Sam Berry

New paper “Proteome-wide model for human disease genetics” is now live at Nature Genetics: rdcu.be/eRu7K
popEVE (pop.evemodel.org) finds the needles in the haystacks of human genetic variation:

YouTube video by Senator Bernie Sanders LIVE: I Won't Support Doubling Health Care Premiums

I’m voting no on the continuing resolution that would double healthcare premiums for 20 million Americans, kick 15 million people off Medicaid & allow 50,000 Americans to die unnecessarily every year.

All to give $1 trillion in tax breaks for billionaires.

Evolutionary analysis reveals the origin of sodium coupling in glutamate transporters - Nature Structural & Molecular Biology Reddy et al. used ancestral protein reconstruction, cryo-electron microscopy and functional assays to elucidate how a secondary active transporter evolved to harness the energy of sodium gradients to ...

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Happy (but mostly relieved) to share my dream project with @boudkerlab.bsky.social, now published in @natsmb.nature.com! We used evolution, protein engineering & cryoEM to uncover how ion coupling in glutamate transporters works, and how it evolved.🧵
Free article: go.nature.com/4oRUC1q

Yes, I think I agree. There are two problems: 1) the approach they use isn’t very accurate even for natural proteins and 2) any model will behave very differently for sequences close to the training set than for those far away, so their result is expected just from how the model is trained

To my knowledge there is no evidence that that networks like ESMFold accurately predict structural perturbations upon mutation? So yeah seems it’s entirely analysis *of the model* not of actual protein biophysics

RFK Jr. is not a vaccine skeptic. He's a vaccine denier whose anti-science extremist views and actions are destroying one of humanity's greatest scientific achievements. He's going to kill a lot of people, and those deaths are on the 52 Republican senators who confirmed him and those enabling him.

This is a very cool ancestral reconstruction study by @krishnareddy.bsky.social et al. that I recommend reading! @rachellegaudet.bsky.social and I thought it was so interesting that we wrote a News & Views about it, check it out: rdcu.be/eCfyl

🚨New paper 🚨

Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇
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🚨 New paper 🚨 RNA modeling just got its own Gym! 🏋️ Introducing RNAGym, large-scale benchmarks for RNA fitness and structure prediction.
🧵 1/9

As a note - AlphaFold and other similar algorithms can still do reasonably well without MSA info. They really have learned principles from the PDB (but these principles are NOT physical protein folding - as evidenced by that they can’t predict destabilizing muts etc)

Couldn't be prouder of my incredibly talented mentee Camille and glad to see her hard work has been acknowledged by winning *both* the Hoopes and Henderson prizes for her undergraduate thesis!

Prevalence of Group II Introns in Phage Genomes Although bacteriophage genomes are under strong selective pressure for high coding density, they are still frequently invaded by mobile genetic elements (MGEs). Group II introns are MGEs that reduce h...

(1/7) Very excited to share my first PhD preprint on the interactions of two of my favorite mobile genetic elements: phages and group II introns!

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

Opinion | The Science I Would Be Doing if I Weren’t in ICE Detention

read this please

www.nytimes.com/2025/05/13/o...

Opinion | The Science I Would Be Doing if I Weren’t in ICE Detention

Lovely article from our colleague Kseniia Petrova, who has been wrongfully imprisoned for months: www.nytimes.com/2025/05/13/o...

Thanks, will check these out!

Do you think it would be be more reasonable to benchmark these kinds of models against raw NMR data (e.g. by simulating NMR data from the predicted ensemble, if that’s possible) or are there still too many sources of variability going into the raw data?

Zero-shot design of drug-binding proteins via neural selection-expansion Computational design of molecular recognition remains challenging despite advances in deep learning. The design of proteins that bind to small molecules has been particularly difficult because it requ...

Super excited to share a new preprint from our lab on design of small-molecule binding proteins using neural networks! The paper has a bit of everything. A new graph neural network, new design algorithms, and experimental validation. www.biorxiv.org/content/10.1...
🧵🧪

AlphaFold is running out of data — so drug firms are building their own version Thousands of 3D protein structures locked up in big-pharma vaults will be used to create a new AI tool that won’t be open to academics.

I think it says everything here that the locked-away industry version of AlphaFold3 they want to build is based on... OpenFold, which was developed to be open-source by academics. Industry is built on the advances of open-source research.

www.nature.com/articles/d41...

A graphic that reads Free Rümeysa Öztürk with a photo of her.

This week, my Somerville constituent Rümeysa Öztürk was abducted in broad daylight by DHS officials and sent to Louisiana to be locked in a detention center. She has not been charged with any crime.

Opinion | What Autocrats Want From Academics: Servility In 1931, Italian scholars were made to take loyalty oaths. Will that happen to us?

"On October 8, 1931, a law went into effect requiring every Italian university professor to sign an oath pledging their loyalty to the government of Benito Mussolini. Out of over 1,200 professors in the country, only 12 refused. All of them were immediately fired." www.chronicle.com/article/what...

Publishing this *now* is so embarrassingly tone-deaf and anti-science I almost can’t believe it - just as this exact ideology is being used in a fascist takeover of the US and the accompanying wholesale attack on science and free speech

NIH ban on renewing senior scientists adds to assaults on its in-house research Policy follows firings of tenure-track scientists and suspension of training programs

Friends, I am at a loss of words for how devastating it would be to lose the entire intramural #NIH program. Some of the biggest medical and scientific breakthroughs have come from scientists in the NIH Intramural program. #SaveTheNIH 🧬🧪 🖥️ 🧠

www.science.org/content/arti...

Structural biology is in an era of dynamics & assemblies but turning raw experimental data into atomic models at scale remains challenging. @minhuanli.bsky.social and I present ROCKET🚀: an AlphaFold augmentation that integrates crystallographic and cryoEM/ET data with room for more! 1/14.

Today in @nature.com we share our back-to-back stories with Ning Zheng’s lab revealing chemical-genetic convergence between a molecular glue degrader & E3 ligase cancer mutations. 1/5

I can’t believe it - after years of advocacy, exclusionary zoning has ended in Cambridge.

We just passed the single most comprehensive rezoning in the US—legalizing multifamily housing up to 6 stories citywide in a Paris style

Here’s the details 🧵

I wrote 50,000 words in November! Of course, leave it to me to do my first NaNoWriMo in 15+ years of writing fiction when I'm supposed to be writing my thesis, not a novel... 🤔

It feels like there’s some magic spice our best models are missing out on. Preorganization of the binding site seems like one huge thing that can get you from 0/100 to 1/100, but I’m super curious what else is out there to learn

This work seems like a big advance in enzyme design, but it’s still fascinating that we can design new proteins that fold with ~90% accuracy, but even with careful biochemical design, DFT, and heaps of machine learning you only get about 1/100 designs with the activity level of natural enzymes!