Shamith Samarajiwa

Microbe with bizarrely tiny genome may be evolving into a virus With DNA focused almost entirely on replication, newly discovered organism blurs the line between cells and viruses

The newly discovered microbe provisionally known as Sukunaarchaeum isn’t a virus.

But like viruses, it seemingly has one purpose: to make more of itself. scim.ag/4e6y0W2

A.I. is improving the accuracy of medical diagnoses. Today for inherited retinal diseases [IRD] (Eye2Gene vs retinal experts)
nature.com/articles/s42...

Cancer vaccines will be a big part of the future of immunotherapy. A new, super review @thelancet.com
www.thelancet.com/journals/lan...

The Catch in Catching Cancer Early New blood tests promise to detect malignancies before they’ve spread. But proving that these tests actually improve outcomes remains a stubborn challenge.

The promise and problems with multi-cancer early detection tests
by Sid Mukherjee @newyorker.com
www.newyorker.com/magazine/202...

Atul Butte died yesterday.
The world lost a giant.
A big bear of a man.
With a huge smile.
With love for everyone.
With energy that could power a room.
I loved everything about Atul.
I loved how he was always happy.
I loved how excited he was about science and helping people.

Bethesda Declaration — STAND UP FOR SCIENCE Support NIH Staff Now!

www.standupforscience.net/bethesda-dec...

Royal Society prize winner returns award in protest over Elon Musk Andrea Sella is latest scientist to express dismay over UK science academy’s refusal to criticise tech billionaire

www.ft.com/content/8778...

Do you remember the Human Genome Project? I’m not sure the Trump administration wants you to The NIH archives of the Human Genome Project could fall victim to Trump administration cuts, writes a former archivist.

Do you remember the Human Genome Project? I’m not sure the Trump administration wants you to www.statnews.com/2025/06/05/n... via @statnews.com

EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals www.nature.com/articles/s41... 🧬🖥️🧪 #Rstats bioconductor.org/packages/Syn...

Open Source Genetic Database Shuts Down to Protect Users From 'Authoritarian Governments' "The risk/benefit calculus of providing free & open access to individual genetic data in 2025 is very different compared to 14 years ago."

The open-source genetic database OpenSNP is shutting down and deleting all user data after 14 years due to the risk posed by Trump administration, law enforcement abuse, authoritarian governments, and 23andMe bankruptcy:

www.404media.co/open-source-...

President Trump’s Tariffs Will Help America Win the War Against Birds President Trump has announced a sweeping plan of tariffs against dozens of nations, including the Antarctic Heard and McDonald Islands, which are u...

I wrote a new piece on an important topic: “President Trump’s Tariffs Will Help America Win the War Against Birds”

www.mcsweeneys.net/articles/pre...

The Royal Society is dead A few months ago, Dorothy Bishop resigned her fellowship in the Royal Society in protest at Elon Musk’s continuing fellowship. This was a highly principled stand. Eight weeks ago, Steven Curr…

as Elon Musk continues to shred science, Mike Taylor reflects on inaction by @royalsociety.org
svpow.com/2025/04/04/t...

Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model Dalal et al. show how AI can be used to systematically uncover the sequence rules that guide how signaling pathways interact with DNA inside cells. This work provides a new lens for discovering the co...

Awesome work showing a super clean + thoughtful application of using genomic deep learning models for discovery.

Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model

www.cell.com/cell-genomic...

The Shingles Vaccine and Reduction of Dementia A compelling new study adds to the body of data supporting some protection provided by the vaccine

A major paper @nature.com this week found a significant decline in dementia after an outdated Shingles vaccine.
I've reviewed the study and many other relevant ones here
erictopol.substack.com/p/the-shingl...

Benchmarking PWM and SVM-based Models for Transcription Factor Binding Site Prediction: A Comparative Analysis on Synthetic and Biological Data www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/InfOmics/PWM...

