Education

Harvard University, Ph.D. 1981

Biosketch

The activities of my research group and collaborations focus on the development of bioinformatics systems essential for functional genomics, genetics and phenotypic research. The sequencing of mouse, human and other genomes and the rapid accumulation of very large data sets has resulted in an overwhelming amount of information from multiple sources containing a variety of content and formats. The challenge is to bring all the data together and make it easily accessible to researchers directly and/or for additional computer analysis. Our current research centers on combining bio-ontologies (defined, controlled, structured vocabularies) and database systems to identify molecular elements that contribute to the processes of particular diseases, such as lung cancer. This work is undertaken as part of the Gene Ontology Consortium, a group of 19 model organism databases and genome annotation centers. My group, as part of the Mouse Geneome Informatics Consortiun at The Jackson Laboratory, is responsible for the functional and comparative annotation of mouse genes.

Research Interests

Functional and Comparative Genome Informatics
My research focuses on functional and comparative genome informatics. I work on the development of systems to integrate and interrogate genetic, genomic and phenotypic information. I am one of the leaders of the Gene Ontology (GO) project and I have been deeply involved with the work of the GO Consortium since its inception. The Gene Ontology project is an international effort to provide controlled structured vocabularies for molecular biology that serve as terminologies, classifications and ontologies to further data integration, analysis and reasoning. My interest in bio-ontologies stems as well from the work I do as a principal investigator with the Mouse Genome Informatics (MGI) project at The Jackson Laboratory. The MGI system is a model organism community database resource that provides integrated information about the genetics, genomics and phenotypes of the laboratory mouse. My current research projects combine bio-ontologies and database knowledge systems to represent disease processes with the objective of discovering molecular elements that contribute to particular pathologies such as respiratory diseases.

The Gene Ontology Consortium

Widespread use of the GO system for functional annotation of genomes enables comparative analysis of genome-size data sets. Understanding and supporting the GO annotation process and bringing new groups into the GO community is essential to the continued development of a broad, integrated network of biological information that can be transparently shared to enable and advance knowledge discovery. The GO Consortium group now consists of 19 model organism databases and genome-annotation groups who work cooperatively to construct the GO bio-ontologies, to provide functional annotations for a wide variety of organisms, and to support a GO information resource. GO participants located at The Jackson Laboratory lead ontology development projects, develop new software applications for the GO project, and provide GO annotations for mouse gene products. Other core groups of the GO project include an ontology development group based at the European Bioinformatics Institute in the United Kingdom, a software and resource development group based at Lawrence Berkeley National Laboratory, and a production database group based at Stanford University.

The Mouse Genome Informatics Project
MGI supports scientific research that uses the laboratory mouse as a model for the study of human biology and disease. MGI data are curated both from the biomedical literature and from co-curated data loads from other major bioinformatics resources. My research group is responsible for the functional and comparative annotation of mouse genes in the MGI resource. This work includes defining the mouse gene set (in co-curation with other informatics resource providers), indexing the biomedical literature for functional annotation, providing official gene nomenclature along with a robust set of synonyms, and extending the representation of relationships between mouse, human and rat genes and genomes. We work closely with the MGI Sequences and Sequence Maps group to resolve sequence-based inconsistencies in the representations of the mouse geneome and transcript data integrated in MGI and between MGI and other informatics resource centers such as the NCBI, Ensembl and the UniProt groups. We also work closely with the MGI Phenotypes group to support the development of standards for the representation of phenotype/genotype data in MGI.

MGI-GO Scientific Curators are using a combination of algorithmic and manual approaches to update annotations of mouse gene products to the GO vocabularies. Currently, more than 17,500 mouse genes have at least preliminary GO annotations and over 9,700 have annotations based on experimental assays in mouse. We use data-mining and other strategies to semi-automate gene annotation to the GO. The highest quality annotations, however, depend on skilled scientific curators who review published literature for information that provides experimental verification for the GO attributions.

Selected Publications

Service

Community Service

• 1995 to 1997 — NSF – Research Collections in Systematics and Ecology Advisory Panel
• 2001 to 2003 — NIH - BISTI pre-National Programs of Excellence in Biomedical Computing (NPEBC) Advisory Panel.
• 2003 to 2009 — External Scientific Advisory Board, Saccharomyces Genome Database (SGD) (NHGRI).
• 2003 to 2009 — External Scientific Advisory Panel for the MDI-BL Toxicogenomics
• 2003 to 2005 — External Scientific Panel for the Pharmacogenetics Research Network
• 2003 to 2006 — External Scientific Advisory Board, TIGR Rice Genome Annotation Project (NSF)
• 2004 to 2009 — TREC Genomics Track - Steering Committee (NIST)
• 2004 to 2004 — NIH: INBRE Review Panel
• 2004 to 2005 — NIH Ad Hoc Study Section Member: Genomics, Computational Biology and Technology (GCAT).
• 2005 to 2005 — Special Editor, PLOS Genetics: Fantom 3 issue.
• 2005 to 2008 — Program Committee – Intelligent Systems for Molecular Biology (ISMB).
• 2005 to 2005 — Program Committee – Pacific Symposium on Biocomputing Meeting
• 2005 to 2005 — Program Committee – European Conference on Computational Biology.
• 2005 to 2005 — Program Committee - Data Integration in the Life Sciences Meeting.
• 2006 to 2009 — NIH Study Section: Genomics, Computational Biology, and Technology (GCAT).
• 2006 to 2006 — NHLBI Cardiovascular Strategic Planning Working Group #11
• 2006 to 2009 — External Scientific Advisory Board, UniProt (Universal Protein Resource)
• 2006 to 2009 — External Scientific Advisory Panel, PharmacoGenetics KnowledgeBase (PharmaGKB)
• 2006 to 2008 — 2006-2008 Program Committee – Bio-Ontologies SIG; ISMB meeting.
• 2008 to 2009 — CIHR (Canada Institutes of Health Research) External Scientific Advisory Board. “Model Organism Interactions and Human Diseases” project.