@raphguerois.bsky.social
Bioinformatics Group leader at Institute of Integrative Cell Biology (I2BC), Paris-Saclay, France. Protein addiction, interaction networks, molecular evolution & engineering, genome integrity
Reposted
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 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
November 26, 2025 at 7:44 AM
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 www.pnas.org/doi/10.1073/...
Reposted
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
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 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
November 28, 2025 at 9:39 AM
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
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
Reposted
How do new centromeres evolve while staying compatible with the division machinery?
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
November 26, 2025 at 4:21 PM
How do new centromeres evolve while staying compatible with the division machinery?
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
Reposted
Structural basis for fork reversal and RAD51 regulation by the SCF ubiquitin ligase complex of F-box helicase 1 pubmed.ncbi.nlm.nih.gov/41256537/ #cryoem
November 21, 2025 at 1:10 AM
Structural basis for fork reversal and RAD51 regulation by the SCF ubiquitin ligase complex of F-box helicase 1 pubmed.ncbi.nlm.nih.gov/41256537/ #cryoem
Reposted
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
www.nature.com/articles/s42...
Latest from the lab. The conclusion is in the title!
Basically, we found that the KMN complex (outer kinetochore) is fully conserved between plants and fungi/animals, showing deep origin. (reminder, you are closer to a mushroom than a mushroom is to a plant.)
Latest from the lab. The conclusion is in the title!
Basically, we found that the KMN complex (outer kinetochore) is fully conserved between plants and fungi/animals, showing deep origin. (reminder, you are closer to a mushroom than a mushroom is to a plant.)
The composition and structure of the outer kinetochore KMN complex is conserved across kingdoms - Communications Biology
Affinity purification in Arabidopsis identified all key subunits of the outer kinetochore KMN complex. Functional analyses revealed a striking conservation of its composition and organization across k...
www.nature.com
November 7, 2025 at 7:02 PM
www.nature.com/articles/s42...
Latest from the lab. The conclusion is in the title!
Basically, we found that the KMN complex (outer kinetochore) is fully conserved between plants and fungi/animals, showing deep origin. (reminder, you are closer to a mushroom than a mushroom is to a plant.)
Latest from the lab. The conclusion is in the title!
Basically, we found that the KMN complex (outer kinetochore) is fully conserved between plants and fungi/animals, showing deep origin. (reminder, you are closer to a mushroom than a mushroom is to a plant.)
Reposted
Among the anti-recombinases, FIGNL1 rules them all. So much that inactivating it brings BRCA2-deficient cells to life. Who is responsible for RAD51 loading without BRCA2/FIGNL1, check out the paper to find out! Great collaboration with @raychaudhurilab.bsky.social
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
October 30, 2025 at 8:41 PM
Among the anti-recombinases, FIGNL1 rules them all. So much that inactivating it brings BRCA2-deficient cells to life. Who is responsible for RAD51 loading without BRCA2/FIGNL1, check out the paper to find out! Great collaboration with @raychaudhurilab.bsky.social
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted
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
Prime editing sensor libraries evaluate diverse genetic variants in their endogenous genomic contexts go.nature.com/49Q1WCQ
rdcu.be/eLVts
rdcu.be/eLVts
High-throughput evaluation of genetic variants with prime editing sensor libraries - Nature Biotechnology
Prime editing sensor libraries evaluate diverse genetic variants in their endogenous genomic contexts.
go.nature.com
October 23, 2025 at 2:19 AM
Prime editing sensor libraries evaluate diverse genetic variants in their endogenous genomic contexts go.nature.com/49Q1WCQ
rdcu.be/eLVts
rdcu.be/eLVts
Reposted
Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 14, 2025 at 6:45 PM
Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted
Thrilled to announce our new preprint, “Protein Hunter: Exploiting Structure Hallucination within Diffusion for Protein Design,” in collaboration with @Griffin, @GBhardwaj8 and @sokrypton.org
🧬Code and notebooks will be released by the end of this week.
🎧Golden- Kpop Demon Hunters
🧬Code and notebooks will be released by the end of this week.
🎧Golden- Kpop Demon Hunters
October 13, 2025 at 3:45 PM
Thrilled to announce our new preprint, “Protein Hunter: Exploiting Structure Hallucination within Diffusion for Protein Design,” in collaboration with @Griffin, @GBhardwaj8 and @sokrypton.org
🧬Code and notebooks will be released by the end of this week.
🎧Golden- Kpop Demon Hunters
🧬Code and notebooks will be released by the end of this week.
