[Computational-biology] CALL FOR PAPERS: COMPUTATIONAL TOOLS FOR NEXT-GENERATION SEQUENCING APPLICATIONS at PSB 2008

Francisco M De La Vega via comp-bio%40net.bio.net (by francisco.delavega from appliedbiosystems.com)
Fri May 4 10:04:52 EST 2007


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


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