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The cancer transcriptome is shaped by genetic changes, variation in gene transcription, mRNA processing, editing and stability, and the cancer microbiome. Deciphering this variation and understanding its implications on tumorigenesis requires sophisticated computational analyses. Most RNA-Seq analyses rely on methods that first map short reads to a reference genome, and then compare them to annotated transcripts or assemble them. However, this strategy can be limited when the cancer genome is substantially different than the reference or for detecting sequences from the cancer microbiome. "Assembly first" (de novo) methods that combine reads into transcripts without any mapping are a compelling alternative. The assembled transcriptome can then be used to identify mutations, splicing patterns, expression levels, tumor-associated microbes, and — if collected from single cells — characterize tumor heterogeneity. There is thus an enormous need for computationally efficient, accurate and user friendly tools for transcriptome reconstruction and analysis in cancer. In this talk, Dr. Regev will describe how the Trinity, a leading software for de novo RNA-Seq assembly, is used to understand exome expression in cancer research.

Session details...


Aviv Regev, a computational and systems biologist, is a professor of biology at MIT, a Howard Hughes Medical Institute Investigator, and the Chair of the Faculty and the director of the Klarman Cell Observatory and Cell Circuits Program at the Broad Institute. She studies the molecular circuitry that governs the function of mammalian cells in health and disease and has pioneered many leading experimental and computational methods for the reconstruction of circuits, including in single-cell genomics.

Dr. Regev is a recipient of the NIH Director’s Pioneer Award, a Sloan fellowship from the Sloan Foundation, the Overton Prize from the International Society for Computational Biology, the Earl and Thressa Stadtman Scholar Award from the American Society of Biochemistry and Molecular Biology, and is a 2016 ISCB Fellow.

Dr. Regev received her M.Sc. from Tel Aviv University, studying biology, computer science, and mathematics in the Interdisciplinary Program for the Fostering of Excellence. She received her Ph.D. in computational biology from Tel Aviv University.


Topic: Using Trinity to Understand the "Expressed Exome"

Speaker: Aviv Regev, Ph.D.

Date: Wednesday, March 15, 2017

Time: 11 AM – 12 PM ET

Room: 2W910-912


Event number: 733 108 535

Event password: $Peakerseries17

You are invited to listen to Dr. Regev's presentation in the NCI Shady Grove Building on Medical Center Drive or via WebEx.

Presentation: A screen cast of the presentation will be available for viewing after the event on the NCI CBIIT Speaker Series YouTube Playlist Exit Disclaimer logo

About the NCI CBIIT Speaker Series:

The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series presents talks from innovators in the research and informatics communities. The biweekly presentations allow thought leaders to share their work and discuss trends across a diverse set of domains and interests. The goals of the Speaker Series are: to share leading edge research; to inform the community of new tools, trends, and ideas; to inspire innovation; and to provide a forum from which new collaborations can begin. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page.

Individuals with disabilities who need reasonable accommodation to participate in this program should contact the Office of Space and Facilities Management (OSFM) at 240-276-5900 or the Federal TTY Relay number 1-800-877-8339.

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