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Sophie Abby

@soabby.bsky.social
831 followers 287 following 25 posts

Researcher at CNRS, TIMC lab, Grenoble France compBio@TrEE group tree-timc.github.io/compbio Archaea & Bacteria Evolution Comparative genomics and Phylogenomics Evolution of Cellular machineries & Metabolic pathways sophieabby.github.io

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Reposted by Sophie Abby
Simonetta Gribaldo @sgribaldo.bsky.social · 23/09/2026
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 🧵👇
nature.com
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Cascales Lab @cascaleslab.bsky.social · 11/09/2026
New paper in Current Biology @currentbiology.bsky.social 🦠 Why do bacteria ditch their T6SS weapon? E. coli keeps it vs susceptible rivals, but loses it when facing immune ones. Great work by @bobytaillefer.bsky.social & Jonas Desjardins! www.cell.com/current-biol...
cell.com
Experimental evolution reveals genetic routes for adaptive loss of the antibacterial type VI secretion system
Taillefer et al. show that a bacterial type VI secretion system is lost or attenuated during experimental evolution when it provides no competitive advantage but is maintained in the presence of susce...
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Reposted by Sophie Abby
Flora Gaudillière-Jami @fgaudilliere.bsky.social · 07/09/2026
Our paper is now out in the @isme-microbes.bsky.social Journal (and selected as editor's choice)! We use an ecological framework to analyze the distribution of small transposable elements in over 30,000 prokaryotic genomes, characterizing their genomic niche doi.org/10.1093/isme...
doi.org
Characterizing the ecological niche of insertion sequences within prokaryotic genomes
Abstract. Insertion sequences (ISs) are widespread prokaryotic transposable elements, often regarded as genomic parasites that primarily cause deleterious
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Société Française de BioInformatique @handle.invalid · 03/09/2026
Une rentrée sur les chapeaux de roue pour la #SFBI qui participe aux Assises pour l'Université et la Recherche à Paris Les Assises s'ouvriront ce 3/09 par un colloque retransmis sur Youtube live : - 3/09 : youtu.be/VYGd2ilBcXE - 4/09 : youtu.be/mDXmhOGV5os Programme : agorasur.fr/assises-pour....
youtu.be
Les assises de la recherche 3 septembre
YouTube video by Politique Des Sciences
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Daniel Tamarit @danieltamarit.bsky.social · 22/05/2026
I'm looking for an enthusiastic student to join my team as a PhD candidate on archaeal genome evolution 🦠💻 Work in beautiful Utrecht, at @binfutrecht.bsky.social, an international group full of caring, amazing scientists, and with frequent cake breaks! www.uu.nl/en/organisat... Please share! 🙏
uu.nl
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Cameron Thrash @jcamthrash.bsky.social · 13/07/2026
Characterizing the ecological niche of insertion sequences within prokaryotic genomes academic.oup.com/ismej/advanc... #jcampubs
academic.oup.com
Characterizing the ecological niche of insertion sequences within prokaryotic genomes
Abstract. Insertion sequences (ISs) are widespread prokaryotic transposable elements, often regarded as genomic parasites that primarily cause deleterious
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Reposted by Sophie Abby
Archaea Biology Vienna @archaea-vienna.bsky.social · 03/07/2026
lewi.univie.ac.at/news-events/...
lewi.univie.ac.at
Christa Schleper elected to the National Academy of Sciences Leopoldina
The German National Academy of Sciences Leopoldina has announced the election of Christa Schleper as a new member in recognition of her outstanding contributions to scientific research. Schleper is a ...
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Sophie Abby @soabby.bsky.social · 03/07/2026
Glad to see it finally out in #mSystems @asm.org! 🥳 See the thread below to read what it is about! journals.asm.org/doi/10.1128/...
journals.asm.org
Global distribution of isoprenoid quinones across Bacteria | mSystems
Isoprenoid quinones are small electron-carrying molecules found in the membranes of organisms that produce energy through photosynthesis or respiration and participate in other important cellular processes. Recent advances in the characterization of their biosynthesis pathways enable their automated annotation from genome analyses. In this article, we performed the genomic analysis of over 26,000 cultured and uncultured bacteria, which was complemented by literature data compiled on over 6,000 cultured bacteria. This enabled us to provide an unprecedented overview of quinone distribution across the bacterial diversity. Creating such a comprehensive data set revealed new information about quinone distribution and evolutionary paths and will facilitate future exploration of various aspects of quinone biology, including their role in the evolution and diversification of bacterial metabolism.
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Michael Sieber @michaelsieber.bsky.social · 01/07/2026
Have ideas for your own, independent research program in Theoretical Biology? Then come and join us as a Group Leader at the @mpi-evolbio.bsky.social in Plön, Germany!
mpg.de
Group Leader in Theoretical Biology (m/f/d)
Experience in Theoretical Biology, Applied Mathematics, Theoretical Physics
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RSG France - JeBiF @jebif.bsky.social · 11/06/2026
🚀 Tu es bioinformaticien·ne (ou en train de le devenir) et tu te poses des questions sur ton avenir pro ? JeBiF vous propose son workshop, une journée dédiée à 𝗹𝗮 𝗽𝗹𝗮𝗰𝗲 𝗱𝗲𝘀 𝗷𝗲𝘂𝗻𝗲𝘀 𝗯𝗶𝗼𝗶𝗻𝗳𝗼𝗿𝗺𝗮𝘁𝗶𝗰𝗶𝗲𝗻·𝗻𝗲·𝘀 𝗱𝗮𝗻𝘀 𝗹𝗲 𝗺𝗼𝗻𝗱𝗲 𝗽𝗿𝗼𝗳𝗲𝘀𝘀𝗶𝗼𝗻𝗻𝗲𝗹. ⚠️ Places limitées 👉 beta.jebif.fr/event/6
