Sequence variations of immune receptors

I am currently research associate at Randall Centre for Cell and Molecular Biophysics, King’s College London, working on the MACSMAF project. MACSMAF aims to define the mechanisms and dynamics behind Class-switch recombination (CSR) in antibodies. The project builds upon expertise of the consortium in studying antibody repertoire, large-scale biological data analysis and in vitro studies of B cell biology.

I contribute to the project in developing bioinformatics tools to analyse antibody sequence variations using data generated with high-throughput sequencing methods. We analyse variations in terms of CSR, somatic hypermutation (SHM) and other diversification mechanisms observed in variable regions of antibodies.

Code

BrepConvert: R package for flexible and detailed annotation of gene conversion events in immunoglobulin repertoire. Designed to analyse repertoire data from primates such as chicken, rabbit etc where gene conversion is prevalent to generate antibody diversity.

BrepPhylo: R package for fast lineage reconstruction, enabling analysis on large samples of clonotypes from BCR repertoire data.

scRNAVeloQuant: R code snippet to quantify transitions between cell types from RNA velocity estimates in single-cell RNA sequencing data analysis.

MACSMAF Publications to which I contributed

Stewart A, Ng JC, Wallis G, Tsioligka V, Fraternali F, Dunn-Walters DK. Single-Cell Transcriptomic Analyses Define Distinct Peripheral B Cell Subsets and Discrete Development Pathways. Front Immunol. 2021 Mar 18;12:602539. doi: 10.3389/fimmu.2021.602539.