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
Protein-protein, protein-RNA & protein-DNA interactions, structure & evolution
ML & DL
Biology of genome maintenance
Women/diversity in science
Personal account
Pinned
🚨 I am super happy to announce that our analysis of how the structure of protein-RNA interfaces evolves is now published (early access) at @plos.bsky.social Computational Biology:
doi.org/10.1371/jour...
🧬🧶
doi.org/10.1371/jour...
🧬🧶
Reposted by Jessica Andreani
Excited to share our new preprint on BioRxiv!
A collaborative effort spanning many years and several labs to uncover what the germline chromosomes of Paramecium really look like. 🔗 www.biorxiv.org/content/10.1...
1/5
A collaborative effort spanning many years and several labs to uncover what the germline chromosomes of Paramecium really look like. 🔗 www.biorxiv.org/content/10.1...
1/5
The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons
Background. Paramecia belong to the ciliate phylum of unicellular eukaryotes characterized by nuclear dimorphism. A diploid germline micronucleus (MIC) transmits genetic information across sexual gene...
www.biorxiv.org
November 10, 2025 at 9:21 AM
Excited to share our new preprint on BioRxiv!
A collaborative effort spanning many years and several labs to uncover what the germline chromosomes of Paramecium really look like. 🔗 www.biorxiv.org/content/10.1...
1/5
A collaborative effort spanning many years and several labs to uncover what the germline chromosomes of Paramecium really look like. 🔗 www.biorxiv.org/content/10.1...
1/5
Reposted by Jessica Andreani
Our new special collection "Protein-Nucleic Acid Interactions: From Origins to Design (2025)" is now published in Current Opinion in Structural Biology. I'm excited to have both co-edited it with Shandar Ahmad and contributed a review!
www.sciencedirect.com/special-issu...
www.sciencedirect.com/special-issu...
LinkedIn
This link will take you to a page that’s not on LinkedIn
lnkd.in
November 10, 2025 at 5:54 PM
Our new special collection "Protein-Nucleic Acid Interactions: From Origins to Design (2025)" is now published in Current Opinion in Structural Biology. I'm excited to have both co-edited it with Shandar Ahmad and contributed a review!
www.sciencedirect.com/special-issu...
www.sciencedirect.com/special-issu...
Reposted by Jessica Andreani
Reposted by Jessica Andreani
wait, wait, what 😱
Direct targeting and regulation of RNA polymerase II by cell signaling kinases in @science.org
www.science.org/doi/10.1126/...
Direct targeting and regulation of RNA polymerase II by cell signaling kinases in @science.org
www.science.org/doi/10.1126/...
November 7, 2025 at 8:32 AM
wait, wait, what 😱
Direct targeting and regulation of RNA polymerase II by cell signaling kinases in @science.org
www.science.org/doi/10.1126/...
Direct targeting and regulation of RNA polymerase II by cell signaling kinases in @science.org
www.science.org/doi/10.1126/...
Reposted by Jessica Andreani
I am very proud to announce that our team has received an ERC synergy grant from @erc.europa.eu. A wonderful recognition of a truly collaborative effort with friends (Julius Lukes, Leos Valasek and Mark Osborn). Excited to begin this journey at @i2bcparissaclay.bsky.social @cnrs.fr
The newly announced ERC Synergy Grant includes research on:
✴️ genetic drug design
✴️ the Big Bang's first microseconds
✴️ crowd movement
✴️ nature-society interactions
👉 buff.ly/ZQhLp4h
Congrats to the 66 awarded research teams!
#FrontierResearch
✴️ genetic drug design
✴️ the Big Bang's first microseconds
✴️ crowd movement
✴️ nature-society interactions
👉 buff.ly/ZQhLp4h
Congrats to the 66 awarded research teams!
#FrontierResearch
buff.ly
November 6, 2025 at 11:40 AM
I am very proud to announce that our team has received an ERC synergy grant from @erc.europa.eu. A wonderful recognition of a truly collaborative effort with friends (Julius Lukes, Leos Valasek and Mark Osborn). Excited to begin this journey at @i2bcparissaclay.bsky.social @cnrs.fr
Reposted by Jessica Andreani
Our latest paper has just been published in Cell!
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
November 5, 2025 at 5:20 PM
Our latest paper has just been published in Cell!
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
Reposted by Jessica Andreani
I'm thrilled to announce that I’m opening my own research team in the Department of Genome Biology at I2BC @i2bcparissaclay.bsky.social ! #ATIP-Avenir
Very excited to start this new adventure! www.i2bc.paris-saclay.fr/equipe-intra...
