Raj Lab:Reading list

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(Developmental biology)
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Here's a list of papers that we think are interesting or useful (still very much a work in progress...):
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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 ==
== Introduction to stochastic effects in gene expression ==
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</biblio>
</biblio>
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== Developmental biology ==
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== Numbers in biology ==
<biblio>
<biblio>
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#turing-ptrslb-52 pmid=2185858
 
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//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
#berg-biophysj-77 pmid=911982
//A classic paper about the physical limits of receptor function.
//A classic paper about the physical limits of receptor function.
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#phillips-pnas-09 pmid=20018695
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//A really cool paper about the role that quantitative measurements can play in studying biology
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</biblio>
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== Developmental biology ==
 +
 +
<biblio>
 +
#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.
#gregor-cell-07 pmid=17632062
#gregor-cell-07 pmid=17632062
#wernet-nature06 pmid=16525464
#wernet-nature06 pmid=16525464

Current revision

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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. . pmid:2167833. PubMed 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. . pmid:12183631. PubMed 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. . pmid:11967532. PubMed 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. . pmid:911982. PubMed HubMed [berg-biophysj-77]
    A classic paper about the physical limits of receptor function.

  2. Phillips R and Milo R. . pmid:20018695. PubMed 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 AM. . pmid:2185858. PubMed HubMed [turing-ptrslb-52]
    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.

  2. Gregor T, Tank DW, Wieschaus EF, and Bialek W. . pmid:17632062. PubMed HubMed [gregor-cell-07]
  3. Wernet MF, Mazzoni EO, Celik A, Duncan DM, Duncan I, and Desplan C. . pmid:16525464. PubMed HubMed [wernet-nature06]
    A technical tour de force in which the authors show that stochastic expression established the retinal mosaic in fruit flies.

  4. Chang HH, Hemberg M, Barahona M, Ingber DE, and Huang S. . pmid:18497826. PubMed HubMed [chang-nature08]
    In this paper, the authors show that stochastic lineage commitment is a result of transcriptome wide variability in gene expression. Cool!

All Medline abstracts: PubMed HubMed
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