CAREER (DBI): Computational Methods for High-Throughput Sequencing and Population Genomics Analysis

This is a CAREER award to support the research of Dr. Yun Song in the Department of Electrical Engineering and Computer Sciences, and Department of Statistics, University of California, Berkeley. Dr. Song is a second-year, tenure-track Assistant Professor. High-throughput sequencing technology has entered a new era and obtaining whole genome sequence information will soon become routine. In one important area of research, the whole-genome description of DNA sequence variation will help us understand the biological mechanisms through which genetic polymorphisms affect phenotypes. In order to understand these mechanisms, the PI is developing tools to improved all aspects of data acquisition, error rate reduction and reduction of the cost of high throughput sequencing by increasing the throughput per run. The PI has used the innovative approach of working closely with the Solexa/Illumina high-throughput sequencing data and the source code for this project. This kind of research is important for setting a high standard for the commercial sector to meet in the future. Further, this project is developing reliable computational methods to annotate genomic variation, including structural variation, and applying them in a large-scale Drosophila resequencing project. Finally, scalable informatics tools for population genomics analysis is being developed. This work is enabling accurate inference of selection and demography on the whole-genome scale in multiple populations and is being applied in a novel approach to the study of human migration patterns.

As a part of his CAREER plan, Dr. Song is integrating research by developing a new undergraduate course in computational biology for students in Electrical Engineering and Computer Science. Furthermore, he is developing effective, open source software packages for the larger community. Finally, the PI is developing bioinformatics modules for courses for students in a minority-serving charter school in the Oakland area. Adam Roberts, a graduate student from Dr. Song?s research group, is teaching at the charter school full time in order to integrate these modules into the curriculum before beginning his own graduate research.

National Science Foundation (NSF)
Division of Biological Infrastructure (DBI)
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Anne Haake
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University of California Berkeley
United States
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