New tools for exploring rare cancer driver mutations.
Large-scale cancer sequencing studies of patient cohorts have statistically implicated many cancer driver genes, with a long-tail of infrequently mutated genes. Our group has developed CHASMplus, a computational method to predict driver missense mutations, which is uniquely powered to identify rare driver mutations within the long-tail. CHASMplus substantially outperforms comparable methods across a wide variety of benchmark sets.
We develop computational models to interpret and predict the impact of individual variation in the genome, transcriptome, and proteome. The models are being applied to cancer genomics, unclassified variants in Mendelian disease genes, and complex disease genetics. In collaboration with clinicians, pathologists, and experimental biologists, we aim to make significant improvements in individualized medicine within the next five years.
Niknafs N et al. (2019) Nat Comm. Nov;10(1):5435 Article
Springer S, Masica D et al. (2019) Sc. Trans. Med Jul 17(11(501) Article
Shao XM et al. (2019) Cancer Immunology Research (in press) bioRxiv preprint
KarchinLab is recruiting new Ph.D students. If you are interested, please read the application instructions
Postdoc Kym Pagel presents a webinar for the National Cancer Institute on the OpenCRAVAT variant interpretation framework. Aug 22.
Ph.D student Ashok Sivakumar defends his disssertation on tools for computational immuno-oncology. Aug. 30 Malone Hall 107 2:30pm. Johns Hopkins Homewood campus.
Ph.D student Ashok Sivakumar and Postdoc Kym Pagel present at AGBT Precision Health meeting September 5-7 in San Diego,
Talk by Rachel about variant interpretation and 3D protein structure at Columbia University Department of Systems Biology Distinguished Speaker series on October 2. New York City.
Postdoc Kym Pagel presents the OpenCRAVAT framework at the American Society for Human Genetics poster session Oct 15-19 Houston.
Talk by Rachel about tumor evolution at the Yale Center for Biomedical Data Science seminar series on November 6. New Haven.
Talk by Rachel about tools for computational immuno-oncology at UCSD Genetics, Bioinformatics and Systems Biology Symposium on January 9. San Diego.