Research

Method development of Third Generation Sequencing

We are interested in methodology research of Third Generation Sequencing (TGS) (e.g., PacBio and Oxford Nanopore sequencing). The Au lab is developing bioinformatics methods for both hybrid sequencing (Second Generation Sequencing (SGS) + TGS) data and TGS-alone data. Our research interests include but not limited to:

Transcriptome:

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.

Epitranscriptome:

RNA modifications and RNA editing;
RNA secondary structure.

Epigenome:

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.

Stem cell biology

The Au lab is applying the hybrid sequencing transcriptome methods and MeSMLR-seq on ESC and iPSC, to deeply study the transcriptomic, epitranscriptomic and epigenetic dynamics over the differentiations from stem cells to different lineage.

University of Michigan, MI 48109.