PSB 2007

Call For Papers, Abstracts and Demonstrations

Pacific Symposium on Biocomputing

Maui -- January 3-7, 2007

The paper submission deadline has passed, and the list of accepted papers has been selected by our referees.

The twelfth Pacific Symposium on Biocomputing (PSB), will be held January 3-7, 2007 at the Grand Wailea Resort on Maui. 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 2007 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, 2005 to present their work in the poster sessions.

Important dates

Paper submissions due: July 17, 2006
Notification of paper acceptance: September 6, 2006
Final paper deadline: September 24, 2006 midnight PT
Abstract deadline: November 10, 2006
Meeting: January 3-7, 2007

Paper format

All papers must be submitted to psb-submit @ in electronic format. The file formats we accept are: postscript (*.ps) and Adobe Acrobat (*.pdf). Attached files should be named with the last name of the first author (e.g. or altman.pdf). 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 (psb-submit @ 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 website soon.

PSB 2007 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.

Biodiversity Informatics: Managing Knowledge Beyond Humans and Model Organisms

Chair: Indra Neil Sarkar

Biomedical informatics is predominated with the design and development of methods for studying a number of key ³model² organisms, which represent only a small fraction of the biodiversity on Earth. This session will be a forum for biodiversity, biomedical, and computational scientists to discuss how methods and principles from each respective discipline are currently used and how they can be adapted for relevant inter-disciplinary studies. Topics that describe methods that traverse traditional biomedical and biodiversity boundaries into a singular framework will be favored.

Indra Neil Sarkar

Computational Proteomics: High-throughput Analysis for Systems Biology

Cochairs: Bobbie-Jo Webb-Robertson and Bill Cannon

High-throughput proteomics is a rapidly developing field that may potentially change the way we study biological systems. This session will focus on the current state-of-the-art informatics research taking place in high-throughput proteomic technologies and proteomics related to systems biology. A special emphasis is places on MS-based proteomics, but research associated with other high-throughput proteomics technologies will also be considered.

Listed are examples of areas of interest, but are not all inclusive.

Contact: Bobbie-Jo Webb-Robertson

DNA-Protein Interactions and Gene Regulation: Integrating Structure, Sequence and Function

Cochairs: Martha Bulyk, Ernest Fraenkel, Alexander Hartemink, and Gary Stormo

Structural information about proteins and about DNA (e.g., chromatin) can be useful in accurately understanding how protein subsequences interact with DNA subsequences at the appropriate sensitivity and specificity, and how these interactions lead to functional consequences in the cell, especially but not exclusively in the context of regulation of gene expression. This session will focus on novel methods and studies that bridge structure, sequence, and function to elucidate previously undiscovered associations between these different aspects of protein-DNA interactions.

Contact: Martha Bulyk

Computational Approaches to Metabolomics

Cochairs: Russ Greiner and David Wishart

This goal of this session is to explore the current state-of-the-art research taking place in the computational sciences for generating and handling of all the data being generated through metabolomics research. This session will focus on the presentation and discussion of new research and methods for the acquisition, management and analysis of metabolomics data. We intend for this session to bring together scientists from pharmacology, biochemistry, genetics, statistics, computing science and bioinformatics to share their efforts in metabolomics.

Contact: Russ Greiner

New Frontiers in Biomedical Text Mining

Cochairs: Pierre Zweigenbaum, Dina Demner-Fushman, Kevin Bretonnel Cohen, and Hong Yu

This session focuses on text mining work that is beyond the majority of that published to date in the field of biomedical language processing, advancing beyond entity identification, relation extraction, and information retrieval. Expected contributions will cover the following topics:

Contact: Pierre Zweigenbaum

Protein Interactions in Disease

Cochairs: Maricel Kann, Yanay Ofran, Marco Punta, and Predrag Radivojac

This session will focus on computational studies of protein interactions involved in disease. Its ultimate goal is to expand current understanding of the molecular basis of disease. Experimental studies indicate that in many diseases, even in some that are considered complex or multifactorial, protein interactions play a key role. The goal of this session is to bring together bioinformaticians, system biologists, biomedical informaticians, physicians, pharmacologists, computer scientists, statisticians, members of the pharmaceutical industry and others to share their experience and scientific findings in this area.

Contact: Maricel Kann

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