Sam Berry

This travel ban has quietly reshaped the personal and scientific futures of many Iranian scholars, including my own. After a full year of planning for a U.S. postdoc, tens of hours of interview preparation, fellowship applications, constant monitoring of whether Harvard’s legal battles would lead to F or J visa revocations, stress over grant freezes, and endless immigration paperwork, the sudden travel ban announced on June 4, 2025 upended everything. After the draft list for the new travel ban appeared in a New York Times article in March, we rushed to reschedule my PhD defense as early as possible. I ended up preparing for my defense in just two weeks in an attempt to get ahead of the ban, which turned out to be pointless. The ban was announced only weeks after my interview at the U.S. Consulate in Toronto, and I have not heard back since. This ban is far more expansive than the one in 2017 and includes no exemptions for F or J visas. When I asked about the possibility of an exemption letter, I was told it was unlikely to help, as this administration appears to view science as no longer being in the U.S. national interest. As @genophoria points out, media coverage and the political response around this ban have been surprisingly limited. I wish more senior academics would speak up. Today, many Iranian and other international students and scholars live in a state of permanent uncertainty, where a single policy change can freeze their careers or force them to leave everything behind. Many do not even feel safe sharing their experiences publicly. In the current political climate for immigrants in the U.S., it is heartbreaking to admit that I feel almost relieved I did not end up there. When you are living with constant fear about your status, buried in paperwork, and know your life can be overturned overnight, how much bandwidth remains to do actual science?

The new travel ban is far more expansive than the one in 2017, yet the political response this time around has been muted to the point of silence. A Republican congresswoman seems to be the loudest voice raising concerns. The cynic in me can't help wondering whether this is payback for immigrant communities not delivering the turnout some Dem politicians expected in 2020. My speculations aside, the impact is very real. The U.S. visa process was already a grueling, dehumanizing maze even in the best of times. International scholars and students now face even more uncertainty about something as basic as freedom to move or change jobs. What’s heartbreaking is how normalized this has become. A century ago, simply landing at Ellis Island meant a chance to start a life by signing your name in a book. Today, the path to "legal entry" is a labyrinth of paperwork, shifting rules, and a political climate where people's lives can be upended overnight depending on who's in office. We should not accept this volatility as the price of wanting to study, work, or build a life in this country. miamiherald.com/news/local/imm…

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:

New online! A structural window into the evolution of secondary transport mechanisms bit.ly/41jEuMm

🚨 New in @ImmunityCP ! EVE-Vax, an AI model that anticipates future viral evolution and designs antigens to proactively test vaccines + therapeutics—before variants even emerge. We envision this work will help make future-proofed vaccines and therapeutics. 👇 (1/7)

Had a great time discussing my recent work with the brilliant @sophiehgibert & @leah_pierson on their @biounethical podcast - check it out!

Still can’t believe I was named to this list! EVEscape and our work on viral evolution prediction and vaccine design has been an amazing collaboration co-led with @deboramarks, @nooryoussef03, @NthadaniN, and @NotinPascal - looking forward to more work to come! ✨

Marks Lab is HIRING!!! If you're a software engineer interested in biology, proteins, RNAs, viruses, genomes, etc etc and ML apply here: shorturl.at/GZOqV

The February issue, with a focus on protein engineering, is live nature.com/nbt/volumes/42… Our cover shows the three data types key to machine learning for functional protein design: structure, sequence and labels, from a Review by Notin et al. go.nature.com/49EPi9x

Be one of the first to take our new ebikes on a supercharged adventure! Just start pedaling and let the ⚡️boost carry you away. Big thanks to our sponsor, @BCBSMA, for supporting the municipalities’ in bringing ebikes to the Bluebikes system. Learn more 👉 blog.bluebikes.com/blog/the-ebike…

Announcing popEVE - a deep generative model of the human proteome that reveal over a hundred novel genes involved in rare genetic disorders medrxiv.org/cgi/content/sh… @Jonnygfrazer @aaronkollasch @H__Spinner @c_sheare @MafaldaFigDias @deboramarks explore at pop.evemodel.org

Ever pined for a deliciously sloppy polymerase? Enter *BadBoy* - Continuous evolution of user-defined genes at 1-million-times the genomic mutation rate. Great work team!! @rix_gordon Rory, Vincent, @deboramarks and @chang_c_liu biorxiv.org/content/10.110…

Previous viral evolution can shed light on future immune evasion. EVEscape, now out in @Nature, is our first step in applying pre-pandemic data to forecast antibody escape through the course of a pandemic. nature.com/articles/s4158… 🧵1/6

How do enzyme dynamics relate to the chemical steps of catalysis? Using DHFR as an example, we address this question with a series of crystallographic perturbation experiments. Solvent access is critical; the DHFR active site has two distinct substates. How does that work? 👇🧵

Multiple New X-ray Snapshots Reveal How Transition Metals Cross Cellular Membranes Through Nramp Transporters [Gaudet Lab] @RachelleGaudet @shamayeetaray @SamPinzkaBerry @eLife mcb.harvard.edu/department/new…

Where do new senses come from? In paired studies, we explore the structural basis of sensory receptor evolution in octopus and squid. @CoreyAHallard @wendyssae @RyanHibbs10 @Nature - nature.com/articles/s4158… - nature.com/articles/s4158…

Outstanding eLife paper from @shamayeetaray, with a supporting cast that includes @SamPinzkaBerry, @abhisekhsingha1 @EricWil39327976, @mrinal1989: High-resolution structures with bound Mn2+ and Cd2+ map the metal import pathway in an Nramp transporter doi.org/10.7554/eLife.…

The hope is that this is a kind of approach that could be applied to other complexes that interact in some but not all species - feel free to reach out if you’re curious, or check out the code on GitHub: github.com/samberry19/evc…

We used an AlphaFold model + EVcomplex intermolecular couplings terms to define an “interaction score” between any MurA/LpxC pair. Kate then tested some of the predictions of this model and they held up in the lab!

I’m so happy to see this paper finally out - in addition to @HummelsKate’s amazing experiments establishing the LpxC/MurA interaction in P. aeruginosa, I thought it was so cool to see that sequence coevolution methods can help predict which bacteria this key complex is formed in!