Diego Javier Zea
@diegozea.bsky.social
Associate Professor at Université Paris-Saclay. Interested in Protein Structure, Interactions and Evolution, Machine Learning, and
Julia programming.
https://diegozea.github.io/
Julia programming.
https://diegozea.github.io/
Reposted by Diego Javier Zea
Scientific Modeling Cheatsheet: SciML has published a quick reference cheatsheet translating hundreds of functions between Julia, Python and MATLAB. Click here for more. sciml.github.io/Scientific_M...
#JuliaLang #SciML #Python #MATLAB #ScientificComputing #DataScience #Cheatsheet #Engineering
#JuliaLang #SciML #Python #MATLAB #ScientificComputing #DataScience #Cheatsheet #Engineering
October 24, 2025 at 3:10 PM
Scientific Modeling Cheatsheet: SciML has published a quick reference cheatsheet translating hundreds of functions between Julia, Python and MATLAB. Click here for more. sciml.github.io/Scientific_M...
#JuliaLang #SciML #Python #MATLAB #ScientificComputing #DataScience #Cheatsheet #Engineering
#JuliaLang #SciML #Python #MATLAB #ScientificComputing #DataScience #Cheatsheet #Engineering
Reposted by Diego Javier Zea
October 18, 2025 at 6:20 AM
🚀 MIToS.jl v3.2.0 brings cleaner substitution matrices, better MSA quality measures, easier MSA merges, and sturdier PDB handling — plus higher test coverage. 🧵
October 17, 2025 at 4:29 PM
🚀 MIToS.jl v3.2.0 brings cleaner substitution matrices, better MSA quality measures, easier MSA merges, and sturdier PDB handling — plus higher test coverage. 🧵
Reposted by Diego Javier Zea
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
📢 Deadline Extended!
The application deadline for the PhD student position has been extended to July 4th. If you haven’t applied yet, there’s still time! 👇
The application deadline for the PhD student position has been extended to July 4th. If you haven’t applied yet, there’s still time! 👇
Great news! I’m hiring a PhD student in structural #Bioinformatics to work on modeling protein conformations and interactions at @i2bcparissaclay.bsky.social
as part of the ANR SPPICES project! 🚀
📅 Start: 1 Sept 2025
⏳ Deadline: 23 June 2025
👉Apply now: emploi.cnrs.fr/Offres/Docto...
as part of the ANR SPPICES project! 🚀
📅 Start: 1 Sept 2025
⏳ Deadline: 23 June 2025
👉Apply now: emploi.cnrs.fr/Offres/Docto...
Portail Emploi CNRS - Offre d'emploi - Doctorant en bioinformatique structurale et évolution des protéines (H/F)
emploi.cnrs.fr
June 24, 2025 at 5:28 AM
📢 Deadline Extended!
The application deadline for the PhD student position has been extended to July 4th. If you haven’t applied yet, there’s still time! 👇
The application deadline for the PhD student position has been extended to July 4th. If you haven’t applied yet, there’s still time! 👇
🚨 We're hiring a Bioinformatics Engineer!
🛠️ Develop #JuliaLang & Python tools to model structural and evolutionary features of IDPs
📅 Start: 1 Sept 2025
🎓 3+ years of higher education (Master’s or engineering diploma preferred)
👉 Apply now: emploi.cnrs.fr/Offres/CDD/U...
🛠️ Develop #JuliaLang & Python tools to model structural and evolutionary features of IDPs
📅 Start: 1 Sept 2025
🎓 3+ years of higher education (Master’s or engineering diploma preferred)
👉 Apply now: emploi.cnrs.fr/Offres/CDD/U...
Portail Emploi CNRS - Offre d'emploi - Ingénieur bioinformaticien – Analyse computationnelle des protéines intrinsèquement désordonnées (H/F)
emploi.cnrs.fr
June 13, 2025 at 11:12 AM
🚨 We're hiring a Bioinformatics Engineer!
🛠️ Develop #JuliaLang & Python tools to model structural and evolutionary features of IDPs
📅 Start: 1 Sept 2025
🎓 3+ years of higher education (Master’s or engineering diploma preferred)
👉 Apply now: emploi.cnrs.fr/Offres/CDD/U...
