PSB 2004

Call for Papers and Abstracts

Pacific Symposium on Biocomputing

The Big Island of Hawaii
January 6-10, 2004

The paper submission deadline has passed; notificaton of paper acceptance will be sent on September 8, 2003.

The ninth Pacific Symposium on Biocomputing (PSB) will be held January 6-10, 2004 at the Fairmont Orchid on the Big Island of Hawaii. PSB brings together top researchers from around the world to exchange research results and address open issues in all aspects of computational biology. PSB provides 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 2004 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, 2003 to present their work in the poster sessions.

Important dates

Paper submissions due: July 14, 2003
Notification of paper acceptance: September 8, 2003
Final paper deadline: September 22, 2003
Abstract deadline: November 1, 2003
Meeting: January 6-10, 2004

Paper format

All papers must be submitted to in electronic format. The file formats we accept are: Adobe Acrobat (*.pdf), Microsoft Word documents (*.doc), and postscript (*.ps). Attached files should be named with the last name of the first author (e.g. altman.pdf, altman.doc, or 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. However, please note that no one is guaranteed travel support. Travel support applications will be available on the website in mid-July.

PSB 2004 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 and Symbolic Systems Biology

Cochairs: Trey Ideker, Eric Neumann and Vincent Schachter

Modeling in Systems Biology is often thought of as systems simulation, but in reality it can involve other forms of models and therefore requires a broader definition. Models may be numerically computable, but they also may be symbolical and accessible to inferential logic. Logical formalisms that describe complex phenomena are just as important as modeling molecular dynamics, and may lead to faster insight where the computational complexities are too great for a full-scale simulation

All co-chairs,,

Joint Learning from Multiple Types of Genomic Data

Cochairs: Alexander Hartemink and Eran Segal

This session will focus on methods in computational genomics that employ joint learning from multiple types of data. Preference will be given to methods that attempt to simultaneously discover patterns appearing in multiple data sources, rather than apply separate methods to each type of data. The performance of the methods should ideally be compared to the performance that can be obtained from learning from one data source at a time.

Contact: Alexander Hartemink

Alternative Splicing

Cochairs: Hui Wang, Ueng-cheng Yang, and Chris Lee

Alternative splicing is an essential yet complicated biological process, involving an estimated 30-60% of all human genes. Bolstered by genomic data and new experimental approaches, bioinformatics is emerging as an important tool for studying this phenomenon. For this first-time session, we are soliciting papers in three major areas:

Contact: All cochairs,,

Computational Tools for Complex Trait Gene Mapping

Cochairs: Francisco de la Vega, Kenneth Kidd & Andrew Collins

The novel computational and statistical approaches required for planning, executing, and analyzing the data of large association studies aimed to elucidate the basis of complex-traits, either common disease, response to environmental impact, or adverse drug response. The goal of the session is the presentation and discussion of new research, methods, algorithms, and tools, that promise to facilitate the elucidation of the connections between genotypes and complex-traits using the data generated by high-throughput genotyping technologies.

Contact: All cochairs,,

Biomedical Ontologies

Cochairs: Olivier Bodenreider, Joyce A. Mitchell, and Alexa T. McCray

Ontologies provide an organizational framework of the concepts involved in biological processes in a system that can be used computationally for reasoning about biomedical knowledge. Ontologies provide a conceptualization of the domain that can be shared among diverse groups of researchers and computational systems. This session will explore the theories, techniques, and applications of biomedical ontologies. The overall session goal is to share new research ideas and achieve a better understanding of current approaches, issues, and challenges in ontology research.

Olivier Bodenreider
+1 (301) 435-3246

Informatics Approaches in Structural Genomics

Cochairs: Sean D. Mooney, Philip E. Bourne, and Patricia C. Babbitt

The goal of structural genomics is to discover and characterize the three dimensional structure of all the proteins and other macromolecules found in nature. Presentations will focus on progress in solving the computational challenges in this field. Topic areas included in the discussions will be (1) Determination of all common scaffolds found in naturally evolved proteins, (2) Structure-based prediction and classification of function and (3) Elucidating structurally defined function.

Sean Mooney
+1 (415) 370-5909

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This page written by Lawrence Hunter, and last updated on April 16, 2003