Clinical metagenomic next-generation sequencing (mNGS), the comprehensive analysis of
microbial and host genetic material (DNA and RNA) in samples from patients, is rapidly …

Lyme disease (also known as Lyme borreliosis) is the most common vector-borne disease in
the United States with an estimated 476,000 cases per year. While historically, the long-term …

Lyme disease (Lyme borreliosis) is a tick-borne, zoonosis of adults and children caused by
genospecies of the Borrelia burgdorferi sensu lato complex. The ailment, widespread …

We introduce alevin, a fast end-to-end pipeline to process droplet-based single-cell RNA
sequencing data, performing cell barcode detection, read mapping, unique molecular …

Network medicine is an emerging area of research dealing with molecular and genetic
interactions, network biomarkers of disease, and therapeutic target discovery. Large-scale …

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus
disease-19 (COVID-19), has emerged as the cause of a global pandemic. We used RNA …

In the United States (US), tick-borne diseases (TBDs) have more than doubled in the past
fifteen years and are a major contributor to the overall burden of vector-borne diseases. The …

Motivation Cell type composition of tissues is important in many biological processes. To
help understand cell type composition using gene expression data, methods of estimating …

Clinical metagenomics (CMg) is the process of sequencing nucleic acid of clinical samples
to obtain clinically relevant information such as the identification of microorganisms and their …

The mammalian host responds to infection with Borrelia spirochetes through a highly
orchestrated immune defense involving innate and adaptive effector functions aimed toward …