Statistical
and Computational Challenges in
Next-Generation Sequencing
Friday, October 10th, 2008
Program [PDF]
Background
For the past decade, microarrays have been the assays of choice for
high-throughput studies of gene expression. Recent improvements in the
efficiency, quality, and cost of genome-wide sequencing are prompting
biologists to rapidly abandon microarrays in favor of so-called
next-generation sequencers, e.g., Applied Biosystems' SOLiD, Helicos
BioSciences' HeliScope, Illumina's Solexa, and Roche's 454 Life
Sciences
sequencing systems. These high-throughput sequencing technologies have
already been applied for studying genome-wide transcription levels
(mRNA-Seq), transcription factor binding sites (ChIP-Seq), chromatin
structure, and DNA methylation status. While sequencing-based gene
expression studies have been touted as overcoming longstanding
limitations of microarray-based studies, these new biotechnologies
raise similar as well as novel statistical and computational
challenges.
The main objectives of this small workshop are to
- outline the statistical and
computational challenges related to next-generation sequencing;
- report on work in progress,
early findings, and promising directions;
- facilitate the hands-on
discussion of practical data handling and software issues;
- foster collaborations between
biologists and statisticians;
- foster collaborations between
academia and industry.
Program
Invited talks and posters: abstracts
Participants (currently
confirmed)
Organizers
Sandrine Dudoit,
Division of Biostatistics and Department of Statistics, University of
California, Berkeley
Terry Speed,
Department of Statistics and Division of Biostatistics, University of
California, Berkeley/Bioinformatics Division, Walter and Eliza Hall
Institute, Melbourne
Margaret Taub,
Department of Statistics, University of California, Berkeley
Speakers
Kasper Hansen,
Biostatistics, UC Berkeley
John
Marioni, Statistics, University of Chicago
Martin
Morgan, Fred Hutchinson Cancer Research Center
Rasmus
Nielsen, Integrative Biology and Statistics, UC Berkeley
Lior
Pachter, Mathematics, UC
Berkeley
Elizabeth Purdom, Biostatistics
and Statistics, UC Berkeley
Devin Scannell, Molecular and
Cell Biology, UC Berkeley
Wendy Schackwitz, Joint Genome
Institute
Barbara
Wold, Biology,
California Institute of Technology
Panelists
Steven Brenner, Plant and Microbial Biology, UC Berkeley
Fiona Hyland, Applied Biosystems
Gavin Sherlock, Genetics, Stanford University
Terry Speed, Statistics and Biostatistics, UC
Berkeley
Paul
Spellman, Lawrence Berkeley National Laboratory
Ed Thayer, Helicos BioSciences
Svilen Tzonev, Illumina
Participants
Henrik Bengtsson,
Statistics, UC Berkeley
Steven Brenner, Plant and Microbial Biology, UC Berkeley
James Bullard, Biostatistics, UC Berkeley
Justing Choi, Functional
Genomics Laboratory, UC Berkeley
Hector Corrada Bravo,
Biostatistics, Johns Hopkins University
Sandrine Dudoit, Biostatistics
and Statistics, UC Berkeley
Mike Duff, Genetics and
Developmental Biology, University of Connecticut Health Center
Steffen Durinck, Illumina
Chris Ellison, PMB, UC Berkeley
Russell Fletcher, Molecular and
Cell Biology, UC Berkeley
Kasper Hansen, Biostatistics, UC Berkeley
Ines Hellmann, Integrative Biology, UC Berkeley
Haiyan Huang, Statistics, UC Berkeley
Fiona Hyland, Applied Biosystems
Rafael Irizarry, Biostatistics, Johns Hopkins University
Wei-Chun Kao, Computer Science, UC Berkeley
Su Yeon Kim, Integrative Biology, UC Berkeley
Doron Lipson, Helicos
BioSciences
John Marioni, Statistics, University of Chicago
Joel Martin, Joint Genome Institute
Oleg Mayba, Statistics, UC Berkeley
Ken McCue, Biology, California Institute of Technology
Martin Morgan, Fred Hutchinson
Cancer Research Center
Ali Mortazavi, Biology, California Institute of Technology
Serban Nacu, Genentech
Pierre Neuvial, Statistics, UC Berkeley
John Ngai, Molecular and Cell Biology, UC Berkeley
Rasmus Nielsen, Integrative Biology and Statistics, UC Berkeley
Lior Pachter, Mathematics, UC
Berkeley
Helder Pedro, Mathematics, UC Berkeley
Franck Picard, Biometrie et Biologie Evolutive, CNRS et
Universite Claude Bernard Lyon I
Christi Preston, Molecular and Cell Biology, UC Berkeley
Elizabeth Purdom,
Biostatistics and Statistics, UC Berkeley
Amrita Ray, Lawrence Berkeley National Laboratory
Stephane Robin, AgroParisTech
Mark Robinson, Walter and Eliza Hall Institute
Devin Scannell, Molecular and
Cell Biology, UC Berkeley
Gary Schroth, Illumina
Meromit Schuster, Computer
Science, UC Berkeley
Wendy Shackwitz, Joint Genome
Institute
Gavin Sherlock, Genetics, Stanford University
Yun Song, Computer Science and
Statistics, UC Berkeley
Terry Speed, Statistics and Biostatistics, UC Berkeley
Paul Spellman, Lawrence Berkeley National Laboratory
Christiana Spyrou, Statistical
Laboratory, University of Cambridge
Jason Stajich, Plant and Microbial Biology, UC Berkeley
Rory Stark, Cambridge Research Institute - Cancer Research UK
Margaret Taub, Statistics, UC Berkeley
Ed Thayer, Helicos BioSciences
Svilen Tzonev, Illumina
Wenyi Wang, Statistics, UC Berkeley
Barbara Wold, Biology, California Institute of Technology
Oh Kyu Yoon, Molecular and Cell Biology, UC Berkeley
Nancy Zhang, Statistics, Stanford
Xiaoyue Zhao, Bionovo
Practical information
Please consult the MSRI website for
information concerning
Directions,
Public Transportation and Parking
Short
Term Housing
Sponsors
We gratefully acknowledge the support of Applied Biosystems and
Illumina.
