Seminars and Invited Talks

Date

Description

Oct 20, 2017 Huan (Helen) Wang, M.S.

Systems Analyst
Department of Biostatistics
Virginia Commonwealth University

Noon
One Capitol Square
Room 305

Nov 3, 2017 Chongzhi Zang, Ph.D.

Assistant Professor
Center for Public Health Genomics
University of Virginia
Charlottesville, VA

Modeling Gene Regulation with Public Genomic Data: From Integration to Prediction

Epigenetic regulation of gene expression plays a critical role in many biological processes including cancer formation and progression. Prediction of enhancers and transcription factors regulating genes with differential expression is an essential problem in functional genomics research. In this talk I will present a series of computational methods for modeling gene regulation using massive publicly-available data from human and mouse. We develop MARGE, a logistic regression and semi-supervised learning-based approach for predicting genomic cis-regulatory profiles that regulate a given gene set by leveraging a compendium of public H3K27ac ChIP-seq datasets. We develop BART to predict transcription factors associated with MARGE-predicted cis-regulatory profiles using thousands of public transcription factor ChIP-seq datasets. Integrating these approaches on The Cancer Genome Atlas (TCGA) molecular profiling data, we reconstruct the functional enhancer profiles and predict active transcription factor targets for each TCGA cancer type. Our work demonstrates the power of utilizing public data for computational studies of epigenomics.

Noon
One Capitol Square
Room 305

Nov 17, 2017 Nathan Sheffield, Ph.D.

Assistant Professor
Public Health Sciences
University of Virginia School of Medicine
Charlottesville, VA

Tools for Epigenome Analysis of Genomic Regions and Data-Intensive Project Management

In this presentation, I will start by introducing two R packages for epigenome analysis. First, LOLA (Locus Overlap Analysis), which identifies enrichments of genomic ranges in public databases, linking newly generated epigenome data to large existing data sets. Second, MIRA (Methylation-based Inference of Regulatory Activity), which uses aggregate DNA methylation patterns data to infer regulatory activity at collections of regions of interest. I will demonstrate the utility of these tools in understanding the rare pediatric cancer Ewing sarcoma. Finally, I will present pepkit, an open toolkit for organizing large-scale, sample-intensive biological research projects around a standardized structure called Portable Encapsulated Projects.

Noon
One Capitol Square
Room 305

Dec 1, 2017 Terrance D. Savitsky, Ph.D.

Research Mathematical Statistician
Office of Survey Methods Research
Bureau of Labor Statistics
Washington, DC

