Louis-Marie Bobay

Version 1.3.2 of PearTree released: github.com/artic-networ... Fixes many of the remaining niggling bugs. WebApp updated at peartree.live

How fast can speciation be? In less than 100 years, certain strains of lab mice have already (partly) lost the ability to hybridize with each others. The molecular mechanism has just been worked out - read below for a genetics detective story ⬇️

🧪 "Mr. Trump’s science adviser, Michael Kratsios, has criticized the agency’s system for deciding which grants to fund ... He also argued the N.S.F. should ... bypass external review panels.” Kratsios lost 90% of assets while CFO of Clarium Capital. Do you trust him with the US science portfolio?

Interested in #archaea, #methane, #cell-envelopes? New paper out @nature.com ! We discovered an enzyme that specifically cleaves the cell wall of methanogens, revealing a new chemical structure of archaeal peptidoglycan, 50 yrs after its first description www.nature.com/articles/s41... #MicroSky 🧵👇

Excited that our new paper with @henrylabsymbio.bsky.social and Kerry Oliver is out @pnas.org! We show that mobile genetic elements can spread adaptive host-benefiting traits across heritable insect symbionts on eco-evolutionary timescales.🧵 www.pnas.org/doi/10.1073/...

New paper from the lab, out in Nature Microbiology. We ran CRISPRi screens to ask what genes E. coli needs in order to live in a gut and what this can tell us about the gut environment itself. https://doi.org/10.1038/s41564-026-02471-8

Now published from a fun collaboration, please see 🧵 academic.oup.com/ismecommun/a...

Dear all, I have the pleasure to inform you that the online course "Resistance to Antibacterial Agents", produced by the Institut Pasteur, will start on November 3, 2026. How does ABR emerge and spread? ... 🔗 www.fun-mooc.fr/en/courses/r...

1/17 Submissions are now open for the 2027 Microbial Population Biology GRC! We expect this meeting to be extraordinarily oversubscribed. If you want to come, time is of the essence--apply ASAP! June 27–July 2 • Andover, NH www.grc.org/microbial-po...

UNC Greensboro Department of Biology is hiring for three positions this year including one in microbiology! spartantalent.uncg.edu/postings/35918

Now published in @asm.org mSystems! journals.asm.org/doi/10.1128/...

Characterizing the ecological niche of insertion sequences within prokaryotic genomes academic.oup.com/ismej/advanc... #jcampubs

Scott Gilbert made a useful critique of our preprint, which we have replied to: doi.org/10.32942/X2W...

Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them academic.oup.com/gbe/article/...

We are actively searching for a postdoc to join the lab! Details provided here - johrilab.org/join Please share. I will be at PEQG and will be happy to chat if you're interested!

New paper about zero-shot predictions of mutational effects. There's a lot of misunderstanding about what such predictions can and cannot do. In brief, they're good at identifying deleterious mutations but bad at predicting fitness improvements. 1/ www.biorxiv.org/content/10.6...

Our preprint, where we infer the fitness effects of new mutations in regulatory regions of the D. melanogaster genome. We find an abundance of weakly deleterious effects - www.biorxiv.org/content/10.6... Led by @adaigle.bsky.social .

Very happy to announce a big new paper from the lab, led by grad students @smishra677.bsky.social and Laia Pomar-Pallarès (in collaboration with @roblanfear.bsky.social). We introduce a new way to study introgression, with accompanying software (DAFT) 1/n 🧵 www.biorxiv.org/content/10.6...

Andy Kern, who doesn't (really) have an account here, would like to share his group's new tool for speeding up pop gen summary stat calculations using GPUs. Check it out here: www.biorxiv.org/content/10.6... And see his thread over at the other place: x.com/pastramimach...

I’m excited to share a new paper out today led by Dr. Younghwan Kwak. Cool story on symbiont genomic variation within individual hosts. (And, also, just an impressive display of -omics skill). academic.oup.com/mbe/advance-...

If you would like the government to know what you think about their proposal to put federal science funding, communication, and travel under strict political control, you can tell them in the public comment section here: www.regulations.gov/commenton/OM...

