Call for Papers

Text and Data Mining for Biomedical Discovery

Pacific Symposium on Biocomputing

January 3-7, 2014

Fairmont Orchid, Big Island

Hawaii, U.S.A.



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:

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


Graciela H. González

Arizona State University




Kevin Bretonnel Cohen

U. Colorado School of Medicine


Maricel G. Kann

University of Maryland, Baltimore County


Casey Greene



Robert Leaman

National Center for Biotechnology Information (NLM/NCBI)


Nigam Shah

Stanford University


Jieping Ye

Arizona State University



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


Paper Format

Please see the PSB paper format template and instructions at


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. 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 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.