Steven L. Salzberg, Johns Hopkins University, “Computational Challenges of Next-Generation Genome Sequence Analysis”

When:
November 5, 2013 @ 12:00 pm – 1:00 pm
2013-11-05T12:00:00-05:00
2013-11-05T13:00:00-05:00

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“Computational Challenges of Next-Generation Genome Sequence Analysis”

Steven Salzberg is a Professor of Medicine and the Director of the Center for Computational Biology in the McKusick-Nathans Institute of Genetic Medicine at Johns Hopkins University. He holds joint appointments as Professor in the Departments of Biostatistics and Computer Science. From 2005-2011, he was the Director of the Center for Bioinformatics and Computational Biology (CBCB) and the Horvitz Professor of Computer Science at the University of Maryland, College Park. From 1997-2005 he was Senior Director of Bioinformatics at The Institute for Genomic Research (TIGR) in Rockville, Maryland, one of the world’s leading DNA sequencing centers at the time.

Full details on Dr. Salzberg’s research is available on his website here.

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Abstract

“Computational Challenges of Next-Generation Genome Sequence Analysis”

Next-generation sequencing technology allows us to peer inside the cell in exquisite detail, revealing new insights into biology, evolution, and disease that would have been impossible to find just a few years ago. The enormous volumes of data produced by NGS experiments present many computational challenges that we are working to address. In this talk, I will discuss some of the latest solutions to two basic alignment problems: (1) mapping sequences onto the human genome at very high speed, and (2) mapping and assembling transcripts from RNA-seq experiments. I will also discuss some of the problems that can arise during analysis of exome data, in which the gene-containing portions of the genome are sequenced in an effort to identify mutations responsible for disease. My group has developed algorithms to solve each of these problems, including the widely-used Bowtie program for fast alignment and the TopHat and Cufflinks programs for assembly and quantification of genes in transcriptome sequencing (RNA-seq) experiments. This talk describes joint work with current and former lab members including Ben Langmead, Cole Trapnell, Daehwan Kim, and Geo Pertea; and with collaborators including Mihai Pop and Lior Pachter.

 

 

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