Biotechnology and Bioinformatics Symposium (BIOT-2006)

October 20-21, 2006

Provo, Utah

Proceedings Here are the 2006 proceedings and individual papers from the symposium. Introduction The Biotechnology and Bioinformatics Symposium (BIOT-2006) was held on October 20-21 in Provo Utah. The symposium will include a keynote discussion on the use of knockout mice in drug development as well as discussions of the the Cancer Biomedical Informatics Grid (caBIG). Accepted papers were presented describing research into Pharmagenomics, cost effective genotyping, human genomic sequencing, protein-DNA interactions, hardware for exon prediction, protein folding, data mining and secondary structure prediction. The program schedule is now available at https://biotconf.org/schedule.shtml A publicity poster is also available. Research and development in biotechnology requires the collaboration of scientists and engineers in the fields of biology, chemistry, computer science, chemical engineering, and electrical engineering. This symposium brings together scientists, engineers and scholars from relevant fields with practitioners from industry in order to help each group to understand progress made in the area as a whole.

Keynote Speakers

Functional Mammalian Genomics and Drug Discovery: How Gene Knockouts are Accelerating Drug Discovery

Access to the completed sequence of the mouse and human genomes has opened up new possibilities for discovering mammalian gene function. Coupled with the molecular biological tools for mutant mouse production, scientists are now able to study gene function on an unprecedented scale. The international mouse genomics community has recently announced an initiative to produce knockout alleles for all mouse genes and to develop a system for open access to data and reagents for the broader scientific community. In addition to these efforts, companies such as Lexicon Genetics are using gene knockout (KO) mice to identify novel drug targets or biotherapeutic proteins for the treatment of a wide variety of diseases. An overview will be presented illustrating the process used by Lexicon Genetics to generate and phenotype 5000 knockout mice as part of an integrated drug discovery program.

D. Wade Walke, Ph.D. is Associate Director of Mining and Curation in the Department of Genetics at Lexicon Genetics Incorporated, a biopharmaceutical company located in The Woodlands, TX. Dr. Walke oversees a research group that has identified more than 5000 genes encoding the most pharmaceutically tractable proteins in the mouse and human genomes and that has cataloged the phenotypes of mice in which these genes have been disrupted. This effort has enabled Lexicon to determine the physiological function of these genes and to validate drug targets for treating human disease. Dr. Walke received his B.S. degree in Biochemistry from Brigham Young University and his Ph.D. degree in Biochemistry from the University of Michigan. He served as a postdoctoral fellow in the Department of Neurobiology at The Scripps Research Institute under the direction of Nobel Laureate Dr. Gerald Edelman, where he studied the regulation of gene expression during neuronal development. He also served as a postdoctoral fellow in the Department of Developmental Neurobiology at St. Jude Children's Research Hospital, where he investigated the molecular mechanisms of apoptosis.

caBIG

The cancer Biomedical Informatics Grid (caBIG) is a National Cancer Institute (NCI) initiative to promote data sharing in the cancer community. It brings together researchers with diverse expertise in clinical trial management systems, in vivo imaging, integrative cancer research, tissue banks, pathology tools, architecture, population sciences, vocabularies and common data elements. The goal is to develop systems that interoperate and exchange useful information across the grid. The caBIG community has developed a consensus based approach founded on the principles of open source, open access, open development and federation. The community has agreed that semantic integration is an essential component in this development of interoperable systems, because it enables researchers to unambiguously describe the data they are exchanging. Semantic integration uses controlled vocabularies and structured, standards-based metadata as part of its tool set to unambiguously describe diverse data sets. The metadata descriptions of these data sets are then used to coordinate the development of systems that provide analytical services on that data across the cancer community.

Lewis Frey, PhD is an assistant professor in the Department of Biomedical Informatics at the University of Utah. During his two year NLM-funded postdoctoral fellowship at Vanderbilt University in the Biomedical Informatics Department, he specialized in cancer biomedical informatics. Dr. Frey holds a doctorate and masters in computer science with a focus on machine learning from Vanderbilt University and a bachelor of science in mathematics from the University of Pittsburgh. Dr. Frey has worked extensively on the cancer Biomedical Informatics Grid (caBIG) for the National Cancer Institute, helping the Vocabulary and Common Data Elements workspace draft the compatibility checklist for reviews of silver level compliance. He is involved in drafting UML Best Practices for caBIGs model driven architecture. Dr. Frey conducts research in computational biomedical informatics, particularly in methods of combining multiple data sets of different types (e.g., microarray, proteomic) for the purpose of knowledge discovery. He has developed methods for combining prior knowledge of biological pathways with expression data for biomarker discovery. He is currently working on methods for identifying robust biomarker signatures in expression data for diagnosis and prognosis of lung, breast and colon cancers.