Day 2 Keynote from GTC: Parallel Processing of the Genomes

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At insideHPC, we are very pleased to bring you live streaming keynotes from the GPU Technology Conference this week in San Jose.

In this video, Erez Lieberman Aiden from the Baylor College of Medicine presents a keynote talk entitled: Parallel Processing of the Genomes, by the Genomes and for the Genomes.

The human genome is a sequence of 3 billion chemical letters inscribed in a molecule called DNA. Famously, short stretches (~10 letters, or “base pairs”) of DNA fold into a double helix. But what about longer pieces? How does a 2 meter long macromolecule, the genome, fold up inside a 6 micrometer wide nucleus? And, once packed, how does the information contained in this ultra-dense structure remain accessible to the cell? This talk will discuss how the human genome folds in three dimensions, a folding enables the cell to access and process massive quantities of information in parallel. To probe how genomes fold, we developed Hi-C, together with collaborators at the Broad Institute and UMass Medical School. Hi-C couples proximity-dependent DNA ligation and massively parallel sequencing. To analyze our data and reconstruct the underlying folds, we, too must engage in massively parallel computation. I will describe how we use NVIDIA’s CUDA technology to analyze our results and simulate the physical processes of genome folding and unfolding.