Noelia Ferruz
@noeliaferruz.bsky.social
Generative models for protein design.
Group leader at CRG
Group leader at CRG
Pinned
Noelia Ferruz
@noeliaferruz.bsky.social
· Mar 26
Today I remembered my first QM parameterization of a small molecule failed miserably (turn volume ON for a full experience)
Reposted by Noelia Ferruz
The CRG PhD call is now open. Exciting opportunities across diverse topics and within a world-class scientific environment.
Our group is offering one PhD position to study chromatin evolution.
Consider applying or share with anyone who might be interested!
www.crg.eu/en/content/t...
Our group is offering one PhD position to study chromatin evolution.
Consider applying or share with anyone who might be interested!
www.crg.eu/en/content/t...
Are you looking for a PhD? Join us in Barcelona! You'll dive into a community of >100 PhD students from 30 countries exploring the frontiers of biology. You can also join an online workshop on 6 November (15:00 CET) to learn how to find the right lab for you.
More info: www.crg.eu/en/content/t...
More info: www.crg.eu/en/content/t...
October 23, 2025 at 11:54 AM
The CRG PhD call is now open. Exciting opportunities across diverse topics and within a world-class scientific environment.
Our group is offering one PhD position to study chromatin evolution.
Consider applying or share with anyone who might be interested!
www.crg.eu/en/content/t...
Our group is offering one PhD position to study chromatin evolution.
Consider applying or share with anyone who might be interested!
www.crg.eu/en/content/t...
Reposted by Noelia Ferruz
Protein Structure Evolution (ProSe) Seminar is now on BlueSky! Every 2nd Tuesday, 4PM GMT.
Sign-Up: tinyurl.com/prose-seminar2
Organized by Claudia Alvarez Carreño, Zachary Ardern, Lars Eicholt, Carolina Sanchez-Rocha,
Sergio Romero Romero and Md. Hassan Uz-Zaman.
Sign-Up: tinyurl.com/prose-seminar2
Organized by Claudia Alvarez Carreño, Zachary Ardern, Lars Eicholt, Carolina Sanchez-Rocha,
Sergio Romero Romero and Md. Hassan Uz-Zaman.
October 25, 2025 at 9:23 PM
Protein Structure Evolution (ProSe) Seminar is now on BlueSky! Every 2nd Tuesday, 4PM GMT.
Sign-Up: tinyurl.com/prose-seminar2
Organized by Claudia Alvarez Carreño, Zachary Ardern, Lars Eicholt, Carolina Sanchez-Rocha,
Sergio Romero Romero and Md. Hassan Uz-Zaman.
Sign-Up: tinyurl.com/prose-seminar2
Organized by Claudia Alvarez Carreño, Zachary Ardern, Lars Eicholt, Carolina Sanchez-Rocha,
Sergio Romero Romero and Md. Hassan Uz-Zaman.
Reposted by Noelia Ferruz
Are you looking for a PhD? Join us in Barcelona! You'll dive into a community of >100 PhD students from 30 countries exploring the frontiers of biology. You can also join an online workshop on 6 November (15:00 CET) to learn how to find the right lab for you.
More info: www.crg.eu/en/content/t...
More info: www.crg.eu/en/content/t...
October 23, 2025 at 7:56 AM
Are you looking for a PhD? Join us in Barcelona! You'll dive into a community of >100 PhD students from 30 countries exploring the frontiers of biology. You can also join an online workshop on 6 November (15:00 CET) to learn how to find the right lab for you.
More info: www.crg.eu/en/content/t...
More info: www.crg.eu/en/content/t...
Reposted by Noelia Ferruz
#Research #Biomedicine
Generative AI is more efficient than nature at designing proteins to edit the genome 🧬💻✂️
This is the conclusion of research published at @natbiotech.nature.com by @marcguellc.bsky.social Integra Therapeutics & @noeliaferruz.bsky.social - @crg.eu
📰 tuit.cat/n7ap6
Generative AI is more efficient than nature at designing proteins to edit the genome 🧬💻✂️
This is the conclusion of research published at @natbiotech.nature.com by @marcguellc.bsky.social Integra Therapeutics & @noeliaferruz.bsky.social - @crg.eu
📰 tuit.cat/n7ap6
October 20, 2025 at 8:31 AM
#Research #Biomedicine
Generative AI is more efficient than nature at designing proteins to edit the genome 🧬💻✂️
This is the conclusion of research published at @natbiotech.nature.com by @marcguellc.bsky.social Integra Therapeutics & @noeliaferruz.bsky.social - @crg.eu
📰 tuit.cat/n7ap6
Generative AI is more efficient than nature at designing proteins to edit the genome 🧬💻✂️
This is the conclusion of research published at @natbiotech.nature.com by @marcguellc.bsky.social Integra Therapeutics & @noeliaferruz.bsky.social - @crg.eu
📰 tuit.cat/n7ap6
Reposted by Noelia Ferruz
This work has been possible thanks to an incredible team effort w/ Alejandro, @marcguellc.bsky.social @noeliaferruz.bsky.social and the integra therapeutics team!
