Epigenomes of Pathogens, Microbiome and Human: going beyond cytosine methylations towards other largely uncharacterized DNA methylations, DNA damages, and more generally, diverse forms of nucleic acid modifications. 

Third-generation Sequencing: single molecule; long reads, >20kb;  real-time; PacBio + Oxford Nanopore, integrated w/ Illumina; unique potential to detect nucleic acid modifications, complex structural variations and full length transcripts, etc.
Multi-scale Systems Biology based study of human diseases: genetic interactions and regulatory networks, highlighting both big and "small" data approaches, both "simple" and deep learning, integrated with innovative technologies and experiments.

Our lab (long read sequencing + experiment + computation) has rich experience in PacBio and Oxford Nanopore sequencing. We pioneered the fast growing field of bacterial epigenomics (Nature Biotechnology, 2012; Nature Reviews Genetics, 2018, Nature Microbiology, 2020). We also pioneered the use of DNA methylation for high resolution microbiome analysis (Nature Biotechnology, 2018; Nature Methods, 2021). In addition, we use long read sequencing to study the human genome, epigenome and transcriptome (Genome Research, 2018; Nature Genetics, 2019).

Innovation. Our research highlights two dimensions of innovations:

Pioneering the development, and novel application, of new technologies: Nature Methods, 2021; Nature Reviews Genetics, 2019; Genome Research, 2018; Nature Biotechnology, 2017; Nature, 2016; Nature Commnications, 2015; Genome Research, 2013; PLoS Compulational Biology, 2013; PLoS Genetics, 2013; Nature Biotechnology, 2012;

Integrating different types of data to characterize pathogens and human diseases: Nature Microbiology, 2020; Trends in Microbiology, 2020; Nature Genetics, 2019; Nature Communications, 2019; Cell Reports, 2016; Molecular Psychiatry, 2014; Nature Commnications, 2014; Biological Psychiatry, 2015; PLoS Genetics, 2015;