Brown Synthetic Biological Systems Seminar Series

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Synthetic Biological Systems Seminar Series, Brown University

Fall 2007 Bio1940t Synthetic Biological Systems Course


Tom Knight

MIT, Computer Science and Artificial Intelligence Laboratory

Foundations of Synthetic Biology September 10th (Monday) CIT 227, 3:30 – 4:30pm


Pam Silver

Harvard, Systems Biology

Designing Biological Systems October 29th (Monday) time and venue TBC


Christina Smolke

Caltech, Chemical Engineering

Metabolic engineering and RNA logic devices

November 5th (Wednesday) CIT 227, 3:30 – 4.30pm


Jim Collins

BU, Biomedical Engineering and Co-Director of the Center for BioDynamics

Engineering Gene Networks:

Integrating Synthetic Biology & Systems Biology”

Distinguished lecture, Host: Center for Computational Molecular Biology

November 7th Wednesday SWIG boardroom, CIT 241, 4-5pm


Chris Voigt

Pharmaceutical Chemistry at the University of California, San Francisco

Programming bacteria: wiring synthetic sensors and circuits to heterologous outputs

November 19th (Monday) Life Sciences Building, Sidney Frank Hall, Room 220, 3:30 – 4.30pm


Sponsored by BIOL 1940T Synthetic Biological Systems

Department of Computer Science

Center for Computational Molecular Biology

Department of Chemistry

Center for Biomedical Engineering

Molecular Biology, Cellular Biology, Biochemistry

Division of Biology and Medicine


Spring 2008

Drew Endy, MIT; Ron Weiss, Princeton; Jay Keasling, UC Berkely


Tom Knight is a senior research scientist in the MIT Computer Science and Artificial Intelligence Laboratory. He has been at MIT since the age of fourteen, working closely with computer scientists to revolutionize that field. In his early years, he developed novel hardware devices, some of the first bitmapped displays, the ITS time sharing system, “Lisp machines,” and parallel symbolic processing computer systems. Having established his name in the field of computer science, he developed an interest in molecular biology, and he brought his expertise in computation to synthetic biology. Tom Knight has been instrumental in developing the Registry of Standard Biological Parts, BioBricks, and iGEM. Ron Weiss, now at Princeton, trained under Tom Knight as a PhD student. In addition to these major contributions to synthetic biology, his current projects include artificial transcriptional terminators, bioinformatics of S-layer proteins, and novel BioBrick vectors. Students in his lab are currently developing ways to measure polymerase arrival rates and engineer transcription based digital logic. Says Tom Knight: “I believe that microbial engineering will be the next important engineering discipline, replacing and augmenting microelectronics as the major focus for the 21st century.”


Pamela Silver is a Professor in the Department of Systems Biology at Harvard Medical School. She is also the first Director of the Harvard University Graduate Program in Systems Biology. Prior to this appointment, she held academic appointments at Princeton University and The Dana Farber Cancer Institute. Her lab works on a variety of projects in systems and synthetic biology. Current projects use the advanced operating system afforded by eukaryotes to create artificial proteins with therapeutic value, a cellular oscillator that could lead to pulsatile drug delivery, a cell division counter for analysis of aging, and manipulation/creation of metabolic pathways to produce bio-hydrogen as an economical energy source. She is also interested in spatial genome organization and transcriptional regulation. Pam Silver has been recognized with a Presidential Young Investigator Award, an Established Investigator Award from the American Heart Association, the NIH Director's Lecture and an NIH MERIT Award.

Christina Smolke is an Assistant Professor of Chemical Engineering at Caltech. She graduated from USC with a B.S. degree in Chemical Engineering with an emphasis in Biology in 1997. She then attended the University of California at Berkeley, where she earned her Ph.D. in 2001 in Chemical Engineering under Jay D. Keasling. Before starting her position at Caltech, Christina conducted a two year postdoctoral fellowship in the Cell Biology Department at UC Berkeley under Karsten Weis. Her lab’s research projects include the design of molecular switches that act in vivo as both biosensors and ligand-controlled regulators of gene expression. This work involves gene regulation mechanisms such as the RNA interference (RNAi) pathway, ribozyme-based cleavage, and the antisense pathway. Her lab hopes to integrate molecular switches into synthetic and endogenous cellular networks and to potentially use nucleic acid switches as molecular recognition components of nanosensor devices.

Jim Collins is a Professor of Biomedical Engineering and Co-Director of the Center for BioDynamics at Boston University. He is often referred to as a founder of synthetic biology. His paper modeling and testing a bi-stable toggle switch, a system the Brown iGEM team is now attempting to replicate and expand, was one of the first defining papers of the field. (Gardner, TS; Cantor CR and Collins JJ (20 Jan 2000). "Construction of a genetic toggle switch in Escherichia coli". Nature 403: 339-342.). Jim Collins has also co-founded Cellicon Biotechnologies, which uses his systems and synthetic biology technology platforms to develop novel antibiotics for overcoming resistance. Currently, Jim Collins' research focuses on developing nonlinear dynamical techniques and devices to characterize, improve and mimic biological function. His specific interests include: (a) systems biology - reverse engineering naturally occurring gene regulatory networks, (b) synthetic biology - modeling, designing and constructing synthetic gene networks, and (c) developing noise-based sensory prosthetics.

Christ Voigt is an Assistant Professor of Pharmaceutical Chemistry at the University of California, San Francisco. Prior to this position, he completed his PhD with Frances Arnold at Caltech. Chris Voigt has been a pioneer in Synthetic Biology. His team has produced some of the most novel and famous systems in the field, including his former iGEM team’s creation of light-sensitive bacterial photo film. His most recent research initiatives include bacteria capable of spinning silk and the invasion of cancer cells by engineered bacteria. Currently, his lab is working to engineer multi-gene prokaryotic organelles for applications in biotechnology. His lab is focusing on the type III secretion system, which pumps proteins from the cytoplasm, through both membranes, to the extracellular environment. This system is being exploited to deliver heterologous proteins to the growth media. This work may help the lab in future endeavors to engineer photosynthetic systems to convert sunlight into energetic and specialty chemicals.

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