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ODE Module Guide

Useful papers

• Rosenfeld N, Elowitz MB, Alon U. Negative autoregulation speeds the response times of transcription networks J Mol Biol. 2002 Nov 8;323(5):785-93.
• Mangan, S., and Alon, U. (2003). Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci U S A 100, 11980-11985.
• Mangan S, Zaslaver A, Alon U.The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks.J Mol Biol. (2003) 334:197-204.
• Mangan S, Itzkovitz S, Zaslaver A, Alon U. The incoherent feed-forward loop accelerates the response-time of the gal system of Escheri chia coli. J Mol Biol. (2006) 356:1073-81.

Wednesday, November 4

• Notes part 1, Notes part 2

Due Friday, November 6:

• Homework 1

By Monday, November 9:

• Set up Matlab!

Wednesday, November 11

• Notes part 3

Due Friday, November 13:

• Homework 2

Friday, November 13

• Notes part 4

Due Friday, November 20:

• Programming Homework 1

Monday, November 16

• Notes part 5

Before next class:

• Paper by Goutsias and Kim, paper by Goutsias and Lee

Wednesday, November 18

Before next class:

• Read at least the Introduction and Materials and Methods sections from Chen et al
• Read Kuttykrishnan et al, skipping the Results and Discussion sections, if necessary
• Bring to class a written list of questions/comments to discuss and turn them in after class

Friday, November 20

• Discussion of Chen et al and Kuttykrishnan et al approaches to modeling regulatory networks using ODEs