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.

View Current Research »


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

View All Publications »

Latest Lab News

Spring 2016

Karchin Lab receives ITCR U24 grant from the NCI for Cancer-Related Analysis of VAriants Toolkit.

HotMAPS algorithm paper "Exome-scale discovery of hotspot mutation regions in human cancer using 3D protein structure" by Tokheim et al. published in Cancer Research Apr 28, 2016.

Ph.D student Chris Douville presents poster "Within Sample Detection of Large Chromosomal Changes" at NHGRI's Research Training and Career Development Annual Meeting in Bethesda, Maryland.

Ph.D student Noushin Niknafs presents SCHISM poster at Cancer as an Evolving and Systemic Disease meeting at Memorial Sloan Kettering Cancer Center, NYC.

Dr. Karchin presents keynote at ISCB NGS 2016 Genome Annotation meeting, Barcelona, Spain.

Lab News Archive »