Call For Papers, Abstracts and Demonstrations

Pacific Symposium on Biocomputing

Honolulu, Hawaii - January 5-9, 2000

The fifth Pacific Symposium on Biocomputing (PSB), will be held January 5-9, 2000 in Honolulu, 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 2000 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 12, 1999
Notification of paper acceptance: August 27, 1999
Final paper deadline: September 24, 1999
Abstract deadline: November 1, 1999
Meeting: January 5-9, 2000

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 2000 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.

Identification of Coordinated Gene Expression and Regulatory Sequences

Cochairs: Jean-Michel Claverie, Minoru Kanehisa, Dan Prestridge, Gary Stormo, Michael Q. Zhang

As more genomes become sequenced and more genes are located, the identification and characterization of gene functions on a large-scale (i.e. functional genomics) is the great new challenge to the various genome projects. The advent of large-scale "transcriptomic" and "proteomic" technologies, provides a new type of data, as well as new approaches to discover and characterize gene expression patterns and associated regulatory sequence elements. Developing and validating these new approaches is essential to the future of functional genomics.

Michael Q. Zhang, Ph.D.
Phone: (516) 367-8393
Fax: (516) 367-8461

Molecular Network Modeling and Data Analysis

Cochairs: Roland Somogyi, Hiroaki Kitano, Miyano Satoru, Qiang Zheng

The growth of activity in the areas of gene expression analysis, proteomics and metabolic analysis has opened dramatic new potential for the modeling and analysis of biomolecular networks. This session will focus on three areas:

Roland Somogyi, Ph.D.
tel: 650-845-4210
fax: 650-845-4255

Analysis, Management and Application of SNP Data

Cochairs: Francisco M. De La Vega, Martin Kreitman

The session "Analysis, Management and Application of SNP Data" aims to provide a timely forum on the computational challenges to handle and analyze the impending flood of polymorphism data, and to address the forthcoming problems in the utilization of this information in human genetics, pharmacogenetics, and populational genetics studies.

Francisco M. De La Vega
Tel: (650) 638-6989
Fax: (650) 638-6666

Protein Evolution and Structural Genomics

Cochairs: Steven E. Brenner, Dmitrij Frishman, Richard A. Goldstein, David D. Pollock

In order to establish an integrated study of the function of proteins, it is necessary to combine sequence, structure, and functional analysis in the context of their evolutionary history and their role in the organismal genome. This track will encompass all aspects of structural genomics. The track will also cover use of evolutionary analysis to infer and explain the structure, function, and the evolutionary dynamics of protein and genome sequences.

David D. Pollock, Ph.D.
Tel: 510-643-6299
Fax: 510-643-6264

Natural Language Processing For Biology

Cochairs: Tatsuhiko Tsunoda, Limsoon Wong

We solicit contributions covering any aspect of the use of natural language processing in extracting information from biology sources such as MEDLINE abstracts, journal articles, and GenBank report annotations. We particularly encourage submissions describing implemented algorithms and techniques and submissions describing novel applications of natural language processing in biology.

Limsoon Wong
tel: (+65) 874 8406
fax: (+65) 774 4990

Protein Structure Prediction in Biology and Medicine

Cochairs: Roland L. Dunbrack, Keith Dunker, Adam Godzik

The Protein Structure Prediction in Biology and Medicine session is dedicated to protein structure prediction and its application to understanding protein function in the context of important biological problems. We will review successful applications of protein structure prediction in cases of general interest for biology and medicine, presenting examples where structure prediction provided unique insights and guidance for experiment. We will also examine other sequence-structure relationships in proteins, including dynamic structural features, that may be important for function. For instance structure flexibility and disorder are often hypothesized as being crucial for many aspects of protein function. Finally, we will evaluate and compare specific assumptions and methodologies used for protein structure prediction, as well as novel methodological developments.

Adam Godzik, PhD
tel: (619) 646 3168
fax: (619) 646 3171

Computer-Aided Combinatorial Chemistry & Cheminformatics

Cochairs: Alex Tropsha, Robert Pearlman

This session will address novel methods and developing ideas in the areas of chemical database analysis and bioactive structure prediction. More specifically, we plan to discuss novel metrics and functions for the description and comparison of organic molecules, current approaches to diversity and similarity sampling of molecular databases, combinatorial library design applications, and quantitative modeling of structure-activity relationships (QSAR).

Alex Tropsha
tel: (919) 966-2955

Applications of Information Theory to Biology

Cochairs: T. Gregory Dewey, Hanspeter Herzel

Information theory offers a number of fertile applications to biology. These applications range from statistical inference to foundational issues. The applications of information theory can be broadly categorized into two main areas. These are:

There are a number of statistical analysis tools that can be considered information theoretical techniques. The two main tools are algorithmic complexity and maximum entropy. Applications of algorithmic complexity include sequence searching and alignment, phylogenetic trees, structural classes in proteins, protein potentials, calcium and neural spike dynamics and DNA structure. Maximum entropy methods have also found widespread applications in spectral analysis and image reconstruction. Additional applications have appeared in nucleotide sequence analysis, protein dynamics, peptide structure and drug absorption. In addition to providing an underpinning for statistical methods, information theory also serves as a foundational framework for discussing fundamental biological processes. 50 years after Shannon's pioneering paper, entropy has become an integral part of several biological disciplines dealing with information storage and transmission. Examples are kin recognition, evolution, or neuronal coding. Information theory is particularly relevant in several areas of molecular biology. Well-studied applications are the recognition of DNA binding sites, multiple sequence alignment and gene-finding using a linguistic approach. Genetic networks have also been investigated using information theoretical approaches. In all these cases, the information content of the system or phenomena is of intrinsic interest in its own right. The goal of this track is to highlight the breadth and diversity of applications of information theory to biological systems.

Greg Dewey
Tel: 303-871-3100
Fax: 303-871-2254

Data Mining and Discovery in Molecular Databases

Cochairs: Janice Glasgow, Igor Jurisica, Raymond Ng

This session will focus on the automated process of discovery of novel and useful patterns or motifs in molecular databases. A primary objective of the session will be on the mining of sequence and structure databases in order to gain an increased understanding of the underlying relationships among sequence, structure and function.

Janice Glasgow
tel: (613) 533-6058
fax: (613) 533-6513

Tools for Visualization and Interaction

Cochairs: Eileen Kraemer, Thomas Ferrin

This session deals with tools and techniques for visualization and interaction in support of computational biology and bioinformatics, including but not limited to, interactive visualization of molecules, sequence data, and databases, interactive steering of computations, and standardization efforts related to visualization of and interaction with biological data. During the conference, we plan to have low- and high-end workstations available for live demonstrations. The ultimate goal of this session is to provide a forum for presentation of recent results and discussion among tool developers, researcher, and practitioners in visualization, user interaction, computational biology, and bioinformatics.

Eileen Kraemer
tel: (706) 542-5799
fax: (706) 542-2966

Further Information

For further information about the conference, registration, possible travel support, submission of papers not covered by the above categories, or other information, please contact the conference coordinator:

    PSB Conference Coordinator
    Kevin Lauderdale
    PSB Coordinator
    Section on Medical Informatics
    SUMC, MSOB X-215
    Stanford, CA, USA 94305-5479
    Telephone: (650) 725-0659 FAX: (650) 725-7944

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This page written by Lawrence Hunter, and last updated on April 19, 1999