Very excited to start this new adventure! www.i2bc.paris-saclay.fr/equipe-intra...
Equipe Courret – Institute for Integrative Biology of the Cell
www.i2bc.paris-saclay.fr
October 24, 2025 at 3:39 PM
I'm thrilled to announce that I’m opening my own research team in the Department of Genome Biology at I2BC @i2bcparissaclay.bsky.social ! #ATIP-Avenir
Very excited to start this new adventure! www.i2bc.paris-saclay.fr/equipe-intra...
Very excited to start this new adventure! www.i2bc.paris-saclay.fr/equipe-intra...
Reposted by Jessica Andreani
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!
October 26, 2025 at 10:40 PM
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!
Reposted by Jessica Andreani
#JobOffer
💼 Un poste susceptible d’être vacant de Professeur en stabilité des génomes devrait s’ouvrir pour la rentrée 2026 au sein de l’Institut Jacques Monod
➡️ Informations concernant ce poste et la procédure de candidature 🔗 www.ijm.fr/poste-de-pro...
💼 Un poste susceptible d’être vacant de Professeur en stabilité des génomes devrait s’ouvrir pour la rentrée 2026 au sein de l’Institut Jacques Monod
➡️ Informations concernant ce poste et la procédure de candidature 🔗 www.ijm.fr/poste-de-pro...
October 28, 2025 at 1:41 PM
#JobOffer
💼 Un poste susceptible d’être vacant de Professeur en stabilité des génomes devrait s’ouvrir pour la rentrée 2026 au sein de l’Institut Jacques Monod
➡️ Informations concernant ce poste et la procédure de candidature 🔗 www.ijm.fr/poste-de-pro...
💼 Un poste susceptible d’être vacant de Professeur en stabilité des génomes devrait s’ouvrir pour la rentrée 2026 au sein de l’Institut Jacques Monod
➡️ Informations concernant ce poste et la procédure de candidature 🔗 www.ijm.fr/poste-de-pro...
Reposted by Jessica Andreani
Looks like OpenFold3 has been formally released in a public "preview". Not quite on parity with AlphaFold3 on a few benchmarks shown, in particular for antibody interactions. All info on the github link. I am sure we will hear more about this from the developers github.com/aqlaboratory...
GitHub - aqlaboratory/openfold-3: OpenFold3: A fully open source biomolecular structure prediction model based on AlphaFold3
OpenFold3: A fully open source biomolecular structure prediction model based on AlphaFold3 - aqlaboratory/openfold-3
github.com
October 28, 2025 at 9:30 AM
Looks like OpenFold3 has been formally released in a public "preview". Not quite on parity with AlphaFold3 on a few benchmarks shown, in particular for antibody interactions. All info on the github link. I am sure we will hear more about this from the developers github.com/aqlaboratory...
Reposted by Jessica Andreani
Chemoproteomics v. Boltz-2:
"These cases...point to the need to re-train ML co-folding tools on datasets enriched in more diverse types of small molecule-protein interactions...to avoid biased predictions derived from memorization of common orthosteric ligand poses"
www.biorxiv.org/content/10.1...
"These cases...point to the need to re-train ML co-folding tools on datasets enriched in more diverse types of small molecule-protein interactions...to avoid biased predictions derived from memorization of common orthosteric ligand poses"
www.biorxiv.org/content/10.1...
Tryptoline Stereoprobe Elaboration Identifies Inhibitors of the GRPEL1-HSPA9 Chaperone Complex
Activity-based protein profiling has identified hundreds of proteins from diverse classes that react at specific cysteine residues with stereochemically defined electrophilic compounds (stereoprobes) ...
www.biorxiv.org
October 27, 2025 at 6:31 PM
Chemoproteomics v. Boltz-2:
"These cases...point to the need to re-train ML co-folding tools on datasets enriched in more diverse types of small molecule-protein interactions...to avoid biased predictions derived from memorization of common orthosteric ligand poses"
www.biorxiv.org/content/10.1...
"These cases...point to the need to re-train ML co-folding tools on datasets enriched in more diverse types of small molecule-protein interactions...to avoid biased predictions derived from memorization of common orthosteric ligand poses"
www.biorxiv.org/content/10.1...
