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

Numbers in biology

  1. Berg HC and Purcell EM. Physics of chemoreception. Biophys J. 1977 Nov;20(2):193-219. DOI:10.1016/S0006-3495(77)85544-6 | PubMed ID:911982 | HubMed [berg-biophysj-77]

    A classic paper about the physical limits of receptor function.

  2. Phillips R and Milo R. A feeling for the numbers in biology. Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):21465-71. DOI:10.1073/pnas.0907732106 | PubMed ID:20018695 | HubMed [phillips-pnas-09]

    A really cool paper about the role that quantitative measurements can play in studying biology

All Medline abstracts: PubMed | HubMed

Developmental biology


  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 (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.

  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!