PSB 2014 - Pacific Symposium on Biocomputing (PSB) 2014

Text and Data Mining for Biomedical Discovery
Pacific Symposium on Biocomputing
January 3-7, 2014
Fairmont Orchid, Big Island
Hawaii, U.S.A.
Motivation
The biggest challenge for text and data mining in biomedical informatics is to impact the discovery process, enabling scientists to generate novel hypothesis to address the most crucial questions for understanding the molecular basis of human diseases. However, formulation of a flexible and general approach for integrating heterogeneous data and knowledge sources for discovery is elusive and highly dependent upon the specific underlying scientific question. Thus, the true impact of text and data mining is only realized if it goes beyond the methods for extraction or pattern recognition, and into enabling understanding of the molecular underpinnings of biological processes.
This session will bring together researchers with a strong background in either text or data mining 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.
Session Topics
We seek contributions where the data or text mining aspects are so tightly coupled to their corresponding biological/pharmacological/genomic aspects for their significance, that neither aspect of the work can be de-emphasized or understood without the other; work where the biology significantly enhances and informs the text and data mining methods, and vice versa.
Some examples of topics of interest to this session include novel approaches that integrate empirical data with knowledge extracted from the literature, curated databases, relevant ontologies and other sources to perform discovery-related tasks such as:
Gene prioritization
Binding site prediction
Gene/protein function prediction,
Prediction of associations (protein-protein, gene-drug, gene-disease, drug-drug, and others)
Pathway generation or validation
for translational applications such as pharmacogenomics and personalized medicine (genome-phenome validation, or disease detection, diagnosis and prognosis). Submissions should clearly state the translational value of their contribution.
Session Organizers
Chair:
Graciela H. González
Arizona State University
ggonzalez-AT-asu.edu
Co-Chairs:
Kevin Bretonnel Cohen
U. Colorado School of Medicine
kevin.cohen-AT-gmail.com
Maricel G. Kann
University of Maryland, Baltimore County
mkann-AT-umbc.edu
Casey Greene
Dartmouth
casey.s.greene-AT-dartmouth.edu
Robert Leaman
National Center for Biotechnology Information (NLM/NCBI)
robert.leaman-AT-nih.gov
Nigam Shah
Stanford University
nigam-AT-stanford.edu
Jieping Ye
Arizona State University
jieping.ye-AT-asu.edu
Submission Information
Please note that the submitted papers are reviewed and accepted on a competitive basis. At least three reviewers will be assigned to each submitted manuscript.
Important Dates
Paper submissions due: July 31, 2013
Notification of paper acceptance: September 9, 2013
Final paper deadline: October 1, 2013 at 11:59pm PT
Registration opens: August 1, 2013 at noon PT
Travel award applications
PSB has been able to offer travel support to many attendees in the past. However, please note that no one is guaranteed travel support.
Available: August 1, 2013 at noon PT
Deadline: October 7, 2013 at noon PT
Decisions will be announced in mid-October.
For details, please see http://psb.stanford.edu/keydates.html
Paper Format
Please see the PSB paper format template and instructions at http://psb.stanford.edu/psb-online/psb-submit.
The file formats we accept 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 will be rejected without review.
Each paper must be accompanied by a cover letter. The cover letter must state the following:
? The email address of the corresponding author.
? The specific PSB session that should review the paper or abstract.
? The submitted paper contains original, unpublished results, and is not currently under consideration elsewhere.
? All co-authors concur with the contents of the paper.
Submitted papers are limited to twelve (12) pages in our publication format. Please format your paper according to instructions found at http://psb.stanford.edu/psb-online/psb-submit/. If figures cannot 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.