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Cascales Lab @cascaleslab.bsky.social · 08/05/2026
T2SS ? T4SS ? CDI ? T6SS ? T7SS ? NO ! The T9SS is also involved in interbacterial competition !! Great work by Maelle Paillat @maellepllt.bsky.social under the supervision of Thierry Doan @thicoz.bsky.social Congratulations to both ! Glad to see this story out !
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Sophie Schbath @sophieschbath.bsky.social · 30/04/2026
PCI statistics & machine learning statml.peercommunityin.org
statml.peercommunityin.org
PCI Statistics and Machine Learning
Peer Community in Statistics and Machine Learning
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Courtney Stairs @cstairs.bsky.social · 11/04/2026
We stumbled upon an unusual gene called 'rqua' in the genome of some freshwater sponges. In microbes, this gene confers the ability to make a ubiquinone analog - rhodoquinone - which can help the respiratory chain run without oxygen.
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Société Française de BioInformatique @handle.invalid · 31/03/2026
🧐 Baisse du nombre d'offres d'emploi (post-doctorants, ingénieurs, permanents ou temporaires) en 2025. 🫵 Besoin de vous pour comprendre les raisons de cette diminution via ce sondage : grist.numerique.gouv.fr/o/docs/forms... 📎 Bilan plus détaillé : www.sfbi.fr/blog/article...
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Reposted by Sophie Abby
Joel Pick @joelpick.bsky.social · 19/03/2026
I'm excited to announce that the @sortee.bsky.social Guidelines for Data and Code Quality Control in Ecology and Evolutionary Biology are now published in Peer Community Journal peercommunityjournal.org/articles/10....
peercommunityjournal.org
The SORTEE guidelines for data and code quality control in ecology and evolutionary biology
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CNRS Biologie @cnrsbiologie.bsky.social · 20/03/2026
#ResultatScientifique🔎| Comment des processus géologiques pourraient-ils avoir favorisé l’apparition de la vie sur Terre ? ✍️ Simon Duval 👋 @cnrs-dr12.bsky.social @univ-amu.fr 📕 @natcomms.nature.com ▶️ buff.ly/BIh13pB
buff.ly
Aux origines de la vie : des « membranes » minérales capables de convertir l’énergie
Comment des processus géologiques pourraient-ils avoir favorisé l’apparition de la vie sur Terre ?
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Eduardo Rocha @epcrocha.bsky.social · 17/03/2026
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
ecoevorxiv.org
From Trading Genes to Crafting New Tricks: How Horizontal Gene Transfer Potentiates the Emergence of Novel Functions
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Vicky Lioy @vslioy.bsky.social · 11/03/2026
Are you investigating the biology of prokaryotic or eukaryotic cells? Are you looking for an excellent scientific environment to establish and lead your own research team? The I2BC is your place and a new call for team leaders is now open. More info👇Deadline 22nd April @i2bcparissaclay.bsky.social
i2bc.paris-saclay.fr
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Tatiana Giraud @tatianagiraud.bsky.social · 07/03/2026
La Biodiversite en Infographies sort ce jeudi 12 mars! Pour comprendre l'effondrement du vivant, pourquoi c'est un grave problème et ce qu'on peut faire de vraiment efficace, avec des données scientifiques représentées clairement..aux editions Tana
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Stephan Köstlbacher @stephkoe.bsky.social · 05/03/2026
🧵 1/10 New paper out in @natmicrobiol.nature.com from my postdoc at @mib-wur.bsky.social! 🎉 How eukaryote-like was the archaeal ancestor of eukaryotes? Sequence searches alone can't tell us — so we used protein structure prediction to look deeper. 🧬 www.nature.com/articles/s41...
nature.com
Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling - Nature Microbiology
A structural catalogue of the Asgard archaeal pangenome reveals hundreds of eukaryotic-like proteins that suggest a higher degree of cellular complexity in the archaeal ancestor of eukaryotes.
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Eduardo Rocha @epcrocha.bsky.social · 03/03/2026
Fantastic collaboration w/ @dbikard.bsky.social @audeber.bsky.social @rayanchikhi.bsky.social labs led by @jmouradesousa.bsky.social : We assessed the rates of variation of anti-phage systems in P4-like satellites and P2 helper phages. Quick conclusion: Huge variation! We focus on 4 key questions/5
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Niko Leisch @nikobiota.bsky.social · 24/02/2026
The best stories are the personal ones. So before we get to the new preprint, stay awhile and listen #MobileLabs #TREC
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Cameron Thrash @jcamthrash.bsky.social · 17/02/2026
Giant multicellular magnetotactic prokaryotes in marine sediments academic.oup.com/ismej/advanc... #jcampubs
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Courtney Stairs @cstairs.bsky.social · 09/02/2026
Check out our latest pre-print of our favourite pets - the breviates. This work was led by Zhezhen Yi in collaboration with @andrewjroger.bsky.social and many others! By studying diverse breviates we were able to see how different metabolic pathways can evolved in response to low-oxygen.
biorxiv.org
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Tobias Warnecke @tobiaswarnecke.bsky.social · 14/08/2025
Archaea are often surrounded by bacteria. But is there ever active conflict between the two? Can archaea kill bacteria? If so, how do they do it? Work by @romainstrock.bsky.social shows that some archaea can kill bacteria by secreting peptidoglycan hydrolases. journals.plos.org/plosbiology/...
