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Umberto Lupo

@umbislupo.bsky.social
810 followers 398 following 71 posts

Senior ML Scientist at Isomorphic Labs

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Reposted by Umberto Lupo
Yo Akiyama @yoakiyama.bsky.social · 21/07/2026
Excited to share our now published paper @cp-cell.bsky.social highlighting advances in modeling the evolution of protein-protein interactions with MSA Pairformer. Big thanks to Zhidian Zhang, Olivia Tang, @eunbelivable.bsky.social @milot.bsky.social @martinsteinegger.bsky.social and @sokrypton.org!
cell.com
Expanding the scope of protein language modeling to protein-protein interactions with MSA Pairformer
Protein language models have excelled at modeling individual proteins, but extending these capabilities to protein complexes remains a major challenge. MSA Pairformer, a parameter-efficient protein la...
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Alisia Fadini @alisiafadini.bsky.social · 21/07/2026
Atomic models powered bioAI's first era. Experiments measure more. @rs-station.bsky.social is joining omsf.io to unlock interpretation of raw exp observables at scale (blog👇); we'll partner with @openfold.io, @openbind.bsky.social , and cryo-EM+X-ray facilities to make this routine. Join us!
omsf.io
Open Molecular Software Foundation
Making bonds Building open source software and communities for the molecular sciences.
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Thomas Dietterich @tdietterich.bsky.social · 13/05/2026
We are implementing a similar policy at @arxiv.bsky.social. If there is incontrovertible evidence of LLM slop in a paper, this means the authors did not take the time to read the LLM output and we can't trust anything else in the paper. Penalty is 1 year ban from arXiv followed by...
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Simon Hammann @simonhammann.bsky.social · 20/04/2026
Don't be shy to take on a little two-week side project. These five months will be the most precious three years of your academic journey.
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Umberto Lupo @umbislupo.bsky.social · 07/04/2026
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Alisia Fadini @alisiafadini.bsky.social · 01/04/2026
ROCKET 🚀 inference-time optimization of AlphaFold to fit structural data is published! rdcu.be/fa9YH Since our preprint, we’ve pushed it to regimes where other methods break: low resolution, weak signal, real experimental edge cases. Here’s what we learned: 1/15
rdcu.be
AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network
Nature Methods - ROCKET improves experimental structure elucidation by integrating implicit structural knowledge from OpenFold, a trainable reimplementation of AlphaFold2, with X-ray...
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jproney @jproney.bsky.social · 13/03/2026
I'm excited to announce some major updates to our ProteinEBM paper with Chenxi Ou @sokrypton.org!
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Mohammed AlQuraishi @moalquraishi.bsky.social · 13/03/2026
New OpenFold3 preview out! (OF3p2) It closes the gap to AlphaFold3 for most modalities. Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratch🧵1/9
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eLife @elife.bsky.social · 05/03/2026
On the nature of the earliest known lifeforms
buff.ly
On the nature of the earliest known lifeforms
Microfossils reported from Archaean BIFs most likely were liposome-like protocells, which had evolved intracellular mechanisms for energy conservation but not for regulating cell morphology and replication.
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Christian Dallago @machine.learning.bio · 26/02/2026
Five years ago, we released FLIP. The core question was: can ML models for protein fitness prediction generalize in the ways that actually matter for protein engineering, i.e. low data, extrapolation to more mutations, out-of-distribution sequences?
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Simon Olsson @smnlssn.bsky.social · 13/02/2026
New pre-print from the lab on scaling transferable implicit transfer operators to protein dynamics. Collaboration with @olewinther.bsky.social lead by @panosantoniadis.bsky.social.
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Patrick Bryant @patrickbryant1.bsky.social · 07/02/2026
Introducing The Structural History of Eukarya (SHE): The first proteome-scale phylogeny constructed entirely from 3D structure. We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)
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Simons Foundation @simonsfoundation.org · 03/02/2026
While most AI models are trained on text and images, the Polymathic AI collaboration has something different in mind: AI trained on #physics: www.simonsfoundation.org/2025/12/09… #science
simonsfoundation.org
These New AI Models Are Trained on Physics, Not Words, and They’re Driving Discovery
These New AI Models Are Trained on Physics, Not Words, and They’re Driving Discovery on Simons Foundation
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Stephanie Wankowicz @stephanieaw.bsky.social · 21/01/2026
New Preprint!! We show that binding entropy can be quantitatively predicted from crystallographic ensemble models, accounting for both protein conformational entropy and solvent entropy! www.biorxiv.org/content/10.6...
