I'm excited to share our new preprint representing the bulk of my PhD work, along with @camillefreedman.bsky.social, @deboramarks.bsky.social and @rachellegaudet.bsky.social. How do transporter proteins control what molecules they bring across the membrane? www.biorxiv.org/content/10.6...

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:

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.

LIVE: I Won't Support Doubling Health Care Premiums

YouTube video by Senator Bernie Sanders

youtube.com

1/14 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

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 ...

go.nature.com

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

A structural window into the evolution of secondary transport mechanisms

Nature Structural & Molecular Biology - Protein sequence signatures suggest that eons ago, a bacterial glutamate transporter lost its sodium coupling to make way for a shift to proton coupling....

rdcu.be

Nature Structural & Molecular Biology@natsmb.nature.com · 12mo ago

New online: Evolutionary analysis reveals the origin of sodium coupling in glutamate transporters

🚨New paper 🚨 Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇 1/12

🚨 New paper 🚨 RNA modeling just got its own Gym! 🏋️ Introducing RNAGym, large-scale benchmarks for RNA fitness and structure prediction. 🧵 1/9

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!

Harvard_MCB@harvardmcb.bsky.social · last yr.

Senior MCB, CPB, and Neuroscience Concentrators Receive the Thomas Temple Hoopes and Henderson Prizes #AcademicSky www.mcb.harvard.edu/department/n... @rachellegaudet.bsky.social @naoshigeuchida.bsky.social @neurovenki.bsky.social @dulaclab.bsky.social @rivaselenarivas.bsky.social

(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...

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...

biorxiv.org

read this please www.nytimes.com/2025/05/13/o...

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

nytimes.com

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

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

nytimes.com

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... 🧵🧪

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...

biorxiv.org

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...

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.

nature.com

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.

"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...

Opinion | What Autocrats Want From Academics: Servility

In 1931, Italian scholars were made to take loyalty oaths. Will that happen to us?

chronicle.com

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

Hemant Mehta@friendlyatheist.com · last yr.

Lol. All the anti-trans, reflexively contrarian, “anti-woke” scientists have contributed to a book about how science is under attack. Somehow, there are no chapters dedicated to how Republicans are decimating research and firing experts.

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...

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

science.org

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... 🤔

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!

Kevin K. Yang 楊凱筌@kevinkaichuang.bsky.social · 2y ago

The Baker lab seems serious about moving into enzyme design. Here, they train a flow-matching model that can be conditioned by atomic coordinates and then use it to design enzymes based on active site geometry specified by density functional theory. www.biorxiv.org/content/10.1...