PSB 2006

Call For Papers, Abstracts and Demonstrations

Pacific Symposium on Biocomputing

Maui -- January 3-7, 2006

The paper submission deadline has passed, and the list of accepted papers has been selected by our referees.

The eleventh Pacific Symposium on Biocomputing (PSB), will be held January 3-7, 2006 at the Grand Wailea Resort on Maui. PSB will bring together top researchers from North America, the Asian Pacific nations, Europe and around the world to exchange research results and address open issues in all aspects of computational biology. PSB will provide 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 intends to attract a balanced combination of computer scientists and biologists, presenting significant original research, demonstrating computer systems, and facilitating formal and informal discussions on topics of importance to computational biology.

To provide focus for the very broad area of biological computing, PSB is organized into a series of specific sessions. Each session will involve both formal research presentations and open discussion groups. The 2006 PSB sessions are:

Papers and posters

The core of the conference consists of rigorously peer-reviewed full-length papers reporting on original work. Accepted papers will be published in a hard-bound archival proceedings, and the best of these will be presented orally to the entire conference. Researchers wishing to present their research without official publication are encouraged to submit a one page abstract by November 1, 2005 to present their work in the poster sessions.

Important dates

Paper submissions due: July 18, 2005
Notification of paper acceptance: September 6, 2005
Final paper deadline: September 23, 2005
Abstract deadline: November 1, 2005
Meeting: January 3-7, 2006

Paper format

All papers must be submitted to 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. or altman.pdf). 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:

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

Contact Russ Altman ( for additional information about paper submission requirements.

Travel support

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 and many graduate students. However, please note that no one is guaranteed travel support. Travel support applications will be available on the website soon.

PSB 2006 Sessions:

Each session has a chair who is responsible for organizing submissions. Please contact the specific session chair relevant to your interests for further information. Links on each of the session titles below lead to more detailed calls for participation for each session.

Computational Approaches for Pharmacogenomics

Cochairs: Marylyn D. Ritchie, Michelle W. Carrillo, and Russell Wilke

This session is designed to explore the current state-of-the-art research taking place in bioinformatics, biostatistics, and computational genetics to develop tools for the handling of all the pharmacogenomics data being generated. The goal of this session is the presentation and discussion of new research, algorithms, and methods for the management and analysis of pharmacogenomics data. We intend for this session to bring together scientists from pharmacology, genetics, statistics, and computational biology/bioinformatics to share their efforts in pharmacogenomics.

Contact: Marylyn Ritchie

Computational Proteomics

Cochairs: Bobbie-Jo Webb-Robertson, Bill Cannon, Joshua Adkins, and Deborah Gracio

This session is designed to bring together scientists in the computational sciences to explore the current state-of-the-art research taking place in all aspects of proteomics with special emphasis on MS-based approaches.

Contact: Bobbie-Jo Webb-Robertson

Design and Analysis of Genetic Studies After the HapMap Project

Cochairs: Andrew G. Clark, Andrew Collins, Francisco M. De La Vega, Kenneth K. Kidd

The goal of this session of the PSB conference is the presentation and discussion of new research, methods, algorithms, and tools that facilitate the planning, executing, and analysis of studies of human genomic variation leveraging the reference survey of variation performed by the HapMap project as well as other genome-wide datasets becoming available on the public domain.

Contact: Francisco M. De La Vega
Email: delavefm @

Linking Biomedical Information Through Text Mining

Cochairs: Kevin Bretonnel Cohen, Olivier Bodenreider, and Lynette Hirschman

This PSB session is intended to stimulate work in this area and to drive progress both in language processing and in the use and development of biological resources. It differs from previous PSB sessions on NLP and on ontologies in that it requires that submissions include both an NLP component and a mapping between at least two publicly available data sources.

Contact: Kevin Bretonnel Cohen

Protein Interactions in Disease

Cochairs: Maricel Kann, Yanay Ofran, Marco Punta, and Predrag Radivojac

We would like to invite contributions addressing the connections between protein interactions and diseases. In this context, submission topics can include but are not limited to:

Contact: Maricel Kann

Semantic Webs for Life Sciences

Cochairs: Robert Stevens, Olivier Bodenreider, and Yves A. Lussier

The Semantic Web is a vision that moves the Web from a form that is only really usable by humans, to one where the data and services are open to autonomous computational agents. This vision relies on the semantics of both the content and services on the Web being accessible to computers. Semantic markup through ontologies developed in OWl or RDF are meant to provide this semantic markup -- OWL is, after all, the web Ontology Language. As the recent biomedical ontology sessions at PSB have revealed, there is much activity within bioinformatics in the field of semantic markup of data. The discipline is well poised to build Semantic Webs for Life Sciences that will afford bioinformatics applications deeper computational access to the knowledge element of bioinformatics resources.

Contact: Robert Stevens

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