Call For Papers, Abstracts and Demonstrations

Pacific Symposium on Biocomputing

Honolulu, Hawaii - January 3-7, 2001

The fifth Pacific Symposium on Biocomputing (PSB), will be held January 3-7, 2001 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 17, 2000
Notification of paper acceptance: August 28, 2000
Final paper deadline: September 25, 2000
Abstract deadline: November 6, 2000
Meeting: January 3-7, 2001

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 2001 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.

Human Genome Variation: Linking Genotypes to Clinical Phenotypes

Cochairs: Francisco De La Vega, Martin Kreitman, Issac Kohane

The session "Human Genome Variation: Linking Genotypes to Clinical Phenotypes" aims to provide a timely forum on the computational challenges to correlate the impending flood of high-throughput genotyping and gene expression profiling data with clinical phenotypes, and to address the forthcoming problems in the utilization of this information in human genetics, pharmacogenetics, populational genetics, and clinical studies.

Isaac Kohane

Natural Language Processing for Biology: Term extraction, Information retrieval, Information extraction, and Corpus Annotation

Cochairs: Limsoon Wong and Junichi Tsujii

We solicit contributions covering any aspect of the use of natural language processing in biology applications. Areas of interest are:

We particularly encourage submissions describing implemented algorithms and techniques and submissions describing novel applications of natural language processing in biology.

Limsoon Wong
+(65) 874 8406

Genome, Pathway and Interaction Bioinformatics

Cochairs: Peter Karp, Eric Neumann and Pedro Romero

This session is intended to be a 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 R. Romero
(650) 859-5669

Phylogenetics in the Post-Genomic Era

Cochairs: Jennifer Steinbachs and Paul Kearney

This session focuses on topics of immediate and emerging importance to the phylogenetic analysis of molecular data in the post-genomic era. The session will bring together researchers from the biological, computational and mathematical sciences with the goal of achieving a better understanding of the current issues and challenges in phylogenetics.

Jennifer Steinbachs
(312) 665-7810

High performance computing for computational biology

Cochairs: Thomas Ferrin, Bruce Foster and Richard Hughey

This session provides a forum to present new algorithms and methods for computational biology, especially those aimed at addressing efficiency, scalability, and cost issues associated with high-performance computing. Computational methods for sequence analysis, structure and function prediction, neural information theory, whole genome analysis, pharmacgenomics, expression microarrays, and large structure and in-vivo imaging are examples of topics of interest.

Richard Hughey
(831) 459-2939

Disorder and Flexibility in Protein Structure and Function

Cochairs: Clay Bracken, A. Keith Dunker and Malin Young

This session examines how structural disorder and flexibility contribute to protein function. Potential topics include: computational analysis of disordered and flexible regions of proteins, biophysical methods of analyzing disordered regions in proteins, computational and biophysical characterization of order to disorder transitions, and novel methods of predicting and assessing protein disorder.

Clay Bracken
(212) 746-6473

DNA Structure, Protein-DNA Interactions, and DNA-Protein Expression

Cochairs: Richard Lathrop and Pierre Baldi

The session seeks computational approaches to understanding the DNA<->Protein<->DNA cycle by which DNA and proteins co-exist, co-regulate, and co-create each other.

Richard Lathrop
(949) 824-4021

Structures, Phylogenies, and Genomes: The Integrated Study of Protein Evolution

The genomic data available to computational biologists represents the product of the complex processes of evolution. It has been long recognized that there is much important information contained in the encoded evolutionary history. The track will cover use of evolutionary analyses to model, infer and explain the structure, function, and evolutionary dynamics of proteins and their sequences.

Cochairs: Richard Goldstein and David Pollock

David Pollock
(505) 665-1923

Bioethics, Fiction Science, and the Future of Mankind

Cochairs: Pierre Baldi and Soren Brunak

This session will have two themes. One is fiction science, i.e. trying to extrapolate current trends and predict what are some of the possible scenarios for the future of mankind and civilization, regardless of their desirability. The second theme is bioethics and will address contemporary issues such as stem cell research, human cloning, and gene/genome patents.

This session will be organized as a discussion only, and we are not expecting full papers. Please contact the session chairs if you are interested in participating.

Pierre Baldi
(949) 824-5809

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, 2000