CALL FOR PAPERS
COMPUTATIONAL TOOLS FOR NEXT-GENERATION SEQUENCING APPLICATIONS
A session of the Pacific Symposium on Biocomputing 2008
January 4-8, 2008
Big Island, Hawaii, USA
Next generation, rapid, low-cost genome sequencing promises to address a
broad range of genetic analysis
applications including: comparative genomics, high-throughput polymorphism
detection, analysis of small RNAs,
identifying mutant genes in disease pathways, transcriptome profiling,
methylation profiling, and chromatin
remodeling. One of the ambitious goals for these technologies is to
produce a complete human genome in a
reasonable time frame for US$100,000, and eventually US$1,000. In order to
do this, throughput must be increased
dramatically. This is achieved by carrying out many parallel reactions.
Despite the fact the read-length is short
(down to 20-35 bp), the overall throughput is enormous, each run producing
up to several hundreds of million reads
and billions of base-pairs of sequence data. As the promise of several of
these next generation sequencing (NGS)
technologies becomes reality, computational methods for analyzing and
managing the massive numbers of the short
reads produced by these platforms, are urgently needed. Algorithms for
genome assembly are in their infancy for
optimizing the use of short reads that often have different error
characteristics, a lack of mate pairs, deeper coverage
potential, and other differences affecting shotgun fragment assembly.
Although variant and SNP discovery from
Sanger sequencing reads is reasonably well understood, the NGS platforms
present new challenges not only for the
massive amount of short reads, but also due to the different underlying
error models that are critical to generate
quality values and distinguishing false positives from real variations.
The utilization of NGS in disease variant
identification needs new statistical methodologies. Furthermore, NGS is
also poised to propel genome-wide gene
expression, promoter, methylation and genomic rearrangement profiling and
new algorithms that can utilize short
paired need development. Given the massive volume of data being produced
by NGS platforms, data management
and analysis becomes a major undertaking for those adopting the new
platforms. The session of PSB 2008
"Computational tools for next-generation sequencing applications" will be
focused on the computational methods,
tools, and algorithms required for utilizing the staggering volumes of
short-read data. The particular challenges that
short reads present and proposed solutions for managing such volumes of
data would be of particular interest. The
session will similarly consider application-specific algorithms, analysis
methods, or study planning and design tools
with emphasis in the new types of biology that these technologies enable.
The session also aims to encourage the
discussion between academic scientists and their industry counterparts,
which are engaged in the development of
such platforms.
CALL FOR PAPERS AND POSTERS
We encourage academic, government, and industrial scientists to submit
manuscripts with original work in the
subject area. PSB will publish accepted full papers in an archival
proceedings indexed in Medline. All contributed
papers will be rigorously peer-reviewed by at least three referees. A
limited number of papers will be selected for
oral presentation to the full assembled conference. Posters and computer
demonstrations are also requested to
complement the session, and require the submission of a one-page abstract.
Accepted poster abstracts will be
distributed at the conference separately from the archival Proceedings. In
addition of the oral presentation of the full
papers, and the poster session, an invited panel discussion devised to
encourage exchange between industry and
academic scientists will be also held.
POSSIBLE SUBMISSION TOPICS
¥ Algorithms for de novo assembly with paired short sequencing reads
¥ Methods for polymorphism discovery and medical resequencing
¥ Design of genetic epidemiology studies with next-generation
sequencing
¥ Algorithms for massive tag-sequencing applications
¥ Tools for metagenomic sampling with next-generation sequencing
¥ Data formats, visualization tools, and informatics infrastructure
KEY DATES
Deadline for full paper submission: July 16, 2007
Full paper author notification: September 5, 2007
Deadline for poster abstracts: November 9, 2007
CONFERENCE INFORMATION
The Pacific Symposium on Biocomputing (PSB 2008) is an international,
multidisciplinary conference for the
presentation and discussion of current research in the theory and
application of computational methods in problems
of biological significance. The symposium is a forum for the presentation
of work in databases, algorithms,
interfaces, visualization, modeling and other computational methods, as
applied to the data-rich areas of molecular
biology. PSB 2008 will be held at the Big Island of Hawaii on January 4-8,
2008.
For more information see the official PSB 2008 Web page:
http://psb.stanford.edu
SESSION CHAIRS
Francisco M. De La Vega
Applied Biosystems
Foster City, CA, USA
E-mail:delavefm from appliedbiosystems.com (Main Contact)
Gabor Marth
Boston College
Boston, MA, USA
Granger Sutton
J. Craig Venter Institute
Rockville, MD, USA
