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Shamith Samarajiwa

@shamith.bsky.social
70 followers 131 following 4 posts

Computational Biologist & Data Scientist @Imperialmed.bsky.social www.samarajiwa-lab.org EpiGenome Regulation & Biomedical AI : Cancer, Immunity, Ageing & Metabolic Disease Prev: University of Cambridge, CRUK Cambridge Institute, Monash Univeristy

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Reposted by Shamith Samarajiwa
PHD Comics @phdcomics.com · 04/03/2026
Data
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Alt CDC (they/them) @altcdc.altgov.info · 20/02/2026
💉 Where can you find accurate vaccine information?💉 American Academy of Pediatrics (AAP): downloads.aap.org/AAP/PDF/AAP-... Other medical societies: cmss.org/programs-and... CIDRAP for in-depth evidence review: vaxintegrity.cidrap.umn.edu/evidence-rev...
cmss.org
Clinical Guidance on Immunization - CMSS
CMSS shares our members’ commitment to ensuring that high-quality, evidence-based healthcare is available and accessible to all patients. We work collaboratively with a broad network of medical societies, healthcare organizations, and patient and public health coalitions to bring forward the latest recommendations and resources to guide quality care. CMSS is pleased to share access to the […]
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Epigenetics Podcast @epigeneticspod.bsky.social · 16/02/2026
In the most recent Episode we talked with Srinjan Basu from Imperial College London to talk about his work on how chromatin architecture and epigenetic mechanisms orchestrate developmental gene expression programs. #podcast #epigenetics Listen here: activemotif.com/podcasts-sri...
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Science Magazine @science.org · 18/06/2025
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
scim.ag
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
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Eric Topol @erictopol.bsky.social · 18/06/2025
A.I. is improving the accuracy of medical diagnoses. Today for inherited retinal diseases [IRD] (Eye2Gene vs retinal experts) nature.com/articles/s42...
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Eric Topol @erictopol.bsky.social · 17/06/2025
Cancer vaccines will be a big part of the future of immunotherapy. A new, super review @thelancet.com www.thelancet.com/journals/lan...
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Eric Topol @erictopol.bsky.social · 16/06/2025
The promise and problems with multi-cancer early detection tests by Sid Mukherjee @newyorker.com www.newyorker.com/magazine/202...
newyorker.com
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.
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euanashley @euanashley.bsky.social · 14/06/2025
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.
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Shamith Samarajiwa @shamith.bsky.social · 12/06/2025
www.standupforscience.net/bethesda-dec...
standupforscience.net
Bethesda Declaration — STAND UP FOR SCIENCE
Support NIH Staff Now!
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Shamith Samarajiwa @shamith.bsky.social · 12/06/2025
www.ft.com/content/8778...
ft.com
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
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Shamith Samarajiwa @shamith.bsky.social · 06/06/2025
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
statnews.com
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.
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Stephen Turner @stephenturner.us · 25/04/2025
EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals www.nature.com/articles/s41... 🧬🖥️🧪 #Rstats bioconductor.org/packages/Syn...
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Jason Koebler @jasonkoebler.bsky.social · 31/03/2025
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-...
404media.co
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."
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Tiffany C. Li @tiffanycli.bsky.social · 03/04/2025
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...
mcsweeneys.net
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...
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Dorothy Bishop @deevybee.bsky.social · 05/04/2025
as Elon Musk continues to shred science, Mike Taylor reflects on inaction by @royalsociety.org svpow.com/2025/04/04/t...
svpow.com
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…
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Jacob Schreiber @jmschreiber91.bsky.social · 05/04/2025
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...
cell.com
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...
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Eric Topol @erictopol.bsky.social · 05/04/2025
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...
erictopol.substack.com
The Shingles Vaccine and Reduction of Dementia
A compelling new study adds to the body of data supporting some protection provided by the vaccine
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Stephen Turner @stephenturner.us · 24/03/2025
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...
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Michael R Photography 🌿 @msriffle.bsky.social · 22/03/2025
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
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Prof Christina Pagel @chrischirp.bsky.social · 10/03/2025
And here is a previous guest post about actual concrete things scientists can do. christinapagel.substack.com/p/eight-thin...
christinapagel.substack.com
Eight things scientists can do right now to stand up to the Trump administration’s attacks on research, public health, and the environment
A guest post by Dr Anne Toomey, author of the book "Science with Impact: How to Engage People, Change Practice, and Influence Policy".
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Eric Topol @erictopol.bsky.social · 01/03/2025
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...
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Srinjan Lab @srinjan.bsky.social · 26/02/2025
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...
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Daniel Drucker @danieljdrucker.bsky.social · 22/02/2025
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
cell.com
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...
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Anshul Kundaje @anshulkundaje.bsky.social · 21/02/2025
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.
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Andrea Junker @strandjunker.com · 13/02/2025
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. 2. 3. 4. 5. 6. 7. 8. 9. 10.
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Nature Reviews Cancer @natrevcancer.nature.com · 11/02/2025
🥳 Our 4th most downloaded article in 2024: Beyond genetics: driving cancer with the tumour microenvironment behind the wheel by @thefuchslab.bsky.social & colleagues bit.ly/42Cvr... @rockefelleruniv.bsky.social @hhmi.bsky.social @natureportfolio.bsky.social #NRCtop10of2024
bit.ly
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.
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Eric Topol @erictopol.bsky.social · 04/02/2025
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...
thelancet.com
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.
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Eric Topol @erictopol.bsky.social · 29/01/2025
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...
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Hank Green @hankgreen.bsky.social · 29/01/2025
My bad.
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Shamith Samarajiwa @shamith.bsky.social · 24/01/2025
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.
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Anshul Kundaje @anshulkundaje.bsky.social · 17/01/2025
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/
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Anshul Kundaje @anshulkundaje.bsky.social · 25/12/2024
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/
biorxiv.org
ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants
Despite extensive mapping of cis-regulatory elements (cREs) across cellular contexts with chromatin accessibility assays, the sequence syntax and genetic variants that regulate transcription factor (T...
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Zamin Iqbal @zaminiqbal.bsky.social · 11/12/2024
This is the most amazing thread since they did a similar thing to cure a cancer
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Carl Zimmer @carlzimmer.com · 12/12/2024
Over 30 prominent scientists call for a ban on the creation of a "mirror cell"--a microbe made of molecules that are mirror images of their natural forms. It could cause a mind-boggling global disaster. Here's my story [gift link] 🧪https://nyti.ms/3OUCXp6
nyti.ms
A ‘Second Tree of Life’ Could Wreak Havoc, Scientists Warn (Gift Article)
Research on so-called mirror cells, which defy fundamental properties of living organisms, should be prohibited as too dangerous, biologists said.
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Kevin Mitchell @wiringthebrain.bsky.social · 12/12/2024
The tech bro fascination with eugenics is so on brand. The idea that you could make accurate, actionable predictions from individual genotypes (with all their complex, non-linear interactions) from averaged, linearly modeled population-level genomic statistics is just another big data fantasy
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