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.
Grading
- Weekly Journals (your own paper summary and those of others) = 30% final grade
- Weekly Presentations = 30% final grade
- Research Proposal by teams = 40% final grade
You must keep hard copies of your weekly journal entries in a 3-ring binder. We will grade these periodically during the semester. You will also keep copies of your papers, any drawings of ideas you have, protocols used in lab, etc.
Scheduling with Doodle
WEEK THREE (January 30 - February 3)
WEEK FOUR (February 6 - 10) WET LAB WEEK
WEEK SIX (February 20 - 24)
Synthetic Seminar 4:30 pm Feb. 23 in VAC classroom and lunch with speaker Dr. Karmella Haynes at Arizona State University
WEEK SEVEN (February 27 - March 2)
WEEK EIGHT (March 5 - 9) SPRING BREAK
WEEK THIRTEEN (April 9 - 13) INCLUDES EASTER BREAK
WEEK SIXTEEN (April 30 - May 4)
WEEK SEVENTEEN (May 7 - 9) READING DAY May 10
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.
We will need to become experts in the magnetosome produced by bacteria. We will need to identify key papers to understand what is known so far. We also need to understand what UW-Seattle iGEM2011 did with this project.
- 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.
- Community Structure in Time-Dependent, Multiscale, and Multiplex Networks
Peter J. Mucha, Thomas Richardson, Kevin Macon, Mason A. Porter, and Jukka-Pekka Onnela
Science. Vol. 328. page 876-878.
- 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.
- A Cultured Greigite-Producing Magnetotactic Bacterium in a Novel Group of Sulfate-Reducing Bacteria
Christopher T. Lefèvre, et al.
Science. Vol. 334. page 1720.
- 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.
