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Workshop II: Transcriptomics and Epigenomics
October 25 - 28, 2011
Organizing Committee |
Scientific Overview |
Speaker List
Application/Registration |
Contact Us
Organizing Committee
Sandrine Dudoit
(University of California, Berkeley (UC Berkeley), Biostatistics and Statistics)
Lior Pachter
(University of California, Berkeley (UC Berkeley), Mathematics)
Matteo Pellegrini
(University of California, Los Angeles (UCLA), Molecular, Cell, and Developmental Biology)
Barbara Wold
(California Institute of Technology, Biology Division)
Wing Wong
(Stanford University, Statistics)
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Scientific Overview
The set of RNA transcripts in cells, collectively referred to as the transcriptome, are of
fundamental importance as they form the substrate for protein synthesis, while also having
the ability to assume functional roles via their secondary and tertiary structure.
Transcriptional regulation is frequently controlled epigenetically, i.e. via mechanisms that
do not depend strictly on the underlying DNA sequence. The collection of epigenetic marks is
known as the epigenome.
Close connections between the transcriptome and epigenome are beginning to be unraveled via
new technologies based on high-throughput sequencing that allow for the measurement of the
transcriptome and epigenome at the resolution of individual nucleotides. For example, using
RNA-seq it is possible to obtain a comprehensive and quantitative view of the cellular
transcriptome. The measurement of the epigenome includes the profiling of cytosine metylation
in the entire genome using approaches known as BS-seq or MethylC-seq. Protein DNA interactions
also play a critical role in epigenetic regulation and chromatin-immunoprecipitation may be
used to identify binding sites for specific proteins, using an approach termed ChIP-seq. Much
work has already been dedicated to mapping histone modifications across the genome and thus
elucidating the “histone code”. Furthermore, nucleosome positions are also important in
regulating transcription and replication, and these can be measured using nuclease-based assays.
As the epigenome of each type of cell is different, profiling epigenomes from stem cells to
differentiated cells presents a daunting challenge for the genomics community.
The analyses of these types of data are presenting the mathematical community a rich set of
challenges. These include the development of algorithms for read mapping, transcript assembly,
peak calling, and prediction of nucleosome positions from the DNA sequence of the genome. All of
these problems require the development of novel statistical and computational techniques, and
mathematical foundations for many of the ideas need to be developed.
The workshop will include presentations that discuss the mathematical challenges in each of
these fields. It will also include a poster session. A request for posters will be sent to
registered participants in advance of the workshop.
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Confirmed Speakers
Orly Alter
(University of Utah)
Henrik Bengtsson
(University of California, San Francisco (UCSF))
Colin Dewey
(University of Wisconsin-Madison)
Sandrine Dudoit
(University of California, Berkeley (UC Berkeley))
Joseph Ecker
(The Salk Institute for Biological Studies)
Nir Friedman
(Hebrew University)
Alexander Hartemink
(Duke University)
Hongkai Ji
(Johns Hopkins University)
Tao Jiang
(University of California, Riverside (UC Riverside))
Christina Kendziorski
(University of Wisconsin-Madison)
Yuval Kluger
(Yale University)
Jigang Li
(Yale University)
Wei Li
(Baylor College of Medicine)
Ali Mortazavi
(University of California, Irvine (UCI))
Matteo Pellegrini
(University of California, Los Angeles (UCLA))
Zhiping Weng
(University of Massachusetts Medical School)
Yi Xing
(University of Iowa)
Zohar Yakhini
(Agilent Labs and the Technion)
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Contact Us:
Institute for Pure and Applied Mathematics (IPAM)
Attn: GENWS2
460 Portola Plaza
Los Angeles CA 90095-7121
Phone: 310 825-4755
Fax: 310 825-4756
Email: ipam@ucla.edu
Website:
http://www.ipam.ucla.edu/programs/genws2/
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