David Rocke — Differential Expression Analysis with RNA-SEQ: Review and Critique
Starts: 9:00 am
Ends: October 17, 2014 - 10:00 am
Location: GBSF 4202
Description: Structural & functional genomics focus group meeting
Speaker: David Rocke, Public Health Sciences and Biomedical Engineering.
RNA-Seq data are increasingly used for whole-genome differential mRNA expression analysis in lieu of gene expression arrays such as those from Affymetrix and Illumina. We review commonly used methods for this type of analysis, including DESeq, edgeR, and Cuffdiff2, by placing them within a common framework that allows comparisons of components of the methods as well as of the overall results. We also review a number of recent studies comparing these methods in terms of false positives and sensitivity, and add additional results of our own. We show that none of the existing methods is fully satisfactory, with most identifying large numbers of genes as differentially expressed even when there are none, but some will lead to better, more reliable results than others. This area is still early in its intellectual development and is changing rapidly. This has important implications for how applied researchers should approach the analysis of their RNA-Seq data and how these analyses should be documented.
Dr Sriram Subramaniam — Applications to HIV/AIDS and signal transduction: cryo-electron microscopy comes of age
Starts: 2:00 pm
Ends: October 17, 2014 - 3:00 pm
Location: LSA 1022
Description: Dr Sriram Subramaniam is from the National Cancer Institute, NIH, Bethesda
Abstract: Recent breakthroughs in the field of cryo-electron microscopy provide new opportunities for determination of the structures of a variety of macromolecular assemblies and small dynamic protein complexes that are not amenable to analysis by X-ray crystallography or NMR spectroscopy. In addition, advances in technologies for imaging whole cells and tissues in 3D at high resolution have opened up new vistas for 3D structural imaging. The long-term mission of our research program is to obtain an integrated molecular understanding of viral and cellular architecture by combining advanced technology development for 3D imaging with novel methods for image segmentation and computational analysis. Specific areas of current interest that I will discuss include: structural biology of HIV entry, mechanisms of membrane transport, and assembly of protein complexes involved in metabolism.
Dr. Charlie Gersbach — Editing the Human Genome and Epigenome with the CRISPR/Cas9 System to Correct Genetic Disease and Program Cell Phenotype
Starts: 10:00 am
Ends: October 20, 2014 - 11:00 am
Location: GBSF 1005
Description: Dr. Gersbach (Duke University) is a leader in genome engineering. He is the 2014 recipient of the Outstanding Young Investigator Award by the American Society for Gene and Cell Therapy (ASGCT), largely for this work with Duchenne Muscular Dystrophy.