Jessica Andreani

AlphaFold Database welcomes community datasets Latest AlphaFold Database update adds high-value datasets for microbial and viral proteins, generated by specialist communities

The AlphaFold Database, jointly developed with Google DeepMind, now contains datasets from specialist communities.

This includes rich datasets for microbes, viruses & parasites associated with tropical diseases.

Explore the new datasets in the AlphaFold Database.

www.ebi.ac.uk/about/news/u...

🔬 C'est la Journée des femmes et filles de science ! #FemmesEnSciences #11février

Envie de découvrir (ou faire découvrir) des femmes scientifiques ? J'ai rassemblé plein de ressources ici ⬇️
www.linkedin.com/pulse/envie-...

Et mon starter pack de chercheuses sur bluesky go.bsky.app/TBEzKC

Multiple protein structure alignment at scale with FoldMason Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...

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/...

PhD position in Jena! Unique German-French collaboration to work on integrating phage genomic modules into VirJenDB.org - make sense of #phages, #big_data, #front_end, #back_end, #database. Please apply here 👇
jobs.uni-jena.de/jobposting/c...

Fresh news on de novo genes! Happy to present our latest work published in Nature communications: www.nature.com/articles/s41...

Keywords not in specific order: intergenic ORFs, de novo genes, GC content, foldability, genetic code, ancestral sequence reconstruction and more :)

Computational design of conformation-biasing mutations to alter protein functions Conformational biasing (CB) is a rapid and streamlined computational method that uses contrastive scoring by inverse folding models to predict protein variants biased toward desired conformational sta...

Can we design mutations that bias proteins towards desired conformational states?

Today in @science.org, we introduce Conformational Biasing (CB), a simple and scalable computational method that uses contrastive scoring by inverse folding models to identify conformation-biasing mutations.

When RNA Degradation 🤝 meets 🤝 Protein Degradation! tinyurl.com/E3TDMD In a collaboration of @bartellab.bsky.social and Schulman lab, we show that, in target-directed microRNA degradation (TDMD), 2-RNA-factors recruit an E3 ligase and induce the degradation of not only a protein but also RNA (1/5).

“There Are Two Possible Futures for American Science.” The Simons Foundation president talks about science philanthropy, the future of the research enterprise, and remaining hopeful.

Folks interested in science philanthropy should read this interview w/Simons Foundation President David Spergel on the role of philanthropy, support of early career scientists (from incentives to a call for more retirements), and the pivot point between future scenarios.

issues.org/american-sci...

Bacteriophages are normally classified as either virulent or temperate. Reality is, of course, more complicated!
Here we show many bacterial isolates contain non-temperate phages that can persist through restreaking.
Thanks to all co-authors for such a great collaboration!

So 2025 turned out to be a big year for de novo antibody design! Here are thoughts and predictions on the state of de novo antibody design heading into 2026 🧵

High-resolution HIV-1 m6A epitranscriptome reveals isoform-dependent methylation clusters and unique 2-LTR transcript modifications Abstract. The N6-methyladenosine (m6A) modification of HIV-1 has been widely studied but the number and precise positions of the m6A sites remain unclear d

I am very pleased to share our latest article published in NAR Genomics and Bioinformatics. A collaborative effort with great colleagues from the I2BC NGS facility.

thanks to @i2bcparissaclay.bsky.social for its financial support through epiRNA programs

academic.oup.com/nargab/artic...

Milestone: >20,000 Structures Deposited to the PDB in 2025 wwPDB has received a record number of depositions this year

wwPDB has received a record number of depositions this year--more than 20,000!

Many thanks to all of our depositors and biocurators more making these important data available to all

Details:

🚀🧬Début de la formation AlphaFold & au-delà à Orsay !
Au programme de ces 3 jours : analyse de structures protéiques en 3D, grâce aux outils d’intelligence artificielle tels qu’AlphaFold et initiation à l’utilisation du supercalculateur Jean Zay (IDRIS - @cnrs.fr ) !

JO du jour : ouverture des postes de CR au CNRS : www.legifrance.gouv.fr/jorf/id/JORF...
Avec une coquille : le titre et la liste des postes disent "chargés de recherche de classe normale" mais l'article 1 dit "directeurs de recherche de 1ère classe". Rectificatif à venir.

Les jours passent et l'arrêté d'ouverture du concours CNRS n'est pas sorti ?

Le concours n'est pas ouvert ?

✨New preprint!

🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al!
Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬

🔗👇

Carte prévisionnelle de la ZAC de Courcelles dans les années 1970 (Gif-Informations, mars 1972). On y voit une partie des magasins actuels, les parkings, et la "bretelle de la vallée de Chevreuse", le long du RER. Texte : "La piste cyclable derrière Intermarché passe sur des terrains réservés pour une grande route en fond de vallée. Celle-ci est abandonnée dans les années 1970, après d'intenses mobilisations des communes."

#Avent2025 1/24 Cette année, je vous emmène sur les traces invisibles des Trente Glorieuses : 24 détails de l'espace Orsay-Saclay qui raconte ce qui fut, ou aurait pu être... Aujourd'hui, la piste cyclable derrière Intermarché à Gif-sur-Yvette : elle raconte une route qui aurait pu exister...

