Raj Lab:Reading list

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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

  1. 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. PubMed ID:2167833 | HubMed [ko-emboj-90]
    A surprisingly modern analysis of non-genetic variability in gene expression in mammalian cells.
  2. 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 | PubMed ID:12183631 | HubMed [elowitz-science-02]
    A beautiful demonstration that variability in gene expression is intrinsically random.
  3. 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 | PubMed ID:11967532 | HubMed [ozbudak-natgen-02]
    Perhaps the first demonstration of the dependence of variability upon biochemical parameters.
All Medline abstracts: PubMed | HubMed

Developmental biology

<biblio>

  1. 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.

  1. berg-biophysj-77 pmid=911982

//A classic paper about the physical limits of receptor function.

  1. gregor-cell-07 pmid=17632062
  2. wernet-nature06 pmid=16525464

//A technical tour de force in which the authors show that stochastic expression established the retinal mosaic in fruit flies.

  1. 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!