Call for Papers and Posters
Dynamics of Biological Networks
A
session at the
Pacific Symposium on Biocomputing
2009
January 5-9, 2009
The
Big
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:
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
tanyabw@uic.edu
Teresa
Przytycka
NCBI, NLM, NIH
przytyck@ncbi.nlm.nih.gov
mona@cs.princeton.edu
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 Formatting and Submission
Papers must be submitted to the PSB 2009 paper management system at
http://acamedics.com/submissions/index.php/psb/psb2009/login
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 altman.ps).
Hardcopy submissions or unprocessed
Each paper must be accompanied by a cover letter. The cover letter must state the following:
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 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.
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 @ gmail.com) for additional information about paper submission requirements.