🛠️ Develop #JuliaLang & Python tools to model structural and evolutionary features of IDPs
📅 Start: 1 Sept 2025
🎓 3+ years of higher education (Master’s or engineering diploma preferred)
👉 Apply now: emploi.cnrs.fr/Offres/CDD/U...
Great news! I’m hiring a PhD student in structural #Bioinformatics to work on modeling protein conformations and interactions at @i2bcparissaclay.bsky.social
as part of the ANR SPPICES project! 🚀
📅 Start: 1 Sept 2025
⏳ Deadline: 23 June 2025
👉Apply now: emploi.cnrs.fr/Offres/Docto...
as part of the ANR SPPICES project! 🚀
📅 Start: 1 Sept 2025
⏳ Deadline: 23 June 2025
👉Apply now: emploi.cnrs.fr/Offres/Docto...
Portail Emploi CNRS - Offre d'emploi - Doctorant en bioinformatique structurale et évolution des protéines (H/F)
emploi.cnrs.fr
June 12, 2025 at 9:33 AM
Great news! I’m hiring a PhD student in structural #Bioinformatics to work on modeling protein conformations and interactions at @i2bcparissaclay.bsky.social
as part of the ANR SPPICES project! 🚀
📅 Start: 1 Sept 2025
⏳ Deadline: 23 June 2025
👉Apply now: emploi.cnrs.fr/Offres/Docto...
as part of the ANR SPPICES project! 🚀
📅 Start: 1 Sept 2025
⏳ Deadline: 23 June 2025
👉Apply now: emploi.cnrs.fr/Offres/Docto...
Reposted by Diego Javier Zea
AlphaFold is amazing but gives you static structures 🧊
In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃
Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...
In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃
Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...
April 17, 2025 at 7:11 PM
AlphaFold is amazing but gives you static structures 🧊
In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃
Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...
In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃
Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...
Reposted by Diego Javier Zea
BioEmu is now easily accessible on Colab. Thank you @martinsteinegger.bsky.social and @jjimenezluna.bsky.social !!
@msftresearch.bsky.social
@msftresearch.bsky.social
Run BioEmu in Colab - just click "Runtime → Run all"! Our notebook uses ColabFold to generate MSAs, BioEmu to predict trajectories, and Foldseek to cluster conformations.
Thanks @jjimenezluna.bsky.social for the help!
🌐 colab.research.google.com/github/sokry...
📄 www.biorxiv.org/content/10.1...
Thanks @jjimenezluna.bsky.social for the help!
🌐 colab.research.google.com/github/sokry...
📄 www.biorxiv.org/content/10.1...
Google Colab
colab.research.google.com
March 29, 2025 at 10:08 AM
BioEmu is now easily accessible on Colab. Thank you @martinsteinegger.bsky.social and @jjimenezluna.bsky.social !!
@msftresearch.bsky.social
@msftresearch.bsky.social
@googlecolab.bsky.social now has native support for #JuliaLang! 🎉 No special setup is needed anymore—start coding and sharing your @julialang.org projects! 🚀
March 6, 2025 at 10:45 AM
@googlecolab.bsky.social now has native support for #JuliaLang! 🎉 No special setup is needed anymore—start coding and sharing your @julialang.org projects! 🚀
Reposted by Diego Javier Zea
🚨 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...
🧬🧶
December 3, 2024 at 10:03 PM
🚨 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 Diego Javier Zea
Chai-1, the open source AF3 clone, is now available with an Apache 2 license github.com/chaidiscover...
November 27, 2024 at 4:58 PM
Chai-1, the open source AF3 clone, is now available with an Apache 2 license github.com/chaidiscover...
