JCVI: About / Bios / Agnes Chan
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Agnes Chan, Ph.D.
Assistant Professor

Research Interests and Accomplishments

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 Ph.D. in Developmental Biology from the University of Cambridge, UK.

Select Publications

Choi Y, Chan AP
PROVEAN Web Server: a Tool to Predict the Functional Effect of Amino Acid Substitutions and Indels.

Bioinformatics (Oxford, England). 2015 Aug 15; 31: 2745-7.[more]

Chan AP, Sutton G, et al.
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 Jun 01; 16: 143.[more]

Krishnakumar V, Choi Y, et al.
A Maize Database Resource That Captures Tissue-specific and Subcellular-localized Gene Expression, via Fluorescent Tags and Confocal Imaging (Maize Cell Genomics Database).

Plant & Cell Physiology. 2015 Jan 01; 56: e12.[more]

Tang H, Krishnakumar V, et al.
An Improved Genome Release (version Mt4.0) for the Model Legume Medicago Truncatula.

BMC Genomics. 2014 Sep 01; 15: 312.[more]

Gottlieb A, Müller HG, et al.
Insular Organization of Gene Space in Grass Genomes.

PloS One. 2013 Sep 01; 8: e54101.[more]

Duangjit J, Bohanec B, et al.
Transcriptome Sequencing to Produce SNP-based Genetic Maps of Onion.

TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 2013 Aug 01; 126: 2093-101.[more]

Choi Y, Sims GE, et al.
Predicting the Functional Effect of Amino Acid Substitutions and Indels.

PloS One. 2012 Sep 01; 7: e46688.[more]

Rivarola M, Foster JT, et al.
Castor Bean Organelle Genome Sequencing and Worldwide Genetic Diversity Analysis.

PloS One. 2011 Sep 01; 6: e21743.[more]

Massa AN, Wanjugi H, et al.
Gene Space Dynamics During the Evolution of Aegilops Tauschii, Brachypodium Distachyon, Oryza Sativa, and Sorghum bicolor Genomes.

Molecular Biology and Evolution. 2011 Sep 01; 28: 2537-47.[more]

Foster JT, Allan GJ, et al.
Single Nucleotide Polymorphisms for Assessing Genetic Diversity in Castor Bean (Ricinus Communis).

BMC Plant Biology. 2010 Sep 01; 10: 13.[more]

Chan, A. P., Crabtree, J., et al.
Draft Genome Sequence of the Oilseed Species Ricinus communis

Nat Biotechnol. 2010 Aug 22; 28(9): 951-6.[more]

Chan, A. P., Melake-Berhan, A., et al.
The Highest-copy Repeats Are Methylated In the Small Genome of the Early Divergent Vascular Plant Selaginella Moellendorffii

BMC Genomics. 2008 Jun 12; 9(1): 282.[more]

Song HW, Cauffman K, et al.
Hermes RNA-binding Protein Targets RNAs-encoding Proteins Involved in Meiotic Maturation, Early Cleavage, and Germline Development.

Differentiation; Research in Biological Diversity. 2007 Jul 01; 75: 519-28.[more]

Chan, A.P., Rabinowicz, P.D., et al.
Plant Database Resources at the Insittute for Genomic Research

Plant Bioinformatics: Methods and Protocols. 2007 Jun 01;: 113-136.[more]

Chan AP, Kloc M, et al.
The Maternally Localized RNA Fatvg Is Required for Cortical Rotation and Germ Cell Formation.

Mechanisms of Development. 2007 May 01; 124: 350-63.[more]

Chan, A. P., Rabinowicz, P. D., et al.
Plant Database Resources at the Institute for Genomic Research

Methods Mol Biol. 2007 Jan 01; 406: 113-36.[more]

Childs, K. L., Hamilton, J. P., et al.
The TIGR Plant Transcript Assemblies Database

Nucleic Acids Res. 2007 Jan 01; 35(0): D846-51.[more]

Bruggmann, R., Bharti, A. K., et al.
Uneven chromosome Contraction and Expansion In the Maize Genome

Genome Res. 2006 Oct 01; 16(10): 1241-51.[more]

Chan, A. P., Pertea, G., et al.
The TIGR Maize Database

Nucleic Acids Res. 2006 Jan 01; 34(0): D771-6.[more]

Haas, B. J., Wortman, J. R., et al.
Complete Reannotation of the Arabidopsis Genome: Methods, Tools, Protocols and the Final Release

BMC Biol. 2005 Mar 22; 3(1): 7.[more]

Lee, Y., Tsai, J., et al.
The TIGR Gene Indices: Clustering and Assembling EST and Known Genes and Integration With Eukaryotic Genomes

Nucleic Acids Res. 2005 Jan 01; 33: D71-4.[more]

Zearfoss NR, Chan AP, et al.
Hermes Is a Localized Factor Regulating Cleavage of Vegetal Blastomeres in Xenopus Laevis.

Developmental Biology. 2004 Mar 01; 267: 60-71.[more]

Whitelaw, C. A., Barbazuk, W. B., et al.
Enrichment of Gene-coding Sequences In Maize by Genome Filtration

Science. 2003 Dec 19; 302(5653): 2118-20.[more]

Wortman, J. R., Haas, B. J., et al.
Annotation of the Arabidopsis Genome

Plant Physiol. 2003 Jun 01; 132(2): 461-8.[more]

Zearfoss NR, Chan AP, et al.
Identification of New Xlsirt Family Members in the Xenopus laevis Oocyte.

Mechanisms of Development. 2003 Apr 01; 120: 503-9.[more]

Wu CF, Chan AP, et al.
Difference in the Maternal and Zygotic Contributions of Tumorhead on Embryogenesis.

Developmental Biology. 2003 Mar 15; 255: 290-302.[more]

Guo W, Chan AP, et al.
A Human Mix-like Homeobox Gene MIXL Shows Functional Similarity to Xenopus Mix.1.

Blood. 2002 Jul 01; 100: 89-95.[more]

Kloc M, Dougherty MT, et al.
Three-dimensional Ultrastructural Analysis of RNA Distribution Within Germinal Granules of Xenopus.

Developmental Biology. 2002 Jan 01; 241: 79-93.[more]

Wu CF, Nakamura H, et al.
Tumorhead, a Xenopus Gene Product That Inhibits Neural Differentiation Through Regulation of Proliferation.

Development (Cambridge, England). 2001 Sep 01; 128: 3381-93.[more]

Kloc M, Bilinski S, et al.
RNA Localization and Germ Cell Determination in Xenopus.

International Review of Cytology. 2001 Sep 01; 203: 63-91.[more]

Chan AP, Etkin LD
Patterning and Lineage Specification in the Amphibian Embryo.

Current Topics in Developmental Biology. 2001 Sep 01; 51: 1-67.[more]

Chan AP, Kloc M, et al.
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 Jan 01; 100: 137-40.[more]

Chan AP, Kloc M, et al.
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 Nov 01; 126: 4943-53.[more]

Kloc M, Larabell C, et al.
Contribution of METRO Pathway Localized Molecules to the Organization of the Germ Cell Lineage.

Mechanisms of Development. 1998 Jul 01; 75: 81-93.[more]

Chan AP, Gurdon JB
Nuclear Transplantation from Stably Transfected Cultured Cells of Xenopus.

The International Journal of Developmental Biology. 1996 Apr 01; 40: 441-51.[more]

Ho WK, Wong MW, et al.
Cloning and Sequencing of the Grass Carp (Ctenopharyngodon Idellus) Growth Hormone Gene.

Biochimica Et Biophysica Acta. 1991 Oct 08; 1090: 245-8.[more]