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Wednesday, August 23, 2017 at 1:45pm to 2:45pm
"Assembling the Transcriptome: Computational Challenges and Genetic Discoveries"
Steven Salzberg
Professor of Biomedical Engineering, Computer Science, and Biostatistics
Director, Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine
Johns Hopkins University School of Medicine
Next-generation sequencing technology allows us to peer inside the cell in exquisite detail, revealing new aspects of biology, evolution, and disease that would have been impossible to discover just a few years ago. The enormous volumes of data produced by NGS experiments present many computational challenges, particularly when analyzing data from RNA sequencing experiments. In recent years, members of my lab have developed several widely-used systems this problem, including the Bowtie, TopHat and Cufflinks programs for alignment and assembly of transcipts from RNA-seq data. In this talk, I will discuss two new systems and the algorithms underlying them: (1) the HISAT system for spliced aligment of NGS reads, a successor to TopHat; and (2) the StringTie program for assembly and quantitation of RNA-seq data, a successor to Cufflinks. I will then describe how we used these systems to analyze nearly 10,000 human RNA-seq experiments and create a comprehensive new human gene catalog, containing thousands of novel genes and gene variants.
This talk describes joint work with Mihaela Pertea, Ph.D. and Daehwan Kim, Ph.D.
Dept. of Biological Statistics and Computational Biology, CALS
Sue Bishop
607-255-5488
Steven Salzberg
Johns Hopkins School of Medicine
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