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Caltech BioControl

We are investigating strategies for the engineering of biological systems

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  • Best of 06-07 (10)
  • Best of 07-08 (6)

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  • Fiona A Chandra (Caltech) created an event
    Meeting
    Friday, December 10, 2010 - 10:00am at Steele Library
    Engineering of a synthetic electron conduit in living cells. Jensen H. M. (2010) Proceedings of the National Academy of Sciences.
    December 9, 2010
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  • Elisa Franco (Caltech) created an event
    Meeting
    Friday, November 19, 2010 - 10:00am at Steele library

    I'll be presenting the paper below, with a few slides.

    An Experimental Design Method Leading to Chemical Turing Patterns. Horvath J. (2009) Science.
    November 10, 2010
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  • Fiona A Chandra (Caltech) created an event
    Restarting BioControl!
    Friday, October 22, 2010 - 9:30am at CDS Library

    Let's restart BioControl for the new school year.

    We'll have breakfast!

    Fundamental limits on the suppression of molecular fluctuations. Lestas Ioannis (2010) Nature.
    October 11, 2010
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  • Elisa Franco (Caltech) created an event
    Next journal club
    Saturday, April 24, 2010 - 1:40pm at Steele 110

    This paper uses all the tools of chemical reaction networks we are talking about this week. I put my notes about CRNs from the BioControl class website, they might be useful to read the paper.
    http://www.cds.caltech.edu/~elisa/CDS270-4-2010/CDS270-4-2010-Week4-1.pdf

    Structural sources of robustness in biochemical reaction networks. Shinar G (2010) Science.
    April 20, 2010
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  • Elisa Franco (Caltech) created an event
    Journal club + CDS 270-4 weekly reading
    Friday, April 9, 2010 - 1:30pm at Steele 110

    In this paper they propose a definition of bifurcations for stochastic systems.
    Seems interesting and an appropriate reading for class and journal club; the paper just came out a month ago. Brian Ingalls was a student with Eduardo Sontag.

    Estimating the stochastic bifurcation structure of cellular networks. Song C (2010) PLoS Comput Biol.
    April 5, 2010
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  • Vanessa Jonsson (Caltech) created an event
    Meeting
    Friday, March 19, 2010 - 11:00am at Steele CDS Library

    This is an old article but it is a standard way of modeling chemical kinetics in biology.

    Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm. Rao Christopher V. (2003) J. Chem. Phys..
    March 16, 2010
    Oh Noes, no one's there... - Zhaoqian Steven Xie (Caltech) March 19, 2010 Comment deleted
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  • Ophelia Venturelli (Caltech) created an event
    Meeting
    Friday, March 12, 2010 - 11:00am at Steele 114 (CDS Library)
    Parameter Estimation and Model Selection in Computational Biology. Lillacci Gabriele (2010) PLoS Comput Biol.
    March 9, 2010
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  • Fiona A Chandra (Caltech) created an event
    BioControl Meeting
    Saturday, March 6, 2010 - 11:00am at Steele Library

    Because this looks pretty cool~
    I'll also try to get us some coffee/snacks!

    Rules for Biologically Inspired Adaptive Network Design. Tero A. (2010) Science.
    March 3, 2010
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  • Zhaoqian Steven Xie (Caltech) created an event
    Meeting
    Friday, February 19, 2010 - 9:00am at CDS Library, Steele 114

    Hi, I'm Steven, a 1st year CDS grad student interested in systems biology. This is the article I picked.

    Shifts in growth strategies reflect tradeoffs in cellular economics. Molenaar Douwe (2009) Mol Syst Biol.
    February 16, 2010
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  • Elisa Franco (Caltech) created an event
    Meeting
    Friday, February 12, 2010 - 9:00am at Steele library
    Is genetic evolution predictable?. Stern DL (2009) Science.
    February 5, 2010
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  • Fiona A Chandra (Caltech)

    next meeting: Friday, February 5, 2010 - 9:00am at Steele Library

    Promoter architecture and the evolvability of gene expression. Tirosh Itay (2009) J Biol.

    February 5, 2010
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  • Ophelia Venturelli (Caltech) created an event
    Meeting
    Saturday, January 23, 2010 - 9:00am at CDS Library (Steele 114)
    Design principles for ligand-sensing, conformation-switching ribozymes. Chen X (2009) PLoS Comput Biol.
    January 21, 2010
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  • Ophelia Venturelli (Caltech) created an event
    Meeting
    Friday, January 15, 2010 - 9:00am at CDS Library (Steele 114)

    Here's the paper for tomorrow!

    Probing the Limits to Positional Information. GREGOR T (2007) Cell.
    January 14, 2010
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  • Elisa Franco (Caltech) created an event
    next meeting?
    Friday, November 27, 2009 - 10:00am at Steele Library

    What about this paper? If you have better ideas, let me know.

    Evolvability and hierarchy in rewired bacterial gene networks. Isalan M (2008) Nature.
    November 20, 2009
    We did that one last year - it made it into the top of '07-'08. I'd suggest the new paper from Wingreen and Bassler (et al.). - Joshua K. Michener (Caltech) November 20, 2009 Comment deleted
    Oh I must have missed that meeting! Thanks for pointing that out... - Elisa Franco (Caltech) November 28, 2009 Comment deleted
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  • Ophelia Venturelli (Caltech)

    Hey everyone-would it be okay if we shifted our meetings to 9am on Fridays? Let me know.

    November 19, 2009
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  • Fiona A Chandra (Caltech) created an event
    Next Meeting
    Friday, November 13, 2009 - 10:00am at CDS Library (Steele)

    There will be bagels for breakfast!

