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BCB
2010
150views Bioinformatics» more  BCB 2010»
13 years 2 months ago
Enzymatic target identification with dynamic states
As a metabolic network reaches from a state to a steady state, a subset of its fluxes gradually change. The sequence of intermediate states, called the dynamic state, shows the pa...
Bin Song, Sanjay Ranka, Tamer Kahveci
BMCBI
2010
259views more  BMCBI 2010»
13 years 2 months ago
Rule-based spatial modeling with diffusing, geometrically constrained molecules
Background: We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our appro...
Gerd Gruenert, Bashar Ibrahim, Thorsten Lenser, Ma...
BIOINFORMATICS
2011
13 years 2 months ago
Integrative network alignment reveals large regions of global network similarity in yeast and human
Motivation: High-throughput methods for detecting molecular interactions have produced large sets of biological network data with much more yet to come. Analogous to sequence alig...
Oleksii Kuchaiev, Natasa Przulj
BMCBI
2011
13 years 2 months ago
easyDAS: Automatic creation of DAS servers
Background: The Distributed Annotation System (DAS) has proven to be a successful way to publish and share biological data. Although there are more than 750 active registered serv...
Bernat Gel, Andrew M. Jenkinson, Rafael C. Jimenez...
BMCBI
2011
13 years 2 months ago
Hierarchical graphs for rule-based modeling of biochemical systems
Background: In rule-based modeling, graphs are used to represent molecules: a colored vertex represents a component of a molecule, a vertex attribute represents the internal state...
Nathan W. Lemons, Bin Hu, William S. Hlavacek
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