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Simon Baker

@drsimonbaker.bsky.social
282 followers 451 following 31 posts

Bladder cell biologist working with normal and cancer human tissue models for @kidneyresearchuk.org and @yorkagainstcancer.bsky.social. We study how bladder cancer is initiated by BK polyomavirus-induced APOBEC3 cytosine deaminases.

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Simon Baker @drsimonbaker.bsky.social · 18/05/2026
This over half-a-million investment in my lab means we can continue our search for ways to tackle BK virus and the diseases it causes. We aim to improve the lives of transplant recipients suffering with BK virus and to address its role in bladder cancer initiation.
George Hatton and Diane Lee working in the microscopy labs at the University of York. They are looking at an image of BK virus infected cells.
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Simon Baker @drsimonbaker.bsky.social · 18/05/2026
We see #bladdercancer as a potential long-term consequence of poorly-controlled BK virus infections but transplant recipients also suffer from acute damage to their kidneys (“BK virus associated nephropathy”) and lower urinary tracts (“ureteric strictures” and “haemorrhagic cystitis”).
We see bladder cancer as a potential long-term consequence of poorly-controlled BK virus infections but transplant recipients also suffer from acute damage to their kidneys (“BK virus associated nephropathy”) and lower urinary tracts (“ureteric strictures” and “haemorrhagic cystitis”).
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Simon Baker @drsimonbaker.bsky.social · 18/05/2026
This senior fellowship will build on the work of my intermediate fellowship where we associated BK virus infections with the APOBEC mutations that initiate bladder cancers (see our recent Science Advances paper for details - www.science.org/doi/10.1126/...).
science.org
Virus-induced APOBEC3 transmutagenesis in bladder cancer initiation
A model for hit-and-run viral carcinogenesis in the bladder.
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Simon Baker @drsimonbaker.bsky.social · 18/05/2026
I’m happy to announce that I have been awarded a five-year senior fellowship jointly funded by two amazing charities: @kidneyresearchuk.org and @yorkagainstcancer.bsky.social. This new fellowship also comes with a permanent academic job @biologyatyork.bsky.social and @ybri-uoy.bsky.social.
Photo of Simon Baker in the labs at the University of York
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Inigo Martincorena @imartincorena.bsky.social · 05/03/2026
Somatic genomics as a discovery engine for biomedicine - a Perspective in Cell www.sciencedirect.com/science/arti...
sciencedirect.com
Somatic genomics as a discovery engine for biomedicine
Somatic mutations, or genetic changes occurring in cells after conception, are widespread in healthy tissues but are conventionally viewed as signs of…
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Open Research at York @uoyopenres.bsky.social · 23/02/2026
Researchers at the Jack Birch Unit @biologyatyork.bsky.social @ybri-uoy.bsky.social revealed how direct communication between cells can help maintain healthy tissue, potentially paving the way for new bladder cancer treatments 🔬 Open access paper in Life Science Alliance doi.org/10.26508/lsa... 🔓 📄
york.ac.uk
Cells that communicate may help hinder bladder cancer from spreading
Researchers at University of York’s Jack Birch Unit have revealed how direct communication between cells can help maintain healthy human tissue - potentially paving the way for new treatments for blad...
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Simon Baker @drsimonbaker.bsky.social · 20/02/2026
Pleased to see Jenny’s first author work on Connexin communication in the urothelium published. It’s a great story.
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Kidney Research UK @kidneyresearchuk.org · 04/02/2026
For World Cancer Day, we're shining a spotlight on Dr Simon Baker and his team at the University of York, and their research into BK virus and bladder cancer. Read more the research here: bit.ly/4pjXEvr
bit.ly
New results suggest that bladder cancer could be caused by the body’s response to common childhood virus - Kidney Research UK
New data from Dr Simon Baker suggests BK virus can drive bladder cancer development, which kidney transplant recipients are at more risk of.
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Simon Baker @drsimonbaker.bsky.social · 24/01/2026
Sounds interesting. Shame it’s not open access.
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Simon Baker @drsimonbaker.bsky.social · 07/01/2026
The relevant recent paper 🔬🔗: www.science.org/doi/10.1126/... Our work is supported by @kidneyresearchuk.org and @yorkagainstcancer.bsky.social, and is hosted by the @biologyatyork.bsky.social and @ybri-uoy.bsky.social.
science.org
Virus-induced APOBEC3 transmutagenesis in bladder cancer initiation
A model for hit-and-run viral carcinogenesis in the bladder.
