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ISMB
2007
15 years 9 months ago
Automatic genome-wide reconstruction of phylogenetic gene trees
Gene duplication and divergence is a major evolutionary force. Despite the growing number of fully sequenced genomes, methods for investigating these events on a genome-wide scale...
Ilan Wapinski, Avi Pfeffer, Nir Friedman, Aviv Reg...
ASM
2008
ASM
15 years 8 months ago
UML-B: A Plug-in for the Event-B Tool Set
UML-B provides a graphical front end for Event-B. It adds support for class-oriented and state machine modelling. UML-B is similar to UML but has its own meta-model. UML-B provides...
Colin F. Snook, Michael J. Butler
ASM
2008
ASM
15 years 8 months ago
Modeling Workflows, Interaction Patterns, Web Services and Business Processes: The ASM-Based Approach
Abstract. We survey the use of the Abstract State Machines (ASM) method for a rigorous foundation of modeling and validating web services, workflows, interaction patterns and busin...
Egon Börger, Bernhard Thalheim
CIBCB
2005
IEEE
15 years 8 months ago
A Transcriptional Approach to Gene Clustering
— We present an integrative method for clustering coregulated genes and elucidating their underlying regulatory mechanisms. We use multi-state partition functions and thermodynam...
Ilias Tagkopoulos
CIBCB
2007
IEEE
15 years 8 months ago
Optimization of Bacterial Strains with Variable-Sized Evolutionary Algorithms
—In metabolic engineering it is difficult to identify which set of genetic manipulations will result in a microbial strain that achieves a desired production goal, due to the co...
Miguel Rocha, José P. Pinto, Isabel Rocha, ...