October 2, 2025 at 6:11 PM
This work has been possible thanks to an incredible team effort w/ Alejandro, @marcguellc.bsky.social @noeliaferruz.bsky.social and the integra therapeutics team!
Reposted by Noelia Ferruz
my father-in-law is a “I know a guy” Guy. sadly all the old Guys are aging out of the Guy Economy. Guys are fundamentally incompatible with Hustle Culture because it’s not about “winning” a deal, it’s about collecting favors and goodwill in a mutually-beneficial cycle. protect your local Guy Economy
August 30, 2025 at 2:51 PM
my father-in-law is a “I know a guy” Guy. sadly all the old Guys are aging out of the Guy Economy. Guys are fundamentally incompatible with Hustle Culture because it’s not about “winning” a deal, it’s about collecting favors and goodwill in a mutually-beneficial cycle. protect your local Guy Economy
Reposted by Noelia Ferruz
CATH turns 30 years old this year!
We are organising a 1-day symposium on September 16th at UCL, highlighting recent AI-based developments to enhance protein family classifications, annotations and analyses.
www.eventbrite.co.uk/e/protein-an...
We are organising a 1-day symposium on September 16th at UCL, highlighting recent AI-based developments to enhance protein family classifications, annotations and analyses.
www.eventbrite.co.uk/e/protein-an...
Protein Annotations in the age of AI
A not-for-profit symposium hosted at UCL - more details about speakers and venue below.
www.eventbrite.co.uk
August 22, 2025 at 10:45 AM
CATH turns 30 years old this year!
We are organising a 1-day symposium on September 16th at UCL, highlighting recent AI-based developments to enhance protein family classifications, annotations and analyses.
www.eventbrite.co.uk/e/protein-an...
We are organising a 1-day symposium on September 16th at UCL, highlighting recent AI-based developments to enhance protein family classifications, annotations and analyses.
www.eventbrite.co.uk/e/protein-an...
Reposted by Noelia Ferruz
Woke up this morning in Greenland. It is game time for my cameras. National Geographic Endurance safely crossed the Denmark Straight and into this fjord! #EastCoastKin #photography #Greenland
August 21, 2025 at 9:28 AM
Woke up this morning in Greenland. It is game time for my cameras. National Geographic Endurance safely crossed the Denmark Straight and into this fjord! #EastCoastKin #photography #Greenland
Reposted by Noelia Ferruz
This preprint from Helen Sakharova is one of the coolest things to come out of my lab: “Protein language models reveal evolutionary constraints on synonymous codon choice.” Codon choice is a big puzzle in how information is encoded in genomes, and we have a new angle. www.biorxiv.org/content/10.1...
Protein language models reveal evolutionary constraints on synonymous codon choice
Evolution has shaped the genetic code, with subtle pressures leading to preferences for some synonymous codons over others. Codons are translated at different speeds by the ribosome, imposing constrai...
www.biorxiv.org
August 7, 2025 at 8:29 AM
This preprint from Helen Sakharova is one of the coolest things to come out of my lab: “Protein language models reveal evolutionary constraints on synonymous codon choice.” Codon choice is a big puzzle in how information is encoded in genomes, and we have a new angle. www.biorxiv.org/content/10.1...
Reposted by Noelia Ferruz
Evaluating zero-shot prediction of protein design success by AlphaFold, ESMFold, and ProteinMPNN [new]
Zero-shot protein design assessment filters, but accuracy predicting success is limited.
Zero-shot protein design assessment filters, but accuracy predicting success is limited.
August 1, 2025 at 8:58 PM
Evaluating zero-shot prediction of protein design success by AlphaFold, ESMFold, and ProteinMPNN [new]
Zero-shot protein design assessment filters, but accuracy predicting success is limited.
Zero-shot protein design assessment filters, but accuracy predicting success is limited.