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Simon Baker @drsimonbaker.bsky.social · 07/01/2026
I chatted with @philiprlang.bsky.social on his podcast about how a virus might be involved in bladder cancer. Since "Phil Lang is Not a Scientist", we made this really accessible. If you're interested in how small sneaky DNA viruses might contribute to the origins of cancers, give it a listen.
creators.spotify.com
Episode 13 - Simon Baker by Phil Lang is Not a Scientist
In this podcast I speak to Simon about his important research into the causes of bladder cancer, as well as his life and career.Story from Kidney Research UK about Simon's important breakthrough: http...
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Alex Reid @alexanderreid.bsky.social · 09/12/2025
I had a lovely chat with Phil Lang on his podcast "Phil Lang is Not a Scientist" where I talk a lot about dreams and sleep! Phil interviews researchers from across the University of York about their work in all sorts of fascinating areas. (creators.spotify.com/pod/profile/...).
creators.spotify.com
Episode 6 - Alex Reid by Phil Lang is Not a Scientist
It was great to talk to Psychology academic Alex Reid today about his work at York.Alex's profile: https://www.york.ac.uk/psychology/staff/academicstaff/amr507/Here's a link to Alex's last paper on sl...
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Liz (TheLongCovidNurse) @thelongcovidnurse.bsky.social · 06/12/2025
Another virus which causes ‘just a cold’ or ‘cold like symptoms’ is actually causing cancer. Tip of the iceberg?
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Simon Baker @drsimonbaker.bsky.social · 04/12/2025
This work was hosted @biologyatyork.bsky.social, @ybri-uoy.bsky.social and @yorkbioscience.bsky.social. With collaborators at @universityofleeds.bsky.social, @lthtresearchcomms.bsky.social, @leedsth.nhs.uk, University of Texas at San Antonio and the National Cancer Institute at Bethesda.
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Simon Baker @drsimonbaker.bsky.social · 04/12/2025
The fantastic authors on Bluesky are @sallyjamesyork.bsky.social, @asmasonomics.bsky.social, @karen-hogg.bsky.social, @imartincorena.bsky.social, @starrett.bsky.social
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Simon Baker @drsimonbaker.bsky.social · 04/12/2025
With thanks to our funders @kidneyresearchuk.org and @yorkagainstcancer.bsky.social for supporting #bladdercancer research which is so often neglected. #cancer #cancerresearch #APOBEC
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Simon Baker @drsimonbaker.bsky.social · 04/12/2025
These findings suggest a model of bladder carcinogenesis where the urothelial response to BK virus infections drives the initiating APOBEC mutations, but the virus is not required in the arising tumour.
A model for bladder cancer initiation where persistent BK virus infections of the kidney reactivate and shed decoy cells into the urine infecting the urothelium. In late-stage infections, the urothelium isolates and apically extrudes infected cells (marked by expression of the Viral capsid major Protein 1 “VP1”). In the viral extrusion microenvironment, bystander cells express interferon-regulated APOBEC3A, which damages the host genome. This is a hypothesis for how bladder cancers become defined by APOBEC3A/B mutagenesis without any virus present in the final tumour.
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Simon Baker @drsimonbaker.bsky.social · 04/12/2025
"Transmutagenesis" describes the observation of bystander cells that were negative for viral proteins and proximal to infected neighbours acquiring APOBEC3A mediated potentially cancer initiating mutations.
Flow cytometry was used to sort a population that was high in antiviral APOBEC3 cytidine deaminase expression but had no detectable viral protein expression. Nanorate sequencing (NanoSeq) was then used to capture the APOBEC mutational signature forming in these cells. Could these cells be the progenitors of bladder cancers with APOBEC mutations in their genome but no trace of viruses?
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Simon Baker @drsimonbaker.bsky.social · 04/12/2025
Chronic (>21 day) BK virus infections of normal human urothelium led to robust inductions of APOBEC3 mutational signatures. APOBEC3A was induced by bystander cells (negative for viral proteins) and in association with apical extrusion of infected cells by interferon signalling.
Histology images showing coordinated apical extrusion of BK virus infected cells by the healthy tissue. APOBEC3 cytidine deaminases were upregulated in bystander cells (without detectable viral proteins) involved in the apical extrusion process.
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Simon Baker @drsimonbaker.bsky.social · 04/12/2025
Our evidence suggests there could be a route to bladder cancer prevention by stopping/controlling the reactivation of persistent BK virus infections.
Mutograph image showing that mutational signatures characteristic of antiviral APOBECs form in the genomes of urothelial cells when cultures are infected with BK virus.
