epcrocha.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

In our latest review, we explore 12 deep-learning tools for metagenomic analysis, covering their strengths, limitations, and key applications. We hope it serves as both a resource and inspiration for new ways to analyze metagenomic data. Great work by Eli Levy Karin! 📄 doi.org/10.1093/nsr/...

submitted 3 days ago • 2 comments

Experimental evolution of evolvability | Science www.science.org/doi/10.1126/...

submitted 4 days ago • 0 comments

Our Opinion on the balance between horizontal and vertical transmission in plasmids and phages is up and looking pretty at Trends in Microbiology! Work with Andrina Bernhard and @claudiaigler.bsky.social

submitted 4 days ago • 0 comments

New paper out in ISME Journal. Social interactions between strains shape bacterial communities. However, their impact on community functioning is lower compared to basic strain identity features. @joskramer.bsky.social @alexfig.bsky.social @simonmarech.bsky.social academic.oup.com/ismej/advanc...

submitted 12 days ago • 0 comments

New version of DefenseFinder available defensefinder.mdmlab.fr (& cli) Now encompassing 263 systems (+111 this year..!). Thanks @ftesson.bsky.social, DefenseFinder grandmaster. Full list of systems here: defense-finder-models/List_system_article.md at master · mdmparis/defense-finder-models

submitted 6 days ago • 1 comment

I'm delighted to announce that the 2025 @microbiologysociety.org meeting on "Understanding and predicting microbial evolutionary dynamics" will be held in Liverpool 26-27 November 2025! Abstract submission will open soon... #microsky 🧪🧫🦠 microbiologysociety.org/event/societ...

submitted 6 days ago • 3 comments

ASM stands firm in its commitment to diversity, equity and inclusion, as such efforts are critical to advancing the microbial sciences for everyone. Read our statement: asm.org/Press-Releas...

submitted 10 days ago • 28 comments

Two more weeks to apply to join us in Paris ! research.pasteur.fr/en/call/call...

submitted 11 days ago • 0 comments

Imagine that you are a low-copy extra-chromosomal genetic elements invading a host cell. What’s your best strategy to survive? Check our new study of prokaryotic #plasmid for the answer! www.biorxiv.org/content/10.1... led by Johannes Effe with @iwangtoknow.bsky.social and more! (not on bsky)

submitted 12 days ago • 0 comments

New mechanism of gene transfer! With @tcostalab.bsky.social @imperialcollegeldn.bsky.social, we discovered that cf-PICIs form tail-less elements that, once released, spread among different bacterial species by hijacking tails from various phages. More exciting news soon! shorturl.at/kRJqE

submitted 12 days ago • 0 comments

Please repost: Postdoc position in AI for drug discovery in a large collaboration with Dominique Beaini, Audrey Durand, Alex Hernández-García, Anne Marinier at Université de Montréal and Montreal Institute for Learning Algorithms (MILA). www.linkedin.com/posts/yves-b...

submitted 13 days ago • 0 comments

#MicroSky #phagesky

submitted 14 days ago • 0 comments

Many years to get this one out, while gaining huge respect for people doing clinical trials (perseverance!). We show that antibiotic treatments spur changes in the phage composition of the human gut, with bursts of virulent phages that may facilitate homeostasis. Check Eugen's thread!👇

submitted 14 days ago • 0 comments

Super excited to finally present the preprint to accompany Kaptive 3 which we released last year! Big thanks to coauthors @kelwyres.bsky.social, @katholt.bsky.social, @genomarit.bsky.social and Iren Löhr. Here's what we did to improve in silico antigen typing 👇🧵 www.biorxiv.org/content/10.1...

submitted 16 days ago • 1 comment

We interrupt your regularly-scheduled chaos to bring you some cool microbiome science. 🦠 🖥️ 🧬 "Longitudinal phage–bacteria dynamics in the early life gut microbiome" now out in Nature Microbiology. We wanted a way to measure bacteria and phage in metagenomes 1/ www.nature.com/articles/s41...

