Martin Pacesa
@martinpacesa.bsky.social
Assistant Professor at the University of Zurich.
🖥️ protein design, machine learning🤖, crystallography💎, cryoEM🔬. Avid weirdness connoisseur 🎩
🖥️ protein design, machine learning🤖, crystallography💎, cryoEM🔬. Avid weirdness connoisseur 🎩
Reposted by Martin Pacesa
In 2017 we showed that homomers evolve on the edge of supramolecular self-assembly. Here we show how to exploit this vulnerability so that ALL homomers can become bona fide drug-🎯. Delighted that Aim 3 of our @erc.europa.eu finally polymerized! Manuscript: 👉 rdcu.be/e27bT
February 9, 2026 at 5:36 PM
In 2017 we showed that homomers evolve on the edge of supramolecular self-assembly. Here we show how to exploit this vulnerability so that ALL homomers can become bona fide drug-🎯. Delighted that Aim 3 of our @erc.europa.eu finally polymerized! Manuscript: 👉 rdcu.be/e27bT
Reposted by Martin Pacesa
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)
We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)
February 7, 2026 at 8:50 AM
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)
We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)
Reposted by Martin Pacesa
Bluesky doesn’t really shine yet as a place to discover papers, especially at the intersection of biology and ML. To help a little, I’m going to start sharing papers I find interesting. To kick things off, here’s one from @petar-v.bsky.social and colleagues at DeepMind
arxiv.org/abs/2601.22950
arxiv.org/abs/2601.22950
Perplexity Cannot Always Tell Right from Wrong
Perplexity -- a function measuring a model's overall level of "surprise" when encountering a particular output -- has gained significant traction in recent years, both as a loss function and as a simp...
arxiv.org
February 3, 2026 at 8:47 AM
Bluesky doesn’t really shine yet as a place to discover papers, especially at the intersection of biology and ML. To help a little, I’m going to start sharing papers I find interesting. To kick things off, here’s one from @petar-v.bsky.social and colleagues at DeepMind
arxiv.org/abs/2601.22950
arxiv.org/abs/2601.22950
Reposted by Martin Pacesa
🗓️ Save the Date!
The 5th European RosettaCon – Crossing Boundaries with Protein Design will take place in Lisbon, Portugal 🇵🇹
🗓️ October 28–30, 2026
Join the protein design community for an inspiring scientific meeting at the intersection of innovation and design.
The 5th European RosettaCon – Crossing Boundaries with Protein Design will take place in Lisbon, Portugal 🇵🇹
🗓️ October 28–30, 2026
Join the protein design community for an inspiring scientific meeting at the intersection of innovation and design.
February 3, 2026 at 6:05 AM
🗓️ Save the Date!
The 5th European RosettaCon – Crossing Boundaries with Protein Design will take place in Lisbon, Portugal 🇵🇹
🗓️ October 28–30, 2026
Join the protein design community for an inspiring scientific meeting at the intersection of innovation and design.
The 5th European RosettaCon – Crossing Boundaries with Protein Design will take place in Lisbon, Portugal 🇵🇹
🗓️ October 28–30, 2026
Join the protein design community for an inspiring scientific meeting at the intersection of innovation and design.
Here are the success rates of de novo pipelines based on which designs I could actually identify the methods for.
January 22, 2026 at 3:48 PM
Here are the success rates of de novo pipelines based on which designs I could actually identify the methods for.
Huge congratulations @nboyd.bsky.social with Mosaic that absolutely killed in the competition! 𝑩𝒊𝒏𝒅𝑪𝒓𝒂𝒇𝒕2 did also pretty well with the second highest hit rate in the competition!
proteinbase.com/collections/...
proteinbase.com/collections/...
proteinbase.com
January 22, 2026 at 8:29 AM
Huge congratulations @nboyd.bsky.social with Mosaic that absolutely killed in the competition! 𝑩𝒊𝒏𝒅𝑪𝒓𝒂𝒇𝒕2 did also pretty well with the second highest hit rate in the competition!
proteinbase.com/collections/...
proteinbase.com/collections/...
Reposted by Martin Pacesa
My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring!
mirdita.org
mirdita.org
Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning
Mirdita Lab builds scalable bioinformatics methods.
mirdita.org
January 20, 2026 at 11:07 AM
My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring!
mirdita.org
mirdita.org
Reposted by Martin Pacesa
🔬 Postdoc position – Infection Biology & Cryo-ET (Zurich) 🇨🇭
We are looking for a motivated Postdoc to join our interdisciplinary team.
