A transcriptome constructed from short-read RNA sequencing (RNA-seq) is an easily
attainable proxy catalog of protein-coding genes when genome assembly is unnecessary …

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

We introduce Scallop, an accurate reference-based transcript assembler that improves
reconstruction of multi-exon and lowly expressed transcripts. Scallop preserves long-range …

Background The use of novel algorithmic techniques is pivotal to many important problems
in life science. For example the sequencing of the human genome (Venter et al., 2001) …

Background Since the invention of next‐generation RNA sequencing (RNA‐seq)
technologies, they have become a powerful tool to study the presence and quantity of RNA …

Transcriptome assemblers aim to reconstruct full-length transcripts from RNA-seq data. We
present TransComb, a genome-guided assembler developed based on a junction graph …

Transcript assembly from RNA-seq reads is a critical step in gene expression and
subsequent functional analyses. Here we present PsiCLASS, an accurate and efficient …

RNA-seq technology is widely used in various transcriptomic studies and provides great
opportunities to reveal the complex structures of transcriptomes. To effectively analyze RNA …

Motivated by multiple genome assembly problems and other applications, we study the
following minimum path flow decomposition problem: Given a directed acyclic graph G=(V …

Motivation Alternative splicing (AS) of introns from pre-mRNA produces diverse sets of
transcripts across cell types and tissues, but is also dysregulated in many diseases …