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yosoykit.bsky.social
Kit Curtius
@yosoykit.bsky.social
920 followers 130 following 33 posts
Assistant Professor at UCSD Medicine, Division of Biomedical Informatics. Researching cancer evolution and early detection. Check out our work at www.qcclab.com
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yosoykit.bsky.social
Kit Curtius @yosoykit.bsky.social · Jan 30
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
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yosoykit.bsky.social
Kit Curtius @yosoykit.bsky.social · 19d
All our methods using open weight LLMs are publicly available to modify for other problems and explained in detail in our paper and SI: github.com/bdj34/llama....
GitHub - bdj34/llama.cpp_data_extraction: Back up code to structure pathology reports. Repository was originally a clone of llama.cpp, then modified for data structuring
Back up code to structure pathology reports. Repository was originally a clone of llama.cpp, then modified for data structuring - bdj34/llama.cpp_data_extraction
github.com
yosoykit.bsky.social
Kit Curtius @yosoykit.bsky.social · 19d
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
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Kit Curtius @yosoykit.bsky.social · Aug 28
thank you for the support Trevor!
yosoykit.bsky.social
Kit Curtius @yosoykit.bsky.social · Jul 17
thank you Adam!
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Kit Curtius @yosoykit.bsky.social · Jul 17
No worries Suzanne, difficult last name club! haha thank you for the support <3
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Kit Curtius @yosoykit.bsky.social · Jul 15
It's open to the public I just walked right on! 7 mins walk from the convention center :)
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Kit Curtius @yosoykit.bsky.social · Jul 15
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”
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Kit Curtius @yosoykit.bsky.social · Jul 2
Next up at #EBECancer25 summer school - hands-on digital pathology workshop with @mihaelaangelova.bsky.social @chandler-gatenbee.bsky.social
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Kit Curtius @yosoykit.bsky.social · Jul 1
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
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Kit Curtius @yosoykit.bsky.social · May 7
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 💛
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Kit Curtius @yosoykit.bsky.social · Apr 15
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 🐘
abc10news.bsky.social
ABC 10News @abc10news.bsky.social · Apr 14
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.
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Kit Curtius @yosoykit.bsky.social · Apr 2
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... ☺️
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Kit Curtius @yosoykit.bsky.social · Feb 25
Will the recording be up on youtube after streaming? Have a meeting at same time but would like to watch :)
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Kit Curtius @yosoykit.bsky.social · Feb 14
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
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Kit Curtius @yosoykit.bsky.social · Feb 14
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
eventswcs.bsky.social
Wellcome Connecting Science Learning and Training @eventswcs.bsky.social · Feb 13
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
Wellcome Connecting Science discussion course Evolutionary Biology and Ecology of Cancer Course dates: 30 June-3 July 2025 Location: Wellcome Genome Campus, UK Application and bursary deadline: 1 April 2025
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yosoykit.bsky.social
Kit Curtius @yosoykit.bsky.social · Feb 14
amyboddy.bsky.social
Amy Boddy @amyboddy.bsky.social · Feb 14
Come learn how to apply approaches in evo-eco to cancer biology 🧬 ✨
eventswcs.bsky.social
Wellcome Connecting Science Learning and Training @eventswcs.bsky.social · Feb 13
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
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yosoykit.bsky.social
Kit Curtius @yosoykit.bsky.social · Jan 30
Finally, we are very hopeful that this genetic test could help prevent cancers in very high-risk patients. We are pushing this work forward still, much more to come! Thank you to the fantastic team I had the pleasure working with the past years @trevorgraham.bsky.social et al @cancerresearchuk.org
yosoykit.bsky.social
Kit Curtius @yosoykit.bsky.social · Jan 30
With independent data from other UK centers, we externally validated this biomarker and found similar risk stratification. As a predictive biomarker for HGD/CRC, both PPV & NPV >90% at 5 years post initial LGD resection time point in the validation. Check out the paper for more!
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Kit Curtius @yosoykit.bsky.social · Jan 30
We found LGD from progressors already harbored significantly more CNAs than non-progressors at index Dx. As a binary biomarker, the odds ratio of developing HGD/CRC for a high CNA score was 36, and this was 6 times higher than OR for even the strongest clinical predictor (invisible/unresected LGD).
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Kit Curtius @yosoykit.bsky.social · Jan 30
Low-grade dysplasia is notoriously hard to risk-stratify, even with some known risk factors for later cancer (e.g., size, multifocality). We hypothesized that the true culprit was underlying altered genomes of cells and conducted a large case-control study to test this at index LGD timepoint.
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yosoykit.bsky.social
Kit Curtius @yosoykit.bsky.social · Jan 30
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
1 7 17
yosoykit.bsky.social
Kit Curtius @yosoykit.bsky.social · Jan 18
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...
www.nature.com
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Kit Curtius @yosoykit.bsky.social · Jan 17
This is just the start of our work to tease apart relationships between host-microbe clonal populations in BE progression from an evolutionary perspective. Thanks for the fun collaboration with labs @ucsdmedschool.bsky.social @ucsandiego.bsky.social @fredhutch.bsky.social !
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Kit Curtius @yosoykit.bsky.social · Jan 17
Finally in model simulations, we found that assuming widely varying growth rates across taxa best reflected EAC data, implying that selection pressures may influence largely niche-based population dynamics in the tumor microenvironment.
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Kit Curtius @yosoykit.bsky.social · Jan 17
We found evidence of mostly neutral processes in normal and precancerous tissue, with the exception of Helicobacter pylori which deviated from a neutral expectation in BE patients who did not progress to EAC. For the EAC microbiome, patterns seem largely non-neutral.
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