Raj Lab:Reading list
Here's a list of papers that we think are interesting or useful (still very much a work in progress...):
Introduction to stochastic effects in gene expression
- Ko MS, Nakauchi H, and Takahashi N. The dose dependence of glucocorticoid-inducible gene expression results from changes in the number of transcriptionally active templates. EMBO J. 1990 Sep;9(9):2835-42.
A surprisingly modern analysis of non-genetic variability in gene expression in mammalian cells.
- Elowitz MB, Levine AJ, Siggia ED, and Swain PS. Stochastic gene expression in a single cell. Science. 2002 Aug 16;297(5584):1183-6. DOI:10.1126/science.1070919 |
A beautiful demonstration that variability in gene expression is intrinsically random.
- Ozbudak EM, Thattai M, Kurtser I, Grossman AD, and van Oudenaarden A. Regulation of noise in the expression of a single gene. Nat Genet. 2002 May;31(1):69-73. DOI:10.1038/ng869 |
Perhaps the first demonstration of the dependence of variability upon biochemical parameters.
- turing-ptrslb-52 pmid=2185858
//This paper talks about how patterns can form from the spatial interactions between diffusing chemical species. Check out the date this paper was published: before the structure of DNA! Also, it's one of the first papers to recognize the role that computer simulations could play in studying these types of problems.
- berg-biophysj-77 pmid=911982
//A classic paper about the physical limits of receptor function.
- gregor-cell-07 pmid=17632062
- wernet-nature06 pmid=16525464
//A technical tour de force in which the authors show that stochastic expression established the retinal mosaic in fruit flies.
- chang-nature08 pmid=18497826
//In this paper, the authors show that stochastic lineage commitment is a result of transcriptome wide variability in gene expression. Cool!