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Synthetic & Systems Biology

Regulation in the galactose utilization
network studied in the Matthew Bennett Lab

One of the most pressing questions for biologists in the post-genomic era is: how can we, as scientists, begin to understand the vast networks of interacting parts that translate genotypes into phenotypes? To answer this question, synthetic and systems biologists bring together diverse fields such as biology, chemistry, physics, mathematics, computer science, and engineering – all in attempt to elucidate the fundamental principles governing gene regulatory networks. The two fields, however, go about this task in slightly different ways. Synthetic biologists use a “bottom-up” approach by creating simplified, de novo gene networks with the aim of understanding the processes by which regulation occur. In contrast, systems biologists use a “top-down” approach by studying large-scale native networks in order to discover the emergent properties and effects of the underlying layers of regulation. While these two disciplines attack the problem from different angles, they share the common belief that computational modeling and engineering techniques will aid the discovery process. Here at Rice’s Department of Biochemistry & Cell Biology, researchers from both fields are working together to eventually come to a complete understanding of cellular regulatory processes.

Faculty links:

George N. Bennett: Response of microbes to stress and use of metabolic engineering to generate strains with beneficial properties (lab home page).

Matthew Bennett: Synthetic biology and the dynamics of gene regulation. The Bennett lab uses a hybrid computational and experimental approach to design, construct and understand gene regulatory networks (lab home page).

Synthetic gene oscillators in bacteria from the Matthew Bennett lab

Herbert Levine: Physics of nonequilibrium processes, especially in the emergence of spatial patterns in extended systems such as Dictyostelium chemotaxis, neuronal circuits, and phenotypic transitions in bacterial colonies.

Seiichi P. T. Matsuda: Recombinant biosynthetic approaches to natural product biosynthesis; directed evolution and DNA shuffling to generate new oxidosqualene cyclases; metabolic engineering to produce terpenes.

Kathleen S. Matthews: Recombinant biosynthetic approaches to natural product biosynthesis; directed evolution and DNA shuffling to generate new oxidosqualene cyclases; metabolic engineering to produce terpenes.

Edward P. Nikonowicz: NMR spectroscopy of RNA and RNA-protein interactions - correlation of structure, function, and dynamics; biophysical studies and engineering of RNA regulatory elements; small molecule-RNA interactions; biophysical and functional studies of tRNA base modification.

John S. Olson: Biochemical, biophysical, and physiological properties of myoglobins, hemoglobins, and red blood cells; genetic engineering of heme protein based blood substitutes; application of rapid kinetic techniques to biological problems (lab home page).

José Onuchic: Biophysical studies and modeling of protein folding and convergent kinetic pathways, the theory of chemical reactions in condensed matter with emphasis on biological electron transfer reactions, and stochastic effects in genetic networks.

George N. Phillips, Jr.: The design or redesign of proteins is still an interesting challenge. The Phillips group is working to develop and test methods for testing the relationship of stability, dynamics, and function and for designing more stable enzymes for potential commercial uses.

Nicholas H. Putnam: Computational comparative genomics, mechanisms and dynamics of genome evolution, studies of genome structure variation in a natural population.

Laura Segatori :  Biotechnology and protein engineering; cell and tissue engineering; protein folding; neurodegenerative diseases (lab home page.)

Yousif Shamoo : The evolutionary and molecular basis for antibiotic resistance, directed evolution of protein structure-function, and the underlying biophysical and physicochemical principles of adaptation within bacterial populations (lab home page).

Schemata of the "weak link approach" for studying evolutionary dynamics at the molecular level (Shamoo)

Jonathan Silberg: Investigation of the processes controlling molecular evolution, particularly the evolution of protein structure, function, and molecular recognition using biochemical, computational, and molecular biological methods (lab home page).

Jeffrey J. Tabor: Use of light and other forms of electromagnetic radiation to control the activities in proteins inside of cells in real time, constructing synthetic transcriptional and post-translational signaling circuits, programming cells to communicate using unnatural signals, and combining all of these technologies to program synthetic multicellular behaviors.

Peter Wolynes: Application of statistical energy landscapes to understand biomolecular regulatory networks, proteing folding kinetics, gene recognition and genetic network regulation. Development of bioinformatically based schemes for predicting structure from sequence using computer simulation.

Weiwei Zhong:  Using the nematode C. elegans as a model to decipher gene interaction networks regulating development and behavior (lab home page).