Featured Research

Computational analysis of genomic and clinical data to aid medical decision making.

In the new "post-genome" era of personalized medicine, many variants critical to disease susceptibilities, prognosis and drug sensitivities will be identified and increased numbers of people will undergo DNA sequencing. We are developing algorithms and tools intended to facilitate this process.


  • Assistant Research Professor David Masica is applying his MOCA algorithm to classify cysts that may be precursors to pancreatic cancer. Read about how Dave's mathematical model is being used in Science Daily.
  • Read about this year's Critical Assessment of Genomes experiment CAGI4 and our team's win in a genotype to phenotype prediction challenge.

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Dr. Rachel Karchin

Associate 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.

Lab Members and More Lab Info »


Featured Software Tool Tutorial

Selected Publications

Mascia DL, Karchin R (2016) PLoS Computational Biology. 12(5):e1004725. Article

Niknafs N, Guthrie VB, Naiman DQ, Karchin R (2015) PLoS Computational Biology 11(10):e1004416 Article

Newest Publication

Tokheim C Bhattacharya R, Niknafs N, Gygax DM, Kim R, Ryan M, Masica DL, Karchin R. May 2016 Article

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Latest Lab News

Autumn 2016

KarchinLab is recruiting new Ph.D students. If you are interested, please read the application instructions.

Dr. Karchin presents Evaluating the Evaluation of Cancer Driver Genes at Canceromatics III Tumor Heterogeneity in Madrid, Spain.

New MuPIT protein structure variant viewer released. Redesigned interface and fast 3D graphics.

Collin Tokheim presents Mutational hotspots in cancer: a protein structure-driver relationship to the JHU Lecture Series in Computational Biophysics.

PLoS Computational Biology launches Focus Feature on Genome Landscapes and Phenotype Prediction of Disease by Dr. Karchin and Dr. Ruth Nussinov.

CRAVAT 4.3 released. Enhanced interactive results pages. New annotations. Dockerized CRAVAT/MuPIT available for local installation!

Lab News Archive »