Disease variants identified by genome-wide association studies (GWAS) tend to overlap
with expression quantitative trait loci (eQTLs), but it remains unclear whether this overlap is …

Pooled CRISPR screens with single-cell RNA sequencing readout (Perturb-seq) have
emerged as a key technique in functional genomics, but they are limited in scale by cost and …

Profiling immunoglobulin (Ig) receptor repertoires with specialized assays can be cost-ineffective
and time-consuming. Here we report ImReP, a computational method for rapid and …

Background Recent advancements in next-generation sequencing have rapidly improved
our ability to study genomic material at an unprecedented scale. Despite substantial …

Pooled CRISPR screens with single-cell RNA-seq readout (Perturb-seq) have emerged as
a key technique in functional genomics, but are limited in scale by cost and combinatorial …

Identifying gene sets that are associated to disease can provide valuable biological
knowledge, but a fundamental challenge of gene set analyses of GWAS data is linking disease-…

Assay-based approaches provide a detailed view of the adaptive immune system by profiling
T and B cell receptor repertoires. However, these methods carry a high cost and lack the …

In this dissertation, I develop new computational and/or experimental methods to elucidate
human disease mechanisms from two different data modalities: (1) genotypes with matched …

Aneuploidy, defined as abnormal chromosome number or somatic DNA copy number, is a
characteristic of many aggressive tumors and is thought to drive tumorigenesis. Gene …

Assay-based approaches provide a detailed view of the adaptive immune system by profiling
immunoglobulin (Ig) receptor repertoires. However, these methods carry a high cost and …