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Agnes Chan, PhD, is an Assistant Professor in the Human Biology and Plant Genomics Departments at the J. Craig Venter Institute, Rockville, MD.

Dr. Chan’s research interests and expertise are in bioinformatics and computational analysis of diseases and traits from microbes to humans, and the sequencing, annotation and analysis of plant genomes.

During her tenure at JCVI, Dr. Chan served as a Program Officer in 2010 at the National Science Foundation to develop project management skills. Dr. Chan also plays an active role to promote science outreach by working closely with the Native American community and organizing molecular biology and genomics workshops for students and faculty from Native American serving institutes and Tribal Colleges.

Dr. Chan received her BS in Biochemistry and Computer Science, and M. Phil. degree in Biotechnology from the Chinese University of Hong Kong, MS in Computer Science from Johns Hopkins University, and PhD degree in Developmental Biology from the University of Cambridge, UK. In her early career, Dr. Chan worked with Prof Sir John Gurdon (2012 Nobel Laureate) on nuclear transplantation at the University of Cambridge, UK.

Research Priorities

Dr. Chan’s research focus are on bioinformatics and computational analysis of diseases and traits from microbes to humans, and the sequencing, annotation and analysis of plant genomes.

Human Genomic Medicine and Microbiome

  • Dissection of the human chronic wound microbiome
  • Computational phasing of human genomes to study disease haplotypes and variants
  • Prediction of SNP and indel impacts on protein function

Plant Genomics

  • Development of a one-stop community data integration portals for the plant model Arabidopsis
  • Mapping regulatory inheritance and gene expression for the bioenergy crop shrub willow
  • Development of a confocal image database of GFP reporter lines for the crop plant maize
  • Sequencing and analyses of plant genomes


Select Publications

Dominance and Sexual Dimorphism Pervade the Salix purpurea L. Transcriptome.
Genome biology and evolution. 2017-09-01; 9.9: 2377-2394.
PMID: 28957462
Araport11: a complete reannotation of the Arabidopsis thaliana reference genome.
The Plant journal : for cell and molecular biology. 2017-02-01; 89.3: 789-804.
PMID: 27862469
ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery.
Plant & cell physiology. 2017-01-01; 58.1: e4.
PMID: 28013278
Electrochemical detection of Pseudomonas in wound exudate samples from patients with chronic wounds.
Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society. 2016-03-01; 24.2: 366-72.
PMID: 26815644
PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels.
Bioinformatics (Oxford, England). 2015-08-15; 31.16: 2745-7.
PMID: 25851949
A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii.
Genome biology. 2015-07-21; 16.143.
PMID: 26195261
Predicting the functional effect of amino acid substitutions and indels.
PloS one. 2012-01-01; 7.3: e46688.
PMID: 23056405
The highest-copy repeats are methylated in the small genome of the early divergent vascular plant Selaginella moellendorffii.
BMC genomics. 2008-06-12; 9.282.
PMID: 18549478
The TIGR Plant Transcript Assemblies database.
Nucleic acids research. 2007-01-01; 35.Database issue: D846-51.
PMID: 17088284
Plant database resources at The Institute for Genomic Research.
Methods in molecular biology (Clifton, N.J.). 2007-01-01; 408.113-36.
PMID: 18287690
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release.
BMC biology. 2005-03-22; 3.7.
PMID: 15784138
The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.
Nucleic acids research. 2005-01-01; 33.Database issue: D71-4.
PMID: 15608288
Annotation of the Arabidopsis genome.
Plant physiology. 2003-06-01; 132.2: 461-8.
PMID: 12805579
Tumorhead, a Xenopus gene product that inhibits neural differentiation through regulation of proliferation.
Development (Cambridge, England). 2001-09-01; 128.17: 3381-93.
PMID: 11546754
The vegetally localized mRNA fatvg is associated with the germ plasm in the early embryo and is later expressed in the fat body.
Mechanisms of development. 2001-01-01; 100.1: 137-40.
PMID: 11118900
fatvg encodes a new localized RNA that uses a 25-nucleotide element (FVLE1) to localize to the vegetal cortex of Xenopus oocytes.
Development (Cambridge, England). 1999-11-01; 126.22: 4943-53.
PMID: 10529413
Nuclear transplantation from stably transfected cultured cells of Xenopus.
The International journal of developmental biology. 1996-04-01; 40.2: 441-51.
PMID: 8793614