Call for Papers and Posters

Molecular Bioinformatics for Diseases: Protein Interactions and Phenomics

 Pacific Symposium on Biocomputing Session

January 4-8, 2008

Fairmont Orchid, Big Island

Hawaii, U.S.A.

Motivation

This session focuses on the emerging fields of protein interactions in diseases and phenomics: from protein-protein interactions to supracellular phenotypes.  Experimental studies indicate that protein interactions play a key role in many diseases, even in some that are considered complex or multifactorial. While altered phenotypes are among the most reliable manifestations of altered gene functions, research focused on systematic analysis of phenotype relationships to study human biology is still in its infancy. We the word phenome and phenomics to describe the physical totality of all traits of an organism (Mahner, J Theor Biol 1997 186:55-63). We are seeking original research that aims to capitalize on novel computational methods and technological developments in informatics to derive disease predictions from protein interactions of phenomic datasets and networks. The goal of this session is to bring together bioinformaticians, systems biologists, biomedical informaticians, physicians, pharmacologists, computer scientists, statisticians, members of the pharmaceutical industry and others to share their experience and scientific findings in this area.

Session Topics

We would like to invite contributions addressing informatics approaches to analyzing how diseases are determined at any scale of biology: from protein interactions to organismsÕ phenotypes. In this context, submission topics can include, but are not limited to:

(i) protein interactions:

á            protein-protein interactions

á            protein-DNA/RNA interactions

á            analysis of protein networks and systems analysis of disease

á            studies in cis/co- regulation

á            effects of SNPs and haplotypes on protein interactions

á            studies in protein misfolding or aggregation as related to the emergence of diseases

á            protein interactions in drug discovery: drug design and target selection

(ii) phenomics:

á            Fundamental properties emerging from phenome-genome networks or new methods to generate associations from these multi-scale networks

á            Comparative phenomics or determination of shared molecular mechanisms of phenotypes from genomic analyses

á            Integrative phenomics or methods to integrate large datasets comprising heterogeneity of measurements and representation at the molecular level and phenotypic levels

á            Discovery systems predicting gene-phenotype associations or supracellular biological processes associated with genes, gene products or molecular functions

á            Significant innovation in standards for exchanging and reusing phenomes or phenotypes associated with genetic or model organism databases or electronic medical records.

á            Original methodologies for quantitative trait loci or other genetic analyses that also include prior probabilities derived from high throughput phenomic studies

á            Visualization systems for cross-scale genome-phenome networks

Other topics within the subject area are welcome. Note that all submitted papers should make clear their relevance for the study of disease. If unsure whether your paper fits the session theme, please contact one of the co-chairs.

Session Co-Chairs (alphabetical order)

Atul Butte 

Stanford University
abutte@stanford.edu

Maricel Kann 

National Center of Biotechnology Information, NIH at the Structure Group
kann@mail.nih.gov

Yves Lussier

The University of Chicago
Lussier@uchicago.edu

yanay Ofran 

Columbia University
yanay.ofran@columbia.edu

Marco Punta

Columbia University
punta@cubic.bioc.columbia.edu

Predrag Radivojac

Indiana University
predrag@indiana.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 16, 2007

Notification of paper acceptance: September 5, 2007

Final paper deadline: September 24, 2007 at midnight PDT

Poster abstract deadline: November 9, 2007

 

 

Paper Format

All papers must be submitted to psb-submit @ helix.stanford.edu in electronic format with PSB in the subject line. The file formats we accept are: Adobe Acrobat (*.pdf) and postscript (*.ps). Attached files should be named with the last name of the first author (e.g. altman.pdf or altman.ps). 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:

á            The email address of the corresponding author

á            The specific PSB session that should review the paper or abstract

á            The submitted paper contains original, unpublished results, and is not currently under consideration elsewhere.

á            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 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 pictures can be printed at the expense of the authors. The fee is $500 per page of color pictures, payable at the time of camera ready submission.


Contact Russ Altman for additional information about paper submission requirements.