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Reposted by Chaitanya K. Joshi

Das Lab @rdaslab.bsky.social · 14d

The results are in: top codes in Stanford #RNA 3D Folding @kaggle.com competition are competitive with CASP16-leading humans Vfold, beat AlphaFold 3. Top team’s trick was template-based modeling, not #DeepLearning. Congrats: john, odat, Eigen, + all 1706 participants! www.kaggle.com/competitions...

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Reposted by Chaitanya K. Joshi

MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 21d

🚨To accommodate the addition of EuroMLSB, we have extended the submission deadline to October 1, 2025 11:59pm AoE.

Find information on paper guidelines at mlsb.io. Submissions will be made through CMT.

MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · Aug 19

📢The submission portal for MLSB 2025 is live! Submissions are due September 26, 2025 11:59 pm AoE. cmt3.research.microsoft.com/MLSB2025

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Reposted by Chaitanya K. Joshi

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 21d

Genome language models can generate new, high-fitness bacteriophages!

@samuelhking.bsky.social @claudiadriscoll.bsky.social
@david-li.bsky.social @danguo.bsky.social @adititm.bsky.social Garyk Brixi @maxewilkinson.bsky.social @brianhie.bsky.social

www.biorxiv.org/content/10.1...

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Reposted by Chaitanya K. Joshi

Samuel King @samuelhking.bsky.social · 21d

Many of the most complex and useful functions in biology emerge at the scale of whole genomes.

Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵

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Reposted by Chaitanya K. Joshi

Jase Gehring @skyjase.bsky.social · 21d

very cool work and a milestone in synthetic biology. how impressive are the new phage genomes?

with generative bioML, i'm always looking at how similar the generated sequences are to known sequences. let's take a look

Samuel King @samuelhking.bsky.social · 21d

Many of the most complex and useful functions in biology emerge at the scale of whole genomes.

Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵

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Reposted by Chaitanya K. Joshi

MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 26d

You asked and we listened... @workshopmlsb.bsky.social is excited to be expanding to Copenhagen, DK at @euripsconf.bsky.social 🎉

Two workshops (San Diego & Copenhagen) will run concurrently to support broader attendance. You can indicate your location preference(s) in the submission portal💫

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Chaitanya K. Joshi @chaitjo.bsky.social · Sep 5

The 3D structure of biomolecules are nature's 'thinking tokens' enroute to the output that we actually truly want to understand: Function.

(Slide from Denny Zhou's Stanford talk on LLM Reasoning)

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Reposted by Chaitanya K. Joshi

Rachael Kretsch @rachael-kretsch.bsky.social · Sep 2

We have restarted our global Nucleic Acid Strcuture webinar series to bring the expiremental and computational communities together to discuss new developments in the field. Join us this Thursday for the next webinar. Sign up to our mailing list here: groups.google.com/g/casp-rna-sig

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Chaitanya K. Joshi @chaitjo.bsky.social · Aug 31

Scaling laws for BioML and wet lab data will eventually work out in the right setting! After all, language data for LLMs was acquired by the largest wet lab experiment ever conducted: Human civilisation 🤯

Reposted by Chaitanya K. Joshi

Nate Corley @ncorley.bsky.social · Aug 15

(1/7)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)

[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)

Accelerating Biomolecular Modeling with AtomWorks and RF3

Deep learning methods trained on protein structure databases have revolutionized biomolecular structure prediction, but developing and training new models remains a considerable challenge. To facilita...

www.biorxiv.org

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Chaitanya K. Joshi @chaitjo.bsky.social · Aug 16

It can train foundation models, but can it train frontier models too? ;)

Chaitanya K. Joshi @chaitjo.bsky.social · Aug 15

📢 Submissions for MLSB 2025 are officially open! We invite researchers to submit their work on the intersection of AI and structural biology.

🗓️ Deadline: September 26, 2025 🔗 More info: cmt3.research.microsoft.com/MLSB2025

MLSB 2025 Workshop

Workshop on Machine Learning in Structural Biology co-located with NeurIPS 2025

www.mlsb.io

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Chaitanya K. Joshi @chaitjo.bsky.social · Aug 15

RosettaFold 3 is here! 🧬🚀

AtomWorks (the foundational data pipeline powering it) is perhaps the really most exciting part of this release!