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Simon Baker @drsimonbaker.bsky.social · 04/12/2025
What causes bladder cancer initiating mutations? Our paper in Science Advances asks the question: can BK virus infections of normal urothelium lead to the APOBEC3 mutational signatures found in bladder cancers? We found that they can!
science.org
Virus-induced APOBEC3 transmutagenesis in bladder cancer initiation
A model for hit-and-run viral carcinogenesis in the bladder.
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Kelly @broadwaybabyto.bsky.social · 27/11/2025
Australia recorded ZERO cases of cervical cancer in women under 25 for the first time since they started tracking the cancer in the 80s. This is the power of vaccines. The HPV vaccine is extremely effective at preventing cancer. Viruses can be oncogenic. Get your vaccines and protect yourself!
www1.racgp.org.au
newsGP - Australia set for world-first cervical cancer elimination
Vaccination programs have played a key role, and GPs remain ‘instrumental’ in boosting screening rates to reach the 2035 target.
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Simon Baker @drsimonbaker.bsky.social · 11/11/2025
Are you a kidney transplant recipient who would like to learn more about post-transplant viral infections? Join @kidneyresearchuk.org funded researchers to hear updates on their research. This online seminar will take place 1-2pm on Friday 28th November 2025, register for free below.
kidneyresearchuk.org
Research webinar - Kidney Research UK
A webinar to hear directly from Kidney Research UK funded researchers as they share the latest updates on projects tackling BK virus and cytomegalovirus.
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Clive McKimmie @clive-mckimmie.bsky.social · 31/10/2025
New PhD opportunity! Can skin inflammation protect us from mosquito-borne viruses like Zika? Join our MRC PhD project at York exploring how psoriasis and eczema change skin immunity to virus. Our grads thrive in academia, biotech & beyond. Apply now 👉 tinyurl.com/bfmd2rf4
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Simon Baker @drsimonbaker.bsky.social · 16/10/2025
I'm really excited to be teaching about mutational signatures and viral aetiologies in #bladdercancer at the "Course on Urothelial Malignancies" in Paris 14-16 January 2026. There are so many great speakers, I'm sure I'll learn lots. Hope to see you there! Contact: c.uro2026@curie.fr
Poster for the 2nd Course on Urothelial Cancers on January 14th-16th 2026 at the Institut Curie in Paris. Theme: Understanding molecular basis of urothelial tumors to improve diagnosis and treatments. Contact: c.uro2026@curie.fr
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John E Milad @johnemilad.bsky.social · 11/10/2025
“Rare” kidney diseases leave a deep and widespread impact. 160,000+ people in the UK are affected — driving 25% of dialysis demand and costing the NHS £263m a year. As a @kidneyresearchuk.org Trustee, I’m calling for faster diagnosis and fairer access to care. 🔗 bit.ly/47Wdp5Z #KidneyHealth
kidneyresearchuk.org
Collectively common, rare kidney disease report - Kidney Research UK
A report about the impact of rare kidney diseases in the UK including diagnosis delays and waits for new treatments.
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Clive McKimmie @clive-mckimmie.bsky.social · 01/10/2025
We all know vaccines target the pathogen, but can you also target the vector? 📢 in a new paper out today in Vaccines, we show that a vaccine targeting mosquito salivary peptides, AGSv-PLUS, enhances human skin immune response to biting. Open access: www.mdpi.com/2076-393X/13... 1/6
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Lori O'Brien @llobrienlab.bsky.social · 26/09/2025
For this #FluorescenceFriday, a gorgeous image of an adult mouse kidney labeled with AQP2 and alpha SMA antibodies. AQP2 (green) marks the collecting duct and distal connecting segment while SMA marks the arterial tree. Courtesy of talented postdoc Sarah McLarnon.
Image of a fluorescently labeled adult mouse kidney showing AQP2 staining of collecting ducts and connecting segment in green and alpha SMA staining of the arterial tree in magenta. The collecting ducts look like squiggly branches.
