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» Adaptive Modeling of Biochemical Pathways
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ENTCS
2010
103views more  ENTCS 2010»
13 years 4 months ago
A Model and Analysis of the AKAP Scaffold
We study the biochemical processes involved in scaffold-mediated crosstalk between the cAMP and the Raf-1/MEK/ERK pathways. We model the system by a continuous time Markov chain w...
Oana Andrei, Muffy Calder
BIBM
2007
IEEE
144views Bioinformatics» more  BIBM 2007»
14 years 1 months ago
Kinetic Modeling Using BioPAX Ontology
Thousands of biochemical interactions are available for download from curated databases such as Reactome, Pathway Interaction Database and other sources in the Biological Pathways...
Oliver Ruebenacker, Ion I. Moraru, James C. Schaff...
BIRD
2008
Springer
158views Bioinformatics» more  BIRD 2008»
13 years 9 months ago
A Computational Method for Reconstructing Gapless Metabolic Networks
Abstract. We propose a computational method for reconstructing metabolic networks. The method utilizes optimization techniques and graph traversal algorithms to discover a set of b...
Esa Pitkänen, Ari Rantanen, Juho Rousu, Esko ...
IV
2008
IEEE
296views Visualization» more  IV 2008»
14 years 1 months ago
Revealing Subnetwork Roles using Contextual Visualization: Comparison of Metabolic Networks
This article is addressing a recurrent problem in biology: mining newly built large scale networks. Our approach consists in comparing these new networks to well known ones. The v...
Romain Bourqui, Fabien Jourdan
ISMB
1998
13 years 8 months ago
BioSim: A New Qualitative Simulation Environment for Molecular Biology
Traditionally, biochemical systems are modelled usingkinetics anddifferential equationsin a quantitative simulator. However,for manybiological processes detailed quantitative info...
Karsten R. Heidtke, Steffen Schulze-Kremer