Karen Eilbeck
Adjunct Professor of Human Genetics and of Biomedical Informatics
B.S. University of Salford, United Kingdom
Ph.D. University of Manchester, United Kingdom
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.
The lab is developing ontology-enabled software. We are developing tools to both view and manage ontology typed sequence data. 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.
Next generation sequence data:
The lab has a strong focus on whole genome sequence data, in particular how to effectively capture and manage that data both for scientific research and also for translational informatics such as electronic medical records. We are actively collaborating with genetic testing and genomic analysis companies, and developed an ontology typed variant file format with various collaborators including the EBI.
User interface to query the Sequence Ontology
References
1. Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, Stein L, Flicek P, Yandell M, Eilbeck K (2010) A standard variation file format for human genome sequences. Genome Biol 11(8):
2. Moore B, Fan G, Eilbeck K (2010) SOBA: sequence ontology bioinformatics analysis. Nucleic Acids Res 38
3. Eilbeck K, Moore B, Holt C, Yandell M (2009) Quantitative measures for the management and comparison of annotated genomes. BMC Bioinformatics 10:67
4. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ; OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.
5. Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M (2005) The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol 6(5)
[Nat Biotechnol (2007) 11:1251-5]
Updated 6/3/2011
