Gene expression is the fundamental level at which the results of various genetic and
regulatory programs are observable. The measurement of transcriptome-wide gene …

RNA sequencing (RNA-seq) has become an exemplary technology in modern biology and
clinical science. Its immense popularity is due in large part to the continuous efforts of the …

Alternative splicing (AS) generates isoform diversity for cellular identity and homeostasis in
multicellular life. Although AS variation has been observed among single cells, little is …

Motivation: The alignment of sequencing reads to a transcriptome is a common and
important step in many RNA-seq analysis tasks. When aligning RNA-seq reads directly to a …

Background Understanding the regulation of gene expression, including transcription start
site usage, alternative splicing, and polyadenylation, requires accurate quantification of …

RNA‐seq is widely used to determine differential expression of genes or transcripts as well
as identify novel transcripts, identify allele‐specific expression, and precisely measure …

Accurately quantifying gene expression levels is a key goal of experiments using RNA-
sequencing to assay the transcriptome. This typically requires aligning the short reads …

Accurate ty** of human leukocyte antigen (HLA) is important because HLA genes play
important roles in immune responses and disease genesis. Previously available …

Background Human leucocyte antigen (HLA) genes play an important role in determining
the outcome of organ transplantation and are linked to many human diseases. Because of …

Motivation: Long read sequencing technology is becoming an increasingly indispensable
tool in genomic and transcriptomic analysis. In transcriptomics in particular, long reads offer …