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» Logic-Based Modeling in Systems Biology
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ISCA
2007
IEEE
196views Hardware» more  ISCA 2007»
15 years 6 months ago
Anton, a special-purpose machine for molecular dynamics simulation
The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle provide answers to some of the ...
David E. Shaw, Martin M. Deneroff, Ron O. Dror, Je...
BMCBI
2010
167views more  BMCBI 2010»
14 years 12 months ago
BisoGenet: a new tool for gene network building, visualization and analysis
Background: The increasing availability and diversity of omics data in the post-genomic era offers new perspectives in most areas of biomedical research. Graph-based biological ne...
Alexander Martin, Maria Elena Ochagavia, Laya C. R...
BMCBI
2005
212views more  BMCBI 2005»
14 years 11 months ago
PAGE: Parametric Analysis of Gene Set Enrichment
Background: Gene set enrichment analysis (GSEA) is a microarray data analysis method that uses predefined gene sets and ranks of genes to identify significant biological changes i...
Seon-Young Kim, David J. Volsky
ICANN
2009
Springer
15 years 4 months ago
Computing with Probabilistic Cellular Automata
Abstract. We investigate the computational capabilities of probabilistic cellular automata by means of the density classification problem. We find that a specific probabilistic ...
Martin Schüle, Thomas Ott, Ruedi Stoop
BMCBI
2010
123views more  BMCBI 2010»
14 years 12 months ago
Computationally efficient flux variability analysis
Background: Flux variability analysis is often used to determine robustness of metabolic models in various simulation conditions. However, its use has been somehow limited by the ...
Steinn Gudmundsson, Ines Thiele