Reposted by Noelia Ferruz
🚀 We’re excited to share our latest publication in collaboration with Verena Ruprecht's group at @crg.eu
Mechanobiology meets Nuclear Metabolism
www.nature.com/articles/s41...
Mechanobiology meets Nuclear Metabolism
www.nature.com/articles/s41...
Mitochondria-derived nuclear ATP surge protects against confinement-induced proliferation defects - Nature Communications
The authors uncover a mechano-metabolic adaptation where confinement induces rapid mitochondrial relocalization to the nuclear periphery, generating localized nuclear ATP surges that support chromatin...
www.nature.com
July 30, 2025 at 10:03 AM
🚀 We’re excited to share our latest publication in collaboration with Verena Ruprecht's group at @crg.eu
Mechanobiology meets Nuclear Metabolism
www.nature.com/articles/s41...
Mechanobiology meets Nuclear Metabolism
www.nature.com/articles/s41...
Reposted by Noelia Ferruz
Thank you everyone for the congratulations and the large number of applications! I want to specifically encourage applications for these positions:
* Postdoc in structural biology (cryoEM, ideally with X-ray too)
* Full time lab manager/technician with wetlab experience
* Postdoc in structural biology (cryoEM, ideally with X-ray too)
* Full time lab manager/technician with wetlab experience
I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!
July 29, 2025 at 6:01 PM
Thank you everyone for the congratulations and the large number of applications! I want to specifically encourage applications for these positions:
* Postdoc in structural biology (cryoEM, ideally with X-ray too)
* Full time lab manager/technician with wetlab experience
* Postdoc in structural biology (cryoEM, ideally with X-ray too)
* Full time lab manager/technician with wetlab experience
Reposted by Noelia Ferruz
Reposted by Noelia Ferruz
🚨🚨🚨
Please RT!
We're looking for a postdoc to join an exciting joint project between our lab @upf.edu & @crg.eu (Barcelona) and the Sander lab @mdc-berlin.bsky.social (Berlin) investigating how alternative splicing and microexons influences the maturation of pancreatic islets.
Deadline: 30/09/25👇
Please RT!
We're looking for a postdoc to join an exciting joint project between our lab @upf.edu & @crg.eu (Barcelona) and the Sander lab @mdc-berlin.bsky.social (Berlin) investigating how alternative splicing and microexons influences the maturation of pancreatic islets.
Deadline: 30/09/25👇
www.upf.edu
July 23, 2025 at 2:28 PM
🚨🚨🚨
Please RT!
We're looking for a postdoc to join an exciting joint project between our lab @upf.edu & @crg.eu (Barcelona) and the Sander lab @mdc-berlin.bsky.social (Berlin) investigating how alternative splicing and microexons influences the maturation of pancreatic islets.
Deadline: 30/09/25👇
Please RT!
We're looking for a postdoc to join an exciting joint project between our lab @upf.edu & @crg.eu (Barcelona) and the Sander lab @mdc-berlin.bsky.social (Berlin) investigating how alternative splicing and microexons influences the maturation of pancreatic islets.
Deadline: 30/09/25👇
Join Martin’s new lab, great location, super cool project, and the best advisor! What’s not to like?
I am looking to interview prospective PhD students, Postdocs and technicians, particularly with wetlab expertise, but computational skills are a bonus.
July 25, 2025 at 11:06 AM
Join Martin’s new lab, great location, super cool project, and the best advisor! What’s not to like?
Reposted by Noelia Ferruz
Struct bio ms titles over the years
1965 - A three-dimensional model of X
1985 - The structure of X
1995 - The structure of X reveals Y
2005 - Structural basis of
2015 - The molecular mechanism of
2025 - Harnessing AlphaFold
1965 - A three-dimensional model of X
1985 - The structure of X
1995 - The structure of X reveals Y
2005 - Structural basis of
2015 - The molecular mechanism of
2025 - Harnessing AlphaFold
July 20, 2025 at 12:28 PM
Struct bio ms titles over the years
1965 - A three-dimensional model of X
1985 - The structure of X
1995 - The structure of X reveals Y
2005 - Structural basis of
2015 - The molecular mechanism of
2025 - Harnessing AlphaFold
1965 - A three-dimensional model of X
1985 - The structure of X
1995 - The structure of X reveals Y
2005 - Structural basis of
2015 - The molecular mechanism of
2025 - Harnessing AlphaFold
Reposted by Noelia Ferruz
The internet remains undefeated 😂😅
July 19, 2025 at 2:16 AM
The internet remains undefeated 😂😅
Reposted by Noelia Ferruz
We are looking to recruit a tenure track group leader in the field of Chemical/Synthetic Biology (in the broadest sense) to lead a research program within the Division of Protein & Nucleic Acid Chemistry ( www.jobs.ac.uk/job/DNW809/r... ) at the MRC Laboratory of Molecular Biology (LMB).