🎧Golden- Kpop Demon Hunters
Reposted
GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio
www.nature.com/articles/s41...
www.nature.com/articles/s41...
GPU-accelerated homology search with MMseqs2 - Nature Methods
Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...
www.nature.com
September 18, 2025 at 8:09 PM
GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 27, 2025 at 4:14 PM
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted
Now online! AI-generated MLH1 small binder improves prime editing efficiency
AI-generated MLH1 small binder improves prime editing efficiency
A compact, AI-generated suppressor of DNA mismatch repair can enhance prime editing in vivo and in vitro and can be integrated into a variety of prime editing architectures.
dlvr.it
August 5, 2025 at 6:52 PM
Now online! AI-generated MLH1 small binder improves prime editing efficiency
Reposted
Reposted
Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
July 7, 2025 at 8:21 AM
Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
Reposted
AI just cracked de novo antibody design with a 100x leap! 🧪
Chai-2, a next-gen multimodal generative model, is shaking up protein design. With a 16% hit rate in fully de novo antibody design—over 100 times better than previous methods—it’s making drug discovery faster and more precise than ever.
Chai-2, a next-gen multimodal generative model, is shaking up protein design. With a 16% hit rate in fully de novo antibody design—over 100 times better than previous methods—it’s making drug discovery faster and more precise than ever.
July 1, 2025 at 2:34 AM
AI just cracked de novo antibody design with a 100x leap! 🧪
Chai-2, a next-gen multimodal generative model, is shaking up protein design. With a 16% hit rate in fully de novo antibody design—over 100 times better than previous methods—it’s making drug discovery faster and more precise than ever.
Chai-2, a next-gen multimodal generative model, is shaking up protein design. With a 16% hit rate in fully de novo antibody design—over 100 times better than previous methods—it’s making drug discovery faster and more precise than ever.
Reposted
Excited to unveil Boltz-2, our new model capable not only of predicting structures but also binding affinities! Boltz-2 is the first AI model to approach the performance of FEP simulations while being more than 1000x faster! All open-sourced under MIT license! A thread… 🤗🚀
June 6, 2025 at 1:46 PM
Excited to unveil Boltz-2, our new model capable not only of predicting structures but also binding affinities! Boltz-2 is the first AI model to approach the performance of FEP simulations while being more than 1000x faster! All open-sourced under MIT license! A thread… 🤗🚀
Reposted
🚀 Excited to release BoltzDesign1!
✨ Now with LogMD-based trajectory visualization.
🔗 Demo: rcsb.ai/ff9c2b1ee8
Feedback & collabs welcome! 🙌
🔗: GitHub: github.com/yehlincho/Bo...
🔗: Colab: colab.research.google.com/github/yehli...
@sokrypton.org @martinpacesa.bsky.social
✨ Now with LogMD-based trajectory visualization.
🔗 Demo: rcsb.ai/ff9c2b1ee8
Feedback & collabs welcome! 🙌
🔗: GitHub: github.com/yehlincho/Bo...
🔗: Colab: colab.research.google.com/github/yehli...
@sokrypton.org @martinpacesa.bsky.social
June 3, 2025 at 1:31 AM
🚀 Excited to release BoltzDesign1!
✨ Now with LogMD-based trajectory visualization.
🔗 Demo: rcsb.ai/ff9c2b1ee8
Feedback & collabs welcome! 🙌
🔗: GitHub: github.com/yehlincho/Bo...
🔗: Colab: colab.research.google.com/github/yehli...
@sokrypton.org @martinpacesa.bsky.social
✨ Now with LogMD-based trajectory visualization.
🔗 Demo: rcsb.ai/ff9c2b1ee8
Feedback & collabs welcome! 🙌
🔗: GitHub: github.com/yehlincho/Bo...
🔗: Colab: colab.research.google.com/github/yehli...
@sokrypton.org @martinpacesa.bsky.social
Reposted
@science.org 🧫🧬❄️🔬 Molecular basis of influenza ribonucleoprotein complex assembly and processive RNA synthesis | Science www.science.org/doi/10.1126/...
@yiweichang.bsky.social www.yiweichanglab.org @jiwasa.bsky.social #virology #Influenza #Cryo-EM #StructuralBiology #RNA #polymerase
@yiweichang.bsky.social www.yiweichanglab.org @jiwasa.bsky.social #virology #Influenza #Cryo-EM #StructuralBiology #RNA #polymerase
May 15, 2025 at 11:12 PM
@science.org 🧫🧬❄️🔬 Molecular basis of influenza ribonucleoprotein complex assembly and processive RNA synthesis | Science www.science.org/doi/10.1126/...
