Biological circuit for one of the early paradigms of eukaryotic gene regulation describing quinic acid (QA) metabolism in the model system Neurospora crassa.

There is an established interdisciplinary team from the Genetics, Physics, Computer Science, and Statistics departments working on identifying biological circuits for fundamental biological processes and validating these biological circuits by fitting them to genomics data. Since the discovery of the structure of DNA 50 years ago, biologists have been taking apart living systems on a finer and finer scale until we have been able to determine the complete genetic blueprint of many organisms. The challenge of the new millennium is "reassembling the pieces," i.e., moving from genomes to life.

One approach to reassembling the pieces is to borrow a metaphor from computer science: the entire chemical reaction network describing what a cell does is a biological circuit. The theme for this genomics and computational biology program is "computing life," i.e., identifying biological circuits for fundamental processes like carbon metabolism and validating these biological circuits by fitting them to genomics data describing what the cell is doing (i.e., RNA and protein profiling data) (PNAS 99: 16904-16909 [2002]). This involves measuring what individual macromolecules are doing within a cell.

	see also:		• Computing Life

EQUIPMENT AND FACILITIES

• Robotics for microarraying

	download articles:		• Metabolomics • An ensemble method for identifying regulatory circuits with special reference to the qa gene cluster of Neurospora crassa • IntelliGEN: A Distributed Workflow System for Discovering Protein-Protein Interactions

SELECTED PUBLICATIONS

HS Kelkar, J Griffith, ME Case, S Covert, R D Hall, C Keith, JS Oliver, MJ Orbach, MS Sachs, J Wagner, MJ Weise, J Wunderlich, and J Arnold. (2001). "The Neurospora crassa genome: cosmid libraries sorted by chromosome." Genetics 157 (March issue), 979-990

Battogtokh, D, DK Asch, ME Case, J Arnold, & H-B Schuttler (2002). "An ensemble method for identifying regulatory circuits with special reference to the qa gene cluster of Neurospora crassa." PNAS USA 99: 16904-16909

Kochut, KJ, J Arnold, A Sheth, J Miller, E Kraemer, B Arpinar, and J Cardoso. (2003). "INTELLIGEN: a distributed workflow system for discovering protein-protein interactions." Parallel and Distributed Databases 13, 43-72

Bennett, J. and J. Arnold (2001). "Genomics of Fungi." The Mycota VIII. Biology of the Fungal Cell. Howard and Gow (eds). pp. 267-297 Springer-Verlag, NY, NY

I. Arnold, J. H.-B. Schuttler, D. Logan, D. Battogtokh, J. Griffith, B. Arpinar, S. Bhandarkar, S. Datta, K. J. Kochut, E. Kraemer, J. A. Miller, A. Sheth, G. Strobel, T. Taha, B. Aleman-Meza, J. Doss, L. Harris, & A. Nyong. (2004). "Metabolomics." In Handbook of Industrial Mycology. Marcel Dekker, NY, NY

About the Center .::. Mission .::. News from the Center .::. Faculty and Research .::. Facilities .::. Contact the Center .::. Home