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» On Timed Models of Gene Networks
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BMCBI
2007
144views more  BMCBI 2007»
13 years 8 months ago
Accelerated search for biomolecular network models to interpret high-throughput experimental data
Background: The functions of human cells are carried out by biomolecular networks, which include proteins, genes, and regulatory sites within DNA that encode and control protein e...
Suman Datta, Bahrad A. Sokhansanj
BMCBI
2008
146views more  BMCBI 2008»
13 years 8 months ago
Rank-based edge reconstruction for scale-free genetic regulatory networks
Background: The reconstruction of genetic regulatory networks from microarray gene expression data has been a challenging task in bioinformatics. Various approaches to this proble...
Guanrao Chen, Peter Larsen, Eyad Almasri, Yang Dai
GD
2009
Springer
14 years 16 days ago
Semi-bipartite Graph Visualization for Gene Ontology Networks
Abstract. In this paper we propose three layout algorithms for semibipartite graphs—bipartite graphs with edges in one partition—that emerge from microarray experiment analysis...
Kai Xu 0003, Rohan Williams, Seok-Hee Hong, Qing L...
CMSB
2006
Springer
13 years 11 months ago
Rewriting Game Theory as a Foundation for State-Based Models of Gene Regulation
We present a game-theoretic foundation for gene regulatory analysis based on the recent formalism of rewriting game theory. Rewriting game theory is discrete and comes with a graph...
Chafika Chettaoui, Franck Delaplace, Pierre Lescan...
APN
2006
Springer
13 years 10 months ago
From Petri Nets to Differential Equations - An Integrative Approach for Biochemical Network Analysis
Abstract. We report on the results of an investigation into the integration of Petri nets and ordinary differential equations (ODEs) for the modelling and analysis of biochemical n...
David Gilbert, Monika Heiner