Research Overview
The Zhang lab at the UCSD Bioengineering department is interested in
developing novel genome technologies towards the applications in
stem cell research, brain mapping and human disease studies.
1. Genome Technology:
We are developing various methods for synthesis, manipulation and sequencing of DNA molecules. Examples include
- single-cell genome sequencing;
- single-cell transcriptome sequencing;
- large-scale DNA synthesis on programmable DNA chips;
- targeted digital analysis of epigenome;
- imaging and cell tracking.
2. Genome Informatics:
Almost every single aspect of our genome-scale studies depends on
bioinformatics. We do large-scale “manipulation” of DNA molecules in
computer before and after processing them in test tubes. Here are some examples:
- designing DNA probes for capturing & sequencing SNPs/Exons/DMRs, which also includes various simulation;
- de novo assembling of single-cell genome sequencing data;
- haplotype assembling and analysis of single molecule sequencing data;
- integrative analyses of transcriptomics and epigenomics data.
3. Biology:
3.1 Single-cell analysis of human brain.
Human
brain is arguably the most complex organ of the body. We are applying
single-cell sequencing and imaging techniques to characterize the
transcriptional diversity and somatic genomic variation of the human
brain, and to related such -omics information to the three dimensional
organization of the human cortex.
3.2 Regenerative medicine.
Recent advances in nuclear programming and reprogramming have
provided extremely powerful tools for manipulating the cell fates. A
holy grail of regenerative medicine is to restore damaged tissues or
organs with another cell type from the same patients with the use of
nuclear reprogramming and genetic engineering techniques. We are
particularly interested in characterizing the process of cell fate conversion, understanding the underlying molecular mechanisms.
3.2 Genetic and environmental determinants for human common diseases.
Another very broad area of our research interest is to understand
genetic and environmental factors that contribute to common human
diseases. For genetic factors, we are focusing on cis-regulatory genetic
variants in the human genome. On the environmental aspect, we are
particularly interested in the microorganisms that reside in different
parts of the human body, also called human microbiome. We are also
working on the characterization of the epigenome, which is an important
layer of cellular memory that captures the effects of both genetic and
environmental factors.
4. Potential graduate student rotation projects:
- Design and fabrication of microfluidic devices for single cell analysis.
- Computational analysis of single-cell transcriptome data sets.
- Epigenetic analysis of human brain and stem cells.
- Live cell imaging and image analysis.
