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Diego Javier Zea

@diegozea.bsky.social
1.9K followers 4.1K following 43 posts

Associate Professor at Université Paris-Saclay. Interested in Protein Structure, Interactions and Evolution, Machine Learning, and Julia programming. diegozea.github.io

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Diego Javier Zea @diegozea.bsky.social · 19/08/2026
7/7 Finally, a huge thanks to Julie Liliane Daniel and Lucas Vitoriano for all their work on AlphaConformers; to Raphaël Guerois, Jessica Andreani and the AMIG team for their feedback and support; and to I2BC, CEA, Université Paris-Saclay, CNRS, ANR/SPPICES and GENCI-IDRIS. 🙏
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Diego Javier Zea @diegozea.bsky.social · 19/08/2026
6/7 I remember #JuliaCon 2024 with only a couple of biology talks. This year there were dedicated sessions on biology, health, and pharma 📈 Great to see #JuliaLang's adoption growing across the life sciences 🧬
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Diego Javier Zea @diegozea.bsky.social · 19/08/2026
5/7 I also presented a poster at #JuliaCon on MIToS.jl, my Julia package for working with protein sequences and structures. AlphaConformers relies heavily on MIToS, and developing the pipeline drove several improvements on it. MIToS: github.com/diegozea/MIT...
Me with my poster presenting the new features of MIToS at JuliaCon Global 2026.
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Diego Javier Zea @diegozea.bsky.social · 19/08/2026
4/7 This software side was the focus of my #JuliaCon talk: Julia as a glue language for reproducible #bioinformatics pipelines, with JLL packages providing versioned, cross-platform command-line tools. Talk (timestamped) ▶️ : www.youtube.com/live/5Ux0rKe...
youtube.com
Muschel N1 | JuliaCon Global 2026 | Day 1
YouTube video by The Julia Programming Language
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Diego Javier Zea @diegozea.bsky.social · 19/08/2026
3/7 The code is open source and available as a Julia package. AlphaConformers brings together #JuliaLang code and external bioinformatics tools in a reproducible workflow. Code💻: github.com/diegozea/Alp...
github.com
GitHub - diegozea/AlphaConformers.jl
Contribute to diegozea/AlphaConformers.jl development by creating an account on GitHub.
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Diego Javier Zea @diegozea.bsky.social · 19/08/2026
2/7 AlphaConformers searches for structurally related proteins and organizes their diversity into structure-derived MSAs and template sets, giving AlphaFold alternative conformational hypotheses to explore. Preprint 📄: www.biorxiv.org/content/10.6...
biorxiv.org
AlphaConformers: Structure-guided sampling enables prediction of multiple protein conformations
Proteins are dynamic molecules capable of adopting multiple conformations. However, AlphaFold2 predominantly generates models around a single conformation, usually representing a ligand-bound state. T...
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Diego Javier Zea @diegozea.bsky.social · 19/08/2026
1/7 Two busy weeks around AlphaConformers: last week I presented it at #JuliaCon Global 2026; this week, our preprint is out on bioRxiv. The question behind it: can structural information help AlphaFold explore alternative protein conformations? 🧵
Here's the image of the apo-form, which serves as the query, alongside the holo-form, the target, along with the closest AlphaConformer model for the holo form, illustrating a successful example.
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JuliaHub @juliahub.bsky.social · 03/12/2025
Join us for a deep dive into JuliaC, the new toolchain for building executables and shared libraries from Julia code. Learn how to create compact binaries and integrate Julia with #C, #C++, #Python, and more. juliahub.com/events/build... #JuliaLang #EmbeddedSystems #TechnicalComputing
juliahub.com
JuliaC: A New Tool for Building Julia Binaries - Event - JuliaHub
Explore how JuliaC builds compact Julia binaries for embedded systems and real-time deployment, simplifying integration across engineering workflows.
