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BIOINFORMATICS

Bioinformatics

Vaccines induce a diverse repertoire of antibody and cellular responses, which can vary significantly in terms of their contribution to vaccine efficacy. We aim to characterize polyclonal immune responses in a repertoire-wide manner by developing statistical analysis and annotation tools that 1) annotate B cell receptor sequences and determine B cell lineages from immunosequencing data and 2) quantitatively compare repertoire-wide antibody and B cell receptor properties.

Software

Publications

Khavrutskii, I. V., S. Chaudhury, S. M. Stronsky, D. W. Lee, J. G. Benko, A. Wallqvist, S. Bavari, and C. L. Cooper. Quantitative Analysis of Repertoire-Scale Immunoglobulin Properties in Vaccine-Induced B-Cell Responses. Frontiers in Immunology. 2017 August 14; 8(910). [PDF]

Chaudhury, S., G. D. Gromowski, D. R. Ripoll, I. V. Khavrutskii, V. Desai, and A. Wallqvist. Dengue virus antibody database: systematically linking serotype-specificity with epitope mapping in dengue virus. PLOS Neglected Tropical Diseases. 2017 February 21; 11(2):e0005395. [PDF]

Lee, D. W., I. V. Khavrutskii, A. Wallqvist, S. Bavari, C. L. Cooper, and S. Chaudhury. BRILIA: integrated tool for high-throughput annotation and lineage tree assembly of B-cell repertoires. Frontiers in Immunology. 2017 January 17; 7:681. [PDF]