ISMB 2009 SIG on Short Read Sequencing

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Short-SIG: ISMB 2009 Special Interest Group on Short Read Sequencing
Call for Papers and Abstracts
In association with Bioinformatics
http://compbio.cs.toronto.edu/ismb09-sig

Key Dates:
• April 20th – Paper submission deadline
• May 11th – Abstract submission deadline
• June 1st – Decisions
• June 28th – Short-SIG in Stockholm, Sweden

Overview:
The ISMB 2009 Special Interest Group on Short Read Sequencing (held prior to the ISMB conference on June 28th in Stockholm, Sweden) will bring together biologists and computational scientists interested in exploring the challenges and opportunities in the analysis of high-throughput short read sequencing technologies. Following up on our successful meeting at Toronto in 2008, that drew together more than 120 people and had 18 scientific presentations we are expanding our program to include full papers as well as oral abstract presentations.

The past year has seen the development of several computational methods for assembly and alignment of short reads. However realizing the full promise of short read technologies requires the development of methods that analyze the resulting assemblies and mappings to infer biological meaning. For this year’s SIG we are especially interested in presentations describing methodology to infer various polymorphisms (SNPs, larger insertions/deletions, copy number variants), methods for analysis of RNA sequencing data (RNA expression, de-novo transcriptome sequencing, novel transcript discovery), and other applications of short read sequencing (transcription factor binding site discovery, nucleosome positioning, methylation profiling, and analysis of metagenomic samples). We also welcome submissions on any other important method related to short read sequencing technologies.
Papers:
We are soliciting high-quality papers that will go through rigorous peer-review and will be published as a special proceedings section of the Bioinformatics journal. Papers will be considered simultaneously for the SIG and Bioinformatics: Papers accepted to the journal will be presented as talks at the SIG, and will be published in a special section of the Bioinformatics journal. Furthermore, Bioinformatics and Oxford University Press are offering a $700 prize or open access charge waiver for the best paper presented at the meeting. Papers requiring extensive revisions will be considered separately for abstract presentations at the SIG and as regular papers at the Bioinformatics journal. All manuscripts should be submitted via the online submission system at (http://mc.manuscriptcentral.com/bioinformatics), and include a cover letter stating the manuscript should be considered for the ISMB Short Read Sequencing SIG.

Abstracts:
Simultaneously we will also select oral presentations from submitted abstracts. The abstracts should target topics of immediate relevance in the field and must describe novel work, not previously published in any journal or proceedings. Abstracts should be submitted by e-mail to [email protected] in PDF, Word, or plain text format.

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In response to several requests we have postponed the paper submission deadline to April 27th.

-Mike