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. . pmid:2167833.
A surprisingly modern analysis of non-genetic variability in gene expression in mammalian cells.
- Elowitz MB, Levine AJ, Siggia ED, and Swain PS. . pmid:12183631.
A beautiful demonstration that variability in gene expression is intrinsically random.
- Ozbudak EM, Thattai M, Kurtser I, Grossman AD, and van Oudenaarden A. . pmid:11967532.
Perhaps the first demonstration of the dependence of variability upon biochemical parameters.
Numbers in biology
- Berg HC and Purcell EM. . pmid:911982.
A classic paper about the physical limits of receptor function.
- Phillips R and Milo R. . pmid:20018695.
A really cool paper about the role that quantitative measurements can play in studying biology
- Turing AM. . 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 (this ref says 1953, but it was actually 1952)! Also, it's one of the first papers to recognize the role that computer simulations could play in studying these types of problems.
- Gregor T, Tank DW, Wieschaus EF, and Bialek W. . pmid:17632062.
- Wernet MF, Mazzoni EO, Celik A, Duncan DM, Duncan I, and Desplan C. . pmid:16525464.
A technical tour de force in which the authors show that stochastic expression established the retinal mosaic in fruit flies.
- Chang HH, Hemberg M, Barahona M, Ingber DE, and Huang S. . pmid:18497826.
In this paper, the authors show that stochastic lineage commitment is a result of transcriptome wide variability in gene expression. Cool!