at 3:48 AM
Reposted by Guillaume GAUTREAU
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.
I've often wondered about what we should call organisms whose similarity might be due to acquired genetic material. It got a little complicated, but I made a stab at it here

Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes academic.oup.com/mbe/article/...
Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes
Abstract. The classification of living systems presents significant challenges due to the prevalence of gene transfer between genomes. Traditional taxonomi
academic.oup.com
October 30, 2025 at 11:36 AM
Reposted by Guillaume GAUTREAU
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-...
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes
Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy
academic.oup.com
October 22, 2025 at 2:20 PM
Reposted by Guillaume GAUTREAU
Bravo !
Après six-ans (à mi-temps), bientôt plus #étudiant !

www.instagram.com/p/DP6FgQRitUJ/
October 17, 2025 at 11:14 AM
Reposted by Guillaume GAUTREAU
Après six-ans (à mi-temps), bientôt plus #étudiant !

www.instagram.com/p/DP6FgQRitUJ/
October 17, 2025 at 10:51 AM
Reposted by Guillaume GAUTREAU
Strainify: Strain-Level Microbiome Profiling for Low-Coverage Short-Read Metagenomic Datasets https://www.biorxiv.org/content/10.1101/2025.10.10.681738v1
October 13, 2025 at 11:47 PM
Reposted by Guillaume GAUTREAU
Efficient and accurate search in petabase-scale sequence repositories www.nature.com/articles/s41... 🧬🖥️🧪
MetaGraph: metagraph.ethz.ch
Code: github.com/ratschlab/me...
October 9, 2025 at 5:10 PM
Reposted by Guillaume GAUTREAU
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
October 1, 2025 at 10:47 PM
Reposted by Guillaume GAUTREAU
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
September 10, 2025 at 9:12 AM
Reposted by Guillaume GAUTREAU
kSanity: A k-mer based application forprecision bacterial strain detection andquantification https://www.biorxiv.org/content/10.1101/2025.09.04.674052v1
September 9, 2025 at 2:48 PM
Reposted by Guillaume GAUTREAU
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...
Clustering of plasmid genomes for genomic epidemiology by using rearrangement distances, with pling
Integration of plasmids into genomic epidemiology is challenging, because there are no clearly defined evolving-units (equivalent to species), and because plasmids appear to evolve as much by structur...
www.biorxiv.org
September 7, 2025 at 2:56 PM
Reposted by Guillaume GAUTREAU
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
High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
September 7, 2025 at 11:35 PM
Reposted by Guillaume GAUTREAU
Clustering of plasmid genomes for genomic epidemiology by using rearrangement distances, with pling https://www.biorxiv.org/content/10.1101/2025.09.02.673752v1
September 7, 2025 at 3:48 AM
Reposted by Guillaume GAUTREAU
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
September 7, 2025 at 3:48 AM
Reposted by Guillaume GAUTREAU
High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
September 7, 2025 at 4:47 AM
Reposted by Guillaume GAUTREAU
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
August 26, 2025 at 3:47 AM
Reposted by Guillaume GAUTREAU
AEMB: a computationally efficient abundance estimation method for metagenomic binning https://www.biorxiv.org/content/10.1101/2025.07.30.667338v1
August 2, 2025 at 3:47 AM
Reposted by Guillaume GAUTREAU
Building pangenomes for domesticated and wild tree species: genomic complexity and strategies https://www.biorxiv.org/content/10.1101/2025.07.22.665893v1
July 26, 2025 at 3:47 AM
Reposted by Guillaume GAUTREAU
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
July 17, 2025 at 4:47 PM
Reposted by Guillaume GAUTREAU
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
July 23, 2025 at 8:20 AM
Reposted by Guillaume GAUTREAU
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
Metagenomic-scale analysis of the predicted protein structure universe
Protein structure prediction breakthroughs, notably AlphaFold2 and ESMfold, have led to an unprecedented influx of computationally derived structures. The AlphaFold Protein Structure Database now prov...
www.biorxiv.org
July 22, 2025 at 9:10 AM