Jerome (he/him) 🧬🏳️‍🌈

Protein language models reveal evolutionary constraints on synonymous codon choice Evolution has shaped the genetic code, with subtle pressures leading to preferences for some synonymous codons over others. Codons are translated at different speeds by the ribosome, imposing constrai...

This preprint from Helen Sakharova is one of the coolest things to come out of my lab: “Protein language models reveal evolutionary constraints on synonymous codon choice.” Codon choice is a big puzzle in how information is encoded in genomes, and we have a new angle. www.biorxiv.org/content/10.1...

Same.

The new special issue @science.org
features Immunity with 4 outstanding review papers, 5★ science.org/toc/science/...
Our immune system over the lifespan (figure at right on path to inflammaging and immunosenescence), sex differences, influence on physiology, and host antiviral defenses

🚨 Join us at #ASHG25!🚨
We’re unveiling a new standard for Predicted Effector Gene (PEG) data - designed to make gene prioritisation more transparent, reusable, and #FAIR.
#HumanGenetics #GeneticsDiscoveries #EffectorGene #GWAS #FunctionalGenomics #PEGstandard👇

Vitamin B2 metabolism promotes FSP1 stability to prevent ferroptosis Ferroptosis, a regulated form of cell death driven by excessive lipid peroxidation, has emerged as a promising therapeutic target in cancer. Ferroptosis suppressor protein 1 (FSP1) is a critical regul...

Excited to share our new preprint, led by Kirandeep Deol! 🤩 Genetic screens uncover mechanisms regulating FSP1 abundance in cancer. Vitamin B2 metabolism promotes FSP1 stability via FAD synth / binding, further linking nutrient metabolism to ferroptosis.
www.biorxiv.org/content/10.1...

EBV induces CNS homing of B cells attracting inflammatory T cells - Nature Epstein–Barr virus infection generates a neuroinvasive B cell subset, which recruits activated T cells to the central nervous system, promoting multiple sclerosis.

How does Epstein- Barr virus induce multiple sclerosis?
The infection leads to B cells that get into the brain, attracting pro-inflammatory T cells (mouse model)
www.nature.com/articles/s41...

This study with @ukbiobank.bsky.social will deepen our understanding of the human genome, support the development of more effective treatments, and pave the way for precision medicine 🧬

Learn more about our journey with UK Biobank here: sangerinstitute.blog/2022/09/26/o...

Whole-genome sequencing of 490,640 UK Biobank participants - Nature A study reports whole-genome sequences for 490,640 participants from the UK Biobank and combines these data with phenotypic data to provide new insights into the relationship between human variation a...

✅ Published in @natureportfolio.nature.com today, the paper describing the initial whole-genome sequencing analysis of 500,000 UK Biobank participants.

Read here: www.nature.com/articles/s41...

We're committed to finding new ways of getting important, original research into scientists’ hands as quickly as possible.

Take a look at the other formats you can publish in, from Tools and Resources to Research Advances to Short Reports: buff.ly/GXKivkm

Scaling DNA sequencing is a notable success story.

Scaling protein analysis is harder since the proteome is a much taller mountain: www.nature.com/articles/s41...

@asimovpress.bsky.social writes about @parallelsq.bsky.social's approach to scale up proteomics.

Yosemite employees worked for weeks with no pay before the government hired them Seasonal employees counting on housing at Yosemite were asked to volunteer for the park while the government was unable

Thanks to Trump's cuts, seasonal employees at Yosemite worked for as long as six weeks without pay.

The National Park Service is one of our most popular government agencies.

It's being gutted to fund enormously unpopular tax cuts for the super-rich.

E Life's new open access publishing agreements. Supporting a more actable and sustainable system.

We’re pleased to offer open access agreements for research institutions in support of a more equitable and sustainable system for scientific publishing, including uncapped and centralised schemes.
buff.ly/wuB4xoO
#OpenScience #AcademicChatter

3 groups use generative AI to design high-specificity pMHC-binding “artificial TCRs” for more precise targeting of tumor antigen @science.org
www.science.org/doi/10.1126/...

