Brown Systems Biology Journal Club

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Who

  • Nicola Neretti <Nicola_Neretti@b>, Assistant Professor, Physics
  • Suzanne Sindi <ssindi@dam.b>, Assistant Professor, Applied Math

When & where

We meet every two weeks in the SWIG Boardroom (2nd floor CIT room 241)

Next Meeting: Wed 4th April, 5:15pm

Sherief Reda will present "Network Motifs: Simple Building Blocks of Complex Networks" by R. Milo et al. Science 298 (824) 2002.

Mailing list

Previous Meetings

Feb. 14: Suzanne Sindi presented Chapter 1 from Computational Modeling of Genetic and Biochemical Networks, Bower and Bolouri (2001).

Feb. 28: Nicola Neretti presented Gardner TS, Cantor CR, Collins JJ: Construction of a genetic toggle switch in Escherichia coli. Nature 2000, 403(6767):339-342. and Jason Lohmueller presented his ongoing work in generalizing their results to a tristable switch.

Nicola's Slides are available at: http://openwetware.org/wiki/Image:SystemsBiologyJC_022807.pdf Jason's Slides are available at: http://openwetware.org/wiki/Image:Tristable_slides.pdf

March 14: Andrianantoandro E, Basu S, Karig DK, Weiss R: Synthetic biology: new engineering rules for an emerging discipline. Molecular systems biology [electronic resource] 2006, 2:2006 0028. Endy D: Foundations for engineering biology. Nature 2005, 438(7067):449-453.

Suggested Papers

Reviews:

Andrianantoandro E, Basu S, Karig DK, Weiss R: Synthetic biology: new engineering rules for an emerging discipline. Molecular systems biology [electronic resource] 2006, 2:2006 0028.

Endy D: Foundations for engineering biology. Nature 2005, 438(7067):449-453.

Aldridge BB, Burke JM, Lauffenburger DA, Sorger PK: Physicochemical modelling of cell signalling pathways. Nature cell biology 2006, 8(11):1195-1203.

Kaern M, Elston TC, Blake WJ, Collins JJ: Stochasticity in gene expression: from theories to phenotypes. Nature reviews 2005, 6(6):451-464.

Sprinzak D, Elowitz MB: Reconstruction of genetic circuits. Nature 2005, 438(7067):443-448.

Raser JM, O'Shea EK: Noise in gene expression: origins, consequences, and control. Science 2005, 309(5743):2010-2013.

Arias AM, Hayward P: Filtering transcriptional noise during development: concepts and mechanisms. Nature reviews 2006, 7(1):34-44.

Austin DW, Allen MS, McCollum JM, Dar RD, Wilgus JR, Sayler GS, Samatova NF, Cox CD, Simpson ML: Gene network shaping of inherent noise spectra. Nature 2006, 439(7076):608-611.


Relevant to iGEM’s candidate project (tri-stable continuation from 2006 project):

Gardner TS, Cantor CR, Collins JJ: Construction of a genetic toggle switch in Escherichia coli. Nature 2000, 403(6767):339-342.

Kramer BP, Fischer C, Fussenegger M: BioLogic gates enable logical transcription control in mammalian cells. Biotechnol Bioeng 2004, 87(4):478-484.


Networks:

Shen-Orr SS, Milo R, Mangan S, Alon U: Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 2002, 31(1):64-68.

Clocks, oscillators, and more:

Kollmann M, Lovdok L, Bartholome K, Timmer J, Sourjik V: Design principles of a bacterial signalling network. Nature 2005, 438(7067):504-507.

Elowitz MB, Leibler S: A synthetic oscillatory network of transcriptional regulators. Nature 2000, 403(6767):335-338.

Garcia-Ojalvo J, Elowitz MB, Strogatz SH: Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing. Proc Natl Acad Sci U S A 2004, 101(30):10955-10960.

Lahav G, Rosenfeld N, Sigal A, Geva-Zatorsky N, Levine AJ, Elowitz MB, Alon U: Dynamics of the p53-Mdm2 feedback loop in individual cells. Nat Genet 2004, 36(2):147-150.

Rosenfeld N, Young JW, Alon U, Swain PS, Elowitz MB: Gene regulation at the single-cell level. Science 2005, 307(5717):1962-1965.


Suel GM, Garcia-Ojalvo J, Liberman LM, Elowitz MB: An excitable gene regulatory circuit induces transient cellular differentiation. Nature 2006, 440(7083):545-550.

Janes KA, Albeck JG, Gaudet S, Sorger PK, Lauffenburger DA, Yaffe MB: A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science 2005, 310(5754):1646-1653.

Janes KA, Gaudet S, Albeck JG, Nielsen UB, Lauffenburger DA, Sorger PK: The response of human epithelial cells to TNF involves an inducible autocrine cascade. Cell 2006, 124(6):1225-1239.

Janes KA, Lauffenburger DA: A biological approach to computational models of proteomic networks. Current opinion in chemical biology 2006, 10(1):73-80.

Janes KA, Yaffe MB: Data-driven modelling of signal-transduction networks. Nat Rev Mol Cell Biol 2006, 7(11):820-828.


Stochasticity:

Raser JM, O'Shea EK: Control of stochasticity in eukaryotic gene expression. Science 2004, 304(5678):1811-1814.

Mettetal JT, Muzzey D, Pedraza JM, Ozbudak EM, van Oudenaarden A: Predicting stochastic gene expression dynamics in single cells. Proc Natl Acad Sci U S A 2006, 103(19):7304-7309.

Acar M, Becskei A, van Oudenaarden A: Enhancement of cellular memory by reducing stochastic transitions. Nature 2005, 435(7039):228-232.

Samadani A, Mettetal J, van Oudenaarden A: Cellular asymmetry and individuality in directional sensing. Proc Natl Acad Sci U S A 2006, 103(31):11549-11554.

Pedraza JM, van Oudenaarden A: Noise propagation in gene networks. Science 2005, 307(5717):1965-1969.

Thattai M, van Oudenaarden A: Stochastic gene expression in fluctuating environments. Genetics 2004, 167(1):523-530.

Becskei A, Kaufmann BB, van Oudenaarden A: Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nat Genet 2005, 37(9):937-944.