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» Adaptive Modeling of Biochemical Pathways
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BMCBI
2005
156views more  BMCBI 2005»
13 years 7 months ago
A new dynamical layout algorithm for complex biochemical reaction networks
Background: To study complex biochemical reaction networks in living cells researchers more and more rely on databases and computational methods. In order to facilitate computatio...
Katja Wegner, Ursula Kummer
BMCBI
2007
126views more  BMCBI 2007»
13 years 7 months ago
Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation
Background: Biochemical investigations over the last decades have elucidated an increasingly complete image of the cellular metabolism. To derive a systems view for the regulation...
Gunnar Schramm, Marc Zapatka, Roland Eils, Rainer ...
CDC
2009
IEEE
133views Control Systems» more  CDC 2009»
14 years 6 days ago
Kinetic perturbations as robustness analysis tool for biochemical reaction networks
— Models of biochemical reaction networks can be decomposed into a stoichiometric part and a kinetic part. The stoichiometric part describes the structural mass flows while the ...
Steffen Waldherr, Frank Allgöwer, Elling W. J...
CMSB
2008
Springer
13 years 9 months ago
Automatic Complexity Analysis and Model Reduction of Nonlinear Biochemical Systems
Kinetic models for biochemical systems often comprise a large amount of coupled differential equations with species concentrations varying on different time scales. In this paper w...
Dirk Lebiedz, Dominik Skanda, Marc Fein
BMCBI
2007
147views more  BMCBI 2007»
13 years 7 months ago
Modeling biochemical transformation processes and information processing with Narrator
Background: Software tools that model and simulate the dynamics of biological processes and systems are becoming increasingly important. Some of these tools offer sophisticated gr...
Johannes J. Mandel, Hendrik Fuß, Niall M. Pa...