Research

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 (cutting edge technology + experiment + computation) pioneered the fast growing field of bacterial epigenomics (m6dA as most abundant form, Nature Biotechnology, 2012). We also pioneered the use of DNA methylation (m6dA) for high resolution microbiome analysis (Nature Biotechnology, 2017). Recent work by us and others discovered that m6dA exists as a novel form of DNA methylation in mammalian genome (Nature 2016), and multiple evidence suggests it has a significant diseases link. We have unique expertise in third generation sequencing based detecting of different types of DNA modifications. We emphasize biological and biomedical impacts in the design of novel methods. We prioritize our efforts on identifying emerging challenges in a relatively young research field and developing novel methods that can fundamentally address these challenges. Our long term goal is to obtain biological insights that can be translated for more accurate disease diagnosis and more effective treatment.

Innovation. Our research highlights three dimensions of innovations:

Pioneering the development, and novel application, of new technologies: Nature Reviews Genetics, 2018; Nature Biotechnology, 2017; Nature, 2016; Nature Biotechnology, 2012; PLoS Genetics, 2013;

Designing foundational methods for
novel technologies: Genome Research, 2018; Nature Commnications, 2015; Genome Research, 2013; PLoS Compulational Biology, 2013.

Novel integration of different types of complementary data: Cell Reports, 2016;
Molecular
Psychiatry, 2014;
Nature Commnications, 2014; Biological Psychiatry, 2015; PLoS Genetics, 2015;

Support