Call For Papers, Abstracts and Demonstrations

Pacific Symposium on Biocomputing

Lihue, Kauai, Hawaii - January 3-7, 2002

The fifth Pacific Symposium on Biocomputing (PSB), will be held January 3-7, 2002 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 2002 PSB sessions are:

Papers, Abstracts and Demonstrations

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, and present their work in discussion, poster and demonstration sessions. Workstations and internet connections will be available for demonstrations. Please submit detailed requests for demonstration facilities along with your paper or abstract.

Important dates

Paper submissions due: July 16, 2001
Notification of paper acceptance: August 20, 2001
Final paper deadline: September 24, 2001
Abstract deadline: November 5, 2001
Meeting: January 3-7, 2002

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., 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, 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 web site soon.

PSB 2002 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.

Genome-wide Analysis and Comparative Genomics

Cochairs: Inna Dubchak, Lior Pachter, 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.

Inna Dubchak

Genome, Pathway and Interaction Bioinformatics

Cochairs: Peter Karp, Eric Neumann, 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
(650) 859-5669

Expanding Proteomics to Glycobiology

Chair: Willi von der Lieth

Carbohydrates contain a higher information density than the other classes of importtant biological macromolecules. The biological functions of carbohydrates are still not completely understood. However, it is clear that glycans are fundamental to many biological processes including fertilization, immune defense, viral replications, parasitic infection, cell growth, cell-cell adhesion and inflammation. The session intends to summarize new biocomputing approaches aiming at a better understanding of the biological functions of complex carbohydrate.

Willi von der Lieth
Tel: +49-6221-424541

Literature Data Mining for Biology

Cochairs: Lynette Hirschman, Jong C. Park, Junichi Tsujii, Limsoon Wong, Cathy Wu

This session will explore techniques and applications of natural language processing to the extraction of biological information from free text and other relevant biology sources. In particular, we are interested in:

Limsoon Wong
+(65) 874 8406

Human Genomic Variation: Disease, drug response, and clinical phenotypes

Cochairs: Isaac Kohane, Clay Stephens, Julie Schneider, Francisco De La Vega

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. The session "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.

Francisco M. De La Vega, Ph.D.
(650) 638-6989

Phylogenetic Genomics and Genomic Phylogenetics

Cochairs: Scott Stanley and Benjamin Salisbury

This session will explore the natural partnership between the co-evolving disciplines of phylogenetics and genomics. The analysis of genome structure and function depends on phylogenetics set it in the full context of evolutionary history and process. Phylogenetic systematics increasingly draws upon genomics, both as a vast source of informative data and as subject matter.

Scott Stanley
(203) 786-3537

Proteins: Structure, Function and Evolution

Cochairs: Peter Clote, Gavin Naylor, Eugene Shakhnovich, and Ziheng Yang

This session is concerned with aspects of protein structure, function and evolution, where techniques employed may include investigations of energy landscapes, folding algorithms, statistical approaches to fold or class recognition, evolutionary genomics for determining more biologically reasonable position-dependent amino acid substitution matrices which reflect coevolutionary patterns in amino acid sequences, etc.

Peter Clote
(617) 552-1332

Back to the main PSB page
This page written by Lawrence Hunter, and last updated on April 30, 2001