Artificial Intelligence Methods and Tools for Systems Biology

Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
Lazy Learning for Predictive Toxicology based on a Chemical Ontology
Eva Armengol and Enric Plaza . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
QSAR Modeling of Mutagenicity on Non-Congeneric Sets of Organic
Compounds
Uko Maran and Sulev Sild . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Characterizing Gene Expression Time Series using a Hidden Markov
Model
Sally McClean, Bryan Scotney and Steve Robinson . . . . . . . . . . . . . . . . . . . . . . 37
Analysis of Large-Scale mRNA Expression Data Sets by Genetic
Algorithms
Chia Huey Ooi and Patrick Tan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
A Data-Driven, Flexible Machine Learning Strategy for the Classification
of Biomedical Data
Rajmund L. Somorjai, Murray E. Alexander, Richard Baumgartner,
Stephanie Booth, Christopher Bowman, Aleksander Demko, Brion Dolenko,
Marina Mandelzweig, Aleksander E. Nikulin, Nicolino J. Pizzi, Erinija
Pranckeviciene, Arthur R. Summers and Peter Zhilkin . . . . . . . . . . . . . . . . . . . . . 67
Cooperative Metaheuristics for Exploring Proteomic Data
Robin Gras, David Hernandez, Patricia Hernandez, Nadine Zangger, Yoan
Mescam, Julien Frey Olivier Martin, Jacques Nicolas and Ron D. Appel . . . . . . 87
Integrating Gene Expression Data, Protein Interaction Data, and
Ontology-Based Literature Searches
Panos Dafas, Alexander Kozlenkov, Alan Robinson and Michael Schroeder . . . . 107
Ontologies in Bioinformatics and Systems Biology
Patrick Lambrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
Natural Language Processing and Systems Biology
K. Bretonnel Cohen and Lawrence Hunter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Systems Level Modeling of Gene Regulatory Networks
Martin Stetter, Bernd Schurmann and Mathaus Dejori . . . . . . . . . . . . . . . . . . . . 175
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Computational Neuroscience for Cognitive Brain Functions
Marco Loh, Miruna Szabo, Rita Almeida, Martin Stetter and Gustavo Deco . . . 197
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217


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