Research Vision

Our lab 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; Science, 2022; Nature Reviews Geneitcs, 2023). We have three primary research strategies:

Epigenomes of Pathogens, Microbiome and Human: New research directions that are largely unexplored; going beyond cytosine methylations towards other largely uncharacterized DNA methylations, DNA damages, and more generally, diverse forms of nucleic acid modifications. 

Third-generation Sequencing: New technologies create unprecedented opportunities; 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: Human diseases are complex, so we need an open mind; genetic interactions and regulatory networks, highlighting both big and "small" data approaches, both "simple" and deep learning, integrated with innovative technologies and experiments.

Computation vs. Experiments: We have a highly interdisciplinary lab culture where members with dry/wet background closely discuss and learn from each other. We do not set any boundary in our mind between computational and experimental approaches because (1) we always keep our eyes on the ultimate biological or biomedical questions/goals, and we try all means to answer/achieve them; (2) we found from our own experience that the best research design often involves a holistic consideration from experiments, to samples, to technology, to data analyses. So, we call ourselves a humid lab.

Mentoring Vision

We believe scientific career development is multi-dimensional. While a strong publication record is undoubtly important, additional abilities (we often call them "soft skills") are equally important, if not more, especially when we aim long: how to approach a problem or a challenge? how to prioritize? how to give  effective presentations? how to improve different types of writing skills? how to communicate with lab members and collaborators? how to overcome failures and strive stronger? and importantly, what basic principles (e.g. integrity, gratitude, and responsibility, and more) should be enforced in research and career? This is why our lab has multiple types of group meetings, project meetings and 1on1 meetings to help trainees with different backgrounds to best develop their research, their skills and their career, and ultimately achieve their unique goals.