Featured Research

Computational analysis of genomic data to aid medical decision making.

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

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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.

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Featured Software Tool Tutorial

Selected Publications

Identifying Mendelian disease genes with the Variant Effect Scoring Tool. BMC Genomics. 14(3) 1-16. Article

SubClonal Hierarchy Inference from Somatic Mutations: automatic reconstruction of cancer evolutionary trees from multi-region next generation sequencing. BioRxiv Nov 26. 2014 [preprint]

A probabilistic model to predict clinical phenotypic traits from genome sequencing. PLoS Computational Biology. Sep 4. 10(9):e1003825 Article

Newest Publication

Masica DL, Sosnay PR, Raraigh KS, Cutting GR, Karchin R (2014) Missense variants in CFTR nucleotide-binding domains predict quantitative phenotypes associated with cystic fibrosis disease severity. Human Mol. Genetics. Dec 8. Epub ahead of print. Article

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Latest Lab News

New release of Mutation Position Imaging Toolbox (MuPIT) interactive features visualization of clustered Cancer Genome Atlas somatic mutations in 14 tumor types and completely redesigned interface. Dec. 22, 2014

New paper by David Masica published Dec 8, 2014 in Human Molecular Genetics from Karchin Lab project with Cystic Fibrosis patient individualized care (inCF) initiative. Featured here in Johns Hopkins Engineering magazine.

Visualization of Ebola mutations. Mutation Position Imaging Toolbox for Ebola virus proteins released, in collaboration with the UCSC Ebola Portal Nov 15, 2014.

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