Computational Approaches to Metabolomics

At the Pacific Symposium on Biocomputing 2007
January 3-7, 2007
Grand Wailea, Maui
http://psb.stanford.edu/cfp-metabolomics.html

Motivation for the Session

The goal of this session is to discuss the latest progress in the study 
of metabolomics  the study of small molecules found in or produced by 
an organism (http://www.metabolomics.ca)  using bioinformatics tools.

 

Metabolomics, or metabolic profiling, is an emerging branch of health 
research that uses metabolites as very sensitive reporters to detect 
tiny changes or mutations that happen to genes or proteins, monitor 
and/or measure the larger-scale physiological changes that occur in 
response to subtle changes in the environment, and assist in the 
improved monitoring of adverse drug reactions. Indeed, metabolomics 
is increasingly being used in a variety of health applications 
including pharmacology, pre-clinical drug trials, toxicology, 
transplant monitoring, newborn screening and clinical chemistry 
using highly automated and high-throughput platforms.

 

Tandem mass spectrometry (MS/MS), capillary electrophoresis (CE), 
Fourier transform MS (FT-MS), infrared spectroscopy (FTIR) and 
NMR spectroscopy are all used in metabolic profiling. These 
technological developments are complemented by a trend to use 
more sophisticated computer techniques to process or deconvolve 
chromatographic, spectroscopic or spectrometric data. These 
instruments generate so much data so quickly, that it is important 
to develop software tools for data reduction, data visualization, 
data classification and analysis. Machine learning tools like 
Bayesian classifiers, decision trees, support vector machines 
and various types of Markov networks will need to be constructed 
and trained to both to produce classifiers of disease state and 
stage as well as identify genetic disease markers. In addition, 
the metabolomics community needs software tools that will analyze 
known biochemical pathway data (from existing resources such as 
KEGG, PUMA, WIT) for various functions, including ways to predict 
candidate gene mutations or disruptions on the basis of metabolite 
abundances.

 

Possible Topics

 

    * Identifying and Interpreting Patterns in Metabolomic Data, both 
      for classification  and to identify markers
    * Novel ways to Acquire, Process and Analyze Metabolomic Data
    * Novel methods for analyzing multiple types of experimental data
    * Relating metabolomics to the other omics, such as genomics and 
      proteomics
    * Experimental designs for metabolic systems.
    * Metabolomics databases, integration and interoperability 

Papers addressing any of the mentioned topics (or other related topics) 
are welcome. The session is especially interested in new methods for 
analyzing multiple types of experimental data and is not limited to 
a specific technological platform.

Session co-chairs

 

Russ Greiner

University of Alberta

greiner_-_cs.ualberta.ca

 

David Wishart

University of Alberta

dwishart_-_cs.ualberta.ca

 

General Information on PSB

 

The Pacific Symposium on Biocomputing (PSB) 2007 is an international, 
multidisciplinary conference for the presentation and discussion of 
current research in the theory and application of computational 
methods in problems of biological significance. Papers and 
presentations are rigorously peer reviewed and are published in 
an archival proceedings volume. PSB 2007 will be held 
January 3-7, 2007 at the Grand Wailea in Wailea, Maui. 
Tutorials will be offered prior to the start of the conference.

 

The PSB has been designed to be responsive to the need for critical 
mass in sub-disciplines within Biocomputing. For that reason, it 
is the only meeting whose sessions are defined dynamically each 
year in response to specific proposals. PSB sessions are organized 
by leaders in the emerging areas and targeted to provide a forum 
for publication and discussion of research in Biocomputing 
"hot topics." In this way, PSB provides an early forum for 
serious examination of emerging methods and approaches in this 
rapidly changing field. More information on the conference can 
be obtained from the conference Web page: http://psb.stanford.edu/.

 

Important Dates

 

    * Submissions are due July 17, 2006 **extended to July 31**
    * Decisions are announced September 6, 2006
    * Camera ready copy due September 25, 2006 

 

Submission Information

 

The conference is focused on rigorously peer-reviewed full-length papers 
on original research. The accepted manuscripts will be published in 
a bound archival proceeding, available online via the PSB website, 
and referenced in online sources such as PubMed. The best of the 
papers will be accepted for oral presentation to the entire conference. 
A poster session is available for researchers who wish to present 
their work without official publication.

 

All papers must be submitted to psb-submit _-_ helix.stanford.edu in 
electronic format. Only files in one of two formats are acceptable: 
postscript (*.ps) or Adobe Acrobat (*.pdf). Attached files should 
be named with the first authors last name (e.g., altman.pdf). 
Hardcopy submission or unprocessed TEX or LATEX files will be 
rejected without review.

 

Each paper must be accompanied by a cover letter with the following 
information:

    * Email address of corresponding author
    * The specific PSB session that should review the paper or abstract
    * A list of 5 individuals qualified to review the paper
    * The submitted papers 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 the official PSB 
publication format. Please format your paper according to these 
instructions, which can be 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.

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