Benjamin
@_benjaminv
Bioinformatics, Coding, Microbial and Meta genomics, Biology. mastodon @[email protected] pronouns: he/him ✡️
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Most genetic reports label variants as ✅ “pathogenic” or ❌ “benign.” But what patients really want to know is: what are my chances of getting the disease? 🚨 In our new Science study, we used AI + 1.3M patient records to better answer that…
If any PhD student working in computational biology is displaced by this most recent tumult and is looking for a new lab, I have room for one (or potentially two) PhD students in my group. Feel free to reach out via email.
Huge result! Not only did a polygenic risk score identify a large number of participants with prostate cancer, many of them were low risk by conventional guidelines AND had medium/high-risk disease. That has been a hard needle to thread in other cancers.
14% of 55-69 men with polygenic risk scores (PRS) in the top 10% had prostate cancer classified as intermediate or higher risk, a higher percentage than would have been identified using PSA or MRI screening. This seems like a strong argument for integrating polygenic risk scores…
Ask any cancer researcher and they’ll point you to emerging studies that suggest mRNA vaccines are about to transform cancer care. Stuff like this is simply throwing lives in the trash. Maybe yours.
Exclusive: NIH officials have advised some scientists to remove references to mRNA vaccines from their grant applications, in expectation the Trump administration intends to abandon most research in the field. By @ArthurAllen202 kffhealthnews.org/news/article/n…
I can never understand how people don’t get how silly it is when they say things like “My grandparents survived childhood measles so it’s not a big deal” Well, no shit - if your grandparents didn’t survive measles, you wouldn’t exist Every person existing has a full set of…
LLMs for coding are just non-deterministic compilers from natural language to programming language. And if you argue that this is what Programming actually is you are the kind of person who's gonna be replaced by them, congratulations.
Quick update: Thanks so much for the outpouring of support and help. We learned a lot in the last week and the tumor is actually a myeloid sarcoma likely derived from early AML, with the hope of possible targeted therapies as well (KMT2Ar). We have a long road ahead of us, but…
It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS, indeterminate dendritic cell histiocytosis…
Enormous lies here from your new HHS Secretary The HPV vaccine (Gardasil) is safe, effective, and is on the way to ELIMINATING cervical cancer! RFK Jr is an anti vaccine fanatic who would rather your daughter got cervical cancer than a vaccine Horrible, horrible man.
This is unbelievable. H5N1 is banging at the door and we're firing the 'disease detectives'? Funny thing about pathogens, they will kill you even if you don't know they are there. statnews.com/2025/02/14/tru…
*Every single* cure for a disease ultimately flowed from basic exploratory research. Stopping basic research is like stopping the mountain rains and expecting rivers of cures to still flow. Examples: 1) studying saliva of Gila monster -> GLP1's 2) studying funghi -> first…
As a taxpayer (irrespective of whether you’re a scientist) would you would be in favor of more of the @NIH budget going to fund efforts to solve specific diseases at the expense of basic exploratory research? Which diseases?
If anyone knows clinicians or patients who have knowledge of pediatric patients with the very rare cancer interdigitating dendritic cell sarcoma (IDCS) or other (non-LCH) dendritic or histiocytoc sarcomas please contact Sri Kosuri. His daughter was recently diagnosed with IDCS.
It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS, indeterminate dendritic cell histiocytosis…
Something to consider next time someone tells you that N=3 should be sufficient. It depends critically, of course, on the question. But many studies are massively underpowered (*many* false negatives) and also run the risk of high false positives. #RNASeq
RNAseq is commonly performed. We compared N=30 wild-type Bl6 mice to an N=30 heterozygotic knockout with a phenotype, and then downsized. We found you need at least an N= 8-12 to avoid a >50% false positive rate. A 2nd line confirmed the finding. biorxiv.org/content/10.110…
Sachs' Covello estimates that a trillion dollars is being invested in propping up generative AI, yet it doesn't solve a one-trillion-dollar problem. It isn't making money, it costs too much, it doesn't create new jobs and doesn't make workers smarter. wheresyoured.at/pop-culture/
Those replacing human beings with AI are doing so because they've no respect/understanding of labor, commoditizing outputs without seeing that a job is both the acquisition of labor and the outsourcing of risk. You don't just hire humans- you trust them. wheresyoured.at/pop-culture/
Newsletter: Goldman Sachs has called BS on Generative AI, and I believe that it's time that everybody follows suit - generative AI is unreliable, unsustainable, requires an entire rebuild of America's power grid, and is most decidedly not the future. wheresyoured.at/pop-culture/
When writing bioinformatics tools, I often need small datasets to test edge cases or invalid file formats, e.g. files that are truncated, unsorted, have extraneous whitespace, etc. I started compiling examples here: github.com/omgenomics/bio…, contributions are welcome!
Rockfish: A transformer-based model for accurate 5-methylcytosine prediction from nanopore sequencing has been published in Nat. Comm!! Great work by @domstanojevic w/ Zhe Li, @sarrabakic and @rsyf2 Paper: nature.com/articles/s4146… Code: github.com/lbcb-sci/rockf…
Hello to all #bioinformatics #rustlang, I often copy code to generate data when writing tests. After 3 or 4 times, I got fed up and created biotest crates. biotest can generate fasta, fastq and vcf, I'm open to any suggestion, feedback or contribution. github.com/natir/biotest
"The filename must always be the last argument, or this program will throw a segmentation error." hmm #Bioinformatics
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