Reposted by Jessica Andreani
Hot off the press! Our paper, “Global comparative structural analysis of responses to protein phosphorylation”, is now out in Nature Communications!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Global comparative structural analysis of responses to protein phosphorylation - Nature Communications
Phosphorylation is central to protein regulation, yet its structural mechanisms remain poorly understood. Here, the authors conduct a global, systematic analysis of phosphorylated versus non-phosphory...
www.nature.com
October 27, 2025 at 10:29 AM
Hot off the press! Our paper, “Global comparative structural analysis of responses to protein phosphorylation”, is now out in Nature Communications!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Jessica Andreani
Thread on the intellectual landscape around LLMs 👇
I love progress and am happy to see investment in it—but wonder if the amounts currently going into genAI are a missed opportunity to invest in more mundane "data plumbing" and digitalisation. Which could eventually have higher societal benefits.
I love progress and am happy to see investment in it—but wonder if the amounts currently going into genAI are a missed opportunity to invest in more mundane "data plumbing" and digitalisation. Which could eventually have higher societal benefits.
I am genuinely impressed by large language models - they can absorb disparate components of text into some consolidated view, they can produce extremely good language and - with the right model - translate pretty well between languages and they are an excellent text based UI for humans to use. But..
October 26, 2025 at 8:30 AM
Thread on the intellectual landscape around LLMs 👇
I love progress and am happy to see investment in it—but wonder if the amounts currently going into genAI are a missed opportunity to invest in more mundane "data plumbing" and digitalisation. Which could eventually have higher societal benefits.
I love progress and am happy to see investment in it—but wonder if the amounts currently going into genAI are a missed opportunity to invest in more mundane "data plumbing" and digitalisation. Which could eventually have higher societal benefits.
Reposted by Jessica Andreani
End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon.
🌐 evedesign.bio
🌐 evedesign.bio
October 22, 2025 at 2:30 PM
End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon.
🌐 evedesign.bio
🌐 evedesign.bio
Reposted by Jessica Andreani
Success rates for Europe’s leading research grants are declining as a surge in applications far outweighs the funds available
go.nature.com/479Sni6
go.nature.com/479Sni6
Is academic research becoming too competitive? Nature examines the data
Applications for European research grants increased in 2025. Scientists say they’re feeling the competition.
go.nature.com
October 17, 2025 at 10:12 AM
Success rates for Europe’s leading research grants are declining as a surge in applications far outweighs the funds available
go.nature.com/479Sni6
go.nature.com/479Sni6
Reposted by Jessica Andreani
Many antiphage systems use NAD+, in many ways.
@hugovaysset.bsky.social reviewed them all!
Read to know more about all their molecular mechanisms, how phages counteract them, their distribution in bacteria and their conservation in eukaryotic immunity!
www.cell.com/molecular-ce...
@hugovaysset.bsky.social reviewed them all!
Read to know more about all their molecular mechanisms, how phages counteract them, their distribution in bacteria and their conservation in eukaryotic immunity!
www.cell.com/molecular-ce...
The multifaceted roles of NAD+ in bacterial immunity
In this review, Vaysset and Bernheim examine how nicotinamide adenine dinucleotide
(NAD+) is a key player in diverse and widespread bacterial antiphage defense systems
and phage counterdefense. The au...
www.cell.com
October 17, 2025 at 5:55 PM
Many antiphage systems use NAD+, in many ways.
@hugovaysset.bsky.social reviewed them all!
Read to know more about all their molecular mechanisms, how phages counteract them, their distribution in bacteria and their conservation in eukaryotic immunity!
www.cell.com/molecular-ce...
@hugovaysset.bsky.social reviewed them all!
Read to know more about all their molecular mechanisms, how phages counteract them, their distribution in bacteria and their conservation in eukaryotic immunity!
www.cell.com/molecular-ce...
Reposted by Jessica Andreani
Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from?
Today, we report the discovery of telomerase homologs in a family of antiviral reverse transcriptases, revealing an unexpected evolutionary origin in bacteria.
doi.org/10.1101/2025...
Today, we report the discovery of telomerase homologs in a family of antiviral reverse transcriptases, revealing an unexpected evolutionary origin in bacteria.
doi.org/10.1101/2025...
October 17, 2025 at 12:47 PM
Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from?
Today, we report the discovery of telomerase homologs in a family of antiviral reverse transcriptases, revealing an unexpected evolutionary origin in bacteria.
doi.org/10.1101/2025...
Today, we report the discovery of telomerase homologs in a family of antiviral reverse transcriptases, revealing an unexpected evolutionary origin in bacteria.
doi.org/10.1101/2025...
Reposted by Jessica Andreani
Now published: EnVhogDB, a large database of viral protein family HMM profiles to help functional annotation of new phage genomes - peercommunityjournal.org/articles/10....