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JuliaHub @juliahub.bsky.social · 24/10/2025
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
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Mehmet Hakan Satman @jbytecode.bsky.social · 18/10/2025
Julia v1.12.1 is out! 🎈🙃 #JuliaLang
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Diego Javier Zea @diegozea.bsky.social · 17/10/2025
#JuliaLang #Bioinformatics
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Diego Javier Zea @diegozea.bsky.social · 17/10/2025
🛡️ Confidence boost: refreshed benchmarks and tests now cover 96%+ of the code. Repo: github.com/diegozea/MIT...
github.com
GitHub - diegozea/MIToS.jl: A Julia package to analyze protein sequences, structures, and evolutionary information
A Julia package to analyze protein sequences, structures, and evolutionary information - diegozea/MIToS.jl
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Diego Javier Zea @diegozea.bsky.social · 17/10/2025
🎨 Better structure viz: edit B-factors so you can color atoms/residues by any variable when plotting (e.g., quality, flexibility, or scores).
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Diego Javier Zea @diegozea.bsky.social · 17/10/2025
🗂️ Combining datasets is simpler: merge MSAs by matching sequence names automatically when pairings aren’t specified.
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Diego Javier Zea @diegozea.bsky.social · 17/10/2025
📈 MSA stats at a glance: estimate the effective number of sequences (down-weight redundancy) and quantify the share of “positive” residue pairs under your chosen matrix.
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Diego Javier Zea @diegozea.bsky.social · 17/10/2025
📊 Alignment quality: get the classic sum-of-pairs score for an MSA using a residue substitution matrix (BLOSUM62 by default), with consistent handling of gaps and unknowns.
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Diego Javier Zea @diegozea.bsky.social · 17/10/2025
🧬 Substitution matrices are now first-class: use built-ins like BLOSUM62 or bring your own from BioJulia’s BioAlignments.
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Diego Javier Zea @diegozea.bsky.social · 17/10/2025
🚀 MIToS.jl v3.2.0 brings cleaner substitution matrices, better MSA quality measures, easier MSA merges, and sturdier PDB handling — plus higher test coverage. 🧵
Dragon showing the Julia colors and the text: MIToS.jl v3.2
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 07/07/2025
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
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Diego Javier Zea @diegozea.bsky.social · 24/06/2025
📢 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! 👇
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Diego Javier Zea @diegozea.bsky.social · 13/06/2025
Join the MAGI team at @i2bcparissaclay.bsky.social as part of the ANR SPPICES project 🌶️ This position involves collaboration with members of the ML4NGP network on machine learning & non-globular proteins Learn more 👉 sppices.notion.site
sppices.notion.site
ANR SPPICES
Scoring and Predicting Protein Interactions and Conformations based on Evolutionary Signals
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Diego Javier Zea @diegozea.bsky.social · 13/06/2025
🚨 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...
emploi.cnrs.fr
Portail Emploi CNRS - Offre d'emploi - Ingénieur bioinformaticien – Analyse computationnelle des protéines intrinsèquement désordonnées (H/F)
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Diego Javier Zea @diegozea.bsky.social · 12/06/2025
Learn more about the SPPICES project (Scoring and Predicting Protein Interactions and Conformations based on Evolutionary Signals) here: sppices.notion.site
sppices.notion.site
ANR SPPICES
Scoring and Predicting Protein Interactions and Conformations based on Evolutionary Signals
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Diego Javier Zea @diegozea.bsky.social · 12/06/2025
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...
emploi.cnrs.fr
Portail Emploi CNRS - Offre d'emploi - Doctorant en bioinformatique structurale et évolution des protéines (H/F)
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 17/04/2025
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...
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Diego Javier Zea @diegozea.bsky.social · 30/03/2025
Book/Course
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Frank Noe @franknoe.bsky.social · 29/03/2025
BioEmu is now easily accessible on Colab. Thank you @martinsteinegger.bsky.social and @jjimenezluna.bsky.social !! @msftresearch.bsky.social
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Diego Javier Zea @diegozea.bsky.social · 06/03/2025
I have the same question. I haven't checked yet.
