Workshop II: Transcriptomics and Epigenomics - IPAM

Workshop II: Transcriptomics and Epigenomics

Part of the Long Program Mathematical and Computational Approaches in High-Throughput Genomics
October 25 - 28, 2011

Schedule

All times in this Schedule are Pacific Time (PT)

Tuesday, October 25, 2011

Morning Session

08:00-09:00
Check-In/Light Breakfast (Hosted by IPAM)
09:00-09:15
Welcome and Opening Remarks
09:15-10:05
Matteo Pellegrini (University of California, Los Angeles (UCLA))
Transgenerational Inheritance of DNA Methylation
10:15-10:45
Break
10:45-11:35
Joseph Ecker (The Salk Institute for Biological Studies)
Transgenerational Epigenetic Instability is a Source of Novel Methylation Variants
11:45-13:00
Lunch (on your own)

Afternoon Session

13:00-13:50
Jigang Li (Yale University)
Transcriptomes and Epigenomes in Specific Plant Developmental Processes
14:00-14:30
Break
14:30-15:20
Wei Li (Baylor College of Medicine)
Transcriptome Instability in Prostate Cancer
16:00-17:00
Public Lecture by Michael Brenner at CNSI Auditorium (Optional)
"The Science of Cooking"

Wednesday, October 26, 2011

Morning Session

08:00-09:00
Continental Breakfast
09:00-09:50
Alexander Hartemink (Duke University)
Computational Advances in Elucidating Cell Cycle Transcriptional Regulation
10:00-10:30
Break
10:30-11:20
Nir Friedman (Hebrew University)
Chromatin and Transcription: Adventures in Disentailing Complex Feedback Loops
11:30-12:00
Break

Afternoon Session

12:00-12:50
Tao Jiang (University of California, Riverside (UC Riverside))
A Combinatorial Approach to the Inference of Isoforms from Short Sequence Reads
13:00-14:30
Lunch (on your own)
14:30-15:20
Sandrine Dudoit (University of California, Berkeley (UC Berkeley))
Normalization and Differential Expression in RNA-Seq
15:30-16:00
Break
16:00-16:50
Christina Kendziorski (University of Wisconsin-Madison)
Identifying DE Isoforms in an RNA-seq experiment
17:00-18:30
Reception and Poster Session (Hosted by IPAM)

Thursday, October 27, 2011

Morning Session

08:00-09:00
Continental Breakfast
09:00-09:50
Zhiping Weng (University of Massachusetts Medical School)
Computational Analysis of Human Epigenome and Regulate
10:00-10:30
Break
10:30-11:20
Yuval Kluger (Yale University)
Title not available
11:30-12:00
Break

Afternoon Session

12:00-12:50
Zohar Yakhini (Agilent Labs and the Technion)
Statistical Enrichment in Ranked Lists with Applications in Transcriptomics and Epigenomics
13:00-14:30
Lunch (on your own)
14:30-15:20
Henrik Bengtsson (University of California, San Francisco (UCSF))
Single-Pair Parent-Specific Copy Number Analysis
15:30-16:00
Break
16:00-16:50
Orly Alter (University of Utah)
Discovery of Mechanisms and Prognosis of Cancers from Matrix and Tensor Modeling of Large-Scale Molecular Biological Data

Friday, October 28, 2011

Morning Session

08:00-09:00
Continental Breakfast
09:00-09:50
Yi Xing (University of California, Los Angeles (UCLA))
Alternative Splicing in Evolution and Development
10:00-10:30
Break
10:30-11:20
Colin Dewey (University of Wisconsin-Madison)
Enabling transcript quantification in non-model organisms with RNA-Seq and generative probabilistic models
11:30-12:00
Break

Afternoon Session

12:00-12:50
Adam Roberts (University of California, Berkeley (UC Berkeley))
eXpress
13:00-14:30
Lunch (on your own)
14:30-15:20
Hongkai Ji (Johns Hopkins University)
Differential principal component analysis of ChIP-seq
15:30-16:00
Break
16:00-16:50
Ali Mortazavi (University of California, Irvine (UCI))
Integrating ChIP-seq and DNAse-seq ENCODE Data From from Multiple Cell Types Using Self-Organizing Maps
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