#ERGAReads | How Did Evolution Halve Genome Size During an Oceanic Island Colonization? 🏝️ 🧬 🕷️ academic.oup.com/mbe/article/... #genomes #evolution #islandevolution #biology @molbioevol.bsky.social @ub.edu @jrozasub.bsky.social

Check out this very nice piece by @gmdouglas.bsky.social and S. Andrew Inkpen. ecoevorxiv.org/repository/v...

A very important preprint to check out: The holobiont is not a useful model for most host-microbiome interactions By Gavin M Douglas an S. Andrew Inkpen ecoevorxiv.org/repository/v...

Very excited to share our new paper out in Nature. Congrats to Xiaoqian (Annie) Yu and all the coauthors. www.nature.com/articles/s41...

IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...

Super excited to share our lab's work led by PhD student Margot Ruffieux on domestication of Saccharomyces cerevisiae, with a focus on sourdough and baking associated yeast! 🍞

Please circulate: I will have a postdoc opening soon, ideally with a start date sometime this summer or fall. If you're interested in empirical population genetics, computational methods development, and/or evolutionary modeling via simulation, don't hesitate to reach out. For more info on the lab:

Diversity-generating retroelements for programmable targeted hypermutagenesis - @dbikard.bsky.social @institutpasteur.bsky.social go.nature.com/3OG2nKN

I am excited to share our latest paper, Uniform bacterial genetic diversity along the gut, now out in Nature Communications! www.nature.com/articles/s41.... (1/n)

Horizontal gene transfer is often depicted as a process distributing pre-existing functions to novel genetic backgrounds. Yet HGT can also increase the rate of functional innovation after transfer. Here's a brief review on the topic: ecoevorxiv.org/repository/v... #evosky #microsky

New preprint where @lbobay.bsky.social and I were motivated by the fact that non-synonymous substitutions are commonly analyzed in molecular evolution studies, but the similarity of the amino acids being substituted is an understudied area. doi.org/10.64898/202...

New paper showing that much of the apparent success of protein language models in predicting mutational effects is a mirage: These models mostly memorize sites. 1/ www.biorxiv.org/content/10.6...

➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔 🧵👇

If you are interested in investigating horizontal gene transfer by phages and virus-like particles using computational approaches, this postdoc position in the Callahan Lab could be for you jobs.ncsu.edu/postings/226...

I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.

@carolinamicro.bsky.social Huang & @lbobay.bsky.social investigated genomic rearrangements across 121 microbial species, showing that rearrangements occur at a variable pace across bacteria and archaea, pointing to different selective constraints. 🔗 doi.org/10.1093/gbe/evag002 #genome #evolution

Now out & nicely formatted in @isme-microbes.bsky.social A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron. A few highlights... 🧵 (1/n) doi.org/10.1093/isme...

Aude Bernheim @audeber.bsky.social and Eugene Koonin discuss one of most interesting questions in the field connecting bacterial and animal immunity! www.nature.com/articles/s41...

My book is available for pre-order! www.routledge.com/Quantitative... Or you can request an inspection copy here: www.routledge.com/textbooks/ev...

🚨 Hiring Alert! 🚨My lab at Institut Pasteur is recruiting several Postdocs! We have exciting open projects in: 🦠 Synthetic Biology and🛡️ Bacterial Immunity. Come do great science with us in the middle of Paris! 🇫🇷🥐 research.pasteur.fr/en/job/postd...

Congrats to @carolinamicro.bsky.social for leading this study! We looked at genome rearrangements over short evolutionary timescales. Among other things, we found that genomes are highly syntenic within most species. However, several bacteria experienced sudden and massive genome rearrangements.

🥁 NEW Our study on infant gut microbiome and #straintransmission is now published in @nature.com: doi.org/10.1038/s415... 1/10

I’m excited to share a new paper by a super talented graduate-student-now-postdoc. Grateful to work with old and new collaborators! Characterizing a novel Symbiopectobacterium MEX strain at the early stages of establishing a symbiotic relationship url: academic.oup.com/gbe/article/...