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Diego Javier Zea @diegozea.bsky.social · 06/03/2025
Yes, before, it was pretty cumbersome and slow. Now, it is the opposite experience 🙂
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Diego Javier Zea @diegozea.bsky.social · 06/03/2025
@googlecolab.bsky.social now has native support for #JuliaLang! 🎉 No special setup is needed anymore—start coding and sharing your @julialang.org projects! 🚀
Screen capture of Google Colab showing their native version of Julia (1.10.8)
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Diego Javier Zea @diegozea.bsky.social · 07/12/2024
Since you knew it, could it have helped more unconsciously, being there feeding the intuitions? 🤔
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Diego Javier Zea @diegozea.bsky.social · 06/12/2024
I am not sure that the Julia's Fibonacci implementation is optimal. Using Val is nice to showcase dispatch, but it hits compilation for every number, and it makes the code type unstable. Conversely, using Val should make the compiler memoize the result for each number. github.com/bddicken/lan...
github.com
languages/fibonacci/julia/code.jl at bf71f98f0a823775c16fdb79f2445438f471edf6 · bddicken/languages
Compare languages. Contribute to bddicken/languages development by creating an account on GitHub.
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Jessica Andreani @jessicaandreani.bsky.social · 03/12/2024
🚨 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
Structural comparison of homologous protein-RNA interfaces reveals widespread overall conservation contrasted with versatility in polar contacts
Author summary Protein-RNA interactions are crucial to many biological functions and can play a role in diseases. We adopted a computational strategy to analyze and compare experimental 3D structures ...
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Diego del Alamo @delalamo.xyz · 27/11/2024
Chai-1, the open source AF3 clone, is now available with an Apache 2 license github.com/chaidiscover...
Chai-1 is released under an Apache 2.0 License, which means it can be used for both academic and commerical purposes, including for drug discovery.
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Diego Javier Zea @diegozea.bsky.social · 23/11/2024
Could you add me to the pack if structural bioinformatics and molecular evolution are welcome?
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Diego Javier Zea @diegozea.bsky.social · 22/11/2024
Thanks :)
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Diego Javier Zea @diegozea.bsky.social · 21/11/2024
Hi! I nominate myself :)
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Jacob S. Zelko @thecedarprince.bsky.social · 08/11/2024
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. 🧪🛟🩺 📊
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Maike Osborne @maosbot.bsky.social · 09/11/2024
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...
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 17/11/2024
This is the first fully open source release of a AF3 like model. Awesome! Congratulations to the team.
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Diego Javier Zea @diegozea.bsky.social · 19/11/2024
Hi! I would love to be added to the pack :) Thanks!
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Diego Javier Zea @diegozea.bsky.social · 18/11/2024
Thank you :)
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Diego Javier Zea @diegozea.bsky.social · 18/11/2024
Thanks! :)
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Diego Javier Zea @diegozea.bsky.social · 18/11/2024
Hi! I would love to be added to the starter pack. Thanks! :)
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Diego Javier Zea @diegozea.bsky.social · 18/11/2024
Hi! I would love to be added to the pack :) Cheers
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Razvan Borza @rborza.bsky.social · 17/11/2024
⚠️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...
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Diego Javier Zea @diegozea.bsky.social · 18/11/2024
Hi! Can you please add me to the list? Thanks :)
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Diego Javier Zea @diegozea.bsky.social · 30/01/2024
🌟 Last but not least, I have huge appreciation for Hélène Bret, Raphaël Guerois, and @jessicaandreani.bsky.social for driving this research forward. Their expertise shone throughout the project. Jinmei Gao and I contributed mainly during the review phase. 8/8
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Diego Javier Zea @diegozea.bsky.social · 30/01/2024
🙏 Special thanks to our insightful reviewers, @arneelof.bsky.social and an anonymous expert, whose feedback immensely enhanced our paper. Your contributions are invaluable! 7/8
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Diego Javier Zea @diegozea.bsky.social · 30/01/2024
💻 Our pipeline is available on GitHub if you want to test it: github.com/i2bc/SCAN_IDR 6/8
github.com
GitHub - i2bc/SCAN_IDR
Contribute to i2bc/SCAN_IDR development by creating an account on GitHub.
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