journals.plos.org
Archaea produce peptidoglycan hydrolases that kill bacteria
Archaea regularly interact with bacteria but reports of archaea killing bacteria are very rare. This study shows that many archaea encode peptidoglycan hydrolases, which specifically target bacterial ...
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Pierre Simon Garcia @pierresimongarcia.bsky.social · 03/02/2026
Passioned by #bioenergetics? Do not miss our new article on the evolutionary history of oxidoreductases with G. Borrel and @sgribaldo.bsky.social @archaeal.bsky.social @valdeanda.bsky.social @pasteur.fr @cnrs.fr @cnrsbiologie.bsky.social @natecoevo.nature.com (www.nature.com/articles/s41...).
nature.com
Evolution and diversity of oxidoreductases involved in redox balance and energy conservation - Nature Ecology & Evolution
HORBEC are protein complexes involved in the regulation of redox balance and energy conservation. The authors develop a bioinformatic tool for HORBEC annotation in bacterial and archaeal genomes and r...
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Laura Eme @lauraeme.bsky.social · 02/02/2026
Comparative Genomics of Unicellular Eukaryotes (San Feliu, Spain): Abstract submission is open, with a short deadline! comparativegenomics2026.com Join us as we explore the most diverse, surprising, and still largely uncharted branches of the eukaryotic tree.
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Buzz Baum @buzzbaum.bsky.social · 23/01/2026
A reminder to sign up for the 2026 EMBO archaeal meeting im Cambridge: meetings.embo.org/event/26-arc.... Registration is open. We are looking forward to hosting you!
meetings.embo.org
Molecular Biology of Archaea: Life Through the Prism of Archaea
In 1977, Woese and colleagues revealed Archaea as a distinct domain of life. Building on this insight, the discovery of Asgard archaea has strengthened the view that many hallmarks of eukaryotic cell…
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Olaya Rendueles @olayarendueles.bsky.social · 15/01/2026
My team at @cbitoulouse.bsky.social is recruiting a postdoc #bioinformatics with solid experience in metagenomic analyses. Interest in evolution, ecology & MGEs is important. The offer stands until the perfect candidate is found, and it could be you 🫵 🔁 🙏 #microSky #phagesky #UTIsky @cnrs.fr
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Michael Wagner @michiwagner4.bsky.social · 19/12/2025
🚨 Postdoctoral Opportunity for Female Scientists🚨 The University of Vienna is awarding at least 20 fully funded 4 year postdoctoral positions to outstanding female scientists Interested? Get in touch via direct message careers.univie.ac.at/en/postdoc/e... #MicroSky 🧪 #PostDoc @univie.ac.at
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Laurent Jacob @laurentjacob.bsky.social · 05/12/2025
legend 2025 will be next Tuesday/Wednesday/Thursday. The detailed program is on legend2025.sciencesconf.org?lang=en If you are not attending the conference you can still follow the presentations online (Zoom links are on the website).
legend2025.sciencesconf.org
legend2025 : Machine Learning for Evolutionary Genomics Data - Sciencesconf.org
Evolutionary genomics and population genetics investigate patterns of genetic diversity between species or between populations within a species and play a fundamental role in many aspects, from theoretical facets of evolution to practical ones, such as conservation genetics and biomedical sciences.
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Archaea Biology Vienna @archaea-vienna.bsky.social · 03/12/2025
Asgard on the move ! Watch our videos! Biorxiv.org/content/10.1101/2025.11.30.690169v1
biorxiv.org
Dynamic protrusions mediate unique crawling motility in Asgard Archaea (Promethearchaeota)
Crawling motility is a hallmark of eukaryotic cells and requires a dynamic actin cytoskeleton, regulated adhesion, and spatially organized signalling pathways1–3. Asgard archaea (phylum Promethearchae...
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Cameron Thrash @jcamthrash.bsky.social · 04/12/2025
Oxygen production as an electron overflow pathway in ammonia-oxidizing archaea www.biorxiv.org/content/10.6... #jcampubs
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CNRS @cnrs.fr · 01/12/2025
From January 1st 2026, the CNRS will cut access to one of the largest commercial bibliometric databases, Clarivate Analytics' Web of Science, along with the Core Collection and Journal Citation Reports.
cnrs.fr
The CNRS is breaking free from the Web of Science
From January 1st 2026, the CNRS will cut access to one of the largest commercial bibliometric databases, Clarivate Analytics'
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Elena Buelow @elenabuelow.bsky.social · 01/12/2025
Exploring the human small intestinal luminal microbiome via a newly developed ingestible sampling device url: academic.oup.com/ismecommun/a.... I am proud to have contributed to this work with Alexandre Tronel, Thomas Soranzo (Pelican Health), @alegouellec.bsky.social + all other co-authors.
academic.oup.com
Exploring the human small intestinal luminal microbiome via a newly developed ingestible sampling device
Abstract. Because accessing the small intestine is technically challenging, studies of the small intestinal microbiome are predominantly conducted in patie
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-Boulet- @bouletcorp.bsky.social · 15/11/2025
Vaccines and Autism, par @zachweinersmith.bsky.social
Une scientifique dit: "Attendez une minute... Les gens sur le spectre autistique sont sur-représentés dans la recherche scientifique. Mais... Mais ça veut dire que..."
Un autre réalise soudain, et murmure: "Mon Dieu..."

