Featured Research
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.
Updates
- CHASMplus manuscript on bioRxiv
- CHASMplus interactive tool
Dr. Rachel Karchin
Professor, The William R. Brody Faculty Scholar, Johns Hopkins University. Institute for Computational Medicine, Department of Biomedical Engineering, Department of Oncology.About the Karchin Lab
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.
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Selected Publications
Guthrie VB et al. (2018) Molecular Biology and Evolution. 35(6):1507-1519 Article
Douville C et al. (2018) Proc Natl Acad Sci U S A 115(8):1871-1876. Article
Newest Publication
Bailey MH, Tokheim C, Porta-Pardo E et al. (2018). Cell. 173(2):371-385.e18. Article
Latest Lab News
Summer/Autumn 2018
KarchinLab is recruiting new Ph.D students. If you are interested, please read the application instructions
OpenCRAVAT beta released! Modular, open tools for Custom Ranked Analysis of VAriants Toolkit.
Dr. Karchin promoted to Full Professor of Biomedical Engineering and Oncology.
Ph.D. student Collin Tokheim wins Martin and Carol Macht award for Young Investigator day at Hopkins Medicine.
Postdoc Violeta Beleva Guthrie's paper on network analysis of the functional impact of multiple adaptive mutations is published Mol. Biol. Evo.
Ph.D. student Collin Tokheim's paper on Driver Mutations in Cancer (co-first author with Matt Bailey and Eduard Porta-Pardo) is publisned in Cell.
CRAVAT/MuPIT tutorial workshop at American Society of Human Genetics annual meeting 2018. San Diego Convention Center Room 31, Upper Level. Friday 10/19/2018 at 7:15-8:45AM.