Call For Papers, Abstracts and Demonstrations

Pacific Symposium on Biocomputing

Kauai, Hawaii - January 3-7, 2003

The seventh Pacific Symposium on Biocomputing (PSB), will be held January 3-7, 2003 in Lihue, Kauai, 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 PSB 2003 sessions are:

In addition, PSB 2003 will offer two panel discussions:

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, 2002, and present their work in the poster sessions.

Important dates

Paper submissions due: July 15, 2002
Notification of paper acceptance: August 19, 2002
Final paper deadline: September 23, 2002
Abstract deadline: November 1, 2002
Meeting: January 3-7, 2003

Paper format

All papers must be submitted to 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:

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, no one is guaranteed travel support. We are no longer accepting PSB travel support requests; applications were due Friday, September 13, 2002. Decisions will be announced around September 20, 2002.

PSB 2003 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.

Informatics Approaches In Structural Genomics

Cochairs: Sean D. Mooney 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 (650) 723-2990

Genome-wide Analysis and Comparative Genomics

Cochairs: Inna Dubchak, Victor Solovyev, and Liping Wei

The sequencing of over 800 complete genomes presents unprecedented opportunities for biological discovery as well as new technical challenges for the computational sciences. This session calls for papers on novel computational algorithms and biological applications in genome-wide analysis and comparative genomics. The session will bring together researchers from the biological, computational and mathematical fields with the goal of sharing new research ideas and achieving a better understanding of the current issues and challenges.

Liping Wei
+1 (650) 960-0640

Linking Biomedical Language, Information and Knowledge

Cochairs: Carol Friedman, Lynette Hirschman, Robin McEntire, and Cathy Wu

This session solicits papers on improving information access to the biomedical literature and databases by leveraging the complementary resources and techniques provided by the literature, databases, nomenclatures, and ontologies. We particularly wish to focus on problems of importance to the biology and biomedical research communities, where such techniques have been demonstrated to provide a quantifiable improvement in performance. The session will give preference to papers that leverage resources or techniques from several areas. We will also give preference to papers describing systems of demonstrated utility to end users

Lynette Hirschman
+1 (781) 271-7789

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

Human Genome Variation: Haplotypes, Linkage Disequilibrium, and Populations

Cochairs: Francisco M. De La Vega, Kenneth Kidd, and Isaac Kohane

The session "Human Genome Variation: Haplotypes, Linkage Disequilibrium, and Populations" will be devoted to the computational and statistical challenges of building genome-wide haplotypes, defining haploytpe blocks and their variation across different populations, and their application for linking genotypes and phenotypes using the data generated by high-throughput SNP genotyping technologies.

Francisco De La Vega
delavefm @
+1 (650) 638-6989

Genome, Pathway, and Interaction Bioinformatics

Cochairs: Peter Karp, Eric Neumann, Alexander Hartemink, and Pedro Romero

This session is intended to be a continuing forum for addressing the advances and needs of computational tools for modeling and managing genomic, pathway and interaction information, including metabolic pathways, signal-transduction pathways, genetic regulatory circuits, protein-protein interactions, and other types of biological interactions.

Pedro Romero
+1 (650) 859-5669

Gene Regulation

Cochairs: Serafim Batzoglou and Lior Pachter

This session is intended to bring together researchers who are developing or using bioinformatics tools for understanding gene regulation in prokaryotic and eukaryotic genomes. Such research includes, but is not limited to, methods for the computational prediction of promoters and other regulatory elements, comparative genomics approaches to gene regulation, prediction of regulatory motifs in genes with common expression patterns, local multiple alignment algorithms, gene expression analyses, and discovery of regulatory networks and pathways.

Serafim Batzoglou

Discussion Panels

Genetic Diversity and DNA-based Identification

The theme of this PSB03 session is to address recently emerging issues that spring from our increasing technical ability to easily and rapidly obtain DNA-based information for large numbers of individuals from throughout the world. With the tremendous increase in DNA-based data, the nature and degree of human genetic variation is now becoming an area of increasing scientific study. With this in mind, the general theme of this session will be on the real and potential uses and abuses of knowledge regarding human genetic variation. Specific topics include:
1. What has science told us about genetic variation within our species? How does society reconcile that fact that genetic variations can have functional effects and underlie or at least contribute to many differences in human characteristics with the societal views about non-discrimination, equal opportunity, and fairness?
2. Current uses of human genetic variation data in DNA-based personal identification strategies (forensics and criminal investigations, genealogical and population studies, medical studies; pharmacogenomics; military; genetic testing, evolutionary studies, etc.).
3. What are known misuses of human genetic variation data (discrimination by employers, insurance companies; racial/ethnic profiling, etc.)?
4. What are potential new uses and misuses of data on human genetic variation and DNA-based personal identification?
5. What policy protections need to be developed in order to prevent misuses while optimizing the beneficial applications of DNA-based personal identification?

Moderated by:
James Sikela and Eric Juengst

James Sikela

Graduate and Undergraduate Bioinformatics Education

Bioinformatics education is an area of rapid expansion. There are new programs at the Bachelor's, Master's, Doctoral, and Postdoctoral levels, but still not enough graduates to satisfy the demands of industry and academia. This panel will discuss different approaches to bioinformatics education at all levels, and the different mixes between the constituent fields. It will provide a forum for panelists and participants to discuss the needs and solutions to bioinformatics program development.

Richard Hughey

The Computational Issues in Bioinformatics minitrack of the Software Technology Track Thirty-sixth Annual Hawaii International Conference on System Sciences may be of interest.

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This page written by Lawrence Hunter, and last updated on May 1, 2002