PSB 2010

Call For Papers, Abstracts and Demonstrations

Pacific Symposium on Biocomputing

Big Island of Hawaii -- January 4-8, 2010

The paper submission deadline has passed; paper decision notification was sent on September 10, 2009. The list of accepted papers has been selected by our referees.

The fifteenth Pacific Symposium on Biocomputing (PSB), will be held January 4-8, 2010 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 2010 sessions are:

Session tutorials

Hour long tutorials of the PSB 2010 sessions will be offered on January 4, 2010.

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 electronically and indexed in PubMed (submission to PubMed Central should be made by the author), 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 13, 2009 midnight PT
Notification of paper acceptance: September 10, 2009
Final paper deadline: September 21, 2009 midnight PT
Abstract deadline: November 9, 2009
Meeting: January 4-8, 2010

Paper format

Please see the PSB paper format template and instructions at

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.

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 2010 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.

Computational Challenges in Comparative Genomics

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

The rapidly increasing collection of full genome sequences is posing new computational challenges in comparative genomics. We invite contributions with a substantial and innovative computational component (such as computational models, algorithms, simulation studies, and computationally innovative analyses of biological data) in all areas of comparative genomics, including, but not limited to, gene family evolution, ancestral genome reconstruction, and integration with population genetics.

Contact: Bernard Moret
Email: bernard.moret at

Computational studies of non-coding RNAs

Co-chairs: Rolf Backofen, Hamidreza Chitsaz, Ivo Hofacker, S. Cenk Sahinalp, and Peter F. Stadler

Recent improvements in sequencing methods introduced high-throughput, low-cost, and cloning-free (thus less labor-intensive) technologies. The revolution in DNA sequencing will shortly result in an enormous collection of sequence data pertaining to the genomes and transcriptomes of various human individuals from different populations and also various species. Exact and approximation, possibly high-throughput, algorithms and tools are therefore needed for non-coding RNA studies. This session will focus on new computational work in the area of non-coding RNAs. It is intended to cover the wide range of computational challenges in this field, including the discovery, structural and functional characterization, and modelling interactions of non-coding RNAs.

Contact: S. Cenk Sahinalp
Email: cenk at

Dynamics of Biological Networks

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

Network analysis provides a unifying language to describe relations within complex systems. This session focused on the changes in the properties of molecular networks in time (cell cycle scale and evolutionary scale) and space, and in response to varying conditions such as stress, diseases, and drug treatment. It will also include work leading to an understanding the natural variability in the interactome caused by sequence polymorphisms present in populations.

Contact: Teresa Przytycka
Email: przytyck at

Multi-resolution Modeling of Biological Macromolecules

Co-chairs: Julie Bernauer, Samuel Flores, Xuhui Huang, Seokmin Shin, and Ruhong Zhou

Molecular modelling of macromolecules and their interactions is one of the major challenges in current computational biology. Structure prediction, dynamics, interactions and data analysis are necessary to better understand biological functions. In the structural genomics and systems biology era, models are thus needed at different resolutions, both in space and time. This session focuses on multi-scale approaches to predict and analyze macromolecular structure, assembly and dynamics.

Contact: Julie Bernauer
Email: julie.bernauer at

Personal Genomics

Co-Chairs: Can Alkan, Michael Brudno, Evan E. Eichler, Maricel G. Kann, S. Cenk Sahinalp

This session focuses on the development of novel computational methods in all aspects of Personal Genomics including genetic and epigenetic variation discovery, genotype-phenotype associations, indexing and cataloguing both normal and disease-related variation, exome capture and resequencing, and personalized medicine. This session has a broad target audience that includes algorithm developers working on sequence analysis, genomics researchers, pharmacogeneticists, and medical geneticists. Papers presenting new methods should provide experimental or empirical evidence of the performance and practicality of the new methods. 

Contact: Can Alkan
Email: calkan at

Reverse Engineering and Synthesis of Biomolecular Systems

Co-Chairs: Gil Alterovitz, Silvio Cavalcanti, May Wang, and Marco F. Ramoni

This PSB session was developed to have a special focus on the reverse engineering and synthesis of biomolecular systems. 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 at

Back to the main PSB page