submitted 20 days ago • 5 comments

Dot plots are an effective (if old school!) way to visualise the pairwise comparison of genomes. For our recent pangenomics project (rdcu.be/d8PZ7), I wrote a small Python package to produce publication ready dot plots. Check it out! github.com/drboothtj/do... pypi.org/project/dotp... 🧪🧬🦠

submitted 18 days ago • 0 comments

The 2nd conference of the Society for Mathematical and Theoretical Population Biology @smtpb.bsky.social will be in Chicago @nitmb.bsky.social June 2-6. Applications are now open, both to attend (junior applicants can apply for financial support), and to present, at www.nitmb.org/modeling-and...

submitted 17 days ago • 0 comments

Next Tuesday Clement Gilbert and myself will discuss impact and extent of HGT in both prokaryotes and eukaryotes! It will be broadcasted on France Culture (in French)

submitted 17 days ago • 0 comments

My brother posted this to Twitter - I had never seen it - he just got it this year Thinking of my dad on the Anniversary of his death by suicide x.com/mbeisen/stat...

submitted 17 days ago • 37 comments

Our latest work: how can compartmentalization emerge in a eukaryotic genome lacking canonical heterochromatin? By investigating bacterial genomes put in yeast, we show that the presence or absence of transcription is sufficient! #chromatin #3Dgenome #generegulation www.science.org/doi/10.1126/... 👇

submitted 17 days ago • 3 comments

🚨 Job alert 🚨 — are you interested in understanding how mobile genetic elements and defence systems shape bacterial genome evolution? 🧬 🧪 🧫 🦠 2x 5-year research positions available in experimental evolution @mermanchester.bsky.social Join us! #microsky www.jobs.manchester.ac.uk/Job/JobDetai...

submitted 18 days ago • 1 comment

This is our first message under a starry blue sky of phages. We are a group of phage addicts, we love phages in all aspects: genomics, evolution, interactions, applications ...

submitted 18 days ago • 0 comments

🚨 🧬 Updated preprint on the completed BASEL collection - what's new? Some fun with bacterial immunity and a new P22 relative infecting E. coli K-12. A thread 🧵

submitted 19 days ago • 4 comments

Happy to share our latest piece of work on the PARIS bacterial immune system. We performed a detailed characterization of the AriB Toprim nuclease, the effector of PARIS immunity. www.biorxiv.org/content/10.1...

submitted 19 days ago • 3 comments

We have an open position PhD position in a project aiming to develop novel methodologies for phylogenomic reconstruction of plasmid evolution. See details and how to apply in the Ad. Candidates who will review the relevant literature (see Ad) have a higher chance to write a successful application.

submitted 20 days ago • 0 comments

We have updated all Logan contigs (now at version 1.1)! Contiguity has been much improved (2x) and a duplicated k-mers bug has been fixed. More information and changelog here: github.com/IndexThePlan...

submitted 21 days ago • 1 comment

Would you expect that Bacteria use an archaellum for swimming? We didn't, but we found that some Chloroflexota do! Find the story here: www.biorxiv.org/content/10.1... A little thread below 1/n

submitted 21 days ago • 1 comment

Exciting to see our paper now published 🙌 www.science.org/doi/10.1126/... In this project co-led with @ostermanilya.bsky.social at @soreklab.bsky.social , we show that a bacterial immune system employs a TIR protein and a caspase-like protease, two typical immune components seen in eukaryotes. 🧵👇

submitted 24 days ago • 2 comments

Hello Everyone! 👋 Nucleic Acids Research is excited to be on Bluesky! Please follow us for the latest #Research, #Breakthrough articles, journal issues and more. Also, please consider adding us to your starter packs!

submitted 24 days ago • 0 comments

🚨 Keynotes at RECOMB-seq 2025! 🚨 🌟 Alicia Oshlack – computational transcriptomics @aliciao.bsky.social 🌟 Rayan Chikhi – sequencing data structures @rayanchikhi.bsky.social 🗓️ Dates: April 24–25, 2025 📍 Seoul, South Korea recomb-seq.github.io/speakers/

submitted 31 days ago • 0 comments

Our new paper out in mSystems! journals.asm.org/eprint/ISRAZ... We created a tool called MANIAC to estimate ANI between virus pairs. We found that: 1) MANIAC can reliably estimate ANI ~70%, 2) dsDNA phages exhibit ANI gap around 80%, 3) taxonomic assignment in temperate phages is tricky. Try it!

