The understanding of the human genome has been greatly improved by the advent of next-
generation sequencing technologies (NGS). Despite the undeniable advantages …

Proper gene expression requires the collaborative effort of multiple macromolecular
machines to produce functional messenger RNA. As RNA polymerase II (RNA Pol II) …

Annotating newly sequenced genomes and determining alternative isoforms from long-read
RNA data are complex and incompletely solved problems. Here we present IsoQuant—a …

GENCODE produces high quality gene and transcript annotation for the human and mouse
genomes. All GENCODE annotation is supported by experimental data and serves as a …

SQANTI3 is a tool designed for the quality control, curation and annotation of long-read
transcript models obtained with third-generation sequencing technologies. Leveraging its …

Most approaches to transcript quantification rely on fixed reference annotations; however,
the transcriptome is dynamic and depending on the context, such static annotations contain …

Determining whether the RNA isoforms from medically relevant genes have distinct
functions could facilitate direct targeting of RNA isoforms for disease treatment. Here, as a …

Abstract The advancement of Long-Read Sequencing (LRS) techniques has significantly
increased the length of sequencing to several kilobases, thereby facilitating the identification …

The lack of benchmark data sets with inbuilt ground-truth makes it challenging to compare
the performance of existing long-read isoform detection and differential expression analysis …

Alternative splicing events are a major causal mechanism for complex traits, but they have
been understudied due to the limitation of short-read sequencing. Here, we generate a full …