PSB 2011

Call For Papers, Abstracts and Demonstrations

Pacific Symposium on Biocomputing

Big Island of Hawaii -- January 3-7, 2011

The paper submission deadline has passed; paper decision notification was sent on September 12, 2010. The list of accepted papers has been selected by our referees.

The sixteenth Pacific Symposium on Biocomputing (PSB), will be held January 3-7, 2011 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 2011 sessions are:

Session tutorials

Hour long tutorials of the PSB 2011 sessions will be offered on January 3, 2011.

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 12, 2010 midnight PT (Note: The Multi-scale Modelling of Biosystems session requests an advance deadline of June 30, 2010.)
Notification of paper acceptance: September 10, 2010 Delayed until the evening of September 12, 2010.
Final paper deadline: September 20, 2010 midnight PT
Abstract deadline: November 29, 2010
Meeting: January 3-7, 2011

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 2011 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 Methods Integrating Diverse Biological and Clinical Data for Translational Science

Co-chairs: Gurkan Bebek, Mark Chance, Mehmet KoyutŸrk, Nathan D. Price

Translational research aims to bridge basic life sciences and medicine by incorporating results obtained from basic science to advance clinical applications, and drive basic science based on insights gained from clinical experience. This session recognizes this challenge and focuses on computational methods that enable translational research through integration of various -omics and/or clinical datasets. The session calls for contributions describing computational models, algorithms, simulation studies, and innovative analyses of biological and/or clinical data with a substantial and innovative computational component.

The call for paper deadline has been extended to July 16 for this session only.

Contact: Gurkan Bebek
Email: gurkan at case dot edu

Genome-wide association mapping and rare alleles: from population genomics to personalized medicine

Co-chairs: Francisco M. De La Vega, Carlos D. Bustamante, Suzanne M. Leal

This session will focus on distilling current knowledge in assessing rare genetic variant functionality and their correlation with complex traits, and bring forth methodological questions in the analysis of GWAS from sequenced genome data.

The call for paper deadline has been extended to July 19 for this session only.

Contact: Francisco M. De La Vega, D.Sc.
Email: delavefm at gmail dot com

Microbiome studies: Understanding how the dominant form of life affects us

Co-chairs: James Foster, Jason Moore

Microbes dominate life on earth, measured by biomass, habitat diversity, phylogenetic diversity, or metabolic potential. Nonetheless, microbiome studies are in their infancy. Most natural ecosystems remain uncharacterized. Many human microbiome sites are unexplored, with very few comparisons of healthy versus diseased individuals. Mechanisms for microbial adaption and ecological engineering are poorly understood. Supporting computational tools are just emerging. This session addresses these needs.

The call for paper deadline has been extended to July 18.

Contact: James Foster
Email: foster at uidaho dot edu

Multi-scale Modelling of Biosystems: from Molecular to Mesoscale

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

The purpose of this session is to focus on multi-scale techniques from molecule studies to cell or organism level. The emphasis is on: structure prediction, dynamics and sampling, mesoscale modeling, molecular assemblies, aggregation and analysis of structural interactions and structure and systems biology. This session should benefit from recent progress in multi-scale molecular modeling and bring computer science and biology communities together to enter the mesoscale era.

The call for paper deadline has been extended to July 15 for this session only.

Contact: Julie Bernauer
Email: julie.bernauer at

Personal Genomics

Co-Chairs: Can Alkan, Emidio Capriotti, Fereydoun Hormozdiari, Eleazar Eskin, Maricel G. Kann

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. 

The call for paper deadline has been extended to July 18.

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.

The call for paper deadline has been extended to July 18.

Contact: Gil Alterovitz
Email: psb-bnas at

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