EnVhogDB: an extended view of the viral protein families on Earth through a vast collection of HMM profiles
peercommunityjournal.org
October 18, 2025 at 7:58 AM
Now published: EnVhogDB, a large database of viral protein family HMM profiles to help functional annotation of new phage genomes - peercommunityjournal.org/articles/10....
Joyeux #anniversaire au CEA qui fête ses 80 ans en 2025🎂 #CEA80ans
Je suis fière aujourd’hui d’y participer à une recherche active en sciences du vivant👩💻✨
Cette recherche est issue d’un riche lien historique entre énergie atomique ⚛ et biologie 🧬🔬 que je vous invite à (re)découvrir ⬇️
Je suis fière aujourd’hui d’y participer à une recherche active en sciences du vivant👩💻✨
Cette recherche est issue d’un riche lien historique entre énergie atomique ⚛ et biologie 🧬🔬 que je vous invite à (re)découvrir ⬇️
October 17, 2025 at 5:34 AM
Joyeux #anniversaire au CEA qui fête ses 80 ans en 2025🎂 #CEA80ans
Je suis fière aujourd’hui d’y participer à une recherche active en sciences du vivant👩💻✨
Cette recherche est issue d’un riche lien historique entre énergie atomique ⚛ et biologie 🧬🔬 que je vous invite à (re)découvrir ⬇️
Je suis fière aujourd’hui d’y participer à une recherche active en sciences du vivant👩💻✨
Cette recherche est issue d’un riche lien historique entre énergie atomique ⚛ et biologie 🧬🔬 que je vous invite à (re)découvrir ⬇️
Reposted by Jessica Andreani
We’re very excited to finally share our latest work:
Phyloformer 2, a deep end-to-end phylogenetic reconstruction method: arxiv.org/abs/2510.12976
Using neural posterior estimation, it outperforms Phyloformer 1 and maximum-likelihood methods under simple and complex evolutionary models.
🧵1/17
Phyloformer 2, a deep end-to-end phylogenetic reconstruction method: arxiv.org/abs/2510.12976
Using neural posterior estimation, it outperforms Phyloformer 1 and maximum-likelihood methods under simple and complex evolutionary models.
🧵1/17
October 16, 2025 at 8:35 PM
We’re very excited to finally share our latest work:
Phyloformer 2, a deep end-to-end phylogenetic reconstruction method: arxiv.org/abs/2510.12976
Using neural posterior estimation, it outperforms Phyloformer 1 and maximum-likelihood methods under simple and complex evolutionary models.
🧵1/17
Phyloformer 2, a deep end-to-end phylogenetic reconstruction method: arxiv.org/abs/2510.12976
Using neural posterior estimation, it outperforms Phyloformer 1 and maximum-likelihood methods under simple and complex evolutionary models.
🧵1/17
Reposted by Jessica Andreani
#CEA80ans | 💙1958 : les Schtroumpfs débarquent dans Spirou et colorent le monde en bleu.
À Orsay, le CEA, éclaire l’invisible en utilisant l’atome au service du vivant. ⚛️
Avec la création du SHFJ, il est un acteur historique de la médecine nucléaire.
Pour en savoir + 👉 bit.ly/medecine-nuc...
À Orsay, le CEA, éclaire l’invisible en utilisant l’atome au service du vivant. ⚛️
Avec la création du SHFJ, il est un acteur historique de la médecine nucléaire.
Pour en savoir + 👉 bit.ly/medecine-nuc...
October 15, 2025 at 7:38 AM
#CEA80ans | 💙1958 : les Schtroumpfs débarquent dans Spirou et colorent le monde en bleu.
À Orsay, le CEA, éclaire l’invisible en utilisant l’atome au service du vivant. ⚛️
Avec la création du SHFJ, il est un acteur historique de la médecine nucléaire.
Pour en savoir + 👉 bit.ly/medecine-nuc...
À Orsay, le CEA, éclaire l’invisible en utilisant l’atome au service du vivant. ⚛️
Avec la création du SHFJ, il est un acteur historique de la médecine nucléaire.
Pour en savoir + 👉 bit.ly/medecine-nuc...
Reposted by Jessica Andreani
The latest #AlphaFold DB update is out!
We synchronised with UniProt release 2025_03, predicted protein isoforms across all species, and provide MSAs used to generate each prediction.
Proud of the team at the PDBe for the hard work that went into this. Grateful to play my part in it!
We synchronised with UniProt release 2025_03, predicted protein isoforms across all species, and provide MSAs used to generate each prediction.
