Human and Molecular Genetics Center


Mary E. Shimoyama, PhD

Assistant Professor, Surgery-Cardiothoracic
Specialization: Medical Informatics, Bioinformatics, Genomics, Genetics


Shimoyama Lab

Mary E. Shimoyama, PhD

Research Interests


Rat Genome Database

During the past 12 years, the Rat Genome Database ( has grown to one of the most highly regarded model organism databases in the world. RGD catalogues and assigns official nomenclature to all rat genes, QTL and strains. In addition to operational management of RGD, my research interests include standardization of genetic and phenotype data, integration of heterogeneous datasets, data mining and visualization tools.

Ontology Development and Implementation

An important component of data standardization is the development and use of standardized vocabularies and ontologies. I have created three ontologies for standardizing phenotype data and have overseen the development or implementation of five others. I am interested in the use of ontologies for functional predictions, identifying networks among diseases, phenotypes, pathways and gene functions and the software tools necessary for such research.

Clinical Data Standardization, Databases, Data Mining and Visualization Tools

I am interested in designing comprehensive data standards and formats for clinical measurements, phenotypes, laboratory results, environmental factors, and demographic data for clinical and genetic studies. Adaptation of existing ontologies and the development of new ones will be part of this effort. I am also interested in the development of the software tools that will allow the physician and researcher to leverage the power of integrated datasets to identify causal factors in disease onset and progression.  

RGD in International Innovations Journal

Recent Publications