- Identification and quantification of transcriptomic events of at the gene isoform level, such as gene isoform identification and quantification, allele-specific expression and gene fusion;
- Identification and quantification of transcriptomic events of repetitive genes and novel genes.
See the primary publications: PNAS, 2013; Nucleic Acids Research, 2015; Nucleic Acids Research, 2016; F1000Research, 2017; Bioinformatics, 2018; Genome Biology, 2019; Genome Biology, 2020.
- RNA modifications and RNA editing;
- RNA secondary structure.
- DNA modifications and chromatin accessibility at repetitive elements;
- Strand-specific epigenome.
See the primary publication: Genome Research, 2019 and media report at GenomeWeb. It was selected as the cover of the Genome Research and recommended by F1000prime as an “exceptional” article.