Caltech Synthetic Biology Journal Club

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Past Reading

SynBio @ Caltech

  • We are a journal club at Caltech, getting graduate students together to discuss synthetic biology and metabolic engineering.


  • First meeting POSTPONED to 1/28/2011, 4pm, location Steele Library.

Weekly Topics

We'll start with a broad introduction to popular topics in synthetic biology, then figure out the logistics for future weeks - this will most likely involve rotating responsibility for presenting material each week. If you think the first few weeks will only cover old papers for you, feel free to jump in later.

  • Week 1: Introduction to Synthetic Biology (Emzo and Joe)
    • Synthetic biology: new engineering rules for an emerging discipline. Andrianantoandro E, Basu S, Karig DK and Weiss R. Mol Sys Bio. 2:2006.0028 [1]
    • Synthetic biology: applications come of age. Khalil AS and Collins JJ. Nature Reviews Genetics 11: 367-379 (2010) [2]

  • Week 2: DNA Level Control (Emzo)
    • Construction of a genetic toggle switch in Escherichia coli. Gardner TS, Cantor CR and Collins JJ. Nature 403: 339-342 (2000). [3]
    • Synthetic gene networks that count. Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ. Science 324:1199-1202 (2009). [4]

  • Week 3: Oscillators & Dynamics (Emzo)
    • A Synthetic Oscillatory Network of Transcriptional Regulators. Elowitz MB, Leibler S. Nature. 403:335-8. (2000) [5]
    • A fast, robust and tunable synthetic gene oscillator. Stricker J, Cookson S, Bennett MR, Mather WH, Tsimring LS, Hasty J. Nature. 456:516-19 (2008) [6]

  • Week 4: RNA Based Regulation (Joe)
    • RNA synthetic biology Issacs FJ, Dwyer DJ, Collins JJ. Nature Biotechnology 24:545-555 (2006) [7]
    • Higher-Order Cellular Information Processing with Synthetic RNA Devices Win MN, Smolke CD. Science. 322:456-460 (2008) [http:/]

  • Week 5: Multiple Genes - Gene Network Engineering (Joe)
    • Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models Lewis NE et al. Molecular Systems Biology 6:390 (2010) [8]
    • Programming cells by multiplex genome engineering and accelerated evolution Wang HH, Issacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM. Nature 460:894-898 (2009) [9]
    • Manufacturing Molecules Through Metabolic Engineering Keasling, JD. Science. 330:1355-1358 (2010) [10]

  • Week 6: Multiple Cells - Quorum Sensing and Cell-Cell Communication (Joe)
    • A synthetic multicellular system for programmed pattern formation Basu S, Gerchman Y, Collins CH, Arnold FH, Weiss R. Nature 434 (2005) [11]
    • A synthetic Escherichia coli predator–prey ecosystem Balagadde FK, Song H, Ozaki J, Collins CH, Barnet M, Arnold FH, Quake SR, You L. Molecular Systems Biology 4:187 (2008) [12]
    • Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’ Tamsir A, Tabor JJ, Voigt CA. Nature (2010) [13]