Chan Pui Yee Agnes

  • Scholarship in 1992 at the University of Cambridge
  • Studentship in 1990 at the Chinese University of Hong Kong

Agnes Chan is an Assistant Professor in the Plant Genomics and Genomic Medicine Departments at the J. Craig Venter Institute, Rockville, MD. Dr. Chan was trained in Molecular Biology, Developmental Biology, Computer Science, and Bioinformatics. In her early research career, Dr Chan worked on nuclear transplantation with Prof Sir John Gurdon (2012 Nobel Laureate) at the University of Cambridge, UK.

At JCVI, Dr Chan’s research interests and expertise are in the design and implementation of bioinformatics data analysis methodologies to study diseases and traits, as well as in genome assembly, analysis and annotation.  Examples include the dissection of the microbiome of chronic wounds in humans, mapping biomass traits to parental alleles in plants, the development of a software tool to predict the impact of sequence variants on protein functions, and other projects. For big data projects, Dr Chan is the Data lead of a multi-institutional collaborative effort to develop a new web-based data portal (Araport) to integrate diverse biological data types for the model plant Arabidopsis thaliana.  The project is aimed to develop a simple and efficient data integration and “one-stop-shop” resource for the research community, that can also be generally applicable to other model organisms. Dr Chan is also part of a research collaboration to generate over one hundred green fluorescent protein (GFP) reporter lines for the crop model plant maize, and develop an image database of maize confocal images. The maize reporter lines serve as an open community resource for tracking and studying gene expression in subcellular compartments and specific cell/tissues during plant development.

Dr Chan joined TIGR in 2001 as part of the efforts to comprehensively annotate the first sequenced plant genome Arabidopsis thaliana. She was part of a research consortium to first apply a cost-effective complexity-reduction sequencing approach to decipher the “gene-space” of the highly repetitive and complex maize genome, an economically important crop plant in the US and worldwide. She played major roles to sequence and study the genomes of the oil seed castor bean, which produces one of the deadliest natural toxins (ricin), and the oil palm tree.

Dr Chan plays an active role in outreach collaborations to promote scientific exchanges between the research community and Native Americans, through molecular and bioinformatics workshops for faculty and students at tribal colleges.

Dr Chan earned the B.Sc. in Biochemistry and Computer Science, and M.Phil. in Biotechnology from the Chinese University of Hong Kong, M.Sc. in Computer Science from Johns Hopkins University, and PhD in Developmental Biology from the University of Cambridge, UK.