Congratulations @simonmathis.bsky.social and team!!! ❤️

bioRxiv preprint: www.biorxiv.org/content/10.1...

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Chaitanya K. Joshi @chaitjo.bsky.social · Aug 5

Great image of organizers space group symmetry!

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Chaitanya K. Joshi @chaitjo.bsky.social · Aug 1

Really insightful post and responses - this is why I keep coming back to science social media!

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Jan 4

We’re getting more and more papers on de novo protein design, but I still don’t really know what it means

What’s your definition of de novo design?

Plot that shows an increasing number of papers about de novo protein design

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Chaitanya K. Joshi @chaitjo.bsky.social · Jul 31

Alex’s explainer thread is a heartfelt one: x.com/Alex__Abruda...

And the preprint is on arXiv link: www.arxiv.org/abs/2507.21938

x.com

Chaitanya K. Joshi @chaitjo.bsky.social · Jul 31

🧬 Protein designers: we keep saying we're getting really good at making static, rock-like proteins...

Introducing Dynamic MPNN - our first step towards truly multi-state and 'programmable' protein design! Great collaboration led by Alex Abrudan and Sebastian Pujalte!

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Reposted by Chaitanya K. Joshi

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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Reposted by Chaitanya K. Joshi

Eterna @eternagame.org · Jul 23

Coming up this weekend, Eternacon will feature presentations about fellow #citsci platform @zooniverse.bsky.social and how participants of both Zooniverse and Eterna have created #machinelearning tools for projects. @noirlabastro.bsky.social

Register for free at eternagame.org/eternacon/2025

Blue image of ROOL nanocage made of RNA with text on top noting Eternacon dates as July 26 and 27.

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Reposted by Chaitanya K. Joshi

Rae Radford @raeradford.bsky.social · Jul 19

#BookSky

550 7.8K 39K

Chaitanya K. Joshi @chaitjo.bsky.social · Jul 16

LLMs transfer knowledge across domains; eg. doing well on maths translates to getting better at programming, too.

Molecular models often don't - We may need unified representations for true generalization.

Chaitanya K. Joshi @chaitjo.bsky.social · Jul 16

Are we hitting a wall with scaling molecular foundation models?

Some thoughts on what I think is one of the most interesting open Qs atm: chaitjo.substack.com/p/transfer-l...

Towards transfer learning in molecular foundation models

Are multi-modal molecular foundation models learning transferable representations across biology and chemistry?

chaitjo.substack.com

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Reposted by Chaitanya K. Joshi

Quanta Magazine @quantamagazine.bsky.social · Jul 14

How does a cell know when it’s been damaged? A molecular alarm, set off by mutated RNA and colliding ribosomes, signals danger. @dsamorod.bsky.social reports: www.quantamagazine.org/rna-is-the-c...

RNA Is the Cell’s Emergency Alert System | Quanta Magazine

How does a cell know when it’s been damaged? A molecular alarm, set off by mutated RNA and colliding ribosomes, signals danger.

www.quantamagazine.org

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Reposted by Chaitanya K. Joshi

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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Reposted by Chaitanya K. Joshi

Kelly Nguyen @kellythd-nguyen.bsky.social · Jul 11

Highly collaborative efforts that involved 6 lab members and the labs of @yiliangding.bsky.social and @rdaslab.bsky.social. We uncovered a telomerase dimer and its potential role in telomere maintenance.

MRC Laboratory of Molecular Biology @mrclmb.bsky.social · Jul 11

Sebastian Balch, Zala Sekne & Elsa Franco-Echevarría in @kellythd-nguyen.bsky.social's group have confirmed the existence of dimeric telomerase and illustrated how it is key to telomere maintenance:
www2.mrc-lmb.cam.ac.uk/first-struct...

#LMBResearch @yiliangding.bsky.social @rdaslab.bsky.social 🧪

Structure of telomerase dimer with key catalytic codes and H/ACA RNPs highlighted with schematic illustrating how dimer disruption leads to shortened telomeres and disease mutations of the dimers causes premature ageing diseases

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