"Text Mining and Agent-based modeling for computational biology."

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"Pattern formation in Zebrafish."

Pattern formation is a broad field that has interested both experimentalists and theoreticians for a long time. Pigment pattern formation in zebrafish, Danio rerio has been one of the latest subjects of research. A model to explain pigment cell pattern formation in zebrafish and its mutants, based on new time sequence experimental data, will be presented. The model stresses the importance of differential intercellular adhesion and the mechanisms of stem cell regulation. All interactions included in the model are local -- long-range signals are not required. The model hypotheses are tested through a mathematical (cellular automaton) model. Simulations show that differential cellular adhesion along with an appropriate mechanism of stem cell regulation can explain pattern formation and maintenance. The results obtained with the simulations are compared with experimental data. Experimental tests to the predictions of the model are possible.

"GO Arabidopsis: using gene ontology annotation to define gene clusters."

With the creation of the Gene Ontology annotation in an universal and computational-friendly structure, it is possible and relatively easy to look for the functions and processes of every gene in an annotated genome. In that way this work proposes to find clusters of neighboring genes with similar function and involved in similar processes, opening the possibility of transcriptional corregulation.