Proud of the team at the PDBe for the hard work that went into this. Grateful to play my part in it!
We’re renewing our collaboration with Google DeepMind!
We'll keep developing the AlphaFold Database to support protein science worldwide 🎉
To mark the moment we’ve synchronised the database with UniProtKB release 2025_03.
www.ebi.ac.uk/about/news/t...
🖥️🧬 #AlphaFold
@pdbeurope.bsky.social
We'll keep developing the AlphaFold Database to support protein science worldwide 🎉
To mark the moment we’ve synchronised the database with UniProtKB release 2025_03.
www.ebi.ac.uk/about/news/t...
🖥️🧬 #AlphaFold
@pdbeurope.bsky.social
October 7, 2025 at 2:40 PM
The latest #AlphaFold DB update is out!
We synchronised with UniProt release 2025_03, predicted protein isoforms across all species, and provide MSAs used to generate each prediction.
Proud of the team at the PDBe for the hard work that went into this. Grateful to play my part in it!
We synchronised with UniProt release 2025_03, predicted protein isoforms across all species, and provide MSAs used to generate each prediction.
Proud of the team at the PDBe for the hard work that went into this. Grateful to play my part in it!
Reposted by Jessica Andreani
We’re renewing our collaboration with Google DeepMind!
We'll keep developing the AlphaFold Database to support protein science worldwide 🎉
To mark the moment we’ve synchronised the database with UniProtKB release 2025_03.
www.ebi.ac.uk/about/news/t...
🖥️🧬 #AlphaFold
@pdbeurope.bsky.social
We'll keep developing the AlphaFold Database to support protein science worldwide 🎉
To mark the moment we’ve synchronised the database with UniProtKB release 2025_03.
www.ebi.ac.uk/about/news/t...
🖥️🧬 #AlphaFold
@pdbeurope.bsky.social
October 7, 2025 at 2:03 PM
We’re renewing our collaboration with Google DeepMind!
We'll keep developing the AlphaFold Database to support protein science worldwide 🎉
To mark the moment we’ve synchronised the database with UniProtKB release 2025_03.
www.ebi.ac.uk/about/news/t...
🖥️🧬 #AlphaFold
@pdbeurope.bsky.social
We'll keep developing the AlphaFold Database to support protein science worldwide 🎉
To mark the moment we’ve synchronised the database with UniProtKB release 2025_03.
www.ebi.ac.uk/about/news/t...
🖥️🧬 #AlphaFold
@pdbeurope.bsky.social
Reposted by Jessica Andreani
👩🔬J'ai commencé un kit de démarrage "chercheuses en France" go.bsky.app/TBEzKC #FemmesEnScience
J'ai besoin de votre aide pour le remplir et donner de la visibilité aux chercheuses que vous connaissez et qui sont sur Bluesky !
▶️Taguez celles que vous connaissez, je les ajoute !
J'ai besoin de votre aide pour le remplir et donner de la visibilité aux chercheuses que vous connaissez et qui sont sur Bluesky !
▶️Taguez celles que vous connaissez, je les ajoute !
September 23, 2025 at 2:22 PM
👩🔬J'ai commencé un kit de démarrage "chercheuses en France" go.bsky.app/TBEzKC #FemmesEnScience
J'ai besoin de votre aide pour le remplir et donner de la visibilité aux chercheuses que vous connaissez et qui sont sur Bluesky !
▶️Taguez celles que vous connaissez, je les ajoute !
J'ai besoin de votre aide pour le remplir et donner de la visibilité aux chercheuses que vous connaissez et qui sont sur Bluesky !
▶️Taguez celles que vous connaissez, je les ajoute !
Reposted by Jessica Andreani
We were wondering: Do protein language models learn epistatic signals during pretraining?
Turns out, yes!
Protein Language Models Capture Structural and Functional Epistasis in a Zero-Shot Setting
www.biorxiv.org/content/10.1...
Turns out, yes!
Protein Language Models Capture Structural and Functional Epistasis in a Zero-Shot Setting
www.biorxiv.org/content/10.1...
September 18, 2025 at 12:01 AM
We were wondering: Do protein language models learn epistatic signals during pretraining?
Turns out, yes!
Protein Language Models Capture Structural and Functional Epistasis in a Zero-Shot Setting
www.biorxiv.org/content/10.1...
Turns out, yes!
Protein Language Models Capture Structural and Functional Epistasis in a Zero-Shot Setting
www.biorxiv.org/content/10.1...