Below are several papers which you may find useful for the rotation.
Statistical Physics and Biology
A First Exposure to Statistical Mechanics for Life Scientists by Hernan G. Garcia, Jané Kondev, Julie A. Theriot, and Rob Phillips. Rejected by Am. J. Phys, 2007. | This paper summarizes the basics of statistical mechanics and presents them in an array of biological contexts.
Transcriptional Regulation by the Numbers 1: Models by Lacramiaora Bintu, Nicolas E. Buchler, Hernan G. Garcia, Ulrich Gerland, Terence Hwa, Jané Kondev, and Rob Phillips. Curr. Op. Gen. Dev. (2005) | This work shows how thermodynamic models are used to describe the behavior of a variety of regulatory architectures.
Transcriptional Regulation by the Numbers 2: Applications by Lacramiaora Bintu, Nicolas E. Buchler, Hernan G. Garcia, Ulrich Gerland, Terence Hwa, Jané Kondev, Thomas Kuhlman, and Rob Phillips. Curr. Op. Gen. Dev. (2005) | Here, our discussion of thermodynamic models of genetic regulation are expanded to examine how these input/output functions can be used to make predictions regarding transcriptional outputs.
Cell Biology by the Numbers by Ron Milo and Rob Phillips. Garland Science (2015) | This is a very useful resources that gives numbers for various biological miscellany.
- Gene Regulation at the Single Cell Level by Nitzan Rosenfeld, Jonathan W. Young, Uri Alon, Peter S. Swain, and Michael B. Elowitz. Science (2005) | This was the first publication of the method of counting proteins by the dilution method. This is the method we will use for counting the number of repressors under varying growth conditions.
Relevant Project Literature
- Quantitative Dissection of the Simple Repression Input-Output Function by Hernan G. Garcia and Rob Phillips. PNAS (2011). | This work laid the foundation upon which all of our studies regarding the fold-change in gene expression