• campus:  a to z index
• map
• directory
• calendar

Search:

Karen Eilbeck

Assistant Professor of Human Genetics

B.S. University of Salford, United Kingdom

Ph.D. University of Manchester, United Kingdom

 

Research

References

 

Karen Eilbeck's PubMed Literature Search

Research

The lab performs bioinformatics research. We are interested in using aspects of computer science to address contemporary genomics and molecular biology questions. We are focused on the management and analysis of biological data using bioinformatics techniques. The biological sciences are data intensive but how the data is organized affects how well it can be analyzed and shared with the community. Ontologies are used to standardize and structure the data to make it more amenable to analysis and allow the user community to communicate with each other using the same language. An ontology is a description of our knowledge about a subject. It contains the classes of the data and the relationships that hold between them. The focus of the lab is to develop ontologies and ontology-enabled software to enhance biological research—doing so is essential for analyzing and managing the kinds of genomic and biological data that exist today.

Genomic annotation: Genome annotations combine biological sequence, the results of bioinformatics analyses, and the knowledge of human curators into models of gene structure. Despite their potential as a resource for studies, to date genome annotations have proven difficult to use. A major reason for this has been the lack of community standards for describing them, which has resulted in the proliferation of arbitrary file formats and database schemas. The Sequence Ontology project aims to solve this problem by providing the means to unify the descriptions of genomic annotations. This project is run from this lab and provides a standardized set of terms and relationships with which to label stretches of sequence; it therefore provides a community resource that will allow the standardization of genome annotation file formats, and model organism database schemas. This, in turn will facilitate the exchange and visualization of genome annotations as well as comparison of and computation upon their contents.

The lab is developing ontology-enabled software. The relationships within the ontology allow us to probe the data in new and interesting ways. Recently we used the principles of Extensional Mereology, a formal logic of part-whole relationships, to examine the contents of genome annotations, leading to a classification of the kinds of alternate splicing.

Functional annotation: To understand the results of large scale biological experiments such as microarray studies of gene expression, scientists will often look at the kinds of genes that appear. The Gene Ontology (GO) provided the community with a resource of the terminology to describe exactly what a gene product does. It is divided into three aspects, cellular location, biological process and molecular function. A gene product may be described by terms from each of the aspects. GO is used to describe what gene products do, e.g. the antennapedia gene encodes a protein with transcription factor activity, located in the nucleus, involved with the process of segment specification. The GO consortium continues to develop an extensive ontology for functional annotation and also provides highly detailed manual curation of genes from the literature for several model organisms. The lab is involved with developing techniques to explore and assess aspects of functional annotation.

References