IJCNN Special Session NN20 - Methods and Algorithms for Pathway Analysis

Description and Scope:

In the post-genomics era high throughput technologies produce multitudes of data sets containing lists of differentially expressed genes. The common challenge faced by all researchers is to translate such lists of differentially expressed genes into a better understanding of the underlying biological phenomena, and in particular to put this in the context of the whole organism as a complex system. Numerous methods currently exist for constructing pathways from expression data and several pathway databases are now available for describing metabolic pathways and gene signaling networks. Yet only a handful of methods have attempted to integrate these resources to provide for more complex and useful analysis focused on the pathway or systems level.

This special session will bring together seasoned researchers and new researchers alike to compare and discuss these latest advances in this important field. The session will also provide a forum for highlighting the open issues and will hopefully bring forth new approaches that address some or all of the limitations of the current techniques.

We welcome papers covering any methodology, tool, technique or specific successful application related to pathway analysis. Approaches originated in machine learning and computational intelligence (e.g. neural networks, hidden Markov models, etc.), information theory (e.g. Bayesian approaches), and natural language processing (e.g. MedLine literature processing) are especially encouraged. Approaches using more than one source of information or type of data will be of particular interest.

Paper addressing all issues in integrated pathway analysis, including but not limited to:

• Methods for automatically incorporating new data into existing pathway representations
  
• Topology change sensitive pathway algorithms
  
• Methods for estimating change in pathways due to changes in gene expression data
  
• Methods for integration of gene networks with gene expression data analysis
  
• Extraction of gene association networks from known molecular pathways
  
• Expression data-pathway data integration tools and approaches

Guidlines for Submissions

Submissions to special sessions will be accepted through the WCCI submission site. You will need to complete a short registration process through the online submission managment system in order to submit your paper. Please be certain to indicate that your paper is to be directed to this special session by choosing Session Mode "Special" and choosing the session entitled "Methods and Algorithms for Pathway Analysis" when you submit your paper

Submissions must follow WCCI 2008 guidelines which are listed on the submission page of the WCCI 2008 website at http://www.wcci2008.org/submission.htm . The following formating guidlines are also included here for your convienence:

Instructions for Authors

• Only papers prepared in PDF format will be accepted.
  
  • Paper Size: US Letter format (8.5" x 11").
    
  • Paper Length: Maximum 8 pages, including figures, tables & references. Up to two additional pages are permitted for a charge of $100.00 per additional page, to be paid through the registration process.
    
  • Paper Formatting: double column, single spaced, 10pt font.
    
  • Margins: Left, Right, and Bottom: 0.75" (19mm). The top margin must be 0.75" (19 mm), except for the title page where it must be 1" (25 mm).
    
  • File Size Limitation: 5.0MB.
    
  • Do not number your manuscript pages.
    
  • Note: Violations of any of the above specifications may result in rejection of your paper.
• At the final stage, IEEE requires that the PDF files submitted for the accepted papers be 100% IEEE Xplore compliant. Please make sure that you follow these helpful instructions on how to produce IEEE Xplore compliant PDF files.
  
  • Click here to download instructions from the IEEE (15 pages).
    
  • Example formating files are available for both Latex and MS Word users in a downloadable zip file this zip archive contains a LaTex docuemnt class file and a MS Word template file as well as sample paper produced using either method.
    
  • If you are a LaTex user, using the document class file you can create a IEEE Xplore compliant PDF file from your dvi file using the commands:
    dvips -o mypaper.ps -G0 -tletter mypaper
ps2pdf mypaper.ps mypaper.pdf

  • Your paper should be formated to look like the sample papers.
    
  • Please make sure that your pdf file passes the IEEE PDF eXpress compliance check. This is an IEEE requirement for the publication of the proceedings. All papers
• accepted and presented at WCCI2008 will be indexed by EI.
  
• For all matters related to paper format, please contact the Publications Chairs: Dr. Zeng-Guang Hou at hou@compsys.ia.ac.cn, or Dr. Nian Zhang at nian.zhang@sdsmt.edu.
  
• Papers must be submitted as a camera-ready PDF file which has been verified as IEEE eXplore compliant using the IEEE PDF eXpress compliance checker at http://216.228.1.34/pdfexpress/log.asp . Use the Conference ID: ijcnn08 when processing your PDF file. Detailed instructions for using IEEE PDF eXpress can be found in the following file: IEEE PDF eXpress Instructions.

Special Session Organizers:

Sorin Draghici
Department of Computer Science
Wayne State University
Detroit, MI 48202
USA
E-mail: sorin [at] wayne.edu
Web page: http://www.cs.wayne.edu/~sod

L. Gwenn Volkert
Department of Computer Science
Kent State University
Kent, OH 44242
USA
E-mail: volkert [at] cs.kent.edu
Web page: http://www.cs.kent.edu/~volkert