Multiscale structure of chromatin condensates explains phase separation and material properties The structure and interaction networks of molecules within biomolecular condensates are poorly understood. Using cryo–electron tomography and molecular dynamics simulations, we elucidated the structur...

@science.org 🧬🔬 Multiscale structure of #chromatin condensates explains phase separation and material properties | Science www.science.org/doi/10.1126/... @janhuemar.bsky.social et al.

Cohesin guides homology search during DNA repair using loops and sister chromatid linkages Accurate repair of DNA double-strand breaks (DSBs) is essential for genome stability, and defective repair underlies diseases such as cancer. Homologous recombination uses an intact homologous sequenc...

I am happy to share that my postdoctoral work in the @gerlichlab.bsky.social at @imbavienna.bsky.social is finally out 🎉!
Our study reveals how cohesin guides focused and accurate homology search.
Read more 👉 www.science.org/doi/10.1126/...
Follow along for key insights and updates! 🧵

Une nouvelle méthode pour suivre de près la transmission des gènes chez les bactéries La conjugaison est un mécanisme de transfert génétique horizontal entre bactéries donneuses et receveuses, responsable, entre autres, de la diss

#ResultatScientifique🔎| Une nouvelle méthode pour suivre de près la transmission des gènes chez les bactéries 🦠

✍️ Yoshiharu Yamaichi
🤝 @cnrs-paris-saclay.bsky.social @i2bcparissaclay.bsky.social @univparissaclay.bsky.social
@cea-paris-saclay.bsky.social
📕 @narjournal.bsky.social | buff.ly/iEqMc04

A tripartite protein complex promotes DNA transport during natural transformation in Firmicutes | PNAS Natural genetic transformation is a conserved mechanism of bacterial horizontal gene transfer, which is directed entirely by the recipient cell and...

Congrats to @chgjohnston.bsky.social , Andreani, Radicella et al.!
Elegant PNAS paper on the ComEC/ComFA/ComFC complex in bacterial transformation. AF3 predictions validated by clever mutagenesis. We tried for years to solve this by cryo-EM/crystallography - never succeeded.

The tRNA epitranscriptomic landscape and RNA modification enzymes in Vibrio cholerae Author summary This study charts the first genome-wide map of transfer RNA (tRNA) modifications in the cholera pathogen, Vibrio cholerae, revealing how chemical marks on tRNAs shape translation and st...

Our new paper maps the tRNA modification landscape in Vibrio cholerae! 💫
We describe differences from E. coli and discuss links to decoding of stress-related codons 🦠
Huge thanks to amazing co-authors and collaborators!
@plos.org #rnasky #microsky #tRNAmodifications

Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes Abstract. Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is st

🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...

En 2024, 82 % des universités respectaient les trois seuils du décret... En 2024, 33 universités ont eu un résultat net comptable négatif et étaient donc en déficit. C’est quatre de plus qu’en 2023. Si le nouveau décret financier...

Remarquable travail de @aefsuprecherche.bsky.social qui a testé l'application du décret financier sur l'ensemble des universités dont les comptes financiers 2024 sont disponibles.

Douze établissements seraient en situation budgétaire jugée "insoutenable" car dépassant l’un des trois critères.

#ESR

Remise des prix science ouverte : édition 2025 La cérémonie de remise des prix science ouverte s’est tenue le 1er décembre 2025, à l’Université Pais-Saclay, lors des Assises nationales des données de la recherche (Andor 2025).

Hier a eu lieu la remise des prix science ouverte 2025. Un moment important pour célébrer la qualité du travail de la communauté scientifique et sa contribution à la science ouverte. www.enseignementsup-recherche.gouv.fr/fr/remise-de... @ouvrirlascience.bsky.social @enseignementsup-recherche.gouv.fr

Rewriting protein alphabets with language models Detecting remote homology with speed and sensitivity is crucial for tasks like function annotation and structure prediction. We introduce a novel approach using contrastive learning to convert protein...

Fresh from bioRxiv our latest work introducing The Embedded Alphabet (TEA), a powerful new representation for protein sequences obtained by discretising ESM2 embeddings into 20 characters.

Pre-print: www.biorxiv.org/content/10.1...

🧵👇(1/n)

#RejoignezLeCNRS 🫵 Les concours chercheurs CNRS 2026 ouvrent le 8/12 !
Envie de faire avancer la science au sein d’un des plus grands organismes de recherche ?
👉 carrieres.cnrs.fr/concours-...

#ConcoursChercheurs #Science #Recherche #Icicarecrute #recrutement

Check this out for the 2026 SISB (phage defense) meeting in NYC. Mark your calendar! (and note the Zoom option, if needed)
sisb2026.rockefeller.edu

Le CNRS s’émancipe du Web of Science À partir du 1er janvier 2026, le CNRS coupera l’accès à l’une des plus importantes bases bibliométriques commerciales : le

Le 1er janvier 2026, le CNRS coupera l’accès au Web of Science, Core Collection et Journal Citation Reports. Une nouvelle étape de sa politique en faveur de la science ouverte pour promouvoir des alternatives ouvertes, transparentes et responsables.