@yiweichang.bsky.social www.yiweichanglab.org @jiwasa.bsky.social #virology #Influenza #Cryo-EM #StructuralBiology #RNA #polymerase
@yiweichang.bsky.social www.yiweichanglab.org @jiwasa.bsky.social #virology #Influenza #Cryo-EM #StructuralBiology #RNA #polymerase
Reposted
Forget liquid-liquid phase separation, here comes solid phase transition 😱
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Solid phase transitions as a solution to the genome folding paradox - Nature
In vitro reconstitution and in vivo live-cell imaging of LHX2–EBF1–LDB1 enhancer hubs in olfactory sensory neurons reveals that these transcription factors form condensates with solid, rathe...
www.nature.com
May 14, 2025 at 6:41 PM
Forget liquid-liquid phase separation, here comes solid phase transition 😱
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted
Pleased to share a new preprint - a great collaboration with @jessicaandreani.bsky.social and the Guerois lab at I2BC, and the Radicella lab at the CEA. Using stuctural modelling, we reveal & validate a 3 protein complex involved in DNA import during transformation.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
A tripartite protein complex promotes DNA transport during natural transformation in firmicutes.
Natural genetic transformation is a conserved mechanism of bacterial horizontal gene transfer, which is directed entirely by the recipient cell and facilitates the acquisition of new genetic traits su...
www.biorxiv.org
May 12, 2025 at 6:14 AM
Pleased to share a new preprint - a great collaboration with @jessicaandreani.bsky.social and the Guerois lab at I2BC, and the Radicella lab at the CEA. Using stuctural modelling, we reveal & validate a 3 protein complex involved in DNA import during transformation.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted
Please see our latest paper on the role of EXO1 in meiosis: "EXO1 promotes the meiotic MLH1-MLH3 endonuclease through conserved interactions with MLH1, MSH4 and DNA". Congratulations to both first authors, Megha Roy and Aurore Sanchez and thanks to all our collaborators!
May 5, 2025 at 7:22 AM
Please see our latest paper on the role of EXO1 in meiosis: "EXO1 promotes the meiotic MLH1-MLH3 endonuclease through conserved interactions with MLH1, MSH4 and DNA". Congratulations to both first authors, Megha Roy and Aurore Sanchez and thanks to all our collaborators!
Reposted
Happy to share our DNA Repair special issue on the replication stress response curated with @vindignilab.bsky.social.
www.sciencedirect.com/special-issu...
www.sciencedirect.com/special-issu...
DNA Repair | The replication stress response: mechanisms and functions | ScienceDirect.com by ElsevierScienceDirect
High-fidelity DNA replication is constantly challenged by a diverse range of obstacles, including endogenous lesions and secondary structures in the DNA template, tightly bound protein-DNA complexes, ...
www.sciencedirect.com
April 17, 2025 at 4:01 AM
Happy to share our DNA Repair special issue on the replication stress response curated with @vindignilab.bsky.social.
www.sciencedirect.com/special-issu...
www.sciencedirect.com/special-issu...
Reposted
📣 Happy to announce that "DprA recruits ComM to facilitate recombination during natural transformation in Gram-negative bacteria" just got published in PNAS www.pnas.org/doi/abs/10.1...
🧬🧶👩🔬👩💻 Collaborative and interdisciplinary work, together with the groups of Ankur Dalia and J. Pablo Radicella
🧬🧶👩🔬👩💻 Collaborative and interdisciplinary work, together with the groups of Ankur Dalia and J. Pablo Radicella
DprA recruits ComM to facilitate recombination during natural transformation in Gram-negative bacteria | PNAS
Natural transformation (NT) represents one of the major modes of horizontal gene transfer
in bacterial species. During NT, cells can take up free D...
www.pnas.org
April 14, 2025 at 5:42 AM
📣 Happy to announce that "DprA recruits ComM to facilitate recombination during natural transformation in Gram-negative bacteria" just got published in PNAS www.pnas.org/doi/abs/10.1...
🧬🧶👩🔬👩💻 Collaborative and interdisciplinary work, together with the groups of Ankur Dalia and J. Pablo Radicella
🧬🧶👩🔬👩💻 Collaborative and interdisciplinary work, together with the groups of Ankur Dalia and J. Pablo Radicella