Noon
One Capitol Square
Room 305

Previous Seminars

Oct 13, 2017 Hua Liang, Ph.D.
Oct 6, 2017 Jianwen Cai, Ph.D.
Sep 29, 2017 CANCELLED: Emily Sheldon-Waniga, Ph.D.
Sep 22, 2017 Yanning Liu, Ph.D.
Sep 8, 2017 Tingting Zhang, Ph.D.
Aug 18, 2017 Student Research Symposium
Jun 19, 2017 Rebecca R. Lehman
Apr 28, 2017 Singdhansu Chatterjee, Ph.D.
Apr 14, 2017 Lukasz A. Kurgan, Ph.D.
Apr 11, 2017 Bhanu M. Evani, M.S.
Apr 7, 2017 Wenbin Lu, Ph.D.
Mar 31, 2017 Sujit K. Ghosh, Ph.D.
Mar 24, 2017 Stacia M. DeSantis, Ph.D.
Mar 10, 2017 Casey S. Greene, Ph.D.
Mar 3, 2017 POSTPONED: Tingting Zhang, Ph.D.
Feb 24, 2017 Montserrat Fuentes, Ph.D.
Feb 17, 2017 Samiran Sinha, Ph.D.
Feb 10, 2017 Xin (Cynthia) Tong, Ph.D.
Jan 27, 2017 Codruta Chiuzan, Ph.D.
Dec 2, 2016 Chao Du, Ph.D.
Nov 28, 2016 Zirui Gu
Nov 18, 2016 Hongkun Wang, Ph.D.
Nov 16, 2016 Kyle L. Ferber
Nov 11, 2016 Yanxun Xu, Ph.D.
Nov 10, 2016 Emily V. Dressler, Ph.D.
Nov 4, 2016 Mikhail Dozmorov, Ph.D.
Nov 3, 2016 Arindam RoyChoudhury, Ph.D.
Oct 28, 2016 Aaron Quinlan, Ph.D.
Oct 21, 2016 Bruce Swihart, Ph.D.
Oct 14, 2016 Bo Cai, Ph.D.
Oct 7, 2016 Helen Wang, M.S.
Sep 23, 2016 Cheng Ly, Ph.D.
Sep 16, 2016 Xiaowei Wu, Ph.D.
Sep 9, 2016 Brian J. Reich, Ph.D.
Aug 25, 2016 Vanda Inacio, Ph.D.
Aug 22, 2016 Hui Wang
Aug 18, 2016 Student Research Symposium
Jul 29, 2016 Kabita Joshi, MPH, M.S.
Jul 22, 2016 Edmund R. Glass
May 6, 2016 Jianlin Cheng, Ph.D.
May 4, 2016 Jenna N. Czarnota
Apr 29, 2016 Eric Vance, Ph.D.
Apr 28, 2016 Lauren P. Grant
Apr 27, 2016 Aobo Wang
Apr 26, 2016 Qing Zhou
Apr 22, 2016 Jenise L. Swall, Ph.D.
Apr 15, 2016 Jay Mandrekar, Ph.D.
Apr 8, 2016 Tom Arodz, Ph.D.
Apr 1, 2016 Jacob Wegelin, Ph.D.
Mar 25, 2016 Frank W. Rockhold, Ph.D.
Feb 12, 2016 Linda Corey, Ph.D.
Jan 29, 2016 Mikhail Dozmorov, Ph.D.
Dec 4, 2015 Timothy York, Ph.D.
Dec 2, 2015 Uma Siangphoe
Nov 20, 2015 Tamas S. Gal, Ph.D.
Nov 13, 2015 Dongjun Chung, Ph.D.
Nov 9, 2015 Andrey Afanasyev
Nov 5, 2015 Frank Harrell, Ph.D.
Oct 28, 2015 Helen Wang, M.S.
Oct 23, 2015 Andrey Rzhetsky, Ph.D.
Oct 9, 2015 Dong-Yun Kim, Ph.D.
Oct 2, 2015 CANCELLED: Helen Wang, M.S.
Sep 18, 2015 Rui Feng, Ph.D.
Aug 21, 2015 Student Research Symposium
Jul 22, 2015 Mateusz Makowski
May 27, 2015 Shanshan Chen, Ph.D.
Apr 24, 2015 Hadiza I. Galadima
Apr 17, 2015 Alicia Y. Toledano, Sc.D.
Apr 10, 2015 CANCELLED: Gregory Buck, Ph.D.
Apr 3, 2015 Julian Rosenman, Ph.D., M.D.
Mar 27, 2015 Dipankar Bandyopadhyay, Ph.D.
Mar 20, 2015 Bridget Thomson-McInnes, Ph.D.
Mar 13, 2015 Chi Song, Ph.D.
Mar 6, 2015 Guofen Yan, Ph.D.
Feb 27, 2015 Michael R. Kosorok, Ph.D.
Feb 13, 2015 Minsun Song, Ph.D.
Feb 6, 2015 Hua He, Ph.D.
Dec 5, 2014 Levent Dumenci, Ph.D.
Nov 25, 2014 Paul T. Manser, M.S.
Nov 21, 2014 Andriy Bandos, Ph.D.
Nov 14, 2014 RESCHEDULED – Levent Dumenci, Ph.D.
Oct 30, 2014 Mary E. Haynes
Oct 10, 2014 Wei Zhang, Ph.D.
Sep 26, 2014 Max Kuhn, Ph.D.
Sep 12, 2014 Frank Samuelson, Ph.D. and David Brown, Ph.D.
Sep 5, 2014 Biostatistics Student Research Symposium Program
Aug 29, 2014 Biostatistics Student Research Symposium Program
Jul 24, 2014 Xiangrong Kong, Ph.D.
Jul 18, 2014 Ying Liu, Ph.D.
Jul 14, 2014 Bo Zhang, Ph.D.
Jun 2, 2014 Chunfeng Ren, M.S., M.P.H.
Apr 30, 2014 Department Graduation Ceremony
Apr 25, 2014 Joan E. Bailey-Wilson, Ph.D.
Apr 21, 2014 Ghalib Bello
Apr 18, 2014 Pam R. Factor-Litvak, Ph.D.
Naha Farhat
Apr 11, 2014 Capt. Katherine A. Batterton
Apr 4, 2014 Scarlett L. Bellamy, Sc.D.
Mar 21, 2014 Yang Feng, Ph.D.
Mar 7, 2014 Qingguo Wang, Ph.D.
More news →