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Research Overview

The Zhang lab at the UCSD Bioengineering department is interested in developing novel genome technologies towards the applications in personalized genome medicine and stem cell research.

Genome Technology:

We are developing various methods for synthesis, manipulation and sequencing of DNA molecules. Examples include

  • genome sequencing of single cells or single chromosomes;
  • transcriptome sequencing of single cells;
  • live cell imaging and lineage tracing;
  • large-scale DNA synthesis on programmable DNA chips;
  • targeted digital analysis of epigenome.

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, which also includes various simulation;
  • mapping and analysis of next-generation DNA sequencing data;
  • de novo assembling of single-cell genome sequencing data;
  • haplotype assembling and analysis of single molecule sequencing data;
  • image analysis (segmentation, feature identification and registration, quantitative analysis);
  • integrative analysis of transcriptomics, epigenomics and genomics data.


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 genetic and epigenetic abnormalities during the process of manipulating cell fates. Our research will not only provide a safety standard for regenerative medicine, but also reveal new insights on the molecular mechanisms of nuclear programming and reprogramming.

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.

Potential graduate student rotation projects:

  • Design and fabrication of microfluidic devices for single chromosome analysis.
  • Development of read mapping strategies for next-generation DNA sequencing data.
  • Functional analysis and annotation of genetic variants/mutations identified in genome resequencing.
  • Analysis of global epigenetic changes in stem cells.