Reposted by Diego Javier Zea
Hey folks! I got a bit swamped with all the new #julialang BlueSky people and made my own mega Julia #programmer starter pack!
go.bsky.app/Hv4RKzM
What other starter packs would you want to see? I'm in health research, mathematics, and open source/science. 🧪🛟🩺 📊
go.bsky.app/Hv4RKzM
What other starter packs would you want to see? I'm in health research, mathematics, and open source/science. 🧪🛟🩺 📊
November 8, 2024 at 5:09 AM
Hey folks! I got a bit swamped with all the new #julialang BlueSky people and made my own mega Julia #programmer starter pack!
go.bsky.app/Hv4RKzM
What other starter packs would you want to see? I'm in health research, mathematics, and open source/science. 🧪🛟🩺 📊
go.bsky.app/Hv4RKzM
What other starter packs would you want to see? I'm in health research, mathematics, and open source/science. 🧪🛟🩺 📊
Reposted by Diego Javier Zea
New here? Interested in AI/ML? Check out these great starter packs!
AI: go.bsky.app/SipA7it
RL: go.bsky.app/3WPHcHg
Women in AI: go.bsky.app/LaGDpqg
NLP: go.bsky.app/SngwGeS
AI and news: go.bsky.app/5sFqVNS
You can also search all starter packs here: blueskydirectory.com/starter-pack...
AI: go.bsky.app/SipA7it
RL: go.bsky.app/3WPHcHg
Women in AI: go.bsky.app/LaGDpqg
NLP: go.bsky.app/SngwGeS
AI and news: go.bsky.app/5sFqVNS
You can also search all starter packs here: blueskydirectory.com/starter-pack...
November 9, 2024 at 9:13 AM
New here? Interested in AI/ML? Check out these great starter packs!
AI: go.bsky.app/SipA7it
RL: go.bsky.app/3WPHcHg
Women in AI: go.bsky.app/LaGDpqg
NLP: go.bsky.app/SngwGeS
AI and news: go.bsky.app/5sFqVNS
You can also search all starter packs here: blueskydirectory.com/starter-pack...
AI: go.bsky.app/SipA7it
RL: go.bsky.app/3WPHcHg
Women in AI: go.bsky.app/LaGDpqg
NLP: go.bsky.app/SngwGeS
AI and news: go.bsky.app/5sFqVNS
You can also search all starter packs here: blueskydirectory.com/starter-pack...
Reposted by Diego Javier Zea
This is the first fully open source release of a AF3 like model. Awesome! Congratulations to the team.
Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!
November 17, 2024 at 5:13 PM
This is the first fully open source release of a AF3 like model. Awesome! Congratulations to the team.
Reposted by Diego Javier Zea
⚠️THREAD OF ALL SCIENCE-RELATED STARTER PACKS! ⚠️
🔄Share to help people finding its topic/field
- STRUCTURAL BIOLOGY
Structural Biology 1: bsky.app/starter-pack...
Structural Biology 2: bsky.app/starter-pack...
Crystallography: bsky.app/starter-pack...
Synchrotron&CryoEM: bsky.app/starter-pack...
🔄Share to help people finding its topic/field
- STRUCTURAL BIOLOGY
Structural Biology 1: bsky.app/starter-pack...
Structural Biology 2: bsky.app/starter-pack...
Crystallography: bsky.app/starter-pack...
Synchrotron&CryoEM: bsky.app/starter-pack...
November 17, 2024 at 6:48 PM
⚠️THREAD OF ALL SCIENCE-RELATED STARTER PACKS! ⚠️
🔄Share to help people finding its topic/field
- STRUCTURAL BIOLOGY
Structural Biology 1: bsky.app/starter-pack...
Structural Biology 2: bsky.app/starter-pack...
Crystallography: bsky.app/starter-pack...
Synchrotron&CryoEM: bsky.app/starter-pack...
🔄Share to help people finding its topic/field
- STRUCTURAL BIOLOGY
Structural Biology 1: bsky.app/starter-pack...
Structural Biology 2: bsky.app/starter-pack...
Crystallography: bsky.app/starter-pack...
Synchrotron&CryoEM: bsky.app/starter-pack...
🎉 Exciting news! Our latest paper in Nature Communications delves into protein-protein interaction networks & IDRs using AlphaFold2. Dive into our findings here! 🧬 #Bioinformatics
1/8
1/8
January 30, 2024 at 1:33 PM
🎉 Exciting news! Our latest paper in Nature Communications delves into protein-protein interaction networks & IDRs using AlphaFold2. Dive into our findings here! 🧬 #Bioinformatics
1/8
1/8
Reposted by Diego Javier Zea
Gonna stop curating structbio/ML preprint & papers for a few weeks. The colab notebook below should mostly do the trick (except arxiv) for anyone interested in catching up on whats going on
colab.research.google.com/drive/17e0pD...
colab.research.google.com/drive/17e0pD...
