PSB 2005

Call For Papers, Abstracts and Demonstrations

Pacific Symposium on Biocomputing

Big Island, Hawaii -- January 4-8, 2005

The tenth Pacific Symposium on Biocomputing (PSB), will be held January 4-8, 2005 at the Fairmont Orchid on Big Island of Hawaii. 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 2005 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, 2004 to present their work in the poster sessions.

PSB 2005 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.

Inferring SNP Function Using Evolutionary, Structural and Computational Methods

Cochairs: Carlos Bustamante, Shamil Sunyaev and Matt Dimmic

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.

Contact: Carlos Bustamante (

Biogeometry: Applications of Computational Geometry to Molecular Structure

Cochairs: Alexander Tropsha and Herbert Edelsbrunner

BioGeometry is an emerging scientific discipline at the interface between computational geometry, biochemistry and biophysics, statistics, and chemistry that brings together specialists in the above disciplines to develop new computational techniques and paradigms for representing, storing, searching, simulating, analyzing, and visualizing biological structures. BioGeometry brings together ideas from a wide range of areas of computer science and mathematics, including algorithms, geometry, topology, graphics, robotics, and databases to address on of the most fundamental biological problems, i.e., structure-function relationships for biological molecules.

Contact: Alex Tropsha (

Inferring Function from Structural Genomics Targets

Cochairs: Patsy Babbitt, Philip Bourne, and Sean Mooney

Currently there are ongoing efforts to develop high-throughput methods for protein structure determination both in industry and in academia. This session will continue to present progress and achievements in the field of structural genomics through the use of computational techniques.

Contact: Sean Mooney (

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 (

Joint Learning from Multiple Types of Genomic Data

Cochairs: Alex Hartemink and Eran Segal

This session will focus on the development and application of methods in computational genomics that employ joint learning from multiple types of data. Preference will be given to methods that attempt to simultaneously (jointly) discover patterns in multiple types of data, rather than apply separate methods in series 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: Alex Hartemink (

Biomedical Ontologies

Cochairs: Olivier Bodenreider, Joyce Mitchell and Alexa 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.

Contact: Olivier Bodenreider (

Back to the main PSB page
This page written by Lawrence Hunter, and last updated on April 12, 2004