Jessica Andreani
jessicaandreani.bsky.social
Jessica Andreani
@jessicaandreani.bsky.social
Researcher in computational biology / bioinformatics at @i2bcparissaclay.bsky.social 🇫🇷
Protein-protein, protein-RNA & protein-DNA interactions, structure & evolution
ML & DL
Biology of genome maintenance
Women/diversity in science
Personal account
Pinned
New paper alert 🚨
I am super happy about it, for many reasons!
👥 It was a great collaborative project with Calum @chgjohnston.bsky.social and J. Pablo Radicella, designed a long time ago (in the pre-AlphaFold era - can you imagine?) together with @polardlab.bsky.social and @raphguerois.bsky.social
Pleased to share our recent article in PNAS - a collaboration with @jessicaandreani.bsky.social & Pablo Radicella, with important roles played by many members of each team.

A tripartite protein complex promotes DNA transport during natural transformation in Firmicutes www.pnas.org/doi/10.1073/...
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...
www.pnas.org
Reposted by Jessica Andreani
🔬 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
February 11, 2026 at 7:33 AM
Reposted by Jessica Andreani
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...
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...
www.science.org
January 30, 2026 at 6:11 AM
Reposted by Jessica Andreani
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...
PhD student bioinformatics: Phage genomic modules: data mining, visualisation, and databasing
jobs.uni-jena.de
January 12, 2026 at 11:41 AM
Reposted by Jessica Andreani
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 :)
January 11, 2026 at 7:43 PM
Reposted by Jessica Andreani
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.
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...
www.science.org
January 8, 2026 at 7:08 PM
Reposted by Jessica Andreani
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).
January 6, 2026 at 8:05 AM
Reposted by Jessica Andreani
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...
“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.
issues.org
January 6, 2026 at 5:14 PM
Reposted by Jessica Andreani
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!
December 29, 2025 at 3:18 PM
Reposted by Jessica Andreani
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 🧵
December 26, 2025 at 11:49 PM
Reposted by Jessica Andreani
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...
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
academic.oup.com
December 21, 2025 at 11:51 AM
Reposted by Jessica Andreani
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:
Milestone: >20,000 Structures Deposited to the PDB in 2025
wwPDB has received a record number of depositions this year
www.rcsb.org
December 17, 2025 at 5:22 PM
Reposted by Jessica Andreani
🚀🧬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 ) !
December 10, 2025 at 3:50 PM
Reposted by Jessica Andreani
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.
www.legifrance.gouv.fr
December 11, 2025 at 6:50 AM
Reposted by Jessica Andreani
Les jours passent et l'arrêté d'ouverture du concours CNRS n'est pas sorti ?

Le concours n'est pas ouvert ?
December 10, 2025 at 8:16 PM
Reposted by Jessica Andreani
✨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🧬

🔗👇
December 9, 2025 at 7:52 AM
Reposted by Jessica Andreani
#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...
December 1, 2025 at 3:33 PM
Reposted by Jessica Andreani
@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.
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...
www.science.org
December 5, 2025 at 5:24 AM
Reposted by Jessica Andreani
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! 🧵
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...
www.science.org
December 4, 2025 at 8:18 PM
Reposted by Jessica Andreani
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.
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...
www.pnas.org
November 25, 2025 at 9:41 PM
Reposted by Jessica Andreani
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
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...
journals.plos.org
November 3, 2025 at 11:58 PM
Reposted by Jessica Andreani
🦠🧪🧬🚨 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-...
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
academic.oup.com
December 3, 2025 at 2:34 AM
Reposted by Jessica Andreani
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
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...
www.aefinfo.fr
December 3, 2025 at 6:08 AM
Reposted by Jessica Andreani
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
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).
www.enseignementsup-recherche.gouv.fr
December 3, 2025 at 6:10 AM