Even when full genomic sequences for an organism are available, the functions and interactions of only a small number of gene components are clear. Presently, the functions of uncharacterized proteins have usually been inferred on the basis of sequence similarities, common structural motifs, gene order, gene fusion events, or similarities in gene expression. Recently, new mathematical and computational methods have been introduced for functional predictions based on the role of genes in networks. These methods allow us to perform functional predictions for proteins independent of homologies in structure or sequence and provide a way to characterize proteins that have not yet been studied using published biological data from high-throughput technologies. This proposal requests partial funding for the workshop "Biocomplexity VII: Unraveling the Function and Kinetics of Biochemical Networks: From Experiments to Systems Biology," organized by the Biocomplexity Institute and the School of Informatics at Indiana University. The Biocomplexity VII workshop aims to bring together specialists in a broad array of methodologies to see how they can combine to explicate the functions of genes and proteins in a network context by developing mathematical and computational approaches suited for the analysis of high-throughput data sets. The objectives of the workshop are to: (i) To explore and present the development of new experimental and theoretical approaches for the purposes of reconstructing complex biochemical networks; (ii) To promote interaction between engineers, physicists, mathematicians, biologists, and chemists with interests in all aspects of reconstructing complex biochemical networks, and (iii) To provide a forum for junior faculty and graduate students to interact with a wide range of experts.
Intellectual merit: The scientific focus of the workshop will be on 1) discussing and developing tools to reconstruct the structure and kinetics of genetic and biochemical pathways, 2) the main mathematical and computational issues which complicate applications of such methods and 3) the best current solutions and existing solutions from mathematics, physics, chemistry, engineering and computer sciences which can be applied to solve the problems in 1). The Workshop will bring together researchers in many disciplines, including mathematics, experimental and theoretical biology, physics, engineering, and computer science.
Broader impact: This workshop will promote collaboration and development of both experimental and theoretical studies of genetic and biochemical network dynamics and to expose a broad range of outside researchers to problems in network reconstruction and function. The Workshop is organized specifically to provide interactions between senior researchers, junior faculty, and graduate students. The poster session will facilitate such interaction. Proceedings of the conference will be compiled and disseminated to all participants, published in a journal special issue and will be made available electronically over the world-wide-web. The methodologies we will be discussing will be applicable to any organism, including humans, where only three to five percent of gene function is known. As we better understand the functions of genes and proteins in a network context, we can better predict and control their responses to internal and external perturbations.
