PSB'2002-Human Genome Variation

Call For Papers & Participation

The recent completion of the first assembly of the human genome has provided an invaluable tool for investigating the biology of our species. Several academic and industrial laboratories are working to add value to this raw genome sequence by generating DNA variation and gene expression data. However, researchers are encountering substantial challenges regarding the management, annotation and analysis of this information.

Many of the critical issues involved in linking genetic variation to clinical phenotypes are complicated by a need to synthesize biological and computational expertise. For example, there is a need to apply and extend population genetic analyses to high-throughput data to elucidate underlying patterns of variation in the human genome. When operating at a high-throughput mode, extensive software architectures are needed, and quality control of the data is essential. Current approaches for molecular profiling call for the combined use of genetics and functional genomics data. New and improved algorithms for class discovery and prediction within the combined data sets are needed.

Furthermore, disparate academic and industrial databases must be integrated in order to connect genomic and clinical information; yet is unclear that the underlying ontologies used in these repositories lead to easy interoperation. However, the rewards for overcoming these challenges will be considerable, including an improved understanding of genetic disease and the entire range of normal phenotypic variation and individual differences in drug response.

An Invitation to Participate

The session of the Pacific Symposium on Biocomputing 2002 "Human Genomic Variation: Disease, drug response and clinical phenotypes" will provide a forum for biologists and computer scientists working in academics, government and industry to discuss and develop new approaches to use high throughput genetic variation and expression data to inform scientific and clinical studies.

We encourage academic, industrial and government scientists to submit manuscripts to the session. In addition to a session for oral presentation of novel peer-reviewed contributions, a panel discussion devised to foster exchange between industry and academic scientists will be scheduled. Participants are invited to discuss their issues with other peers in this panel session. Posters and computer demonstrations are also requested to complement the the panel and the peer-reviewed papers.

Submission Topics

The contributions should pose and discuss a novel problems and approaches that need to be addressed in the current post-genomic era. The accepted contributions are expected to describe models, propose specific solutions, or address computational or theoretical aspects of topics related to the challenges posed above.

Among the anticipated topics are:

Lessons from single gene variation analyses studies on human disease and drug response
Algorithms and methods for analyzing association, linkage disequilibrium, and QTL studies using SNPs in candidate gene sets and whole genome scans
Laboratory Information Management Systems for high-throughput genotyping and functional genomics
Methods, algorithms and procedures for QC/QA in high- throughput genotyping-functional genomics operations
Algorithm and methods for molecular classification from genotypic-phenotypic databases
Correlation finding and knowledge discovery in genotypic-phenotypic databases
Ontologies, control vocabularies, data exchange formats, and data models for genotypic-gene expression-phenotypic data
Examples of data integration and data mining of genotyping, gene expression and clinical phenotypic databases
Visualization of large-scale genotypic-gene expression data
Evolutionary models of genome variability and linkage disequilibrium vs. empirical data findings

Full Paper Submissions

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 a oral presentation to the full assembled conference. Accepted poster abstracts will be distributed at the conference separately from the archival Proceedings. To be eligible for Proceedings publication, each full paper must be accompanied by a cover letter stating that it contains original unpublished results not currently under consideration elsewhere.

All papers must be submitted to altman@smi.stanford.edu in electronic format. The file formats we accept are: postscript (*.ps), adobe acrobat (*.pdf) and Microsoft Word documents (*.doc). Attached files should be named with the last name of the first author (e.g. altman.ps, 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.

Submitted papers are limited to twelve (12) pages in our publication format. Please format your paper according to instructions found at:

ftp://ftp-smi.stanford.edu/pub/altman/psb/.

If figures can not 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. 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.

Posters and Computer Demonstrations

The poster session at PSB is another possibility to present results or to share ideas in the Conference. Posters are exhibited several days during the conference and include topics from all PSB sessions.

Computer stations for live software or Web site demonstrations are also available during the conference and are encouraged as a complement to a poster or presentation.

In order to be included in the Abstracts booklet to be distributed at the conference, one-page posters abstracts should be submitted by November 5 to altman@smi.stanford.edu. Posters are not peer-reviewed nor indexed in MEDLINE.

Dates and Deadlines

Paper submissions due: July 16, 2001
Notification of paper acceptance: August 20, 2001
Camera ready of accepted papers copy due: September 24, 2001
Abstract deadline: November 5, 2001
Meeting: January 3-7, 200

FAQ

Q1. How can my paper be included in PSB's hardbound proceedings?

PSB publishes peer-reviewed full papers in an archival proceedings. Each accepted paper will be allocated 12 pages in the proceedings volume. Paper authors are required to register (and pay) for the conference by the time they submit their camera-ready copy, or the paper will not be published.

Q2. How does a PSB publication compare to a journal publication?

PSB papers are strenuously peer reviewed, and must report significant original material. PSB proceedings are indexed in Medline and other indexing services. All accepted full papers will be indexed just as if they had appeared in a journal. It is too early to assess the impact of a PSB paper quantitatively, but we will take every action we can to improve the visibility and significance of PSB publication.

Q3. If I do not want to submit a full paper to PSB, but wish to participate?

Authors who do not wish to submit a full paper are welcome to submit one page abstracts, which will be distributed at the meeting separately from the archival proceedings, and are also welcome to display standard or computer-interactive posters.

Q4. How can I obtain travel support to come to PSB?

We have been able to offer partial travel support to many PSB attendees in the past, including most authors of accepted full papers who request support. However, due to our sponsoring agencies' schedules, we are unable to offer travel awards before the registration (and payment) deadlines for authors. NO ONE IS GUARANTEED TRAVEL SUPPORT. Travel support applications will be available on our web site (http://psb.stanford.edu).

Conference Information

The Pacific Symposium on Biocomputing (PSB 2002) 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 2002 will be held January 3-7, 2002, in Lihue, Kauai at the Kauai Marriott Resort and Beach Club.

For more information see the official PSB 2002 Web page

Session Chairs
Francisco De La Vega Applied Biosystems Foster City, CA, USA E-mail:delavefm@appliedbiosystems.com (Main Contact)
Isaac Kohane Children's Hospital of Boston and Harvard Medical School, Cambridge, MA, USA. E-mail: isaac_kohane@harvard.edu
Joel Claiborne Stephens Julie Schneider Genaissance Pharmaceuticals Inc. New Haven, CT, USA E-mail: j.schneider@genaissance.com