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 30/01/2026
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social. 📄 www.science.org/doi/10.1126/... 🌐 search.foldseek.com/foldmason 💾 github.com/steineggerla...
science.org
Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
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The Get More Smarter Podcast 🧠🏔️ @getmoresmarter.com · 20/01/2026
Important perspective from Greenland.
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John Morgan @johnmorgan3.bsky.social · 19/01/2026
UK Research and Innovation, plus its research councils, quietly quit X. Via @robinbisson.bsky.social @sophieatrpn.bsky.social www.researchprofessionalnews.com/rr-news-uk-r...
researchprofessionalnews.com
UK Research and Innovation and its councils quietly quit X - Research Professional News
Funding agency has “been using alternative platforms” amid ongoing controversies over social media company
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Umberto Lupo @umbislupo.bsky.social · 19/01/2026
I found the secret Pret at Heathrow Terminal 5
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Umberto Lupo @umbislupo.bsky.social · 15/01/2026
This was fun work and a remarkable effort across the computational and wet-lab teams! Strategies for in-silico filtering and ranking of antibody designs have been under-discussed in the literature, e.g. in most technical reports on antibody design that I've seen. Let's talk about these here! [1/n]
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Umberto Lupo @umbislupo.bsky.social · 14/01/2026
At Absci, we performed de novo antibody design campaigns against "zero-prior" epitopes—lacking structural data from antibody-antigen or protein-protein complexes. Model architectures, training data curation, and scoring protocols are fully described. Preprint: www.absci.com/wp-content/u...
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Umberto Lupo @umbislupo.bsky.social · 13/01/2026
fine.house.gov/news/documen...
fine.house.gov
Congressman Fine Introduces Greenland Annexation and Statehood Act to Strengthen U.S. National Security and Put Our Adversaries on Notice
Today, Congressman Fine (FL-06) introduced the Greenland Annexation and Statehood Act, landmark legislation focused on securing America’s strategic national security interests in the Arctic and counte...
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Reposted by Umberto Lupo
Carl Quintanilla @carlquintanilla.bsky.social · 09/01/2026
GERMAN PRESIDENT STEINMEIER: “.. the United States has broken with the values that it helped to establish .. “.. we have now moved beyond the stage where we can lament the lack of respect for international law or the erosion of the international order; we are far beyond that, I believe.”
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Umberto Lupo @umbislupo.bsky.social · 07/01/2026
Recently found out about @jvkersch.bsky.social's `tmtools` github.com/jvkersch/tmt.... It works nicely! Being able to pass user-defined sequence alignments is a nice (if simple) feature that is missing from OpenStructure's own `tmtools` @torstenschwede.bsky.social.
github.com
GitHub - jvkersch/tmtools: Python bindings for the TM-align algorithm and code for protein structure comparison developed by Zhang et al.
Python bindings for the TM-align algorithm and code for protein structure comparison developed by Zhang et al. - jvkersch/tmtools
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Edward Vogel @mathartforall.bsky.social · 06/01/2026
Black swan moment for energy production and storage?
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Umberto Lupo @umbislupo.bsky.social · 29/10/2025
🏛️ 🔍 👀 "There are no optical corrections in the Parthenon"
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 02/10/2025
Visiting Ephesus at #embointegmod25 to look for the missing AlphaFold 3 code
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Lenka Zdeborová @zdeborova.bsky.social · 30/09/2025
Would you like to come to my lab for a postdoctoral position? Apply for the EPFL AI Centre fellowship: epfl.ch/research/fun.... FYI, I have funding (ERC & Simon's collaboration) also for 1-2 top candidates who will not secure the fellowship. Same for @krzakalaf.bsky.social lab.
epfl.ch
EPFL AI Center and Swiss AI Initiative Postdoctoral Fellowships
The 2nd call is now open with a deadline for submissions of 3 November (17.00 CET)!Applications are encouraged from researchers at the postdoctoral level with a keen interest in collaborative, interdi...
