I recently received my PhD from the Department of Biostatistics at the Johns Hopkins Bloomberg School of Public Health. For my dissertation work, I developed statistical methods to characterize antibody responses to various antigens using phage-immunoprecipitation sequencing technology (PhIP-Seq) with Dr. Ingo Ruczinski and Dr. H. Benjamin Larman. My research interests include Bayesian statistics, statistical genomics and proteomics, data analysis and data analysis teaching, and immunology.
Bayesian method for identifying enriched antibody responses from PhIP-Seq data.
Package defining an S4 class for PhIP-Seq experiments. PhIPData allows users to coordinate metadata with experimental data in analyses.
Extension of the kTSP classifier to longitudinal data to identify recent infections for HIV cross-sectional incidence estimation.
Annotated antigen library derived from metagenomic sequencing of stool samples and analyzed data with the new library.
Analyzed and assessed challenges facing current single-particle modeling methods of biochemical systems.
Phage ImmunoPrecipitation Sequencing (PhIP-Seq) is a recently developed technology to assess antibody reactivity, quantifying antibody binding towards hundreds of thousands of candidate epitopes. The output from PhIP-Seq experiments are read count matrices, similar to RNA-Seq data; however some important differences do exist. In this manuscript we investigated whether the publicly available method edgeR for normalization and analysis of RNA-Seq data is also suitable for PhIP-Seq data. We find that edgeR is remarkably effective, but improvements can be made and introduce a Bayesian framework specifically tailored for data from PhIP-Seq experiments (Bayesian Enrichment Estimation in R, BEER).
As availability and use of antiretroviral treatment increase worldwide, algorithms that do not include HIV viral load and are not impacted by viral suppression are needed for cross-sectional HIV incidence estimation. Using a phage display system to quantify antibody binding to over 3300 HIV peptides, we present a classifier based on top scoring peptide pairs that identifies recent infections using HIV antibody responses alone.
Graduate Teaching AssistantResponsibilities
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2016-2017 Undergraduate Teaching AssistantResponsibilities
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