La légende dit: "L'autisme cause les vaccins."
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Sarah Dellière @sarah-delliere.bsky.social · 13/11/2025
🔥 At conferences, who asks the questions shapes who gets seen. Across 24 ID&CM meetings, women were 55% of delegates but asked 36% of questions. 💬 When women moderate or speak first, others follow. Let’s change the pattern bit.ly/47VL0eH 🙏 @maudsalmona.bsky.social & MicroID EmpowHERment consortium
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Nicolas Galtier @nicolasgaltier.bsky.social · 07/11/2025
So Nature-Springer, which absorbs several billion dollars in research funding each year, provides us with an API that attributes all citations to the first article in the volume. Well done Springer Nature, at least I know where not to submit my next paper.
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DEEMteam_Orsay @deemteam.bsky.social · 02/11/2025
This paper has been a must! Great collaboration with @mkrupovic.bsky.social and @yifanzhou.bsky.social, a N&V by a legend of halophilic archaea tinyurl.com/yc3dcv72, and one picture of one of our expeditions to Dallol making the cover of the November issue of @natmicrobiol.nature.com rdcu.be/eLtCH
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Anne Chevallereau @annechevallereau.bsky.social · 22/10/2025
JOB OFFER #PhageSky We have a postdoc position opening in my group to investigate phage-MGE interactions ! We're based in the very nice city of Lyon, France @mmsb-lyon.bsky.social Contact me for more info ! >> Apply on the CNRS webpage emploi.cnrs.fr/Offres/CDD/U...
emploi.cnrs.fr
Portail Emploi CNRS - Offre d'emploi - Postdoctoral researcher Microbiology (M/F)
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Roey Angel @roeyangel.bsky.social · 13/10/2025
📣 New PhD student position opening in my lab! Soils are full of microbes, but how many are active? Surprisingly, we still lack reliable methods to answer this. If you are interested in microbial dormancy and are fascinated by the Alps and glacier forefields, contact me. 🏔️ 🦠 💤 🧬 🎓
The team at our research site in the alps
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Cascales Lab @cascaleslab.bsky.social · 09/10/2025
Open position to work on Type IX secretion (#T9SS) in our lab, in collaboration withe the group of Eric Reynolds at the Dental School of the University of Melbourne. Please spread the word, and forward to anyone potentially interested ! Apply here: emploi.cnrs.fr/Offres/Docto...
emploi.cnrs.fr
Portail Emploi CNRS - Offre d'emploi - Thèse en Microbiologie-Biochimie (H/F)
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Laurent Jacob @laurentjacob.bsky.social · 08/10/2025
The decisions for LEGEND are out: legend2025.sciencesconf.org/data/book_le... I'm really looking forward to hearing these 21 exciting presentations (and additional 30 posters) next December. If you want to attend too, registration is open until October 17th through legend2025.sciencesconf.org
Exploring the space of self-reproducing RNA using generative models, Martin Weigt

