Difference between revisions of "Synthetic Biology Network Research"

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[[WEEK SIX (February 20 - 24)]] Synthetic Seminar Feb. 23 and '''lunch''' with [http://haynes.lab.asu.edu/index.html speaker Dr. Karmella Haynes] at Arizona State University
  
  
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[[WEEK EIGHT (March 5 - 9)]] '''SPRING BREAK'''
 
[[WEEK EIGHT (March 5 - 9)]] '''SPRING BREAK'''
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[[WEEK TEN (March 19 - 23)]]
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[[WEEK ELEVEN (March 26 - 30)]]
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[[WEEK TWELVE (April 2 - 6)]]
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[[WEEK THIRTEEN (April 9 - 13)]] '''INCLUDES EASTER BREAK'''
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[[WEEK FOURTEEN (April 16 - 20)]]
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[[WEEK FIFTEEN (April 23 - 27)]]
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[[WEEK SIXTEEN (April 30 - May 4)]]
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[[WEEK SEVENTEEN (May 7 - 9)]] '''READING DAY May 10'''
  
  

Revision as of 13:26, 26 January 2012

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 ONE (January 17 - 20)


WEEK TWO (January 23 - 27)


WEEK THREE (January 30 - February 3)


WEEK FOUR (February 6 - 10) WET LAB WEEK


WEEK FIVE (February 13 - 17)


WEEK SIX (February 20 - 24) Synthetic Seminar Feb. 23 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 NINE (March 12 - 16)


WEEK TEN (March 19 - 23)


WEEK ELEVEN (March 26 - 30)


WEEK TWELVE (April 2 - 6)


WEEK THIRTEEN (April 9 - 13) INCLUDES EASTER BREAK


WEEK FOURTEEN (April 16 - 20)


WEEK FIFTEEN (April 23 - 27)


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.


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.

  • 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.



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