📩 Interested? Check out the job advert:
www.imm.uzh.ch/dam/jcr:cb17...
👉 More info on the lab: www.weiss-laboratory.com
Please share with interested colleagues!
We are looking for a motivated Postdoc to join our interdisciplinary team.
📩 Interested? Check out the job advert:
www.imm.uzh.ch/dam/jcr:cb17...
👉 More info on the lab: www.weiss-laboratory.com
Please share with interested colleagues!
January 19, 2026 at 1:15 PM
🔬 Postdoc position – Infection Biology & Cryo-ET (Zurich) 🇨🇭
We are looking for a motivated Postdoc to join our interdisciplinary team.
📩 Interested? Check out the job advert:
www.imm.uzh.ch/dam/jcr:cb17...
👉 More info on the lab: www.weiss-laboratory.com
Please share with interested colleagues!
We are looking for a motivated Postdoc to join our interdisciplinary team.
📩 Interested? Check out the job advert:
www.imm.uzh.ch/dam/jcr:cb17...
👉 More info on the lab: www.weiss-laboratory.com
Please share with interested colleagues!
Reposted by Martin Pacesa
Perfect birthday gift 🙌 happy this one is out!
A good end to 2025: rhodamine-binders for bioimaging in JACS: pubs.acs.org/doi/10.1021/...
Fast, Bright, and Reversible Fluorescent Labeling of Rhodamine-Binding Proteins
Rhodamine dyes conjugated to targeting ligands can yield exceptionally bright fluorescent probes for live-cell imaging. However, the limited permeability of such rhodamine derivatives restricts their ...
pubs.acs.org
December 31, 2025 at 2:03 PM
Perfect birthday gift 🙌 happy this one is out!
Fully circular double rainbow appeared today while snowboarding
December 30, 2025 at 2:54 PM
Fully circular double rainbow appeared today while snowboarding
Super excited about our 𝑩𝒊𝒏𝒅𝑪𝒓𝒂𝒇𝒕 pipeline being highlighted as one of @twistbioscience.com favourite publications of 2025!
We did synthesize all binder genes with Twist ❤️
We did synthesize all binder genes with Twist ❤️
BindCraft, an open-source and automated pipeline for de novo protein binder design is presented by Bruno Correia, Martin Pacesa, Lennart Nickel, and Christian Schellhaas:
“One-shot design of functional protein binders with BindCraft”
“One-shot design of functional protein binders with BindCraft”
One-shot design of functional protein binders with BindCraft - Nature
BindCraft, an open-source, automated pipeline for de novo protein binder design with experimental success rates of 10–100%, leverages AlphaFold2 weights to generate binders with nanomolar affinity wit...
www.nature.com
December 29, 2025 at 3:15 PM
Super excited about our 𝑩𝒊𝒏𝒅𝑪𝒓𝒂𝒇𝒕 pipeline being highlighted as one of @twistbioscience.com favourite publications of 2025!
We did synthesize all binder genes with Twist ❤️
We did synthesize all binder genes with Twist ❤️
Repeat after me: GENE 👏 EXPRESSION 👏 PROFILING 👏 DOES 👏 NOT 👏 A 👏 VIRTUAL 👏 CELL 👏 MAKE 👏
December 26, 2025 at 12:11 PM
Repeat after me: GENE 👏 EXPRESSION 👏 PROFILING 👏 DOES 👏 NOT 👏 A 👏 VIRTUAL 👏 CELL 👏 MAKE 👏
Reposted by Martin Pacesa
I've been thinking about the "virtual cell" concept and wanted to write up a few thoughts. Specifically on how I think the prior experience in GWAS informs the most likely way these models will be useful.
andrewcarroll.github.io/2025/12/23/t...
andrewcarroll.github.io/2025/12/23/t...
The Virtual Cell Will Be More Like Gwas Than Alphafold
There has been significant discussion recently on the concept of the “virtual cell.” I want to summarize the key concepts regarding what the field wants from a virtual cell and the challenges we face....
andrewcarroll.github.io
December 24, 2025 at 1:52 AM
I've been thinking about the "virtual cell" concept and wanted to write up a few thoughts. Specifically on how I think the prior experience in GWAS informs the most likely way these models will be useful.
andrewcarroll.github.io/2025/12/23/t...
andrewcarroll.github.io/2025/12/23/t...
