"An S phase-dependent commitment switch activates erythroid transcription and global DNA demethylation"
Virology Seminar - Speaker: Christian Cuevas - 209 Johnson Pavilion
The IBI is offering a free one day RNA-Sequencing analysis workshop for Penn and CHOP researchers. Open to Graduate Students, Postdocs, Staff, and Faculty. The workshop will be led by Greg Grant, Research Assistant Professor of Genetics. It will run from 9:30am to 4:30pm on Tuesday February 25th. There will be lunch provided and coffee/tea.
This workshop is aimed at bioinformaticians and statisticians who may be responsible for setting up and/or running the computational pipelines that take raw data all the way through to high level analysis. We will focus on basic to advanced analysis using a UNIX command line environment to run open-source RNA-Seq software. Participants should have a basic knowledge of the UNIX environment and a basic understanding of statistical methods. The first hour will be spent reviewing some of the relevant UNIX concepts.
We will first discuss the nature of the data and then we will learn about alignment, normalization, quantification, statistical analysis and data management. We will not take the standard push-button out-of-the-box approach to RNA-Seq analysis, but will instead look deeper into the issues that make every study a special case, with the aim of getting more out of the data than the lowest hanging fruit. In other words, we are not just going to show you how to run Tophat and Cufflinks, instead we will evaluate many available methods and look closely at issues that have been largely ignored, but which have considerable impact on the power of the downstream analysis.
This is a practical workshop which will provide down-to-earth material and hands on experience. You will learn how to perform the analyses on the UPenn PMACS compute cluster. Participants will need to bring a laptop with an ssh client in order to connect remotely to the PMACS system.
Please sign up as soon as possible as we have limited space and we expect it to fill up quickly.
RSVP to firstname.lastname@example.org.
February 25, 2014 - 2:00 pm - Austrian Auditorium Clinical Research Building
Erhu Cao, Ph.D.
University of California, San Francisco
Title of seminar:
"Functional and Structural Insights into TRPV1 Activation"
The Institute for Diabetes, Obesity, and Metabolism; the Division of Endocrinology, Diabetes, and Metabolism; and the Diabetes Research Center Combined Spring 2014 Seminar Series presents:
Changhong Li, M.D., Ph.D.
Children's Hospital of Philadelphia
“Fuel Metabolism and Function Correlation in Pancreatic Islets”
February 25, 2014
Smilow Center for Translational Research, 12th Floor
“Role of TCR Specificity in Thymic and Peripheral Regulatory T Cell Development”
"On the Definition and Estimation of the Causal Effect of a Continuous Exposure: Theory and Applications"
Iván Díaz, PhD Postdoctoral Fellow Department of Biostatistics Johns Hopkins Bloomberg School of Public Health
Abstract: The definition of a causal effect typically involves counterfactual variables resulting from interventions that modify the exposure of interest deterministically. A stochastic intervention generalizes this concept to define counterfactuals in which the post-intervention exposure is stochastic rather than deterministic. In this talk I will present a new approach to causal effects based on stochastic interventions. I will focus on an application of this methodology to the definition and estimation of the causal effect of a shift of a continuous exposure. This parameter is of general interest since it generalizes the interpretation of the coefficient in a main effects regression model to a nonparametric model. I will discuss three estimators of the causal effect: an inverse probability of treatment weighted (IPTW) estimator, and augmented IPTW estimator, and a targeted minimum loss based estimator (TMLE). I will discuss the methods in the context of an application to the evaluation of the effect of physical activity on all-cause mortality in the elderly.
Lumena Louis (M.Chou Lab) -
"Regulation of Ubiquitin-like Modification by Tre17/USP6."
Ian Henrich (E. Smyth Lab) -
"HDL-based Nanotherapeutic Approach to Inhibition of Macrophage COX-2 as a Novel Breast Cancer Treatment"