Google Colaboratory
colab.research.google.com
January 26, 2024 at 10:11 AM
Gonna stop curating structbio/ML preprint & papers for a few weeks. The colab notebook below should mostly do the trick (except arxiv) for anyone interested in catching up on whats going on
colab.research.google.com/drive/17e0pD...
colab.research.google.com/drive/17e0pD...
Reposted by Diego Javier Zea
Happy to share our research on using AlphaFold2 to predict how peptides from disordered regions bind proteins, just published in NatureComms
rdcu.be/dwlLa
Work done with Hélène Bret and Raphael Guerois and for the revised version with great contributions from @diegozea.bsky.social and Jinmei Gao.
🧬🧶
rdcu.be/dwlLa
Work done with Hélène Bret and Raphael Guerois and for the revised version with great contributions from @diegozea.bsky.social and Jinmei Gao.
🧬🧶
rdcu.be
January 18, 2024 at 4:59 PM
Happy to share our research on using AlphaFold2 to predict how peptides from disordered regions bind proteins, just published in NatureComms
rdcu.be/dwlLa
Work done with Hélène Bret and Raphael Guerois and for the revised version with great contributions from @diegozea.bsky.social and Jinmei Gao.
🧬🧶
rdcu.be/dwlLa
Work done with Hélène Bret and Raphael Guerois and for the revised version with great contributions from @diegozea.bsky.social and Jinmei Gao.
🧬🧶
Reposted by Diego Javier Zea
New experiment: I will work on a project (starting question: what antibiotic resistance genes co-occur in genomes/metagenomes and does it matter?) completely in the open
Everyone is welcome!
Everyone is welcome!
Extremely Open Science Part 1 : introduction
#science #presentationLuis Pedro Coelho introduces the Extremely Open Science Project for 2024Links:- https://www.big-data-biology.org/extremely-open-science...
youtu.be
January 15, 2024 at 8:53 AM
New experiment: I will work on a project (starting question: what antibiotic resistance genes co-occur in genomes/metagenomes and does it matter?) completely in the open
Everyone is welcome!
Everyone is welcome!
Reposted by Diego Javier Zea
CASP16 will start later this year, so to celebrate that here is a short thread on the uncanny valley separating experimental structures & computational models of proteins. Even though the latter are extremely accurate, there are still some weird differences that are hard to pin down. 🧪🧶🧬🧵
January 3, 2024 at 9:47 AM
CASP16 will start later this year, so to celebrate that here is a short thread on the uncanny valley separating experimental structures & computational models of proteins. Even though the latter are extremely accurate, there are still some weird differences that are hard to pin down. 🧪🧶🧬🧵
Reposted by Diego Javier Zea
My wish for 2024 is that all authors are this direct with their findings
December 31, 2023 at 8:39 AM
My wish for 2024 is that all authors are this direct with their findings
Reposted by Diego Javier Zea
Joris K. - Building Fast Packages Faster: #Julialang as a Backend to #Python and #R (#RStats) Using Julia instead of C or Fortran for package internals can have many advantages for Python and R users, since the language acts more similar to the higher level languages
www.youtube.com/watch?v=JD8H...
www.youtube.com/watch?v=JD8H...
Joris K. - Building Fast Packages Faster: Julia as a Backend to Python and R
Using Julia instead of C or Fortran for package internals can have many advantages for Python and R users, since the language acts more similar to the higher...
www.youtube.com
December 25, 2023 at 12:56 PM
Joris K. - Building Fast Packages Faster: #Julialang as a Backend to #Python and #R (#RStats) Using Julia instead of C or Fortran for package internals can have many advantages for Python and R users, since the language acts more similar to the higher level languages
www.youtube.com/watch?v=JD8H...
www.youtube.com/watch?v=JD8H...