Shamith Samarajiwa
@shamith.bsky.social
Computational Biologist & Data Scientist @Imperialmed.bsky.social https://www.samarajiwa-lab.org
EpiGenome Regulation & Biomedical AI : Cancer, Immunity, Ageing & Metabolic Disease
Prev: University of Cambridge, CRUK Cambridge Institute, Monash Univeristy
EpiGenome Regulation & Biomedical AI : Cancer, Immunity, Ageing & Metabolic Disease
Prev: University of Cambridge, CRUK Cambridge Institute, Monash Univeristy
Reposted by Shamith Samarajiwa
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
But like viruses, it seemingly has one purpose: to make more of itself. scim.ag/4e6y0W2
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
scim.ag
June 18, 2025 at 1:27 PM
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
But like viruses, it seemingly has one purpose: to make more of itself. scim.ag/4e6y0W2
Reposted by Shamith Samarajiwa
A.I. is improving the accuracy of medical diagnoses. Today for inherited retinal diseases [IRD] (Eye2Gene vs retinal experts)
nature.com/articles/s42...
nature.com/articles/s42...
June 18, 2025 at 1:59 PM
A.I. is improving the accuracy of medical diagnoses. Today for inherited retinal diseases [IRD] (Eye2Gene vs retinal experts)
nature.com/articles/s42...
nature.com/articles/s42...
Reposted by Shamith Samarajiwa
Cancer vaccines will be a big part of the future of immunotherapy. A new, super review @thelancet.com
www.thelancet.com/journals/lan...
www.thelancet.com/journals/lan...
June 17, 2025 at 10:38 PM
Cancer vaccines will be a big part of the future of immunotherapy. A new, super review @thelancet.com
www.thelancet.com/journals/lan...
www.thelancet.com/journals/lan...
Reposted by Shamith Samarajiwa
The promise and problems with multi-cancer early detection tests
by Sid Mukherjee @newyorker.com
www.newyorker.com/magazine/202...
by Sid Mukherjee @newyorker.com
www.newyorker.com/magazine/202...
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.
www.newyorker.com
June 16, 2025 at 2:17 PM
The promise and problems with multi-cancer early detection tests
by Sid Mukherjee @newyorker.com
www.newyorker.com/magazine/202...
by Sid Mukherjee @newyorker.com
www.newyorker.com/magazine/202...
Reposted by Shamith Samarajiwa
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.
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.
June 14, 2025 at 6:35 PM
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.
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.
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
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.
www.statnews.com
June 6, 2025 at 4:15 PM
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
Reposted by Shamith Samarajiwa
EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals www.nature.com/articles/s41... 🧬🖥️🧪 #Rstats bioconductor.org/packages/Syn...
April 25, 2025 at 8:00 PM
EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals www.nature.com/articles/s41... 🧬🖥️🧪 #Rstats bioconductor.org/packages/Syn...
Reposted by Shamith Samarajiwa
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-...
www.404media.co/open-source-...
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."
www.404media.co
March 31, 2025 at 4:14 PM
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-...
www.404media.co/open-source-...
Reposted by Shamith Samarajiwa
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...
www.mcsweeneys.net/articles/pre...
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...
www.mcsweeneys.net
April 3, 2025 at 5:55 PM
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...
www.mcsweeneys.net/articles/pre...
Reposted by Shamith Samarajiwa
as Elon Musk continues to shred science, Mike Taylor reflects on inaction by @royalsociety.org
svpow.com/2025/04/04/t...
svpow.com/2025/04/04/t...
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…
svpow.com
April 5, 2025 at 1:21 AM
as Elon Musk continues to shred science, Mike Taylor reflects on inaction by @royalsociety.org
svpow.com/2025/04/04/t...
svpow.com/2025/04/04/t...
Reposted by Shamith Samarajiwa
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...
Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model
www.cell.com/cell-genomic...
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...
www.cell.com
April 5, 2025 at 4:48 PM
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...
Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model
www.cell.com/cell-genomic...
Reposted by Shamith Samarajiwa
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...
I've reviewed the study and many other relevant ones here
erictopol.substack.com/p/the-shingl...
The Shingles Vaccine and Reduction of Dementia
A compelling new study adds to the body of data supporting some protection provided by the vaccine
erictopol.substack.com
April 5, 2025 at 6:06 PM
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...
I've reviewed the study and many other relevant ones here
erictopol.substack.com/p/the-shingl...
Reposted by Shamith Samarajiwa
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...
March 24, 2025 at 3:30 PM
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...
Reposted by Shamith Samarajiwa
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
March 22, 2025 at 10:51 AM
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
Reposted by Shamith Samarajiwa
And here is a previous guest post about actual concrete things scientists can do.
christinapagel.substack.com/p/eight-thin...
christinapagel.substack.com/p/eight-thin...
March 10, 2025 at 4:39 PM
And here is a previous guest post about actual concrete things scientists can do.
christinapagel.substack.com/p/eight-thin...
christinapagel.substack.com/p/eight-thin...
Reposted by Shamith Samarajiwa
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...
www.nytimes.com/2025/03/01/u...
March 1, 2025 at 6:07 PM
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...
www.nytimes.com/2025/03/01/u...
Reposted by Shamith Samarajiwa
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...
www.biorxiv.org/content/10.1...
February 26, 2025 at 6:07 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Shamith Samarajiwa
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
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...
www.cell.com
February 22, 2025 at 4:48 PM
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
Reposted by Shamith Samarajiwa
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.
Disease diagnostics using machine learning of B cell and T cell receptor sequences
www.science.org/doi/10.1126/...
TL;DR: BCRs ARE ALL YOU NEED!
(Well actually .... keep reading) 1/
www.science.org/doi/10.1126/...
TL;DR: BCRs ARE ALL YOU NEED!
(Well actually .... keep reading) 1/
Disease diagnostics using machine learning of B cell and T cell receptor sequences
Clinical diagnosis typically incorporates physical examination, patient history, various laboratory tests, and imaging studies but makes limited use of the human immune system’s own record of antigen ...
www.science.org
February 21, 2025 at 1:33 AM
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.
Reposted by Shamith Samarajiwa
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.
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.
February 13, 2025 at 5:05 PM
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.
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.
Reposted by Shamith Samarajiwa
🥳 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
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
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.
bit.ly
February 11, 2025 at 2:01 PM
🥳 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
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
Reposted by Shamith Samarajiwa
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...
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...
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.
thelancet.com
February 4, 2025 at 3:00 AM
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...
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...
Reposted by Shamith Samarajiwa
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...
"Using our lifecycle-wide single-cell dataset covering 13 age groups over the extent of the human lifespan...."
www.nature.com/articles/s41...
January 29, 2025 at 7:57 PM
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...
"Using our lifecycle-wide single-cell dataset covering 13 age groups over the extent of the human lifespan...."
www.nature.com/articles/s41...