Call for Papers and Posters

Dynamics of Biological Networks

A session at the
Pacific Symposium on Biocomputing 2010

January 4-8, 2010

The Big Island of Hawaii

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Network analysis provides a unifying language to describe relations within complex systems and has played an increasingly important role in understanding biological systems. Over the past decade, computational methods have been developed to infer, analyze, and predict the structure of gene and protein networks. The majority of these approaches have focused on the topology, rather than the dynamics of these networks. Yet most biological networks change over time, space and context. For example, the properties of molecular networks dynamically change in response to stress or other environmental changes. It is important to understand the quantitative dynamics of signaling networks activated by growth factors, cytokines, and the extracellular matrix as defects in signaling pathways are associated with serious diseases, including for example cancer. Understanding cellular dynamics will also aid in efforts to reverse engineer cellular networks and uncover causal relationships.

Therefore, in addition to considering these networks as simply collections of proteins and interactions, researchers have begun to elucidate dynamic properties of such networks. In molecular networks, information about dynamics can be obtained by, for example, integrating static interactions (such as protein-protein or regulatory interactions) with time-dependent gene expression data or information about localization. Additionally, computational methods for inference and analysis of dynamic networks are currently being developed in other domains, such as social networks, and recently some of these approaches for topology reconstruction, identification of clusters, and prediction of dynamic networks are starting to be successfully applied to biological networks.

Session Topics

We invite contributions presenting new computational methods for analysis of biological networks that explicitly address the dynamic nature of these networks, new models of dynamic behavior of biological networks, simulation software for generating dynamic networks, or evaluations of existing methods and validations of existing models. Papers presenting new methods should provide experimental or empirical evidence of the performance of the new methods. In addition, papers that present novel empirical evidence of the dynamic behavior of biological networks are welcome.

In this context, submission topics can include, but are not limited to:

• Reverse engineering of signaling and regulatory networks
• Inference and modeling of regulatory interactions
• Predictive modeling of signaling pathways
• Predicting and analyzing context and time dependence in protein interactions
• Changes in the properties of molecular networks in response to varying conditions such as stress, diseases, and drug treatment, and   sequence polymorphisms present in populations.
• Modeling and analyzing the dynamics of molecular, cellular, and social networks

Other topics within the subject area are welcome. Note that all submitted papers should demonstrate the relevance to this topic. If unsure whether your paper fits the session theme, please contact one of the co-chairs.

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Session Co-Chairs

Tanya Berger-Wolf University of Illinois at Chicago tanyabw@uic.edu

Teresa Przytycka NCBI, NLM, NIH przytyck@ncbi.nlm.nih.gov

Mona Singh Princeton University mona@cs.princeton.edu

Donna Slonim Tufts University slonim@cs.tufts.edu

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General Information on Papers and Presentations

The scientific core of the conference consists of rigorously peer-reviewed full-length papers reporting on original work. Accepted papers will be published in an archival proceedings volume (fully indexed in PubMed), and a number of the papers will be selected for presentation during the conference. Researchers wishing to present their research without official publication are encouraged to submit a one-page abstract, and present their work in a poster session.

Important Dates

• Paper submission deadline: July 13, 2009
• Notification of paper acceptance: September 10, 2009
• Camera ready paper deadline: September 21, 2009
• Meeting: January 4-8, 2010

Paper Formatting and Submission

Please see the PSB paper format template and instructions at http://psb.stanford.edu/psb-online/psb-submit.

The only acceptable file formats 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:

• 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 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.

Contact Russ Altman (psb.hawaii @ gmail.com ) for additional information about paper submission requirements.