Our paper "Automated phenotyping with AI predicts future advanced neoplasia risk in colitis-associated low-grade dysplasia" out today in Clin Gastro Hep! Led by PhD student Brian Johnson-showcases power of LLMs to pull out relevant risk factors in huge EHR datasets www.cghjournal.org/article/S154...

DBMI is seeking applicants for our 2026 Postdoctoral Fellowships in Biomedical Informatics! Join our NIH NLM–funded fellowship. Eligibility: U.S. citizens, non-citizen nationals, or permanent residents (I-551). Apply: dbmi.ucsd.edu/education/nl...

Our new paper is out today! PhD student Brian Johnson tour de force in applying and validating LLMs for phenotyping in massive EHR databases. Opens up many exciting opportunities for disease research using population-scale data #mathonco bmjopengastro.bmj.com/content/12/1...

Large language models for extracting histopathologic diagnoses of colorectal cancer and dysplasia from electronic health records

Objective Accurate data resources are essential for impactful medical research, but available structured datasets are often incomplete or inaccurate. Recent advances in open-weight large language mode...

bmjopengastro.bmj.com

Gorgeous week in Edmonton, Alberta for #SMB2025 @smbmathbiology.bsky.social Fred Adler giving us the laughs we all need with his plenary on “Education, Bureaucracy and Corruption”

Next up at #EBECancer25 summer school - hands-on digital pathology workshop with @mihaelaangelova.bsky.social @chandler-gatenbee.bsky.social

here this week learning with all of our students at #EBECancer25 @eventswcs.bsky.social ! having a lot of Sudoku-type fun at our “grammar of somatic evolution” with tutor @afrankell.bsky.social

That’s a wrap for QCC lab representation at #DDW2025! So fun to work with these people everyday. I’m also rocking yellow for osteogenesis imperfecta awareness day each May 6th #WishboneDay 💛

Quite an earthquake today in SD! We're all good, but I loved watching the elephants' reaction to a natural threat at our beloved SD Zoo Safari Park 🐘

ABC 10News@abc10news.bsky.social · last yr.

WATCH: Elephants at the San Diego Zoo Safari Park react to Monday's 5.2 magnitude earthquake that shook San Diego County. The elephants formed an "alert circle" meant to protect the young and the entire herd from any threats, according to the San Diego Zoo Wildlife Alliance.

Congrats to @cgucci.bsky.social on successfully defending her PhD on pi day! First PhD from our lab, so grateful for her dedication to our team and her supportive thesis committee (not pictured: Ludmil Alexandrov, sorry Ludmil!). Very excited to see all she does next... ☺️

Our Division at UCSD Medicine is hiring postdocs in biomedical informatics on our T15 grant. Please apply if interested or share with others who might be! @ucsdmedschool.bsky.social @ucsandiego.bsky.social @ucsdhealth.bsky.social

Applications are open for our Evolutionary Biology and Ecology of Cancer summer course at the Wellcome Genome Campus, UK! This is a great opportunity for early career scientists/trainees to get plugged into this field #mathonco @amyboddy.bsky.social @trevorgraham.bsky.social @afrankell.bsky.social

Wellcome Connecting Science Learning and Training@eventswcs.bsky.social · 2y ago

Working in #CancerBiology? Join us at our expert-led #EBECancer25 course, to discover how insights on the #evolutionary and ecological aspects of #cancer are shaping the future for improved clinical treatments.💊 📅 30 June-3 July 2025 ⏰Apply by 1 April! 📎bit.ly/40nLdDD @sysbiocurie.bsky.social

Today our study using copy number alterations (CNAs) from low-coverage WGS to predict FUTURE colorectal cancer in patients with IBD is published, details in thread! 1/5 gut.bmj.com/content/earl...

Low-coverage whole genome sequencing of low-grade dysplasia strongly predicts advanced neoplasia risk in ulcerative colitis

Background The risk of developing advanced neoplasia (AN; colorectal cancer and/or high-grade dysplasia) in ulcerative colitis (UC) patients with a low-grade dysplasia (LGD) lesion is variable and dif...

gut.bmj.com

Our work on filtering host DNA from WGS data is also out today in @naturecomms.bsky.social! Congrats to first authors Caitlin Guccione and Lucas Patel - their methods were used in our new preprint and are freely available to use on your own data 🧬 www.nature.com/articles/s41...

Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data - Nature Communications

Here, the authors apply novel pangenome indexes created from diverse human references to facilitate computationally efficient removal of host genetic information, preserving biological accuracy and pr...

nature.com

How do microbial communities assemble during precancer and cancer evolution? Excited to share our new preprint on modeling of microbial evolution in Barrett's esophagus and esophageal adenocarcinoma! 🦠 Led by PhD student Caitlin Guccione #barretts #mathonco more in 🧵 www.biorxiv.org/content/10.1...

Devastated for those who lost everything in the horrible LA fires. Please send me any links to boost here to help those who need to rebuild <3

Kari Kretch@karikretch.bsky.social · 2y ago

We are so grateful to everyone who has reached out to offer support as we face this horrifying tragedy. We have a long road ahead and are comforted to know we are not alone. If you would like to contribute: gofund.me/95387a92

So cool to see this go to an amazing mathematical biologist, congrats!! And I’m honored to win the Leah Edelstein-Keshet prize this year from SMB @smbmathbiology.bsky.social can’t wait for Edmonton, Canada next year 🌲🏔️ #mathonco

The Fields Institute@fieldsinstitute.bsky.social · 2y ago

Congratulations to Dr. Leah Edelstein-Keshet, Professor Emerita at the University of British Columbia, for winning the 2025 CRM-Fields-PIMS prize! Dr. Edelstein-Keshet is a trailblazer in mathematical biology. Read more about her work at tinyurl.com/pb9f8w6w

Thankful this Thanksgiving break for this scientific community refresh to share with! PhD student Brian Johnson led our new preprint up today on using LLMs for extracting diagnoses in large EHR data- extremely accurate + easy to use for (pre)cancer Dx, go Brian! www.medrxiv.org/content/10.1...

Large language models for extracting histopathologic diagnoses from electronic health records

Background & Aims Accurate data resources are essential for impactful medical research. To date, most large-scale studies have relied on structured sources, such as International Classification of Dis...

medrxiv.org