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» The Factor Graph Network Model for Biological Systems
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RECOMB
2010
Springer
13 years 11 months ago
Incremental Signaling Pathway Modeling by Data Integration
Constructing quantitative dynamic models of signaling pathways is an important task for computational systems biology. Pathway model construction is often an inherently incremental...
Geoffrey Koh, David Hsu, P. S. Thiagarajan
BMCBI
2011
12 years 11 months ago
Properties of Metabolic Graphs: Biological Organization or Representation Artifacts?
Background: Standard graphs, where each edge links two nodes, have been extensively used to represent the connectivity of metabolic networks. It is based on this representation th...
Wanding Zhou, Luay Nakhleh
INFOCOM
2007
IEEE
13 years 11 months ago
Performance Evaluation of Loss Networks via Factor Graphs and the Sum-Product Algorithm
— Loss networks provide a powerful tool for the analysis and design of many communication and networking systems. It is well known that a large number of loss networks have produ...
Jian Ni, Sekhar Tatikonda
RECOMB
2005
Springer
14 years 5 months ago
Comparative Systems Biology of the Sporulation Initiation Network in Prokaryotes
Many years of experimental and computational molecular biology of model organisms such as Escherichia coli and Saccharomyces cerevisiae has elucidated the gene regulatory network i...
Michiel J. L. de Hoon, Dennis Vitkup
ATAL
2003
Springer
13 years 10 months ago
A multi-agent system for the quantitative simulation of biological networks
We apply the multi-agent system (MAS) platform to the task of biological network simulation. In this paper, we describe the simulation of signal transduction (ST) networks using t...
Salim Khan, Ravi Makkena, Foster McGeary, Keith S....