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Wen Ding @wyd20.bsky.social · 25/09/2025
Having a fantastic time listening to all the progress in kidney research in the UK @kidneyresearchuk.org driving discoveries. Fantastic talk @willkidney.bsky.social about how large well designed trials have changed our practice in nephrology
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QUOD Biobank @quod-biobank.bsky.social · 24/09/2025
QUOD's National Operational Coordinator, Sarah Cross, is at the Kidney Research UK #DrivingDiscoveries conference today in Bristol and is ready to talk to you about how the QUOD biobank can support your kidney research. Come and say hello! 👋 @nhsbt.bsky.social @ndsurgicalsci.bsky.social @ox.ac.uk
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The Francis Crick Institute @crick.ac.uk · 04/09/2025
Congratulations to @gregfindlay.bsky.social on being awarded a €1.5 million Starting Grant from the @erc.europa.eu to take a closer look at possible disease variants hiding in the dark genome. www.crick.ac.uk/news/2025-09...
crick.ac.uk
€1.5 million to uncover disease risk hiding in non-coding DNA
Greg Findlay, Group Leader of the Genome Function Laboratory at the Francis Crick Institute, has been awarded a Starting Grant from the European Research Council for €1.5 million to take a deep dive i...
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Simon Baker @drsimonbaker.bsky.social · 03/09/2025
The Leeds Transplant teams are amazing humans. Great to see this celebration.
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Simon Baker @drsimonbaker.bsky.social · 08/08/2025
If you're a kidney transplant recipient who has been diagnosed with BK virus infection, please consider reading our evidence-based patient information leaflet that was co-developed alongside BK nephropathy patients. We hope it helps and welcome any feedback to develop it. www.kidney.org.uk/bk-virus
kidney.org.uk
BK Virus
What is BK Virus? BK virus is an infection almost everyone gets during childhood. The symptoms are like a mild cold, so most people don't notice when they catch it. After infection, the virus hides in...
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Daniel Hurdiss @danielhurdiss.bsky.social · 19/07/2025
"A highly potent human antibody neutralizing all serotypes of BK polyomavirus" journals.plos.org/plospathogen...
journals.plos.org
A highly potent human antibody neutralizing all serotypes of BK polyomavirus
Author summary BK polyomavirus (BKPyV) is a common virus that infects most people during childhood and typically remains dormant in the kidneys without causing harm. However, in kidney transplant pati...
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Andrew Holding @andrewholding.bsky.social · 24/04/2025
YBRI (@ybri-uoy.bsky.social) are hosting @alanawelm.bsky.social for an online seminar on 9th May 2pm BST. Prof Welm will be presenting her work on "Modeling metastatic breast cancer to advance therapeutic strategies". Please share, and register to join at www.eventbrite.co.uk/e/ybri-onlin...
eventbrite.co.uk
YBRI Online Biomedical Sciences Seminar 2025
Join our online biomedical sciences seminar open to UG, PG students, postdocs, ECRs and Group Leaders!
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Cancer Research UK @cancerresearchuk.org · 24/04/2025
🚨 Breaking News: The Tobacco and Vapes Bill has passed its Second Reading in @ukhouseoflords.bsky.social! 🚨 This marks another hugely important step towards ending cancers caused by smoking. Please share to show your support for a #SmokefreeUK 🔁
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Kidney Research UK @kidneyresearchuk.org · 23/04/2025
We’re #hiring! It’s an exciting time as we expand and create brand new roles within our passionate charity, committed to changing lives for people with kidney disease. Take a look and share with your network. Find out more and apply here: bit.ly/3umf9kS #Recruitment #CharityJobs
[Image description: ‘We’re hiring’ sits bold on the page. Top right sits the Kidney Research UK logo. To the left, a full-length professional image of their logo from on outdoor event is present. To the right lists two jobs, brand and marketing officer and volunteering officer. Underneath it reads ‘As part of the charity’s growth, new positions have been introduced.’ And lists six more roles: Peer educator manager, health equalities lead, director of translational science and technology assessment, translational research and innovation project officer, health data specialist, and head of data.]
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Jeffrey Townsend @jeffreytownsend.bsky.social · 23/03/2025
APOBEC drives genetic variation in lung tumors, especially in response to tyrosine kinase inhibitor therapy 🧪. Inhibition of APOBEC during use of tyrosine kinase inhibitors could improve outcomes. In a paper just out in Lung Cancer, we show how much. www.sciencedirect.com/science/arti...
sciencedirect.com
Precision projections of the delay of resistance mutations in non-small cell lung cancer via suppression of APOBEC
Genomic instability driven by stress-response-dependent mutagenesis is a key factor in cancer progression. Tyrosine kinase inhibitor therapy, a common…
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Action Bladder Cancer UK @abcuk.bsky.social · 10/03/2025
Excited for the AJ Bell Great North Run 2025? There’s still time to join Team Action Bladder Cancer UK and run for a great cause! Whether you’re a seasoned runner or a first-timer, it’s an event you won’t want to miss. 🏅 events@actionbladdercanceruk.org #GreatNorthRun #BladderCancer #Fundraising
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Simon Baker @drsimonbaker.bsky.social · 10/03/2025
Sorry to hear this Gabe. Hope she finds something soon. Best wishes to you all.