Reposted by Martin Pacesa
JOB ALERT: Operations Director (DCI–Lausanne).
The DCI, a joint initiative of EPFL, UNIL, UNIGE and UNIBE, is recruiting an Operations Director to lead the cryo-EM facility in Lausanne.
📩 Questions: CEO of the DCI: @chgenoud.bsky.social
🔗 Apply here: careers.epfl.ch/job/Lausanne...
The DCI, a joint initiative of EPFL, UNIL, UNIGE and UNIBE, is recruiting an Operations Director to lead the cryo-EM facility in Lausanne.
📩 Questions: CEO of the DCI: @chgenoud.bsky.social
🔗 Apply here: careers.epfl.ch/job/Lausanne...
December 17, 2025 at 12:00 PM
JOB ALERT: Operations Director (DCI–Lausanne).
The DCI, a joint initiative of EPFL, UNIL, UNIGE and UNIBE, is recruiting an Operations Director to lead the cryo-EM facility in Lausanne.
📩 Questions: CEO of the DCI: @chgenoud.bsky.social
🔗 Apply here: careers.epfl.ch/job/Lausanne...
The DCI, a joint initiative of EPFL, UNIL, UNIGE and UNIBE, is recruiting an Operations Director to lead the cryo-EM facility in Lausanne.
📩 Questions: CEO of the DCI: @chgenoud.bsky.social
🔗 Apply here: careers.epfl.ch/job/Lausanne...
Reposted by Martin Pacesa
Are you interested in integrative structural biology, but feel a bit lost?
Don't worry, we have you covered with our FEBS Advanced Course, Lost in Integration Vol. 2 — probing biomolecules with AI and experiments
probingbiomolecules2026.febsevents.org
network.febs.org/posts/integr...
Don't worry, we have you covered with our FEBS Advanced Course, Lost in Integration Vol. 2 — probing biomolecules with AI and experiments
probingbiomolecules2026.febsevents.org
network.febs.org/posts/integr...
December 18, 2025 at 7:27 PM
Are you interested in integrative structural biology, but feel a bit lost?
Don't worry, we have you covered with our FEBS Advanced Course, Lost in Integration Vol. 2 — probing biomolecules with AI and experiments
probingbiomolecules2026.febsevents.org
network.febs.org/posts/integr...
Don't worry, we have you covered with our FEBS Advanced Course, Lost in Integration Vol. 2 — probing biomolecules with AI and experiments
probingbiomolecules2026.febsevents.org
network.febs.org/posts/integr...
This is an amazing position, DCI Lausanne is looking for a new director! It is one of the best cryoEM centers out there, with an fantastic infrastructure and some of the most exceptional experts in microscopy that I ever had the chance to work with!
careers.epfl.ch/job/Lausanne...
careers.epfl.ch/job/Lausanne...
Operations Director of DCI-Lausanne
Operations Director of DCI-Lausanne
careers.epfl.ch
December 17, 2025 at 1:32 PM
This is an amazing position, DCI Lausanne is looking for a new director! It is one of the best cryoEM centers out there, with an fantastic infrastructure and some of the most exceptional experts in microscopy that I ever had the chance to work with!
careers.epfl.ch/job/Lausanne...
careers.epfl.ch/job/Lausanne...
Reposted by Martin Pacesa
🚨 Today, I formally introduced articles of impeachment against Robert F. Kennedy, Jr.
RFK Jr. has turned his back on science and the safety of the American people. Michiganders cannot take another day of his chaos.
RFK Jr. has turned his back on science and the safety of the American people. Michiganders cannot take another day of his chaos.
December 10, 2025 at 1:10 PM
🚨 Today, I formally introduced articles of impeachment against Robert F. Kennedy, Jr.
RFK Jr. has turned his back on science and the safety of the American people. Michiganders cannot take another day of his chaos.
RFK Jr. has turned his back on science and the safety of the American people. Michiganders cannot take another day of his chaos.
Reposted by Martin Pacesa
Excited to share our first work on protein design! Huge thanks to the entire team, and especially to Bel, Evan, to the Doudna, Jacobsen, Cate, Banfield labs, all co-authors, and my D-lab mates! 💫
✨New preprint!
🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al!
Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬
🔗👇
🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al!
Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬
🔗👇
December 9, 2025 at 6:04 PM
Excited to share our first work on protein design! Huge thanks to the entire team, and especially to Bel, Evan, to the Doudna, Jacobsen, Cate, Banfield labs, all co-authors, and my D-lab mates! 💫
Es ist gar hübsch von einem großen Herrn,
So menschlich mit dem Teufel selbst zu sprechen.
So menschlich mit dem Teufel selbst zu sprechen.
Which lines of poetry live rent-free in your head?
December 7, 2025 at 8:42 AM
Es ist gar hübsch von einem großen Herrn,
So menschlich mit dem Teufel selbst zu sprechen.
So menschlich mit dem Teufel selbst zu sprechen.
Reposted by Martin Pacesa
oh, this is nice: x.com/proteinbase/.... only a few lines of code…
December 3, 2025 at 7:26 PM
oh, this is nice: x.com/proteinbase/.... only a few lines of code…
And now it's going to get cut.
December 3, 2025 at 8:42 AM
And now it's going to get cut.
Let's do some community voting on some of the coolest binder designs against the Nipah virus in the @adaptyvbio competition! I think I am definitely going to favour wacky designs...
proteinbase.com/competitions...
proteinbase.com/competitions...
Nipah Binder Competition
Design a protein capable of neutralizing the Nipah virus, a pathogen with up to 75% mortality rate and high pandemic potential, currently lacking effective treatments.
proteinbase.com
December 3, 2025 at 8:41 AM
Let's do some community voting on some of the coolest binder designs against the Nipah virus in the @adaptyvbio competition! I think I am definitely going to favour wacky designs...
proteinbase.com/competitions...
proteinbase.com/competitions...
Reposted by Martin Pacesa
📢 We have multiple open PhD positions to study bacterial immune systems using cutting-edge cryo-EM, microbiology, and biochemistry in our group! Join us and uncover how bacterial defenses eliminate predators and engineer next-gen biotech tools.
🔥 Apply by Jan 8, 2026
Details: phd.pages.ista.ac.at
🔥 Apply by Jan 8, 2026
Details: phd.pages.ista.ac.at
phd.pages.ista.ac.at
December 2, 2025 at 8:44 AM
📢 We have multiple open PhD positions to study bacterial immune systems using cutting-edge cryo-EM, microbiology, and biochemistry in our group! Join us and uncover how bacterial defenses eliminate predators and engineer next-gen biotech tools.
🔥 Apply by Jan 8, 2026
Details: phd.pages.ista.ac.at
🔥 Apply by Jan 8, 2026
Details: phd.pages.ista.ac.at
Reposted by Martin Pacesa
Been excited about this one for a while! What would you do with a new alphabet and the wealth of protein sequence bioinformatics at your disposal? We're also around at #EMBOComp3D Heidelberg and MLSB Copenhagen this week to discuss
Fresh from bioRxiv our latest work introducing The Embedded Alphabet (TEA), a powerful new representation for protein sequences obtained by discretising ESM2 embeddings into 20 characters.
Pre-print: www.biorxiv.org/content/10.1...
🧵👇(1/n)
Pre-print: www.biorxiv.org/content/10.1...
🧵👇(1/n)
Rewriting protein alphabets with language models
Detecting remote homology with speed and sensitivity is crucial for tasks like function annotation and structure prediction. We introduce a novel approach using contrastive learning to convert protein...
www.biorxiv.org
December 1, 2025 at 10:58 AM
Been excited about this one for a while! What would you do with a new alphabet and the wealth of protein sequence bioinformatics at your disposal? We're also around at #EMBOComp3D Heidelberg and MLSB Copenhagen this week to discuss
The Tiger Lillies
Billy Talent
System of a Down
The Offspring
Blink 182
Billy Talent
System of a Down
The Offspring
Blink 182
Introduce yourself with 5 concerts you’ve seen:
Nirvana
Built to Spill
The Shins
Blonde Redhead
Beach House
Nirvana
Built to Spill
The Shins
Blonde Redhead
Beach House
Introduce yourself with 5 concerts you’ve seen:
The Pogues (with Shane)
Super Furry Animals
Cornershop
Nick Cave
Linton Kwesi Johnson
The Pogues (with Shane)
Super Furry Animals
Cornershop
Nick Cave
Linton Kwesi Johnson
November 29, 2025 at 7:38 AM
The Tiger Lillies
Billy Talent
System of a Down
The Offspring
Blink 182
Billy Talent
System of a Down
The Offspring
Blink 182