Networks: From Biology to Theory

During the past decades, we have witnessed the thriving development of new mathematical, computational and theoretical approaches such as bioinformatics and neuroinformatics to tackle some fundamental issues in biology. These scientific approaches focus no longer on individual units, such as nerve cells or genes, but rather on the emerging dynamic patterns of interactions between them. These concentrate on the interplay between the local dynamics and activity transmissions on one side and the global structure of the underlying connection scheme on the other hand.

In this light, the concept of a network emerges as a powerful and stimulating research paradigm in mathematics, physics and computer science, and demonstrates a very lively interaction between experimental findings, simulation studies, and theoretical investigations that then in turn lead to new experimental questions.

Introduction.- Part I: Theory.- The Category of X-Nets.- Networks with Delays.- Dynamical Networks.- Part II: Applications in Neuroscience.- Neuronal Computation Using High Order Statistics.- Neuronal Model of Decision Making.- Estimation of Spike Train Statistics in Spontaneously Active Biological neural Networks.- Physiology and Related Models of Associative Visual Processing.- Gestalt Formation in a Competitive Layered Neural Architecture.- Part III: Applications in Bioinformatics.- Regulatory Signals in Genomic Sequences.- Dynamic Properties of Cell-cycle and Life-cycle networks in Budding Yeast.- Understanding Protein-protein Interactions: From Domain Level to Motif Level.- An Efficient Algorithm for Deciphering Regulatory Motifs.- The Stochastic Model and Metastability of Gene Network.- Messenger RNA Information ? Its Implication in Protein Structure Determination and Others.