A bluebird of happiness. This little one, sitting on a fence close by, was happy to pose for a portrait. And then off it was after bringing joy to my late afternoon walk. #photography #birds #wildlife #wildlifephotography #EastCoastKin

And here is a previous guest post about actual concrete things scientists can do.

christinapagel.substack.com/p/eight-thin...

Francis Collins, the NIH Director for 12 years, led the Human Genome Project and other NIH efforts for 32 years, resigned today. Key words from his resignation letter
www.nytimes.com/2025/03/01/u...

New #preprint from the Basu & Stewart labs! We discover a non-catalytic role for H3K4me3 methyltransferase MLL2 in modulating 3D chromatin organisation and mobility as pluripotent cells are primed for differentiation.

www.biorxiv.org/content/10.1...

Caloric restriction prevents inheritance of polycystic ovary syndrome through oocyte-mediated DNA methylation reprogramming Liu et al. reveal that oocytes independently mediate the transgenerational inheritance of PCOS. Caloric restriction effectively hinders this transmission by restoring disrupted DNA methylation in insu...

Caloric restriction (CR) in F1 or F2 prevented the transmission of #PCOS in mice by restoring disrupted DNA methylation in oocyte genes related to insulin secretion and AMPK signaling pathways #fertility @cp-cellmetabolism.bsky.social www.cell.com/cell-metabol... #epigenetics

If you think this work is cool, do note that it was done by graduate students, PDs and staff in academic labs funded by federal tax payer dollars. Which means if no federal funding, a lot less of this kind of research. Use your voice to protect federally funded research which is under attack.

DISEASES ERADICATED OR DECIMATED BY SCIENCE:
1. Chickenpox
2. Diphtheria
3. Measles
4. Pertussis
5. Pneumococcal Infection
6. Polio
7. Tetanus
8. Typhoid
9. Yellow Fever
10. Smallpox

DISEASES ERADICATED OR DECIMATED BY RFK JR. OR PRAYER:
1.
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10.

Beyond genetics: driving cancer with the tumour microenvironment behind the wheel - Nature Reviews Cancer In their Review article, Fuchs and colleagues discuss how a single or a few mutations in adult cells can lead to invasive cancers without a high mutational burden, demonstrating that non-genetic factors induce the epigenetic changes necessary for tumorigenesis.

🥳 Our 4th most downloaded article in 2024:

Beyond genetics: driving cancer with the tumour microenvironment behind the wheel by @thefuchslab.bsky.social & colleagues

https://bit.ly/42Cvr...

@rockefelleruniv.bsky.social @hhmi.bsky.social @natureportfolio.bsky.social #NRCtop10of2024

Screening performance and characteristics of breast cancer detected in the Mammography Screening with Artificial Intelligence trial (MASAI): a randomised, controlled, parallel-group, non-inferiority, ... The findings suggest that AI contributes to the early detection of clinically relevant breast cancer and reduces screen-reading workload without increasing false positives.

New: The largest medical A.I. randomized controlled trial yet performed, enrolling >100,000 women undergoing mammography screening
The use of AI led to 29% higher detection of cancer, no increase of false positives, and reduced workload compared with radiologists w/o AI thelancet.com/journals/lan...

Immune cell sequencing from birth to old age
"Using our lifecycle-wide single-cell dataset covering 13 age groups over the extent of the human lifespan...."
www.nature.com/articles/s41...

My bad.

Deleted my X account. Science twitter was great but the amount of pseudoscience, misinformation and hate on X was overwhelming. X’s owners antics was the final straw.

We share a lot of our ideas, code, datasets (that we spend years sanitizing) early. Often way before we release preprints. We do this so that others can use, build on, improve & even "beat" our approaches. But I want to say a few things about some simple expectations 1/

Our ChromBPNet preprint out!

www.biorxiv.org/content/10.1...

Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/

This is the most amazing thread since they did a similar thing to cure a cancer