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Patrick Kidger @patrickkidger.bsky.social · 12/09/2025
💥 We are *also* organizing Machine Learning for Structural Biology @ EurIPS, Copenhagen!! Topics include anything in the ML+bio intersection. Submit your ML+bio short papers! Authors can even present in both locations if they have people in both locations 🚀
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Umberto Lupo @umbislupo.bsky.social · 04/09/2025
Cool-looking work by @piompons.bsky.social @albecazzaniga.bsky.social @fra-cutu.bsky.social, going beyond existing works on sampling different conformational ensembles with AF2.
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Nature @nature.com · 29/08/2025
Posts about research on Bluesky receive substantially more attention than similar posts on X, formerly called Twitter go.nature.com/45Ftiw4
go.nature.com
Research posts on Bluesky are more original — and get better engagement
Bluesky posts about science garner more likes and reposts than similar ones on X.
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Umberto Lupo @umbislupo.bsky.social · 29/08/2025
Two exciting openings with us! 🤖🧬🆎🧫💉 - AI Scientist 👉 lnkd.in/eDXHH4E8 - AI Scientist, Drug Creation 👉 lnkd.in/eEvGyaTR You'll work on antibody sequence/structure design, antibody-antigen co-folding, antibody-antigen binding prediction, physics-based methodologies, and more! DMs welcome!
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Damiano Sgarbossa @damianosg.bsky.social · 21/08/2025
🎉 Excited to share that the last paper of my PhD is now published in PRX Life! We introduce RAG-ESM, a retrieval-augmented framework that makes pretrained protein language models (like ESM2) homology-aware with minimal training cost. 📄 Paper: journals.aps.org/prxlife/abst...
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Umberto Lupo @umbislupo.bsky.social · 21/08/2025
@cyrilmalbranke.bsky.social is 🦋! "ProteomeLM significantly outperforms DCA in recovering experimentally validated interactions. In H. sapiens, ProteomeLM achieves an AUC of 0.83, compared to 0.73 for DCA. Among the top 10 million scored pairs, it recovers 50% of known PPI, versus only 20% for DCA"
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Paolo De Los Rios @paolodelosrios.bsky.social · 21/08/2025
A no-miss opportunity to join EPFL. We are a vibrant (had to use it 😉) community working in all branches of basic sciences and engineering, and interdisciplinary studies are strongly encouraged. If you want more information, contact the committee heads, or feel free to DM me. tinyurl.com/bd27ky7p
tinyurl.com
Assistant/associate Professor of AI-assisted Biophysics at the Ecole polytechnique fédérale de Lausanne (EPFL) and Group Leader at the Paul Scherrer Institute (PSI)
The School of Basic Sciences (Physics, Chemistry and Mathematics) at EPFL and the Paul Scherrer Institute (PSI) jointly seek to appoint a Tenure Track Assistant or tenured Associate Professor in AI-As...
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Umberto Lupo @umbislupo.bsky.social · 19/08/2025
"When even the most benign activities are subject to capricious disruption and political interference, the luxury of disengagement is no longer a viable option."
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Kieran Didi @kdidi.bsky.social · 15/08/2025
AtomWorks is out! Building upon @biotite_python, we built a toolkit for all things biomolecules and trained RF3 with it. All open-source, test it via `pip install atomworks`! AtomWorks: github.com/RosettaCommo... RF3: github.com/RosettaCommo... Paper: tinyurl.com/y2w4z65b 1/6
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Noah Giansiracusa @profnoahgian.bsky.social · 04/06/2025
From social media apps to bank loans and hiring/firing decisions to search engines and shopping sites, are you tired of living a life ruled by opaque algorithms? Pre-order now to Take Back Control on August 5. bit.ly/4idpeGr
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Yo Akiyama @yoakiyama.bsky.social · 05/08/2025
Excited to share work with Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org biorxiv.org/content/10.1... TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
biorxiv.org
Scaling down protein language modeling with MSA Pairformer
Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...
