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Sam Berry

@sberry.bsky.social
1.1K followers 718 following 25 posts

Harvard Biophysics PhD candidate studying protein evolution with a focus on transporters in the Gaudet and Marks labs. Occasional fiction writer. Proud cat dad.

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Sam Berry @sberry.bsky.social · 21/04/2026
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...
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Debora Marks @deboramarks.bsky.social · 24/11/2025
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:
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Senator Bernie Sanders @sanders.senate.gov · 10/11/2025
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.
youtube.com
LIVE: I Won't Support Doubling Health Care Premiums
YouTube video by Senator Bernie Sanders
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Krishna Reddy @krishnareddy.bsky.social · 12/09/2025
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
go.nature.com
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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David Ho @davidho.bsky.social · 31/08/2025
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.
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Sam Berry @sberry.bsky.social · 26/08/2025
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
rdcu.be
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....
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Sarah Gurev @sarahgurev.bsky.social · 17/08/2025
🚨New paper 🚨 Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇 1/12
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Pascal Notin @pascalnotin.bsky.social · 18/06/2025
🚨 New paper 🚨 RNA modeling just got its own Gym! 🏋️ Introducing RNAGym, large-scale benchmarks for RNA fitness and structure prediction. 🧵 1/9
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Sam Berry @sberry.bsky.social · 30/05/2025
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!
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Liana Merk @bacteriyay.bsky.social · 24/05/2025
(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...
biorxiv.org
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...
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Chris Hayes @chrislhayes.bsky.social · 13/05/2025
read this please www.nytimes.com/2025/05/13/o...
nytimes.com
Opinion | The Science I Would Be Doing if I Weren’t in ICE Detention
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Sam Berry @sberry.bsky.social · 13/05/2025
Lovely article from our colleague Kseniia Petrova, who has been wrongfully imprisoned for months: www.nytimes.com/2025/05/13/o...
nytimes.com
Opinion | The Science I Would Be Doing if I Weren’t in ICE Detention
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Nick Polizzi @nickpolizzi.bsky.social · 28/04/2025
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... 🧵🧪
biorxiv.org
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...
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Sam Berry @sberry.bsky.social · 01/04/2025
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...
nature.com
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.
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Congresswoman Ayanna Pressley @pressley.house.gov · 29/03/2025
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.
A graphic that reads Free Rümeysa Öztürk with a photo of her.
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Stephanie M. Lee @stephaniemlee.bsky.social · 21/03/2025
"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...
chronicle.com
Opinion | What Autocrats Want From Academics: Servility
In 1931, Italian scholars were made to take loyalty oaths. Will that happen to us?
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Sam Berry @sberry.bsky.social · 28/02/2025
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
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Stephanie Hicks @stephaniehicks.bsky.social · 27/02/2025
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...
science.org
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
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Alisia Fadini @alisiafadini.bsky.social · 24/02/2025
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.
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Brian Liau @brianliau.bsky.social · 12/02/2025
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
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Vice Mayor Burhan Azeem @burhanazeem.bsky.social · 11/02/2025
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 🧵
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Sam Berry @sberry.bsky.social · 01/12/2024
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... 🤔
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Sam Berry @sberry.bsky.social · 16/11/2024
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!
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