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: Molecular biology of prokaryotes, especially analysis of the function of genes and proteins involved in metabolic pathways (lab home page).

Matthew Bennett: Studies of the dynamics of gene regulation - from small-scale interactions such as transcription and translation, to the large-scale dynamics of gene regulatory networks, using a hybrid experimental and computational approach (lab home page).

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.

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.

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.: X-ray crystallography and other biophysical and computational methods are used to relate the three-dimensional structure and dynamics of proteins to their biological functions. Applications of some of the laboratory projects include enzyme discovery for natural product biosynthesis, improving the thermostability of proteins for potential commercial improvements, and contributing basic science results to the development of biofuels, particularly from cellulosic biomass.

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.

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

Yousif Shamoo : In vivo pathways of molecular evolution:  directed evolution of protein structure-function; DNA replication and its relationship to cancer; sequence specific protein-RNA interactions in eukaryotic RNA processing proteins (lab home page).

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:  Development of high-throughput technologies for genetic studies, modeling and analysis of genetic interaction networks, performing large-scale genetic screens in the model system C. elegans (lab home page).

Metabolic gene regulation studies in the Matthew Bennett Lab