As sequencing technologies become more affordable, it is now realistic to propose studying
the evolutionary history of virtually any organism on a genomic scale. However, when …

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 using the latest single-molecule sequencing instruments produces reads
that are thousands of nucleotides long. The ability to assemble these long reads can greatly …

Alternative splicing generates multiple transcript and protein isoforms from the same gene
and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is …

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

Alternative splicing plays an essential role in many cellular processes and bears major
relevance in the understanding of multiple diseases, including cancer. High-throughput RNA …

Genotype estimates from short-read sequencing data are typically based on the alignment of
reads to a linear reference, but reads originating from more complex variants (for example …

Accurate characterisation of splice junctions (SJs) as well as transcription start and end sites
in reference transcriptomes allows precise quantification of transcripts from RNA‐seq data …

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 …

RNA sequencing is widely used to measure gene expression across a vast range of animal
and plant tissues and conditions. Most studies of computational methods for gene …