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Reposted by Noelia Ferruz

Dimitrije @biodimi.bsky.social · 6d

This work has been possible thanks to an incredible team effort w/ Alejandro, @marcguellc.bsky.social @noeliaferruz.bsky.social and the integra therapeutics team!

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ceej @ceej.online · Aug 30

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

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Noelia Ferruz @noeliaferruz.bsky.social · Aug 27

👀

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Noelia Ferruz @noeliaferruz.bsky.social · Aug 25

What is this marvel of the universe?🤯

www.nature.com/articles/s41...

A fluorescent-protein spin qubit - Nature

An optically addressable fluorescent-protein spin qubit is realized using enhanced yellow fluorescent protein; the qubit can be coherently controlled at liquid-nitrogen temperatures and the spin detec...

www.nature.com

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CATH-Gene3D @cathgene3d.bsky.social · Aug 22

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...

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

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Loretta Robinson @lorettarobinson.bsky.social · Aug 21

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

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Liana Lareau @lianafaye.bsky.social · Aug 7

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

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AI x Bio Discovery @aixbiobot.bsky.social · Aug 1

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.

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Noelia Ferruz @noeliaferruz.bsky.social · Aug 1

But independent of this, what I find is that since Bill Degrado coined the term in the 80s, the field has evolved so much that it no longer captures today’s methods.

E.g in this (all-time favourite!) review, Baker and Po-ssu define de novo in a way that would exclude most AI methods today:

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Noelia Ferruz @noeliaferruz.bsky.social · Aug 1

That’s an interesting paper, I must read 🙂

A bit off-tangent now, but I forgot to mention that Pubmed isn’t normalized, and all terms look as they are increasing exponientially, see for example banana 😄 (1/n)

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Sdelci Lab @sdelcilab.bsky.social · Jul 30

🚀 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...

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

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Noelia Ferruz @noeliaferruz.bsky.social · Jul 31

Interestingly, diffusion models can naturally sample proteins with 0% seq identity!
In any case, last time I said we had generated de novo sequences with a pLM a bunch of reviewers avalanched toward my paper with knives and axes and I had to use “artificial”🤣

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Noelia Ferruz @noeliaferruz.bsky.social · Jul 31

Before AI we reserved that term for proteins with no evolutionary history, i.e., designed from first principles, and consequently often had sequence identities ca. 0%. pLMs, unless steered, tend to naturally sample at >30-40% seqid and rarely explore novel folds.

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Martin Pacesa @martinpacesa.bsky.social · Jul 29

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

Martin Pacesa @martinpacesa.bsky.social · Jul 25

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!

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Gina El Nesr @ginaelnesr.bsky.social · Jul 28

Uncancelled! 🥳

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Manuel Irimia @mirimiam.bsky.social · Jul 23

🚨🚨🚨

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

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Noelia Ferruz @noeliaferruz.bsky.social · Jul 25

Join Martin’s new lab, great location, super cool project, and the best advisor! What’s not to like?

Martin Pacesa @martinpacesa.bsky.social · Jul 25

I am looking to interview prospective PhD students, Postdocs and technicians, particularly with wetlab expertise, but computational skills are a bonus.

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Noelia Ferruz @noeliaferruz.bsky.social · Jul 25

Wohoooo 😍😍😍🚀🚀🚀

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Michael Hothorn @structplantbio.bsky.social · Jul 20

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

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BK. Titanji @boghuma.bsky.social · Jul 19

The internet remains undefeated 😂😅

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Phil Holliger @philholliger.bsky.social · Jul 14

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

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Noelia Ferruz @noeliaferruz.bsky.social · Jul 16

What

🌟Collapsing your wave function🌟 @hemamenon.bsky.social · Jul 14

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

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Noelia Ferruz @noeliaferruz.bsky.social · Jul 15

Congrats Angel!!😍

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Noelia Ferruz @noeliaferruz.bsky.social · Jul 13

Aaah I could speak about this for hours😄. For PLMs trained with autoregressive task, I’d say they suffer from the two, with the latter being most problematic because they fail to generalize even in regions that are close by; except when we steer/reinforce them (requiring considerable manual tuning)

Noelia Ferruz @noeliaferruz.bsky.social · Jul 13

I was absolutely thinking this but ran out of characters😂