Beroukhim Lab

Scalable Tracking of Symptoms in the Electronic Health Record using Large Language Models in Patients with Central Nervous System Cancers Undergoing Therapy AbstractBackground. Advances in large language models (LLMs) provide a means for scalable tracking of patient symptoms in clinical trials and post-marking

This was a fun project with John Rhee and Charlotta Lindvall on using LLMs to scour medical records. It has been wonderful to work with them!
secure-web.cisco.com/1QgAtJ9SFoCj...

Every dollar invested by the federal government on health research returns $2.60 in economic activity, not to mention the benefits to our health. The federal government spends very little on biomedical research as it is; it is so counterproductive to cut what remains. ☹️

Devastating news. The Pediatric Brain Tumor Consortium has lost its ability to apply for federal funding upon which it is structured. Without this, it cant exist. This threatens access to clinical trials for children.
These children need MORE funding and MORE trials, not less.
They deserve better

Recurrent breakpoints in the BRD4 locus reduce toxicity associated with gene amplification Wala et al. identify recurrent focal BRD4 deletions in tumors harboring larger amplifications, suggesting that these deletions may serve to limit toxic BRD4 overexpression. A CRISPR-Cas9 cell line mod...

📣 Online now! Our study shows how recurrent focal deletions constitute a mechanism by which cancer cells can dampen toxicity due to gene amplification.

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

🧵👇:

But now she is ineligible to apply for similar grants--so she has been punished for her successful application. This is like many other policies that seem vindictive towards fundamentally good people at vulnerable points in their lives. 2/2

My postdoc received a perfect "10" on her MOSAIC K99/R00 application and is half a year in. She just got an email that the program is being terminated and, it seems, she won't be funded for future years.

This really was a wonderful collaboration, and I recommend
@foijer-lab.bsky.social, @ms01.bsky.social, @vrendo.bsky.social, and @bendavidlab.bsky.social as collaborators to anyone!

A compendium of Amplification-Related Gain Of Sensitivity genes in human cancer Nature Communications - In cancer, the impact on cellular fitness of copy-number gains affecting collaterally-amplified genes remains poorly understood compared to oncogenes. Here, the authors...

Supper happy to see the results of our longstanding collaboration in @naturecomms.bsky.social. We identify RBM14 as an ARGOS gene to modulate cGAS-STING signalling. Driven by @ms01.bsky.social and @vrendo.bsky.social with @bendavidlab.bsky.social and @rameenberoukhim.bsky.social. rdcu.be/d7Mky

Our paper on an MDM2 inhibitor window-of-opportunity trial in GBM came out recently. I think it's a great example of the power of tissue collection trials to guide therapeutic development. Thanks to the many, many people who worked hard to make it possible!

A window-of-opportunity trial reveals mechanisms of response and resistance to navtemadlin in patients with recurrent glioblastoma In patients with glioblastoma, navtemadlin resistance is not mediated by TP53-inactivating mutations, and combination with TMZ may improve efficacy.

A window-of-opportunity trial reveals mechanisms of response and resistance to navtemadlin in patients with recurrent glioblastoma | Science Translational Medicine www.science.org/doi/abs/10.1...

Deep learning to decode sites of RNA translation in normal and cancerous tissues - Nature Communications RNA translation is a core cell process that is deregulated in cancer. Here, the authors show that a machine learning approach, RiboTIE, can reconstruct RNA translation in cancer and non-cancer cells. ...

Looking to see how #RiboSeq can improve your cancer research?

Check out how we've been developing new methods to study #medulloblastoma and other forms of #childhoodcancer.

Out in @naturecomms.bsky.social now. Thanks to Jim Clauwaert and Gerben Menschaert as well!

www.nature.com/articles/s41...

Thanks for starting this, Adrian! Please add me, though I don't post much