Old Journal Club Info

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  • Design Principles of Genetic Circuits
  • tentative: Every other Tuesday, 4PM (maybe 3PM?)

The location will alternate between two venues:

Berkeley West Biocenter
717 Potter St
Room 248
Holmes Lab
Hearst Memorial Mining Building
UC-Berkeley campus
Room 425

Transportation between the two venues: LBL-Potter St shuttle. Or, you can arrange a ride with someone driving. Post requests to the list!

Rules: We avoid discussing papers co-authored by anyone in the group. One paper per meeting, no review articles (unless we are having a special "survey of topics" meeting, which will occur, but rarely). Everyone has to present. That's it.

Schedule for Fall 2006:

Date Presenter Paper/Topic Venue
10/17 N/A Postponed in favor of going to the bioenergy journal club that is starting up Thursday the 19th: Berkeley West Biocenter, Sudar Auditorium (room 120), 5-6PM N/A
10/03 Yuri Bendana Pedraza & van Oudenaarden: Noise propagation in gene networks. Science 2005;307:1965-9. Berkeley West Biocenter
09/26 Andrew Uzilov review of reviews:
- Voigt &: Genetic parts to program bacteria. Curr. Opin. Biotechnol. 2006;17:548-57. (thanks to Karsten Temme for the suggestion)
- Isaacs et al.: RNA synthetic biology. Nat. Biotechnol. 2006;24:545-54.
Holmes lab

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Suggestions for Papers and Other Resources

Suggestions for future discussion:

  • Chan et al.: Refactoring bacteriophage T7. Mol. Syst. Biol. 2005;1:2005.0018.
    • We've all (hopefully) refactored code at some point or another... but have you refactored a genome?
  • Maytals T, Horace A. The Morphology of Audio below 170Hz when Predicting Variable Levels of Jah Glory. Or, from Version to Dub: Rasta Man Science Inna the Dancehall
    • What makes the selectah rewind one track, while the crowd ignores the next selection? A fascinating view into an oft overlooked scientific nook, and a pleasant diversion from RNA. If you are on snack duty for this week, plan ahead!
  • Deamer, D. The First Cell Membranes. Astrobiology, Dec 2002, Vol. 2, No. 4: 371-381.
    • OK, what's a paper from Astrobiology doing here? Well, it's a long shot, but:
      • Deamer gave a talk at UC-Berkeley (RealAudio feed here) about artificial life "from scratch," not just reconstituting components of existing systems. That is, you find the minimum possible set of components to have a working, reproducing cell. The goal is pretty far down the line, but it might be nice to consider a completely engineered system where you have total control, instead of tweaking/hacking known life.
      • Deamer also works mainly in membrane self-assembly, which is kind of relevant if you want to encapsulate your genetic circuits in cellular organelles. Yes, that is also quite down the line, but we can dream...
  • Not a paper, just a pointer that there are some interesting talks recorded from the synthetic biology seminar at UC-Berkeley in Fall 2005, which you can download here.

Papers relevant to questions that have come up in the journal club:


Schedule from Spring 2006:

Date Presenter Paper Venue
04/10 Ian Holmes Penchovsky & Breaker: Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes. Nat. Biotechnol. 2005;23:1424-33. Berkeley West Biocenter
04/17 Darren Platt Kobayashi et al.: Programmable cells: interfacing natural and engineered gene networks. Proc. Natl. Acad. Sci. U.S.A. 2004;101:8414-9. Berkeley West Biocenter
04/24 Yuri Bendana Bayer & Smolke: Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat. Biotechnol. 2005;23:337-43. Berkeley West Biocenter
05/01 Robert Bradley Guido et al.: A bottom-up approach to gene regulation. Nature 2006;439:856-60. Berkeley West Biocenter
05/08 Andrew Uzilov Benenson et al.: An autonomous molecular computer for logical control of gene expression. Nature 2004;429:423-9. Holmes lab
05/15 Sharon Chao Lederman et al.: Deoxyribozyme-based three-input logic gates and construction of a molecular full adder. Biochemistry 2006;45:1194-9. Holmes Lab
05/22 cancelled due to Synthetic Biology 2.0 conference at UC-Berkeley
05/29 cancelled due to Memorial Day holiday
06/05 postponed
06/12 postponed
06/19 postponed
06/26 Darren Platt recap of Synthetic Biology 2.0 conference - see the talks you missed via this webcast Berkeley West Biocenter
07/03 - 08/21 in hiatus for the summer
08/28 Fall classes begin - resume journal club (?)
09/04 academic & administrative holiday - cancel (?)

For earlier discussion of times, topics, etc, see journal club planning. -- Ian Holmes - 18 Apr 2006

Moved from Journal Club -- Ian Holmes - 29 Sep 2008