PSB 2009

Call For Papers, Abstracts and Demonstrations

Pacific Symposium on Biocomputing

Big Island of Hawaii -- January 5-9, 2009

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

The fourteenth Pacific Symposium on Biocomputing (PSB), will be held January 5-9, 2009 at the Fairmont Orchid on the Big Island of 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 2009 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 the abstract deadline listed below to present their work in the poster sessions.

Important dates

Paper submissions due: July 14, 2008
Notification of paper acceptance: September 8, 2008
Final paper deadline: September 22, 2008 midnight PT
Abstract deadline: November 7, 2008
Meeting: January 5-9, 2009

Paper format

Papers must be submitted to the PSB 2009 paper management system at

Please click the "Not a user? Create an account with this site" link to create an author account and upload your paper.

All papers must be submitted in electronic format to the paper management system.

The accepted file formats 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 or electronic submissions not submitted through the paper management system will be rejected without review.

Each paper must be accompanied by a cover letter. The cover letter should be the first page of your paper submission. The cover letter must state the following:

Submitted papers are limited to twelve (12) pages (not including the cover letter) 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.hawaii @ 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, please note that no one is guaranteed travel support. Travel support applications will be available on the website soon.

PSB 2009 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.

Biomolecular Networks: From Analysis to Synthesis

Co-chairs: Gil Alterovitz and Marco Ramoni

This PSB session was developed to have a special focus on design and synthesis of biological networks. This session aims to introduce novel engineering and other mathematical / computational methods within this area of focus. The methods should be shown to have significant biological applications.

Contact: Gil Alterovitz
Email: psb-bnas @

Computational Challenges in Comparative Genomics: Gene Family Evolution, Ancestral Genome Reconstruction, and Applications to Human Genetics

Co-chairs: Webb Miller, Bernard Moret, Pavel Pevzner, and David Sankoff

The rapidly increasing collection of full genome sequences is posing new computational challenges in comparative genomics (CG). We invite papers on gene identification, homology and orthology assignments, sorting out gene duplications and losses in the presence of various rearrangements, detecting horizontal gene transfers, and particularly on inferring ancestral genomes, recognizing ancient reticulations and whole-genome duplications, and applying CG methods in human genetics.

Contact: Bernard Moret
Email: bernard.moret @

Dynamics of Biological Networks

Co-chairs: Tanya Berger-Wolf, Teresa Przytycka, and Mona Singh

Network analysis provides a unifying language to describe relations within complex systems. Computational methods have been used to infer, analyze, and predict the structure and function of gene and protein networks. This session focuses on the computational techniques that explicitly address the dynamic nature of these networks.

Contact: Teresa Przytycka
E-mail: przytyck @

Emerging Challenges in Multi-Scale Modeling in Biology

Co-chairs: Peter Arzberger, James Bassingthwaighte, Roy Kerckhoffs, and Jeff Reinbolt

Physiology functions at all scales from molecules up to the whole-organism level. Therefore, to better understand human physiology and pathophysiology, multi-scale computational models and methods are of utmost importance. This session will be aimed at challenges to be overcome in multi-scale modeling, with an eye towards the development of mechanistic multi-scale patient-specific models to guide and predict the response to therapy in many aspects of medicine

Contact: Roy Kerckhoffs
Email: roy @

Knowledge-Driven Analysis and Data Integration for High-Throughput Biological Data

Co-chairs: Michael Ochs, John Quackenbush, Ramana Davuluri, and Habtom Ressom

The integration of diverse data types and the inclusion of a priori biological knowledge to address the curse of dimensionality are linked problems in high-throughput biology. Data, such as from microarrays, SNP chips, and mass spectrometry measurements, can have millions of measurements for a single system, and each system is defined by its phenotypic responses. Methods for integration and analysis of such data and phenotypes are the focus of this session.

Contact: Michael Ochs
Email: mfo @

Molecular Bioinformatics for Diseases

Co-chairs: Atul Butte, Maricel Kann, Yves Lussier, Yanay Ofran, Predrag Radivojac

This session focuses on computational analysis of the molecular mechanisms that underlie diseases. We are interested in studies that promote understanding of the molecular underpinnings of diseases and pathologies and in studies that could enhance diagnosis, analysis of prognosis and treatment. A main goal of this session is to bring together bioinformaticians, systems 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. Of particular interest are studies that integrate biological, clinical, genomic and molecular data to provide disease-related predictions.

Contact: Maricel Kann
Email: mkann @

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