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Gabe Starrett @starrett.bsky.social · 09/03/2025
If anyone is looking for a lab technician/manager with nucleic acid isolation, library prep, and sequencing analysis experience preferably in the DMV, my former biologist is looking for a job. She was unfortunately terminated in Feb as part of the probationary employee firings. DM me for her info
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Kidney Research UK @kidneyresearchuk.org · 10/03/2025
Did you know that blood in your urine or needing to urinate frequently are symptoms of kidney disease? This #WorldKidneyDay, let’s help more people spot the early warning signs with our ‘Take a wee look’ campaign. What do the colours mean? Find out more: www.kidneyresearchuk.org/2025/02/21/b...
Image of a urine hydration chart on a toilet seat with sections labelled 1 to 7 indicating various hydration levels from 'Drink more water' to 'Ideal Colour.' The chart advises 'Take a wee look.' to detect early signs of kidney disease
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uofytechs.bsky.social @uofytechs.bsky.social · 05/03/2025
#job 🚨for a laboratory technician in the Wright group within dept. Biology/HYMS and @ybri-uoy.bsky.social to work on creating genome-scale arrays of human cell surface receptors to discover new host-pathogen interactions. Apply by 20/3/2025: jobs.york.ac.uk/vacancy/labo...
jobs.york.ac.uk
Jobs - The University of York
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Nath Jones @drnathjones.bsky.social · 04/03/2025
New preprint: results from a collaborative project funded by the GCRF Global Network for NTDs investigating Leishmania deubiquitinase 16 as a potential drug target. @ybri-uoy.bsky.social @mottramlab.bsky.social www.biorxiv.org/content/10.1...
biorxiv.org
Structure and Activity of the Essential UCH Family Deubiquitinase DUB16 from Leishmania donovani
In Leishmania parasites, as for their hosts, the ubiquitin proteasome system is important for cell viability. As part of a systematic gene deletion study, it was discovered that four cysteine protease...
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Julie Talbot @julietalbot.bsky.social · 07/03/2025
As scientists we are often exposed to upsetting findings and we should not have to bury the feelings that our research elicit - I'm glad it's adressed openly here (and yes these results are bleak)
cbc.ca
Scientists brought to tears by huge loss of U.S. butterflies | CBC News
Scientists calculated just how much U.S. butterfly populations have declined in the past 20 years. The results brought some scientists to tears, and have them warning about dire implications for other...
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Henry Scowcroft @oh-henry.bsky.social · 05/03/2025
I've written a big feature piece for @cancerresearchuk.org's News site, about a cutting-edge new brain tumour trial they're supporting. It's aimed at the researcher community so a bit techier than usual, but was great fun pulling together. news.cancerresearchuk.org/2025/03/04/a...
news.cancerresearchuk.org
Accelerating the search for new glioblastoma treatments - Cancer Research UK - Cancer News
Henry Scowcroft looks at a pioneering new clinical platform trial set to offer more options to UK glioblastoma patients and kick-start progress
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Patrick Hickey, MD @pwhickey.bsky.social · 28/02/2025
The HPV vaccine is an anti-cancer vaccine
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The New York Times @nytimes.com · 28/02/2025
The Trump administration terminates funding for polio, HIV, malaria and nutrition programs around the world. “People will die,” said Dr. Catherine Kyobutungi of the African Population and Health Research Center, “but we will never know, because even the programs to count the dead are cut.”
nytimes.com
U.S. Terminates Funding for Polio, H.I.V., Malaria and Nutrition Programs Around the World
Here are some of the 5,800 contracts the Trump administration formally canceled this week in a wave of terse emails.
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Simon Baker @drsimonbaker.bsky.social · 25/02/2025
Disturbing to see another rise in recreational ketamine use in the UK. We did some of the early work showing how ketamine kills the cells that line our bladders: www.sciencedirect.com/science/arti... It's sad to think of all the pain and lifelong consequences for young people caused by ketamine.
bbc.co.uk
Generation K: The disturbing rise of ketamine abuse among young people
Increasing numbers of young people are using the drug, experts say. The health impacts can be catastrophic.
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Simon Baker @drsimonbaker.bsky.social · 06/02/2025
The "Nous-209" vaccine for people with Lynch syndrome includes some 209 neoantigens. Including neoantigens on this scale in a single vaccine gives some hope for a vaccine that could offer protection against bladder cancer despite its extreme genomic heterogeneity.
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