Call for Papers and Participation

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Computational Methods for Inferring SNP Function:

Integrating Evolutionary, Structural, and Comparative Genomics

 

A Pacific Symposium on Biocomputing 2005 Session

January 4-8 at the Fairmont Orchid, Hawaii

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Summary | Session Topics | Contributions | Session Chairs

Conference Deadlines | Manuscript Format | Travel Support | Conference Information

Summary

Single nucleotide polymorphisms (SNPs) are the most prevalent form of genetic variation within populations. Recent technological advances have enabled the accumulation of massive amounts of data on SNPs (>15 million entries in dbSNP) from within a wide range of species (e.g., human, Drosophila, Anopheles, mouse, dog, Arabidopsis, maize, and Plasmodium).  Upcoming sequences of the chimpanzee and rat genomes provide the possibility for comparison of population genetic variation with species divergence at the genome scale.

 

Although the majority of SNPs are likely to be neutral both evolutionarily and functionally, some SNPs can alter the structure or function of DNA, RNA, or proteins. If these molecular changes affect the organism’s phenotype, natural selection can operate on the SNP alleles. Because evolution acts on phenotypes which impact survival and reproduction, the identification of functionally important variation is integral to important research problems ranging from medicine and agriculture to basic genetics. 

 

This session will focus on statistical and computational methods for inferring functional SNPs and their consequences, with an emphasis on novel approaches that merge population and comparative genomics. The recent avalanche of SNP data has led to rapid development of new techniques and models in a variety of research disciplines, and we encourage manuscript submissions that combine approaches from fields such as bioinformatics, computational biology, evolutionary and human genetics, and molecular and cellular biology.

Session Topics

Possible manuscript topics include (but are not limited to):

 

·         Comparative genomic methods for detecting SNPs that affect gene regulation

·         Biophysical studies investigating the effect of SNPs on protein structure and function

·         Association (linkage) studies pursuing the detection of correlation among SNP variants with specific phenotypes

·         Population genetic models for detecting natural selection on SNPs

·         Novel approaches for integrating microarray data and evolutionary analysis

Papers, Oral Presentations, Posters, and Demonstrations

The core of the conference consists of peer-reviewed full-length papers reporting on original work. All submitted papers will be subject to rigorous review by several referees, and must represent original, unpublished results which are not currently under consideration elsewhere. Accepted papers will be fully indexed in Medline and published by PSB in its hard-bound archival proceedings. In addition, a limited number of papers will be selected for oral presentation. Because PSB sessions are conducted sequentially, these talks will be presented to the entire conference.

 

Researchers who wish to present their research without publication in the proceedings are encouraged to share their results and ideas in the poster session. Posters will be displayed throughout the conference, and computer workstations are also available for software demonstrations and Web site presentation. To be included in the poster abstract book distributed at the conference, a one-page abstract must be submitted by November 1 to Larry Altman at altman@smi.stanford.edu. Poster abstracts are not peer-reviewed.

Session Chairs

·         Carlos Bustamante, Cornell University

cdb28@cornell.edu

·         Shamil Sunyaev, Brigham & Women's Hospital, Harvard Medical School

ssunyaev@rics.bwh.harvard.edu

·         Matt Dimmic, Cornell University

            mwd8@cornell.edu

Conference Deadlines

·         Full manuscript submissions due: July 19, 2004

·         Notification of paper acceptance: September 8, 2004

·         Camera ready manuscript of accepted papers due: September 22, 2004

·         Poster/demo abstract deadline: November 1, 2004

·         Meeting: January 4-8, 2005

Manuscript Format

Contributions should address emerging problems and approaches in the area of functional SNP inference. Because the purpose of the conference is to bring together scientists and ideas from different biological and computational fields, ideally the writing should be accessible to an interdisciplinary audience. Please email the session chairs if you have any questions regarding paper content.

 

Submitted papers are limited to 12 pages. Please format your paper according to instructions found at http://psb.stanford.edu/psb-online/psb-submit/. If figures cannot be easily resized and placed precisely in the text, then it should be clear that with appropriate modifications, the total manuscript length would be within the page limit. Papers from previous PSB proceedings are available for examination at the conference website.

 

All papers must be submitted to russ.altman@stanford.edu in electronic format. The file formats we accept are Adobe Acrobat (*.pdf) and Microsoft Word documents (*.doc). Attached files should be named with the last name of the first author (e.g. altman.pdf or altman.doc). Hardcopy submissions or unprocessed TEX or LATEX files will be rejected without review.

 

Each paper must be accompanied by a cover letter. The cover letter must state the following:

·         The email address of the corresponding author

·         The specific PSB session that should review the paper or abstract

·         The submitted paper contains original, unpublished results, and is not currently under consideration elsewhere.

·         All co-authors concur with the contents of the paper.

 

Color pictures can be printed at the expense of the authors. The fee is $500 per page of color pictures, payable at the time of camera ready submission.

 

Contact Russ Altman for additional information about paper submission requirements.

Travel Support

The conference has been able to offer partial travel support to many PSB attendees in the past, however travel support is not guaranteed. Travel support applications will be available on the website in mid-July.

Conference Information

The Pacific Symposium on Biocomputing (PSB) 2005 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. Papers and presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2005 will be held January 4-8, 2005 at the Fairmont Orchid on The Big Island of Hawaii. Tutorials will be offered prior to the start of the conference.

 

PSB 2005 will bring together top researchers from the US, the Asian Pacific nations, and around the world to exchange research results and address open issues in all aspects of computational biology. PSB is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.

 

PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders in the emerging areas and targeted to provide a forum for publication and discussion of research in biocomputing's "hot topics." In this way, PSB provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field.

 

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Summary | Possible Topics | Session Chairs | Conference Deadlines

Contributions | Manuscript Format | Travel Support | Conference Information

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