submitted 26 days ago • 2 comments

The contribution of natural transformation for the acquisition of novel genes has been notoriously difficult to quantify because it relies on recombination (which is affected by other processes). Here's a first estimate : doi.org/10.1101/2025... (for the very busy: 1-6% of gene gains) #MicroSky

submitted 28 days ago • 1 comment

BREAKING NEWS ‼️ Les 6️⃣ #keynote speakers pour #JOBIM2025 ont été sélectionnés ! A eux 6️⃣, nos orateurs et nos oratrices représentent un large panel des domaines de la bioinformatique, dans plusieurs villes de France ainsi que dans des pays voisins. 🤯 Parmi ces domaines, on compte : ⤵️

submitted 35 days ago • 1 comment

We are thrilled to share that our paper entitled "Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history" is officially out in MBE! academic.oup.com/mbe/advance-...

submitted 31 days ago • 2 comments

🚨 New preprint! We know that plasmids are associated with very variable fitness costs in their different bacterial hosts. But, what is the contribution of each of the plasmid-genes in these host-specific effects? Study led by @jorgesastred.bsky.social, @sanmillan.bsky.social and myself! 1/14

submitted 31 days ago • 4 comments

A collection of researchers working on bacterial defense and offense systems, including secretion systems, immunity mechanisms, bacterial warfare, and microbial arms races. Please share and let me know if you'd like to be added (or removed) from the list.

submitted 104 days ago • 26 comments

Deadline extended to 27th January!

submitted 34 days ago • 0 comments

This preprint makes a point that is valid for a lot of machine learning approaches. Organisms or genes are linked by evolutionary history; they are not independent. This results in correlation between learning and test sets, and often in over-optimistic evaluations of the methods' outcome.

submitted 37 days ago • 3 comments

🧬 Save the date! The EMBO Workshop "The Immune System of Bacteria" will uncover groundbreaking insights into bacterial defense systems. Join us April 8-10, 2025, at Institut Pasteur, Paris. Submit your abstracts by Feb. 28 👉 https://www.sisb2025.conferences-pasteur.org/home

submitted 39 days ago • 0 comments

ESKAPE pathogens are outsmarting us. Our latest paper in @naturemicrobiol.bsky.social reveals alarming ease of resistance evolution to antibiotics in development. Collaborative work with @csabapallab.bsky.social‬ and Kintses Lab

submitted 41 days ago • 0 comments

👋 Hi antiphage defense community, we are soon releasing an update of DefenseFinder. We are doing our best to include all the great discoveries from the community, but with so much going on we might miss things. Please answer wt preprints/papers with new systems or mail/git them to us. 🙏

submitted 42 days ago • 3 comments

🚨 Excited to share that our new study, “ESKAPE pathogens rapidly develop resistance against antibiotics in development in vitro” is published in @naturemicrobiol.bsky.social. For details, see the 🧵below and read the paper here: www.nature.com/articles/s41...

submitted 42 days ago • 1 comment

"The pathway to resolve dimeric forms distinguishes plasmids from megaplasmids in Enterobacteriaceae | Nucleic Acids Research | Oxford Academic" academic.oup.com/nar/article/...

submitted 42 days ago • 0 comments

Our paper on 🦠queuosine 34 modification of tRNA tyrosine and antibiotic response is finally out in its final form in @eLife ... and quite different from the preprint version. Many thanks to reviewers, editors and kudos to all authors🙏 elifesciences.org/articles/96317

submitted 43 days ago • 4 comments

🚨PhD studentship opportunity! Bacteria protect themselves with a huge arsenal of defences, but does this affect how they gain new traits on plasmids? 🧫🦠💫 Apply for a funded 4y position with me @livuni-ives.bsky.social, @brockhurstlab.bsky.social @jojofoth.bsky.social & @multidefence.bsky.social ⬇️

submitted 45 days ago • 2 comments