Synthetic Biology Network Research

This page is designed as a community page for students at MWSU and Davidson College who are using synthetic biology to learn more about graph theory and network topology.

Davidson College

Our first meeting will be on Thursday, January 19, 2012. We will meet at 11 am (the common hour) in the Think Tank in the back of Belk computer lab.

We will start slowly with some introductory activities and a brief discussion of some news stories from the recent issue in Science that focused on synthetic biology. Read these pieces:

1. The Allure of Synthetic Biology
2. The Life Hacker
3. Algae's Second Try
4. A Lab of Their Own
5. Visions of Synthetic Biology

Be ready to discuss these stories in general. What did you learn? What surprised you? What felt familiar?

Over the next 14 weeks, we will read a series of papers. We have chosen some to help us get started, but as the semester progresses, you will take the lead in identifying papers. Some of these papers will be easy for you, but others will be more difficult. We will work as a group to understand what is going on. In all cases, we will use these papers to help us frame a research project that will be conducted this summer by 8 Davidson students.

Some possible papers

• The creativity crisis.
  

Po Bronson and Ashley Merryman
Newsweek. July 19, 2010. page 44.

• Synthetic Biology Moving into the Clinic
  

Warren C. Ruder,* Ting Lu,* James J. Collins
Science. Vol. 333. page 1248.

• Engineering bacteria to solve the Burnt Pancake Problem.
  

Haynes, Karmella, et al.
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

• Solving a Hamiltonian Path Problem with a Bacterial Computer.
  

Baumgardner, Jordan et al.
Journal of Biological Engineering. Vol. 3:11

• Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter.
  

Brianna Pearson*, Kin H. Lau* et al.
Interdisciplinary Bio Central. Vol. 3, article no. 10

• DNA assembly for synthetic biology: from parts to pathways and beyond
  

Tom Ellis,*ab Tom Adieac and Geoff S. Baldwin

Integr. Biol., 2011, 3, 109–118

• Information Transduction Capacity of Noisy Biochemical Signaling Networks
  

Raymond Cheong, Alex Rhee, Chiaochun Joanne Wang, Ilya Nemenman, Andre Levchenko
Science. Vol. 334, page 354.

• Synthetic Biology: Regulating Industry Uses of New Biotechnologies
  

Brent Erickson, Rina Singh, Paul Winters
Science. Vol. 333, page 1254.

• Synthetic Biology: Integrated Gene Circuits
  

Nagarajan Nandagopal and Michael B. Elowitz
Science. Vol. 333, page 1244.

• Stochastic Pulse Regulation in Bacterial Stress Response
  

James C. W. Locke,* Jonathan W. Young,* Michelle Fontes, María Jesús Hernández Jiménez, Michael B. Elowitz
Science. Vol. 334. page 366.

• Synthetic biology: applications come of age
  

Ahmad S. Khalil* and James J. Collins
Nature Review Genetics. Vol. 11. page 367.

• Five hard truths for synthetic biology.
  

Roberta Kwok
Nature. Vol. 463. page 288.

• Controllability of complex networks
  

Yang-Yu Liu1,2, Jean-Jacques Slotine3,4 & Albert-La ́szlo ́ Baraba ́si
Nature. Vol. 473. page 167.