PSB 2012

Call For Papers, Abstracts and Demonstrations

Pacific Symposium on Biocomputing

Big Island of Hawaii -- January 3-7, 2012

The list of accepted papers has been selected by our referees.

The seventeenth Pacific Symposium on Biocomputing (PSB), will be held January 3-7, 2012 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 2012 sessions are:

Session tutorials

Hour long tutorials of the PSB 2012 sessions will be offered on January 3, 2012.

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 11, 2011 midnight PT
Notification of paper acceptance: September 9, 2011
Final paper deadline: September 23, 2011 midnight PT
Abstract deadline: November 28, 2011
Meeting: January 3-7, 2012

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 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 2012 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.

Identification of Aberrant Pathway and Network Activity from High-Throughput Data

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

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.

Contact: Rachel Karchin
Email: karchin at jhu dot edu

Intrinsically Disordered Proteins: Analysis, Prediction, Simulation, and Biology

Co-chairs: Jianhan Chen, Jianlin Cheng, Keith Dunker

This session focuses on all aspects of computation in IDP research. The goal is to introduce and discuss 1) important advances in all frontiers of computational "IDPology", 2) available computational capabilities in prediction, analysis and simulation of IDPs, and importantly, 3) outstanding challenges, further directions and key biological questions to be addressed. Another goal is to promote communication and collaboration between scientists working different areas of IDP computation and between experiment and computation.

Call for papers deadline extended to July 18 midnight PST.

Contact: Jianhan Chen
Email: jianhanc at ksu dot edu

Microbiome studies: Analytical Tools and Techniques

Co-chairs: James A. Foster, Jason Moore, Jack Gilbert, John Bunge

Microbes (bacteria, archea, viruses and microscopic eukarya) dominate life on earth. Nonetheless, microbiome studies are in their infancy. Most natural ecosystems remain uncharacterized and many human microbiome sites are only superficially explored. New sequencing technologies make it much easier to gather environmental "omic" data. But progress depends on developing computational, statistical, and data mangement tools and techniques-which are the objectives of this session.

Call for papers deadline extended to July 25 midnight PST (extension applies to this session only).

Contact: James Foster
Email: foster at uidaho dot edu

Modeling host-pathogen interactions: Computational biology and bioinformatics for infectious disease research

Co-chairs: Jason McDermott, Pascal Braun, Daniel Hyduke, Richard Bonneau

The purpose of this session is to bring together research in various aspects of computational analysis and modeling of infectious disease. In particular, emphasis will be on: new experimental approaches to understand host-pathogen interactions in plants and animals, systems biology and regulatory networks of virulence, data integration and approaches to identifying virulence determinants, modeling host-pathogen interactions, and drug target identification for antibiotics and antivirals.

Call for papers deadline extended to July 18 midnight PST.

Contact: Jason McDermott
Email: Jason dot McDermott at

Personalized Medicine: from genotypes and molecular phenotypes towards computed therapy

Co-chairs: Jennifer Listgarten, Oliver Stegle, Fritz Roth, 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-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.

Call for papers deadline extended to July 18 midnight PST.

Contact: Jennifer Listgarten
Email: jennl at microsoft dot com

Text and knowledge mining for pharmacogenomics: Genotype-phenotype-drug relationships

Co-chairs: Kevin Bretonnel Cohen, Yael Garten, Nigham Shah, Udo Hahn

The technical area of this session is text and knowledge mining for pharmacogenomics, particularly focusing on genotype-phenotype-drug relationships. Broad categories of work that have been well-studied in the past are included, specifically text mining and reasoning, but submissions are restricted to applications of that work to the constrained area of pharmacogenomics, and particularly genotype-phenotype-drug relationships.

Call for papers deadline extended to July 18 midnight PST.

Contact: Kevin Bretonnel Cohen
Email: kevin dot cohen at

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