Colloquia Archive
Bibliome Informatics and Complex Networks in Proteomics and Systems Biology
January 23, 2009
AbstractLiterature mining (bibliome informatics) is useful to infer bio-chemical and functional information about groups of genes and proteins; its objective is to sort automatically through huge collections of literature and suggest the most relevant information for a specific analysis. Until now, literature mining has been used to help annotate genes and proteins. In the next few years the field is expected to move into bolder pursuits, such as the discovery of novel protein-protein and gene-disease interactions. Indeed, the second Biocreative competition, which we participated in, included a series of tasks on the extraction of protein-protein interaction information from the literature. We describe our complex network approach to biomedical literature mining in proteomics. We also describe our work on the large-scale validation of bibliome algorithms.
The complex network approach is also useful in the characterization of collective computation in biological networks. While there have been many advances toward understanding the structure of natural networks, as well as on modeling specific biological systems as networks of automata, how the dynamics of complex networks can lead to emergent, collective computation and how to control or “program” it to perform specific tasks are still largely open questions. We discuss a new methodology based on Holland’s schemata, for characterizing the dynamics of large automata networks, such as cellular automata and Boolean networks. We focus on examples from the systems biology literature, such as the segment polarity network of the Drosophila Melanogaster (21 nodes), and a large biochemical intracellular signal transduction network (139 nodes). We discuss how our approach is useful to characterize regulation, control, robustness, modularity and collective computation in networks of automata.
Luis M. Rocha is an Associate Professor of Informatics and a member of the Complex Systems Group. He is currently the director of the complex systems PhD track in Informatics. He is also a core faculty member of the Cognitive Science Program, Adjunct Associate Professor in Computer Science, and affiliated with the Biocomplexity Institute and Center for Complex Networks and Systems at Indiana University, Bloomington, USA. He is also the director of the Computational Biology Collaboratorium and in the Direction of PhD program in Computational Biology at the Instituto Gulbenkian da Ciencia, Portugal.