    Unlimited multistability in multisite phosphorylation systems. Thomson M (2009) Nature.
    November 11, 2009
    How did this paper get into nature? - Elisa Franco (Caltech) November 13, 2009 Comment deleted
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  • Elisa Franco (Caltech) created an event
    Next meeting
    Friday, October 30, 2009 - 10:00am at Steele Library

    Paper about noise...

    Molecular Systems Biology 5 Article number: 318 doi:10.1038/msb.2009.75
    Published online: 13 October 2009
    Citation: Molecular Systems Biology 5:318

    Listening to the noise: random fluctuations reveal gene network parameters

    Brian Munsky1, Brooke Trinh2 & Mustafa Khammash3

    October 26, 2009
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  • Elisa Franco (Caltech) created an event
    Next meeting
    Friday, October 16, 2009 - 10:00am at Steele library
    Kinetic Buffering of Cross Talk between Bacterial Two-Component Sensors. Groban Eli S. (2009) Journal of Molecular Biology.
    October 9, 2009
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  • Elisa Franco (Caltech) created an event
    Next meeting
    Wednesday, October 7, 2009 - 10:30am at Steele Library

    Potential date for starting our meetings again! I picked a random paper...

    Synthetic biology: The yin and yang of nature. Gore Jeff (2009) Nature.
    September 10, 2009
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  • Elisa Franco (Caltech) is following 6 new articles in Best of 07-08
    Evolvability and hierarchy in rewired bacterial gene networks. Isalan M (2008) Nature.
    Molecular computation of solutions to combinatorial problems. Adleman LM (1994) Science.
    Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate. Santos SD (2007) Nat Cell Biol.
    Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics. Bashor CJ (2008) Science.
    Real-time kinetics of gene activity in individual bacteria. Golding I (2005) Cell.
    The frequency dependence of osmo-adaptation in Saccharomyces cerevisiae. Mettetal JT (2008) Science.
    September 10, 2009
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  • Elisa Franco (Caltech) is following 10 new articles in Best of 06-07
    Accurate prediction of gene feedback circuit behavior from component properties. Rosenfeld N (2007) Mol Syst Biol.
    Enzyme-free nucleic acid logic circuits. Seelig G (2006) Science.
    Transient dynamics of genetic regulatory networks. Bennett MR (2007) Biophys J.
    Physical limits to biochemical signaling. Bialek W (2005) Proc Natl Acad Sci U S A.
    Stochastic focusing: fluctuation-enhanced sensitivity of intracellular regulation. Paulsson J (2000) Proc Natl Acad Sci U S A.
    Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems. Angeli D (2004) Proc Natl Acad Sci U S A.
    Improving lycopene production in Escherichia coli by engineering metabolic control. Farmer WR (2000) Nat Biotechnol.
    RNA synthetic biology. Isaacs FJ (2006) Nat Biotechnol.
    Network motifs: simple building blocks of complex networks. Milo R (2002) Science.
    Guiding bacteria with small molecules and RNA. Topp S (2007) J Am Chem Soc.
    September 10, 2009
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  • Elisa Franco (Caltech) created the Caltech BioControl journal club.
    September 10, 2009
  • Elisa Franco (Caltech) created an event
    Week3-27
    Wednesday, May 13, 2009 - 10:00am at Steele Library

    Phosphorelays

    Complexity in bacterial cell-cell communication: quorum signal integration and subpopulation signaling in the Bacillus subtilis phosphorelay. Bischofs IB (2009) Proc Natl Acad Sci U S A.
    October 9, 2009
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  • Elisa Franco (Caltech) created an event
    Week3-26
    Wednesday, May 6, 2009 - 10:00am at Steele Library

    signaling network
    integration of multiple signals
    EGF, Insulin MAPK cascades

    Systems-level interactions between insulin-EGF networks amplify mitogenic signaling. Borisov N (2009) Mol Syst Biol.
    October 9, 2009
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  • Elisa Franco (Caltech) created an event
    Week3-25
    Wednesday, April 29, 2009 - 10:00am at Steele Library

    * Leibler
    * evolution of cooperation

    Simpson's paradox in a synthetic microbial system. Chuang JS (2009) Science.
    October 9, 2009
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  • Elisa Franco (Caltech) created an event
    Week3-24
    Wednesday, April 22, 2009 - 10:00am at Steele Library

    Ultrasensitivity and molecular titration

    Molecular titration and ultrasensitivity in regulatory networks. Buchler NE (2008) J Mol Biol.
    October 9, 2009
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  • Elisa Franco (Caltech) created an event
    Week3-23
    Wednesday, April 15, 2009 - 10:00am at Steele Library

    Negative feedback and linearization

    Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression. Nevozhay D (2009) Proc Natl Acad Sci U S A.
    October 9, 2009
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  • Elisa Franco (Caltech) created an event
    Week3-22
    Wednesday, April 8, 2009 - 10:00am at Steele Library

    Stress transient transcriptional responses

    Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Shalem O (2008) Mol Syst Biol.
    October 9, 2009
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  • Elisa Franco (Caltech) created an event
    Week3-21
    Wednesday, April 8, 2009 - 10:00am at Steele Library

    Modeling and experiments to understand mechanisms of gene regulation by sRNA in bacteria

    Quantitative characteristics of gene regulation by small RNA. Levine E (2007) PLoS Biol.
    October 9, 2009
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  • Elisa Franco (Caltech) created an event
    Week3-20
    Wednesday, March 18, 2009 - 10:00am at Steele Library

    Control of Stem Cell Proliferation and Lineages

    Cell lineages and the logic of proliferative control. Lander AD (2009) PLoS Biol.
    October 9, 2009
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