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
How does messenger RNA (mRNA) get out of the nucleus to become a protein? Eukaryotic mRNA is packaged, exported, and then translated in the cytoplasm. But how do these steps work? And what are open questions? Check out our new review for our take: www.annualreviews.org/content/jour... (1/3)
November 21, 2025 at 5:37 PM
How does messenger RNA (mRNA) get out of the nucleus to become a protein? Eukaryotic mRNA is packaged, exported, and then translated in the cytoplasm. But how do these steps work? And what are open questions? Check out our new review for our take: www.annualreviews.org/content/jour... (1/3)
Reposted by Jessica Andreani
Messenger RNA is made in the nucleus before it is exported to the cytoplasm for translation. But how are only correctly made mRNAs chosen and remodeled in the nucleus for export?
Our new paper investigates the nuclear events leading to human mRNA export. www.nature.com/articles/s41.... (1/4)
Our new paper investigates the nuclear events leading to human mRNA export. www.nature.com/articles/s41.... (1/4)
November 21, 2025 at 5:02 AM
Messenger RNA is made in the nucleus before it is exported to the cytoplasm for translation. But how are only correctly made mRNAs chosen and remodeled in the nucleus for export?
Our new paper investigates the nuclear events leading to human mRNA export. www.nature.com/articles/s41.... (1/4)
Our new paper investigates the nuclear events leading to human mRNA export. www.nature.com/articles/s41.... (1/4)
Reposted by Jessica Andreani
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
November 19, 2025 at 9:16 PM
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
Reposted by Jessica Andreani
Let’s wrap things up: my commentary on the Asgard hypernucleosomes.
Congratulations to all the authors of the paper 🍾!
kwnsfk27.r.eu-west-1.awstrack.me/L0/https:%2F...
Cryo-EM reveals open and closed Asgard chromatin assemblies: Molecular Cell www.cell.com/molecular-ce...
Congratulations to all the authors of the paper 🍾!
kwnsfk27.r.eu-west-1.awstrack.me/L0/https:%2F...
Cryo-EM reveals open and closed Asgard chromatin assemblies: Molecular Cell www.cell.com/molecular-ce...
Cryo-EM reveals open and closed Asgard chromatin assemblies
Ranawat et al. show the cryo-EM structures of Asgard archaeal chromatin assemblies,
revealing that the histone HHoB assembles into both compact closed and extended open
hypernucleosomes. The closed co...
www.cell.com
November 20, 2025 at 4:23 PM
Let’s wrap things up: my commentary on the Asgard hypernucleosomes.
Congratulations to all the authors of the paper 🍾!
kwnsfk27.r.eu-west-1.awstrack.me/L0/https:%2F...
Cryo-EM reveals open and closed Asgard chromatin assemblies: Molecular Cell www.cell.com/molecular-ce...
Congratulations to all the authors of the paper 🍾!
kwnsfk27.r.eu-west-1.awstrack.me/L0/https:%2F...
Cryo-EM reveals open and closed Asgard chromatin assemblies: Molecular Cell www.cell.com/molecular-ce...
Reposted by Jessica Andreani
Chemical proteomics decrypts the kinases that shape the dynamic human phosphoproteome https://www.biorxiv.org/content/10.1101/2025.11.18.689017v1
November 18, 2025 at 11:03 PM
Chemical proteomics decrypts the kinases that shape the dynamic human phosphoproteome https://www.biorxiv.org/content/10.1101/2025.11.18.689017v1
Reposted by Jessica Andreani
Congratulations to Richard Durbin on being awarded our Genetics Society Medal!
November 14, 2025 at 12:40 PM
Congratulations to Richard Durbin on being awarded our Genetics Society Medal!
Reposted by Jessica Andreani
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
Proteome-wide in silico screening for human protein-protein interactions
Protein-protein interactions (PPIs) drive virtually all biological processes, yet most PPIs have not been identified and even more remain structurally unresolved. We developed a two-step computational...
biorxiv.org
November 12, 2025 at 9:26 PM
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
Reposted by Jessica Andreani
The next ProSE Seminar will be given by Joana Pereira @joanampereira.bsky.social (VIB, KU Leuven)
🗓️ November 11th, 5pm CET
Registration is now open: tinyurl.com/prose-seminar2
Please share!
🗓️ November 11th, 5pm CET
Registration is now open: tinyurl.com/prose-seminar2
Please share!
October 28, 2025 at 12:53 PM
The next ProSE Seminar will be given by Joana Pereira @joanampereira.bsky.social (VIB, KU Leuven)
🗓️ November 11th, 5pm CET
Registration is now open: tinyurl.com/prose-seminar2
Please share!
🗓️ November 11th, 5pm CET
Registration is now open: tinyurl.com/prose-seminar2
Please share!
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...