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 🎩
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
Reposted by Martin Pacesa
ProteinCHAOS runs entirely in the browser and lets you choose how to visualize your protein structures.
It supports PDB files from the PDB and AlphaFold servers and offers several visual themes so you can "paint" abstract art with protein traces. I hope it helps you create some interesting images!
It supports PDB files from the PDB and AlphaFold servers and offers several visual themes so you can "paint" abstract art with protein traces. I hope it helps you create some interesting images!
November 23, 2025 at 11:18 PM
ProteinCHAOS runs entirely in the browser and lets you choose how to visualize your protein structures.
It supports PDB files from the PDB and AlphaFold servers and offers several visual themes so you can "paint" abstract art with protein traces. I hope it helps you create some interesting images!
It supports PDB files from the PDB and AlphaFold servers and offers several visual themes so you can "paint" abstract art with protein traces. I hope it helps you create some interesting images!
Reposted by Martin Pacesa
POV: you are a young woman celebrating a recent academic success
November 17, 2025 at 7:20 PM
POV: you are a young woman celebrating a recent academic success
Reposted by Martin Pacesa
Very happy to share our collaborative project on FAM118 proteins - noncanonical sirtuins that form filaments and process NAD in human and other vertebrate cells.
Filament formation and NAD processing by noncanonical human FAM118 sirtuins
Nature Structural & Molecular Biology - Baretić and Missoury et al. identify vertebrate proteins FAM118B and FAM118A as sirtuins similar to bacterial antiphage enzymes and show that...
rdcu.be
November 17, 2025 at 11:37 AM
Very happy to share our collaborative project on FAM118 proteins - noncanonical sirtuins that form filaments and process NAD in human and other vertebrate cells.
Very happy to be this year’s recipient of the 𝗣𝗲𝘁𝗲𝗿 𝗮𝗻𝗱 𝗧𝗿𝗮𝘂𝗱𝗹 𝗘𝗻𝗴𝗲𝗹𝗵𝗼𝗿𝗻 𝗙𝗼𝘂𝗻𝗱𝗮𝘁𝗶𝗼𝗻 𝗥𝗲𝘀𝗲𝗮𝗿𝗰𝗵 𝗔𝘄𝗮𝗿𝗱 together with @jenspuschhof.bsky.social
www.engelhorn-stiftung.de/forschungspr...
www.engelhorn-stiftung.de/forschungspr...
FORSCHUNGSPREIS — Peter&TraudlEngelhornStiftung
www.engelhorn-stiftung.de
November 14, 2025 at 12:20 PM
Very happy to be this year’s recipient of the 𝗣𝗲𝘁𝗲𝗿 𝗮𝗻𝗱 𝗧𝗿𝗮𝘂𝗱𝗹 𝗘𝗻𝗴𝗲𝗹𝗵𝗼𝗿𝗻 𝗙𝗼𝘂𝗻𝗱𝗮𝘁𝗶𝗼𝗻 𝗥𝗲𝘀𝗲𝗮𝗿𝗰𝗵 𝗔𝘄𝗮𝗿𝗱 together with @jenspuschhof.bsky.social
www.engelhorn-stiftung.de/forschungspr...
www.engelhorn-stiftung.de/forschungspr...
Reposted by Martin Pacesa
The Center for Microscopy and Image Analysis at the University of Zurich is seeking a new Head:
jobs.uzh.ch/job-vacancie...
It is super fun to work with them, tons of expertise and cutting edge instrumentation in ❄️🔬
Application deadline: December 15, 2025.
jobs.uzh.ch/job-vacancie...
It is super fun to work with them, tons of expertise and cutting edge instrumentation in ❄️🔬
Application deadline: December 15, 2025.