Exploring the archaic introgression landscape of admixed populations through
joint ancestry inference, Jazeps Medina Tretmanis [et al.]

Predicting natural variation in the yeast phenotypic landscape with machine
learning, Sakshi Khaiwal [et al.]

Phylodynamic modeling with unsupervised Bayesian neural networks, Marino
Gabriele [et al.]

Likelihood-free inference of phylogenetic tree posterior distributions, Luc Blas-
sel [et al.]

Generative continuous time model reveals epistatic signatures in protein evolu-
tion, Barrat-Charlaix Pierre

Neural posterior estimation for high-dimensional genomic data from complex pop-
ulation genetic models, Jiseon Min [et al.]

A differentiable model for detecting diversifying selection directly from alignments
in large-scale bacterial datasets, Leonie Lorenz [et al.]

Detecting interspecific positive selection using transformers, Charlotte West [et al.]

Predicting Multiple Sequence Alignment Uncertainty via Machine Learning, Lucia
Martin-Fernandez [et al.]

Graph Neural Networks for Likelihood-Free Inference in Diversification Mod-
els, Amélie Leroy [et al.]

Popformer: learning general signatures of genetic variation and natural selection
with a self-supervised transformer, Leon Zong [et al.]PRIVET: PRIVacy metric based on Extreme value Theory, Antoine Szatkownik [et
al.]

