First q-bio Summer School: Gene Regulation

Back to The First q-bio School.

These lectures will cover topics related to gene regulation, including: mathematical modeling of genetic regulatory circuits, mechanisms of transcription and translation, reverse engineering of regulatory networks, and biological design principles.

Please contact Michael Wall (mewall@lanl.gov) for questions.

Lecture 1

Scope

Design Principles

Lecturer

Michael Wall

Materials

Lecture notes

PDF Lecture notes

Relevant websites

EcoTFs

Key References

• ME Wall, WS Hlavacek, MA Savageau. Design of gene circuits: lessons from bacteria. Nat Rev Genet 5:34-42 (2004)
• ME Wall, MJ Dunlop, WS Hlavacek. Multiple functions of a feed-forward-loop gene circuit. J Mol Biol 349:501-514 (2005)

Additional Reading

• DF Browning, SJ Busby. The regulation of bacterial transcription initiation. Nat Rev Microbiol 2:57-65 (2004)
• M Ptashne, A Gann. Genes & Signals. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, New York (2002).

or alternatively

M Ptashne, A Gann. Transcriptional activation by recruitment. Nature 386:569-577 (1997)

M Ptashne. Regulated recruitment and cooperativity in the design of biological regulatory systems. Pilos Transact A Math Phys Eng Sci 361:1223-1234 (2003)

Lecture 2

Scope

Boolean models for genetic regulatory networks

Lecturer

Cynthia Olson Reichhardt

Materials

PDF Lecture notes

References

J. Phys. A: Math. Theor. 40, 4339 (2007)

Lecture 3

Scope

Protein Translation

Lecturer

Kevin Sanbonmatsu

Materials

Lecture notes

Relevant websites

References

Lecture 4

Scope

Reverse Engineering Genetic Networks: Predictive Models

Lecturer

Chris Wiggins

Materials

Lecture notes

Relevant websites

References