EMBL researchers and their collaborators have provided exciting new insights into human genetic variation by building upon the 1000 Genomes Project dataset.

The two studies constitute what may be the most complete overview of the human genome to date.

www.embl.org/news/science...

In the world of sphere packing, there’s been debate about whether order or a dash of chaos will give the best results. A recent proof marks a win for order. www.quantamagazine.org/new-sphere-p...

This spot is always empty

Eric Green was the first institute director forced out of NIH. He still hasn’t been told why Eric Green said the process leading to his ouster as a NIH institute director by the Trump administration remains "shrouded in mystery"

STAT story about Eric Green, former director of the National Human Genome Research Institute

www.statnews.com/2025/06/26/n...

1/n

This a really exciting leap forward for genomic sequence to activity gene regulation models. It is a genuine improvement over pretty much all SOTA models spanning a wide range of regulatory, transcriptional and post-transcriptional processes. 1/

This so amusingly absurd 😂

Insanity
today @newyorker.com

Cocrystal structure reveals the mechanism of FSP1 inhibition by FSEN1 | PNAS FSP1 is an FAD-dependent oxidoreductase that uses NAD(P)H to regenerate the reduced forms of lipophilic quinone antioxidants, such as coenzyme Q10 ...

Thrilled this paper is out! We solved the first cocrystal structure of FSP1 with an inhibitor (FSEN1), providing mechanistic insight & a foundation for medchem. Led by Amalia Megarioti & Sitao Zhang. A terrific collaboration with Da Jia.
Brief Skytorial!
1/9

Industry friends, now is the time for MUCH more speaking out on behalf of academic colleagues under duress. Here are core open source methods that many of your products doubtlessly depend on either directly or indirectly (see en.wikipedia.org/wiki/HMMER) being abruptly defunded. Make noise.

Just commented here too - can be anonymous, and standing up for NSF/NIH takes less time than standing in line at the grocery store checkout!!

Was happy to provide a little excerpt, along with others, about the recent @hhmi.org Hanna Grey decision last week as an applicant and a former Gilliam Fellow that knows how important these fellowships are for early career scientists with limited resources.

A photograph of Louis Bamberger, seated on the right, wearing a mustache and bowler hat, and his sister Caroline Bamberger Fuld, standing on the left, wearing a fur hat and shawl

Let's talk about these two department store owners: brother and sister Louis Bamberger and Caroline Bamberger Fuld. From Newark, New Jersey.

They are random people, basically. But in the late 1920s, with fascism taking over Europe, they made a choice that profoundly changed the world: 🧵

What losing billions in federal grants means for universities, and the nation The Trump administration has so far frozen about $11 billion in research funding. University leaders say no other source can fill the void.

What cutting science and biomedical grants mean for the nation...

www.npr.org/2025/04/25/n...

MAGA’s War on Science Why do these people believe that ignorance is strength?

open.substack.com/pub/paulkrug...

Number of genetic differences between random pairs of African individuals (black points) and a corresponding random European (blue points). 20 random samples. One instance: a person from Russia has fewer differences to a Kenyan than that same Kenyan to a Namibian.

a small curly-haired brown pup balances on one back leg with their other one extending behind them in a lovely little arabesque pose. their front paws reach around in a little circle in front of their body, and they’re smiling with their eyes and their little pink tongue. this is a dance move we’re not even sure we could confidently pull off, but they’re crushing it. in the background, a white fluffy dog lays on their side in a light beige dog bed while wearing a flower-shaped inflatable cone around their neck. they’re looking at their energetic friend with a hint of disdain.

This is Arang and Aro. Aro is giving them the ol' razzle dazzle, and Arang is giving nothing at all. 12/10

RFK Jr. to End 'Godsend' Narcan Program That Helped Reduce Overdose Deaths Despite His Past Heroin Addiction Despite overcoming heroin addiction himself, RFK Jr. is backing plans to cut a critical Narcan program that helped reduce overdose deaths.

RFK Jr. is ending the federal Narcan distribution program credited with the recent steep decline in overdose deaths. This despite his own past heroin addiction and his own brother dying of a drug overdose in 1984.