Other active projects
Single cell analysis of cell fate
An important question to cell biology is how cells break the symmetry during mitotic divisions. During mammalian preimplantation embryonic development, the embryo has to decide how to set apart the first two cell populations. It remains an open question when and how the first cell fate decision is made. Cell-fate associated inter-blastomere differences of transcript and protein concentrations were reported from as early as the 8-16 cell stage. However, it is not clear whether these are the earliest differences. Using deep single-cell RNA-seq of matched sister blastomeres, we found highly reproducible differences among the single cells within early stage (2- and 4-cell) mouse embryos [Genome Res,
Single-cell data, especially time-course single cell transcriptomic data demand new statistical methods. We developed a time-variant clustering method for this need [PNAS,
2014]. Time-variant clustering is a Hidden Branching Process. At each
time point, this model degenerates into a finite mixture model.
Single-molecule RNA imaging
We are developing single-molecule RNA FISH
techniques with high sensitivity and simple operation precedure. We
leveraged quantum dots for single-molecule imaging and
quantification [see Figure 3, Nat
Internet search engine on genomic data
Unlike text-based search engines, our
search engine is based on pattern matching of functional genomic regions.
This enables searches inside a new data type, namely the genome-wide
intensity files including WIG and bigWig files [Nucleic
Acd Res, 2016].
PREVIOUS RESEARCH PROJECTS
Evolution of mammalian gene regulatory networks
Genetic and epigenetic re-wiring of transcription
Thermodynamic modeling of interactions among
transcription factors, DNA, and epigenome
Temporal epigenomic changes and dynamics of gene