Joint CMU-Pitt Ph.D. Program in Computational Biology and Department of Computational and Systems Biology Seminar

  • Gates Hillman Centers
  • ASA Conference Room 6115
  • Professor of Computer Science
  • Co-Director, Center for Genomics and Bioinformatics
  • Indiana University, Bloomington

Algorithms for Precision Genomics with Scalability, Security and Privacy Constraints

As high throughput genomic data becomes central to clinical decision making, computational bottlenecks involving scalability, security and privacy call for effective and efficient solutions.

In this talk we will go through some of the recent developments in the compression of high throughput sequence data, such as our new tool for "light genomic assembly" for improved de novo compression and the MPEG benchmarking effort towards establishing genomic sequence representation standards. We will also discuss some of the new developments in secure, collaborative genomic data processing through the use of Intel SGX (Software Guard Extensions) architectures and differentially private querying of population stratified genomic (SNV) data for genome-wide association studies (GWAS). Time permitting, we will also go through some of the algorithmic developments on cancer genome sequence analysis, especially in the context of driver gene and module identification based on new measures of random walk distances in molecular interaction networks.

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