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BMCBI
2008
111views more  BMCBI 2008»
13 years 10 months ago
GENOMEPOP: A program to simulate genomes in populations
Background: There are several situations in population biology research where simulating DNA sequences is useful. Simulation of biological populations under different evolutionary...
Antonio Carvajal-Rodríguez
RECOMB
2009
Springer
14 years 10 months ago
An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations
Collective behavior involving distally separate regions in a protein is known to widely affect its function. In this paper, we present an online approach to study and characterize ...
Arvind Ramanathan, Pratul K. Agarwal, Maria Kurnik...
RECOMB
2007
Springer
14 years 10 months ago
Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions
Abstract. Given the substantial computational requirements of stochastic simulation, approximation is essential for efficient analysis of any realistic biochemical system. This pap...
Hiroyuki Kuwahara, Chris J. Myers
BMCBI
2008
118views more  BMCBI 2008»
13 years 10 months ago
Drug interaction prediction using ontology-driven hypothetical assertion framework for pathway generation followed by numerical
Background: In accordance with the increasing amount of information concerning individual differences in drug response and molecular interaction, the role of in silico prediction ...
Takeshi Arikuma, Sumi Yoshikawa, Ryuzo Azuma, Kent...
AB
2008
Springer
14 years 4 months ago
An Algorithm for Qualitative Simulation of Gene Regulatory Networks with Steep Sigmoidal Response Functions
A specific class of ODEs has been shown to be adequate to describe the essential features of the complex dynamics of Gene-Regulatory Networks (GRN). But, the effective exploitatio...
Liliana Ironi, Luigi Panzeri, Erik Plahte