Research Group Leader in Chemical/Synthetic Biology at MRC Laboratory of Molecular Biology
Start your UK & international job search for academic jobs, research jobs, science jobs and managerial jobs in leading universities and top...
www.jobs.ac.uk
July 14, 2025 at 12:10 PM
We are looking to recruit a tenure track group leader in the field of Chemical/Synthetic Biology (in the broadest sense) to lead a research program within the Division of Protein & Nucleic Acid Chemistry ( www.jobs.ac.uk/job/DNW809/r... ) at the MRC Laboratory of Molecular Biology (LMB).
What
The team built mathematical models detailing how infrared photons could impact the myelin sheath & impart energy to embedded C-H bonds, spurring biphoton generation with many pairs exhibiting entanglement, and serve as a type of “quantum communication resource” within the nervous system.
Quantum Entanglement in Your Brain Is What Generates Consciousness, Radical Study Suggests
This controversial idea could completely change how we understand the mind.
www.popularmechanics.com
July 16, 2025 at 5:43 AM
What
An insightful thread by Miguel as usual! - worth reading
🧵 1/9 I want to share some (inconclusive) thoughts about the generalization capabilities of protein language models under this main question: ¿what does it mean IN distribution generalization and what does it mean OUT of distribution generalization in (protein) biology?
July 9, 2025 at 7:31 PM
An insightful thread by Miguel as usual! - worth reading
Reposted by Noelia Ferruz
In our newest preprint, we discuss current explainable AI (XAI) methods. We divided the workflow of a generative decoder-only model into four information contexts for XAI: training dataset, input query, model components, and output sequence. See here: arxiv.org/abs/2506.19532
@aichemist.bsky.social
@aichemist.bsky.social
June 25, 2025 at 11:37 AM
In our newest preprint, we discuss current explainable AI (XAI) methods. We divided the workflow of a generative decoder-only model into four information contexts for XAI: training dataset, input query, model components, and output sequence. See here: arxiv.org/abs/2506.19532
@aichemist.bsky.social
@aichemist.bsky.social
Reposted by Noelia Ferruz
Are you curious about what protein language models learn? Check out our newest preprint! 🚀https://arxiv.org/abs/2506.19532
We reviewed explainable AI (XAI) techniques across all parts of the generative protein design workflow and discussed their applications, limitations, and untapped potential!
We reviewed explainable AI (XAI) techniques across all parts of the generative protein design workflow and discussed their applications, limitations, and untapped potential!
June 25, 2025 at 11:16 AM
Are you curious about what protein language models learn? Check out our newest preprint! 🚀https://arxiv.org/abs/2506.19532
We reviewed explainable AI (XAI) techniques across all parts of the generative protein design workflow and discussed their applications, limitations, and untapped potential!
We reviewed explainable AI (XAI) techniques across all parts of the generative protein design workflow and discussed their applications, limitations, and untapped potential!
Noooo😭
This was the BEST workshop at NeurIPS!!
This was the BEST workshop at NeurIPS!!
Unfortunately, the MLSB Workshop @ NeurIPS (@workshopmlsb.bsky.social) was rejected this year.
Feedback from the deciding committee indicates it was a coin flip decision, with 283 proposals & a number related to “computational biology”
More on the future of MLSB soon…
Feedback from the deciding committee indicates it was a coin flip decision, with 283 proposals & a number related to “computational biology”
More on the future of MLSB soon…
July 7, 2025 at 5:37 PM
Noooo😭
This was the BEST workshop at NeurIPS!!
This was the BEST workshop at NeurIPS!!
This is absolutely nuts and I wonder how the future of peer review is gonna look like
After all these reports of authors adding language instructions for LLM reviews in their papers I wanted to check this myself and I downloaded the .tex source from one of these papers.
Here is an example.
(I will not share the identity of the paper)
Here is an example.
(I will not share the identity of the paper)
July 5, 2025 at 8:29 PM
This is absolutely nuts and I wonder how the future of peer review is gonna look like