PSB 2013

Call For Papers, Abstracts and Demonstrations

Pacific Symposium on Biocomputing

Big Island of Hawaii -- January 3-7, 2013

The paper submission deadline has passed; paper decision notification has been sent. The list of accepted papers has been selected by our referees and will be announced soon.

The eighteenth Pacific Symposium on Biocomputing (PSB), will be held January 3-7, 2013 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 2013 sessions are:

Session tutorials

Hour long tutorials of the PSB 2013 sessions will be offered on January 3, 2013.

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 31, 2012 midnight PT
Notification of paper acceptance: September 10, 2012
Final paper deadline: October 1, 2012 midnight PT
Abstract deadline: November 28, 2012 midnight PT
Meeting: January 3-7, 2013

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. Color images are accepted for publication at no additional charge.

Contact PSB (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 2013 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.

Aberrant Pathways

Co-chairs: Rachel Karchin, Michael Ochs, Josh Stuart, Joel Bader, and Trey Ideker

The session will focus on computational approaches to interpret very large, high-dimensional data sets, generated by epigenetic and genomic studies of cancer, functional elements in the human genome, GWAS, proteomic and metabolomic studies. We are particularly interested in data integration methods that include pathway and network modeling and in tools that can be used to mine the complex databases in which results of these studies are being stored.

Paper submission deadline extended to August 5, 2012 for this session.

Contact: Rachel Karchin
Email: rachel dot karchin at gmail dot com

Computational drug repositioning

Co-chairs: Zhiyong Lu, Pankaj Agarwal, and Atul Butte

De novo drug discovery continues to be a lengthy and resource-consuming process in spite of all the advances in life sciences and technology. In response, there is an ever-growing effort to apply computational power to improve this process. In recent years, a new set of computational methods are being developed at a system level for discovering alternative uses of known drugs. In this session, all aspects of computational drug repositioning research will be considered, with emphasis on novel approaches and their applications.

Paper submission deadline extended to August 5, 2012 for this session.

Contact: Zhiyong Lu
Email: zhiyong dot lu at nih dot gov


Co-chairs: Alexander J. Hartemink, Manolis Kellis, William Stafford Noble, and Zhiping Weng

This session will focus on computational methods for the analysis and interpretation of various types of epigenomic data, including histone modifications, DNA methylation, nucleosome positioning, chromatin structure and accessibility, and DNA-DNA interaction. The session will include papers that describe methods for building computational models of physical phenomena as well as methods for interpreting the functional significance of epigenomic data.

Paper submission deadline extended to August 8, 2012 for this session.

Contact: William Noble
Email: william-noble at uw dot edu

Personalized medicine: from genotypes and molecular phenotypes towards therapy

Co-chairs: Oliver Stegle, Jennifer Listgarten, Steven Brenner, Robert Nussbaum, and Quaid Morris

This session will address open and new problems pertaining to genotype data, intermediate phenotypes, clinical variables and disease. Problem areas within the scope include methods for genome sequencing, genome-wide association studies, gene expression modeling with relevance to disease, and causal modeling integrating information from multiple sources. The session is intended to have a broad target audience including method developers and practitioners in the fields of medical and human genetics, statistical genetics and related areas.

Paper submission deadline extended to August 5, 2012 for this session.

Contact: Oliver Stegle
Email: oliver dot stegle at tuebingen dot mpg dot de

Phylogenomics and Population Genomics: Models, Algorithms, and Analytical Tools

Co-chairs: Luay Nakhleh, Noah Rosenberg, and Tandy Warnow

Phylogenomics and population genomics involve analyzing the evolutionary relationships among genomes from different species as well as different individuals of the same species. This session is about developing and using new mathematical models and computational techniques for enabling these two fields.

Paper submission deadline extended to August 5, 2012 for this session.

Contact: Luay Nakhleh
Email: nakhleh at rice dot edu

Post-NGS: analysis of -omes generated by NGS

Co-chairs: Gurkan Bebek, Mehmet Koyuturk, Ben Raphael, Thomas LaFramboise, and Mark Chance

The Post-NGS session recognizes the vast amount of information generated by next generation sequencing (NGS) methods and will provide a forum for methods and algorithms developed for analysis of finalized NGS data. Novel computational methods that interpret post-NGS data for research and clinical applications are invited to this session.

Paper submission deadline extended to August 8, 2012 for this session.

Contact: Gurkan Bebek
Email: gurkan at case dot edu

Text and Data Mining for Biomedical Discovery

Co-chairs: Graciela H. Gonzalez, Kevin Bretonnel Cohen, Casey Greene, Udo Hahn, Maricel G. Kann, Robert Leaman, Nigam Shah, Jieping Yie

This session will bring together researchers with a strong text or data mining background who are collaborating with bench scientists for the deployment of integrative approaches in translational bioinformatics. It serves as a unique forum to discuss novel approaches to text and data mining methods that respond to specific scientific questions, enabling predictions that integrate a variety of data sources and can potentially impact scientific discovery.

Paper submission deadline extended to August 5, 2012 for this session.

Contact: Graciela Gonzalez
Email: Graciela dot Gonzalez at asu dot edu

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