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. |
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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; |