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Cecilia Clementi @cecclementi.bsky.social · 18/07/2025
Our development of machine-learned transferable coarse-grained models in now on Nat Chem! doi.org/10.1038/s415... I am so proud of my group for this work! Particularly first authors Nick Charron, Klara Bonneau, Aldo Pasos-Trejo, Andrea Guljas.
doi.org
Navigating protein landscapes with a machine-learned transferable coarse-grained model - Nature Chemistry
The development of a universal protein coarse-grained model has been a long-standing challenge. A coarse-grained model with chemical transferability has now been developed by combining deep-learning m...
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Umberto Lupo @umbislupo.bsky.social · 06/06/2025
Proved that the diabolical Einstein field equations can be formulated as a well-posed initial value problem, paving the way for huge progress in mathematical general relativity that continues to this date. Goodbye, Madame Choquet-Bruhat
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Umberto Lupo @umbislupo.bsky.social · 04/06/2025
#Postdoc opportunity in #protein #evolution at #EPFL I can highly recommend working with Anne-Florence Bitbol! You'll bounce ideas off a world-class scientist with an awe-inspiring range of interests and a sharp mind—without sacrificing quality of life or a lake view. tinyurl.com/ProteinPostdoc
Anne-Florence Bitbol
Tenure Track Assistant Professor at EPFL (École polytechnique fédérale de Lausanne)

I am pleased to announce an opening for a postdoctoral position about protein evolution in my group at EPFL in Switzerland. More information: 
https://lnkd.in/e5an5FRS. hashtag#hiring.
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The Guardian @theguardian.com · 19/03/2025
French scientist denied US entry after officers find phone messages criticizing Trump
theguardian.com
French scientist denied US entry after officers find phone messages criticizing Trump
France’s research minister said the scientist was traveling to Houston for a conference when his phone was searched France’s research minister said a French scientist was denied entry to the US this month after immigration officers at an airport searched…
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Jay 🦋 @jay.bsky.team · 13/03/2025
Bluesky is the place for science.
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Sassy0210 @sassy0210.bsky.social · 11/03/2025
Go Sweden! 🇸🇪
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Ilia Igashov @igashov.bsky.social · 11/03/2025
🚨 Check out DrugFlow, our new generative model for structure-based drug design. DrugFlow provides an atom-level confidence score for each designed molecule, and can adjust molecular size on the fly! Additional details in thread 🧵 #ICLR2025
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Umberto Lupo @umbislupo.bsky.social · 10/03/2025
Thank you @seanmcarroll.bsky.social: x.com/seanmcarroll.... This has an effect. People want to keep hearing from you and they too will migrate here.
x.com
Sean Carroll on X: "Most of my social-media activity is elsewhere, but I've been hanging around X to advertise the podcast and occasionally make a political point. But it's become too unpleasant, I have better ways to spend my time. And ultimately I do agree with this sentiment. https://t.co/zittDXKrBz" / X
Most of my social-media activity is elsewhere, but I've been hanging around X to advertise the podcast and occasionally make a political point. But it's become too unpleasant, I have better ways to spend my time. And ultimately I do agree with this sentiment. https://t.co/zittDXKrBz
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Alexis Licht @alexislicht.bsky.social · 07/03/2025
Dear US colleagues, In response to the Trump administration, my university @univ-amu.fr is setting up a new program dedicated to welcoming American scientists wishing to pursue their work in France. There are several M$ in the budget. www.univ-amu.fr/en/public/ac...
univ-amu.fr
Safe Place For Science: Aix Marseille Université ready to welcome American scientists | Aix Marseille Université
In a context where some scientists in the United States may feel threatened or hindered in their research, our university is announcing the launch of the Safe Place For Science program, dedicated to w...
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Umberto Lupo @umbislupo.bsky.social · 06/03/2025
Hello American friends here. Please consider making gigantic protests great again. This platform is too small. A centralized app for coordination seems a good idea to me.
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Nirmalya Kajuri @kajunut.bsky.social · 20/02/2025
POV >Be Ettore Majorana >Discover neutron-proton model of nucleus and predict the neutron first but refuse to publish > Quantize complex scalars but refuse to publish >Predict new kind of fermion >Show possibility of particles with arbitrary spin >Quit physics at 32 >Refuse to explain >Leave ⚛️🧪
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