Generative models for inferring the evolutionary history of the malaria vector
Anopheles gambiae, Amelia Eneli [et al.]

Language Models Outperform Supervised-Only Approaches for Conserved Ele-
ment Comprehension, Eyes Robson [et al.]

Identification and Classification of Orphan Genes, Spurious Orphan Genes, and
Conserved Genes from the human microbiome, Chen Chen

Neural Simulation-based inference of demography and selection, Francisco De
Borja Campuzano Jiménez [et al.]

Species Identification and aDNA Read Mapping Using k-mer Embeddings, Filip
Thor [et al.]

Contrastive Learning for Population Structure and Trait Prediction, Filip Thor [et
al.]

Protein and genomic language models chart a vast landscape of antiphage de-
fenses, Mordret Ernest

The Phylogenomics and Sparse Learning of Trait Innovations, Gaurav Diwan [et
al.]
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Tobias Warnecke @tobiaswarnecke.bsky.social · 29/09/2025
Become my colleague @oxfordbiochemistry.bsky.social ! 2 Associate Professorships in the areas of - prokaryotic/eukaryotic microbiology - metabolism my.corehr.com/pls/uoxrecru...
my.corehr.com
Job Details
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Julie Boisard @protistsforthewin.bsky.social · 27/09/2025
Now completely published :) Really proud of this paper led with Karla at @cstairs.bsky.social lab. doi.org/10.1093/isme...
doi.org
Anaerobic breviate protist survival in microcosms depends on microbiome metabolic function
Abstract. Anoxic and hypoxic environments serve as habitats for diverse microorganisms, including unicellular eukaryotes (protists) and prokaryotes. To thr
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Sophie Abby @soabby.bsky.social · 18/09/2025
Really glad to announce a new preprint from our lab: Global distribution of quinones in Bacteria! We here combine comparative genomics and text mining to leverage information on quinones distribution from thousands of articles describing new species and from dozens of thousands of genomes! 1/5
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ATLASea @atlasea.bsky.social · 17/09/2025
ATLASea #recrute: Ingénieur développeur - DevOps (H/F) à RENNES IT en contrat CDD de 13 mois Date d'embauche prévue : 1 novembre 2025 Plus d'informations: emploi.cnrs.fr/Offres/CDD/U... #hiring #job
emploi.cnrs.fr
Portail Emploi CNRS - Offre d'emploi - Ingénieur développeur - DevOps (H/F)
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cemess_vienna @cemess.bsky.social · 10/09/2025
Deadline approaching on Sept 17! We are hiring a Full Professor of Environmental Biogeochemistry of Metals at #CeMESS at the University of Vienna. Learn more: 🔗 edge.univie.ac.at/news-talks/n... @edge-vienna.bsky.social @univie.ac.at #EnvironmentalBiochemistry
edge.univie.ac.at
We are hiring: Full Professor of Environmental Biogeochemistry of Metals
Human activities are driving rapid environmental change on a global scale, with pollutants playing a critical role in pushing planetary systems beyond safe limits. These changes have profound conseque...
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Hervé Cottin @hcottin.bsky.social · 10/09/2025
Après plus de deux ans de travail, et grâce à l'implication de près de 30 collègues chercheuses et chercheurs de presque tous les champs des sciences, voici enfin dans toutes les librairies "Le Grand Livre de l'Exobiologie". @lisa-ipsl.bsky.social @upecofficiel.bsky.social @ipsl.bsky.social @cnes.fr
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Tobias Warnecke @tobiaswarnecke.bsky.social · 08/09/2025
Please re-post: Interested in chromatin and its evolution? Good news! There's still time to join us in beautiful Catalonia (9-12 Dec) to discuss eukaryotic, bacterial, archaeal, and viral chromatin and how it all hangs together meetings.embo.org/event/24-evo... Abstract deadline: 30 September
meetings.embo.org
EvoChromo: Evolutionary approaches to research in chromatin
Chromatin is the complex of DNA, RNA and protein that is found making up the chromosomes in eukaryotic cells. Chromatin is essential for proper genome function and is involved in chromosome segregati…
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