Next-generation sequencing (NGS) technology has advanced our understanding of the
human microbiome by allowing for the discovery and characterization of unculturable …

Since the days of Sanger sequencing, next-generation sequencing technologies have
significantly evolved to provide increased data output, efficiencies, and applications. These …

Mitochondrial genome (mitogenome) plays important roles in evolutionary and ecological
studies. It becomes routine to utilize multiple genes on mitogenome or the entire …

We performed the first proteogenomic characterization of hepatitis B virus (HBV)-related
hepatocellular carcinoma (HCC) using paired tumor and adjacent liver tissues from 159 …

Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently
available microbial genomes. This is being addressed by advances in sequencing …

Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes that are
increasingly used in high-throughput sequencing experiments. Through a UMI, identical …

Abstract RNA-sequencing (RNA-seq) has a wide variety of applications, but no single
analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data …

Abstract We introduce the Microenvironment Cell Populations-counter (MCP-counter)
method, which allows the robust quantification of the absolute abundance of eight immune …

Motivation: Detection of random errors and systematic biases is a crucial step of a robust
pipeline for processing high-throughput sequencing (HTS) data. Bioinformatics software …

The human microbiome has emerged as a major player in regulating human health and
disease. Translational studies of the microbiome have the potential to indicate clinical …