Bioinformatics Core 2 - Zeldovich, UMASS Medical School Core 2 will provide bioinformatics support to the Program Project, developing a laboratory information management system (LIMS) integrated with deep sequencing data analysis pipeline, identification of mutations critical for drug resistance, and HIV genome browsing and visualization tools. Core 2 will develop a LIMS with web front end and MySQL database engine, which will capture the experimental conditions for multiple samples of HIV grown in the presence and absence of protease inhibitors. The database will be integrated with data analysis pipeline, which will identify statistically significant resistance mutations. We will use population genetics simulations to build null models of HIV sequence evolution, and compare the results with deep sequencing data to identify sites undergoing statistically significant selection. For those sites, we will determine selection coefficients, and provide this information to Projects 1-3 for experimental follow up and integration into the I-READSS model of interaction of HIV protease with inhibitors.

Public Health Relevance

Bioinformatics Core 2 - Zeldovich, UMASS Medical School Core 2 will provide bioinformatics support to the Program Project, developing a laboratory information management system (LIMS) integrated with deep sequencing data analysis pipeline, identification of mutations critical for drug resistance, and HIV genome browsing and visualization tools. The LIMS will be integrated with data analysis pipeline, which will identify statistically significant resistance mutations, and determine their selection coefficients. Using the tools developed, Core 2 will be also responsible for public dissemination of the data generated by the Program Project.

Agency
National Institute of Health (NIH)
Type
Research Program Projects (P01)
Project #
1P01GM109767-01A1
Application #
8789529
Study Section
Special Emphasis Panel (ZRG1)
Project Start
Project End
Budget Start
Budget End
Support Year
1
Fiscal Year
2014
Total Cost
Indirect Cost
City
Worcester
State
MA
Country
United States
Zip Code
01655