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PSB 2012
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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:
Please see the PSB paper format template and instructions at http://psb.stanford.edu/psb-online/psb-submit/index.html.
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. altman.ps 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 http://psb.stanford.edu/psb-online/psb-submit/. 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 @ gmail.com) for additional information about paper submission requirements.
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
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
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
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 pnnl.gov
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
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 gmail.com