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Rachel Karchin
Assistant Professor, Department of Biomedical Engineering
Address:
3400 N. Charles Street
Computational Science & Engineering Building, Room 217a
Baltimore, MD 21218
Phone: (410) 516-5578
Fax: (410) 516-5294
E-mail: karchin@jhu.edu
Website: http://www.karchinlab.org/
Research Interest Statement
We use computation to study the impact of genetic variation at the molecular level. Genetic variation is critical to human susceptibility to diseases and response to medications. Yet the functional consequences of most genetic variants are unknown. We are working to predict these consequences using computation, by integrating information from molecular modeling and sequence analysis with clinical patient data and in vitro functional studies, through collaborations with physicians, genetic counselors, and experimental biologists. We are particularly interested in inherited cancer susceptibilities and gain of function mutations in tumor genomes.
Current Projects
Computational analysis of protein evolution and structure to aid medical decision making in high-risk breast, ovarian, prostate, and colorectal cancer families
Predicting the impact of somatic variation in cancer genomes with molecular modeling
Large scale annotation of human genetic variation
Molecular modeling of point mutations in proteins
SNPs and X-linked mental retardation
Publications
Carvalho M., M.A. Pino, R. Karchin, J. Beddor, M. Godinho-Netto, R.D. Mesquita, R.S. Rodarte, D.C. Vaz, V.A. Monteiro, S. Manoukian, M. Colombo, C. Ripamonti, R. Rosenquist-Brandell, G. Suthers, A. Borg, P. Radice, S.A. Grist, A.N.. Monteiro, B. Billack (2009). "Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1." Mutation Research, 660(1-2): 1-11.
Pieper U., N. Eswar, B.M. Webb, D. Eramian, L. Kelly, D.T. Barkan, H. Carter, P. Mankoo, R. Karchin, M.A. Marti-Renom, F.P. Davis, A. Sali (2009). "MODBASE, a database of annotated comparative protein structure models and associated resources." Nucleic Acids Res., 37 (Database Issue): D347-54.
Mankoo P., S. Sukumar, R. Karchin (2009). "PIK3CA somatic mutations in breast cancer: Mechanistic insights from Langevin dynamics simulations." Proteins, 75(2): 499-508.
Carter H., S. Chen, L. Isik, S. Tyekucheva, V.E. Velculescu, K.W. Kinzler, B. Vogelstein, R. Karchin (2009). "Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations." Cancer Research, 69(16): 6660-7.
Karchin R. (2009). "Next generation tools for the annotation of human SNPs." Breif Bioinform., 10(1): 35-52.
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