UZH: Head of the Center for Microscopy and Image Analysis (Core Facility)
The Center for Microscopy and Image Analysis (ZMB) is a nationally and internationally recognized Core Facility at the University of Zurich (UZH), providing access to state-of-the-art light and electr...
jobs.uzh.ch
November 12, 2025 at 6:42 PM
The Center for Microscopy and Image Analysis at the University of Zurich is seeking a new Head:
jobs.uzh.ch/job-vacancie...
It is super fun to work with them, tons of expertise and cutting edge instrumentation in ❄️🔬
Application deadline: December 15, 2025.
jobs.uzh.ch/job-vacancie...
It is super fun to work with them, tons of expertise and cutting edge instrumentation in ❄️🔬
Application deadline: December 15, 2025.
Reposted by Martin Pacesa
After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...
An updated evolutionary classification of CRISPR–Cas systems including rare variants - Nature Microbiology
An exploration of previously undescribed variants from the long tail of the CRISPR–Cas distribution.
www.nature.com
November 6, 2025 at 1:49 PM
After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...
Reposted by Martin Pacesa
With the US government absent from the COP30 global climate summit, it will be up to others to avert catastrophe
go.nature.com/4ofcrH6
go.nature.com/4ofcrH6
How to fight climate change without the US: a guide to global action
With the US government absent from the COP30 global climate summit, it will be up to others to avert catastrophe.
go.nature.com
November 3, 2025 at 4:59 PM
With the US government absent from the COP30 global climate summit, it will be up to others to avert catastrophe
go.nature.com/4ofcrH6
go.nature.com/4ofcrH6
So exciting to be able to do a binder design workshop using BindCraft in Mexico 🇲🇽, with such a fantastic community of scientists! The designs to probe interesting biological problems looked amazing! The GPU compute was very generously provided by @aaronmring.bsky.social and AriaX.bio 🖥️
October 28, 2025 at 11:53 PM
So exciting to be able to do a binder design workshop using BindCraft in Mexico 🇲🇽, with such a fantastic community of scientists! The designs to probe interesting biological problems looked amazing! The GPU compute was very generously provided by @aaronmring.bsky.social and AriaX.bio 🖥️
Reposted by Martin Pacesa
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
October 28, 2025 at 6:30 PM
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
Reposted by Martin Pacesa
BIG BIG congratulations to our PhD student
@roman-bushuiev.bsky.social for receiving the Google PhD Fellowship 2025 in Health Research! 🎉💰 goo.gle/43wJWw8
@roman-bushuiev.bsky.social for receiving the Google PhD Fellowship 2025 in Health Research! 🎉💰 goo.gle/43wJWw8
October 25, 2025 at 12:44 AM
BIG BIG congratulations to our PhD student
@roman-bushuiev.bsky.social for receiving the Google PhD Fellowship 2025 in Health Research! 🎉💰 goo.gle/43wJWw8
@roman-bushuiev.bsky.social for receiving the Google PhD Fellowship 2025 in Health Research! 🎉💰 goo.gle/43wJWw8
Reposted by Martin Pacesa
We (@sobuelow.bsky.social) developed AF-CALVADOS to integrate AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale
See preprint for:
— Ensembles of >12000 full-length human proteins
— Analysis of IDRs in >1500 TFs
📜 doi.org/10.1101/2025...
💾 github.com/KULL-Centre/...
See preprint for:
— Ensembles of >12000 full-length human proteins
— Analysis of IDRs in >1500 TFs
📜 doi.org/10.1101/2025...
💾 github.com/KULL-Centre/...
October 20, 2025 at 11:26 AM
We (@sobuelow.bsky.social) developed AF-CALVADOS to integrate AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale
See preprint for:
— Ensembles of >12000 full-length human proteins
— Analysis of IDRs in >1500 TFs
📜 doi.org/10.1101/2025...
💾 github.com/KULL-Centre/...
See preprint for:
— Ensembles of >12000 full-length human proteins
— Analysis of IDRs in >1500 TFs
📜 doi.org/10.1101/2025...
💾 github.com/KULL-Centre/...