@soabby.bsky.social
Researcher at CNRS, TIMC lab, Grenoble France compBio@TrEE group https://tree-timc.github.io/compbio Archaea & Bacteria Evolution Comparative genomics and Phylogenomics Evolution of Cellular machineries & Metabolic pathways https://sophieabby.github.io
The team at our research site in the alps
📣 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.
🏔️ 🦠 💤 🧬 🎓
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...
![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.]](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:7x5c6ifrcznmg4mzhfuc2a6r/bafkreidur7bz43o2jhwr4gbt36awozawqthbkkfeszxjkxf4kvhyh7q6du@jpeg)
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.]](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:7x5c6ifrcznmg4mzhfuc2a6r/bafkreig4akadduemzbit67bv7jnr7x2ircwiriykabg2imuf3phy6hhube@jpeg)
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.]
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
Become my colleague @oxfordbiochemistry.bsky.social !
2 Associate Professorships in the areas of
- prokaryotic/eukaryotic microbiology
- metabolism
my.corehr.com/pls/uoxrecru...
Now completely published :)
Really proud of this paper led with Karla at @cstairs.bsky.social lab.
doi.org/10.1093/isme...
We would like to thank the scientists across the world who characterize quinones in newly described species and publish their work e.g. in IJSEM from @microbiologysociety.org, Antonie van Leeuwenhoek, Archives of Microbiology and Systematic and Applied Microbiology. Quinones rock! 🤩 5/5
18.09.2025 10:10 — 👍 3 🔁 0 💬 0 📌 0...and after the study brilliantly conducted by Dr. Chobert on the dynamics of the quinone repertoire in Pseudomonadota that accompanied their metabolic diversification, also published earlier this year in the ISME Journal from @isme-microbes.bsky.social. 4/5
doi.org/10.1093/isme...
This much-needed compendium of quinones in bacteria is the last chapter of S. Chobert's PhD thesis. This comes after the discovery of a high potential quinone, the methylplastoquinone, led by @lipidorama.bsky.social and colleagues published earlier in @pnas.org... 3/5
doi.org/10.1073/pnas...
Among other discoveries, we show that the two menaquinone pathways tend to replace one another frequently, and that a lineage outside of Pseudomonadota unexpectedly show the potential to produce ubiquinone, a high redox potential usually found in Pseudomonadota and Eukaryota. 2/5
18.09.2025 10:10 — 👍 2 🔁 1 💬 1 📌 0Really 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
18.09.2025 10:10 — 👍 11 🔁 5 💬 1 📌 1ATLASea #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
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
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
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
While journal publishing has always been deeply problematic, hurting both the pace and trajectory of science, something is happening in this moment that is finally causing the system to crumble under its own weight and cost.
1/
To all post-docs: The Genome Biology dept @embl.org
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
graphical abstract of the article the extended mobility of plasmids
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/...
23.07.2025 07:35 — 👍 185 🔁 94 💬 4 📌 9
Photo de groupe prise avec les participants et participantes à JOBIM 2025.
👏 Ca y est, #JOBIM2025 est officiellement fini !
Au nom de toute l'équipe, merci pour votre participation, et pour toutes ces discussions scientifiques intenses et stimulantes.
Merci aussi pour votre enthousiasme, votre bienveillance et tous ces rires échangés pendant la conférence.
1/2 ⤵️
‼️ Le programme détaillé des #JOBIM2025 est en ligne ‼️
📍Rendez-vous sur jobim2025.labri.fr/detailed_pro...
After 5 amazing years @pilhoferlab.bsky.social I'm starting my lab @embl.org Grenoble this November embl.org/wollweber
We'll image Asgard archaea and many other strange microbes ( #archaeasky, #protistsonsky..) to understand eukaryogenesis
First job ad: #teamtomo scientist!🔬❄️ tinyurl.com/2rdu2ze6
Voici le lien correct pour candidater : emploi.cnrs.fr/Offres/CDD/U...
27.06.2025 19:37 — 👍 0 🔁 0 💬 0 📌 0Nous recrutons un IE en bioinformatique pour faire de l'analyse évolutive de séquences biologiques (CDD de 22 mois) dans le cadre d'un projet ANR.
L'offre est disponible ici : emploi.cnrs.fr/Gestion/Offr...
N'hésitez pas à partager ! Merci ! 🙏
Me contacter pour toute info supplémentaire.
Programme synthétique de JOBIM2025
‼️Le #programme synthétique de @jobim2025.bsky.social est en ligne‼️
📍Rendez-vous sur jobim2025.labri.fr pour toutes informations concernant #JOBIM2025
We are looking for new recommenders to join Peer Community in Genomics! The position of “recommender” is analogous to an associate editor at a traditional journal. However, recommenders are not obliged to handle any manuscripts.
12.06.2025 06:02 — 👍 1 🔁 3 💬 1 📌 1Looking for a postdoc on bacterial-insect symbiosis, combining evolution and molecular mechanisms? I'll have one open in my lab starting Sept 2025. If interested contact me (or find me at the GRC on Animal-microbe symbiosis if you'll be there). #SymbioSky
29.05.2025 20:11 — 👍 34 🔁 36 💬 0 📌 1NIH 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.
22.05.2025 12:42 — 👍 288 🔁 232 💬 37 📌 46Our friends of atacamensis.cl have just published this short video about our fieldtrip to the Atacama Desert in March.
24.05.2025 18:24 — 👍 19 🔁 4 💬 0 📌 0
Join the Blokesch lab (@EPFL) as a postdoc in Molecular Microbiology 🤩
Study Vibrio cholerae defense systems (phage/plasmid) in a dynamic, collaborative environment in Lausanne close to Lake Geneva in 🇨🇭!
Please visit my lab's webpage for details about the position and how to formally apply.
The programme and list of abstracts of selected talks and posters for the upcoming MCEB 2025 in Granada, Spain are now available. Please check out the conference website: mceb2025.sciencesconf.org?lang=en
25.04.2025 09:14 — 👍 0 🔁 1 💬 0 📌 1
Excited to announce the Molecular Biology of Archaea (MBoA) 2026!
Join us in Cambridge, UK, from 6–10 July 2026 for the only international meeting dedicated to Archaea.
