Call for Papers and Posters


Dynamics of Biological Networks


A session at the
Pacific Symposium on Biocomputing 2009

January 5-9, 2009

The Big Island of Hawaii



Network analysis provides a unifying language to describe relations within complex systems and has played an increasingly 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. Therefore, in addition to a description of these networks as collections of nodes and edges, researchers have begun to elucidate dynamic properties of such networks. In molecular networks, this is frequently obtained by integrating static interactions (such as protein-protein or regulatory interactions) with time dependent gene expression data. Such an approach has been used, for example, to analyze the dynamics of assembly of protein complexes during the yeast cell cycle.

The properties of molecular networks dynamically change in the response to stress or other environmental changes. It is very important to understand quantitative dynamics of signaling networks activated by growth factors, cytokines, and the extracellular matrix. Defects in signaling pathways are associated with many serious diseases, including for example cancer. This necessitates the development of predictive computational approaches that can be used to model the underlying dynamics of signaling networks, and may have important ramifications in drug discovery and development.

Understanding cellular dynamics will play a key component in efforts to reverse engineer cellular networks. Gene expression or molecular activity data (such as phophorylation state) collected in different time points or under different conditions can be used to infer direct or indirect connections between genes or gene products and, thus, to infer networks. Such reverse network engineering is increasingly more successful thanks to the accumulating availability of biological data and the development of new computational methods. Moreover, 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 dynamics 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
  • 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.


Session Co-Chairs

Tanya Berger-Wolf
University of Illinois at Chicago

Teresa Przytycka

Mona Singh
Princeton University


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 20, 2008 (deadline extended for this session only)
  • Notification of paper acceptance: September 8, 2008
  • Final paper deadline: September 22, 2008
  • Poster abstract deadline (non-reviewed): November 7, 2008
  • Meeting: January 5-9, 2009


Paper Formatting and Submission

Papers must be submitted to the PSB 2009 paper management system at

Please click the "Not a user? Create an account with this site" link to create an author account and upload your paper.

All papers must be submitted in electronic format to the paper management system.

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 Hardcopy submissions or unprocessed TeX or LaTeX files or electronic submissions not submitted through the paper management system 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 and submit your paper according to these instructions, which can be 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.

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 (psb.hawaii @ for additional information about paper submission requirements.