@xavierdidelot.bsky.social et al. present the R package DiagnoDating for diagnosing issues in a reconstructed dated phylogeny, including outlier detection, posterior predictive checking, and residual analysis. 🔗 doi.org/10.1093/molbev/msag093 #evobio #molbio #compbio #phylogeny

🔈Paper out! We turned the most fascinating phage host-switch mechanism, diversity-generating retroelements, into a programmable mutagenesis tool, DGRec. You can perform targeted hypermutation of any 50-200bp sequence directly in vivo in E. coli www.nature.com/articles/s41...

FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social. 📄 www.science.org/doi/10.1126/... 🌐 search.foldseek.com/foldmason 💾 github.com/steineggerla...

Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...

L’Union européenne capitule pour éviter une guerre commerciale avec Trump Par @romaricgodin.bsky.social

Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...

1/8 - New in @natcomms.nature.com ! ☣️ Meet Yersinia enterocolitica (Ye) — a lesser-known but still dangerous cousin of Yersinia pestis. We uncover how this invasive pathogen can survive and adapt for 14 years inside a human host under constant antibiotic pressure 👇 www.nature.com/articles/s41...

Excited to share this preprint focused on the genomic taxonomy of C. diphtheriae #diphtheria ➡️ www.biorxiv.org/content/10.1... Hope it helps advance research and surveillance of this relevant bacterial pathogen. Thanks to @sylvainbrisse.bsky.social and BEBP and BIGSdb teams for making it possible!

Avis aux amateurs : France Travail propose environ 12 millions d'euros pour lui développer un "agent conversationnel" pour échanger avec les demandeurs d'emplois par SMS. www.boamp.fr/pages/avis/?...

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

RAxML-NG v2.0 beta is here github.com/amkozlov/rax... Features 1. Difficulty prediction academic.oup.com/mbe/article/... 2. Adaptive search academic.oup.com/mbe/article/... 3. Early Stop www.biorxiv.org/content/10.1... 4. Model selection 5. Rapid bootstrapping academic.oup.com/mbe/article/...

Au même moment, les agences fédérales de la Défense ont reçu ordre d'annuler toutes activités autour de 11 évènements annuels sur la diversité américaine, dont le Black History Month, le Women History Month, la LGBT Pride Month, le Holocaust Remembrance Day... www.nbcnews.com/politics/don...

Donald Trump lance sa guerre commerciale mondiale Par Martine Orange

Le groupe TotalEnergies fait des dons à l’université de Strasbourg, notamment pour l’école de chimie. Une convention de mécénat dévoile l’emprise que la multinationale souhaite établir dans l’enseignement supérieur et la recherche. https://www.mediapart.fr/journal/france/310125/strasbourg-contre-so…

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

La conversion de tout le secteur de la technologie au trumpisme est le fruit de son modèle économique. Pour poursuivre sa logique prédatrice, il a trouvé dans l’extrême droite un débouché politique utile. https://www.mediapart.fr/journal/economie-et-social/190125/les-big-tech-basculent-l-extreme-dr…

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.

L'équipe de Mediapart arrive progressivement sur Bluesky Les comptes à suivre sont dans notre starter pack 👇 go.bsky.app/5ueP6wM

University websites are like distant stars, when you look at them you see the scientists as they used to be many years ago

First paper from my student Daria Frolova's PhD now on biorxiv: www.biorxiv.org/content/10.1... The key question: plasmids change structurally ~as fast as they mutate, so how can we decide whether 2 plasmids are "the same plasmid" for epi purposes? 1/n

New paper from the lab, the mysteries involving the genetic elements that move by being mobilized by other MGEs. Hitcher Genetic Elements are distinctive, ancient and diverse. ecoevorxiv.org/repository/v...

New job offer: we search a postdoc (bioinformatics) to work on mobile genetic elements and gene flow in bacteria, with a focus on antibiotic resistance within a consortium including bioinformatics, synthetic biology, epidemiology & biochemistry. See research.pasteur.fr/en/job/postd... #MicroSky

New preprint out now - stable bacterial strain nomenclature with Life Identification Numbers using a gene-by-gene approach. From our wonderful collaborators at the Institut Pasteur. www.biorxiv.org/content/10.1...

First step in a community project to provide a uniformly assembled, annotated and searchable set of bacterial genomes, our preprint on our initial release of 1.9 million genome assemblies+taxonomic estimates. (figure compares with previous 661k dataset) www.biorxiv.org/content/10.1... #microsky

Our latest work is finally out! How #capsule serotypes of #Klebsiella pneumoniae influences #phage adsorption and infection, and #plasmid conjugation efficiency. Plasmids care about size-phages dont! Great work led by Matthieu Haudiquet in the lab @epcrocha.bsky.social doi.org/10.1038/s414...

I recently made a comic complaining that NASA refuses to listen to my good ideas for improving the Solar System (xkcd.com/2750). To my delight, NASA’s Science Mission Directorate has sent me an actual expert panel evaluation of my “flatten the planets” proposal! Sadly, they decided not to fund it.

New from the lab. We were stuck studying plasmid mobility because we ignored most origins of transfer by conjugation. Using the occurrences of known oriT, we developed a method to find novel unrelated families. Works well. We now cover most conjugative plasmids of E coli, K pneumo & A baumannii.

Oh non ! James Herbert Brennan, l'auteur de l'incroyable cycle Quête du Graal des Livres Dont Vous Êtes Le Héros, s'en est allé rejoindre le funestre paragraphe 14 à l'âge de 83 ans. Il laisse derrière lui une génération de jeunes Pip endeuillés. RIP :'( rip.ie/death-notice...

The paper is "Pseudogenes act as a neutral reference for detecting selection in prokaryotic pangenomes"! (I was excepting a thumbnail of the link address to appear, but apparently I have much to learn about BlueSky!)

"REPLAY" will make the jump from French to English on March 19, 2024! www.jordanmechner.com/en/books/rep... Un grand merci to everyone who shared the adventure in 2023. Happy New Year! #bandedessinee #graphicnovel #retrogaming #videogames #gamedev #memoir

"BATH matches the accuracy of HMMER3 for annotation of sequences containing no errors, and produces superior accuracy to all tested tools for annotation of sequences containing nucleotide indels."

Fully automated assessment of correlated evolution on phylogenetic trees: now out in OA: doi.org/10.1111/2041... Thanks to all authors (not yet here). This explains the methodological basis of our recent work on epistatic interactions in the evolution of quinolone resistance: doi.org/10.1093/molb...

This website is brilliant: an interactive look at what video games boxes looked like “back in the day”, and all the good stuff you got inside! (by the way, I’m still looking to complete my collection of Ultima boxes, if you have some)

Here is Hybracter, our tool for generating automated hybrid & long-read-only bacterial genome assemblies. Github: github.com/gbouras13/hy... Docs: hybracter.readthedocs.io/en/latest/ Preprint: www.biorxiv.org/content/10.1... @npbhavya.bsky.social @linsalrob.bsky.social #Microsky

New postdoc position in our lab for a project led by Marie Touchon (bioinformatics) and with O Tenaillon (experiments) on the evolution and dynamics of microbial genomes to understand their diversification by gene flow. Check research.pasteur.fr/en/job/postd...