Sam Berry
@sberry.bsky.social
Harvard Biophysics PhD candidate studying protein evolution with a focus on transporters in the Gaudet and Marks labs. Occasional fiction writer. Proud cat dad.
Reposted by Sam Berry
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.
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
www.youtube.com
November 10, 2025 at 1:39 AM
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.
All to give $1 trillion in tax breaks for billionaires.
Reposted by Sam Berry
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
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
September 12, 2025 at 12:08 AM
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
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
Reposted by Sam Berry
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.
August 31, 2025 at 7:45 PM
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
August 26, 2025 at 4:28 AM
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
Reposted by Sam Berry
🚨New paper 🚨
Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇
1/12
Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇
1/12
August 17, 2025 at 3:42 AM
🚨New paper 🚨
Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇
1/12
Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇
1/12
Reposted by Sam Berry
🚨 New paper 🚨 RNA modeling just got its own Gym! 🏋️ Introducing RNAGym, large-scale benchmarks for RNA fitness and structure prediction.
🧵 1/9
🧵 1/9
June 18, 2025 at 7:35 PM
🚨 New paper 🚨 RNA modeling just got its own Gym! 🏋️ Introducing RNAGym, large-scale benchmarks for RNA fitness and structure prediction.
🧵 1/9
🧵 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!
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
www.mcb.harvard.edu/department/n... @rachellegaudet.bsky.social @naoshigeuchida.bsky.social @neurovenki.bsky.social @dulaclab.bsky.social @rivaselenarivas.bsky.social
Senior MCB, CPB, and Neuroscience Concentrators Receive the Thomas Temple Hoopes and Henderson Prizes - Harvard University - Department of Molecular & Cellular Biology
Six graduating seniors in our MCB, Chemical and Physical Biology (CPB), and Neuroscience concentrations have received the prestigious Thomas Temple Hoopes Prize. These prizes, which carry a $5,000 […]
www.mcb.harvard.edu
May 30, 2025 at 2:25 PM
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!
Reposted by Sam Berry
(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...
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...
www.biorxiv.org
May 24, 2025 at 7:20 PM
(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...
www.biorxiv.org/content/10.1...
Reposted by Sam Berry
Opinion | The Science I Would Be Doing if I Weren’t in ICE Detention
www.nytimes.com
May 13, 2025 at 12:49 PM
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
www.nytimes.com
May 13, 2025 at 12:33 PM
Lovely article from our colleague Kseniia Petrova, who has been wrongfully imprisoned for months: www.nytimes.com/2025/05/13/o...
Reposted by Sam Berry
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...
www.biorxiv.org
April 28, 2025 at 3:22 PM
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...
🧵🧪
🧵🧪
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...
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.
www.nature.com
April 1, 2025 at 3:03 PM
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...
www.nature.com/articles/d41...
Reposted by Sam Berry
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.
March 29, 2025 at 2:27 PM
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.
Reposted by Sam Berry
"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?
www.chronicle.com
March 21, 2025 at 10:45 PM
"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
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.
Somehow, there are no chapters dedicated to how Republicans are decimating research and firing experts.
February 28, 2025 at 1:23 PM
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
Reposted by Sam Berry
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...
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
www.science.org
February 27, 2025 at 12:04 PM
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...
www.science.org/content/arti...
Reposted by Sam Berry
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.
February 24, 2025 at 12:23 PM
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.
Reposted by Sam Berry
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
February 12, 2025 at 4:20 PM
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
Reposted by Sam Berry
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 🧵
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 🧵
February 11, 2025 at 1:46 AM
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 🧵
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... 🤔
December 1, 2024 at 4:22 AM
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!
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...
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...
November 16, 2024 at 1:04 AM
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!