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Caltech BioControl
We are investigating strategies for the engineering of biological systems
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2010
Engineering of a synthetic electron conduit in living cells. Jensen H. M. (2010) Proceedings of the National Academy of Sciences.
An Experimental Design Method Leading to Chemical Turing Patterns. Horvath J. (2009) Science.
Fri 22 Oct
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.
Sat 24 Apr
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.
Fri 09 Apr
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.
Fri 19 Mar
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..
Parameter Estimation and Model Selection in Computational Biology. Lillacci Gabriele (2010) PLoS Comput Biol.
Sat 06 Mar
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.
Fri 19 Feb
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.
Is genetic evolution predictable?. Stern DL (2009) Science.
Design principles for ligand-sensing, conformation-switching ribozymes. Chen X (2009) PLoS Comput Biol.
Probing the Limits to Positional Information. GREGOR T (2007) Cell.
2009
Evolvability and hierarchy in rewired bacterial gene networks. Isalan M (2008) Nature.
Unlimited multistability in multisite phosphorylation systems. Thomson M (2009) Nature.
Fri 30 Oct
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
Kinetic Buffering of Cross Talk between Bacterial Two-Component Sensors. Groban Eli S. (2009) Journal of Molecular Biology.
Synthetic biology: The yin and yang of nature. Gore Jeff (2009) Nature.
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.
Systems-level interactions between insulin-EGF networks amplify mitogenic signaling. Borisov N (2009) Mol Syst Biol.
Simpson's paradox in a synthetic microbial system. Chuang JS (2009) Science.
Molecular titration and ultrasensitivity in regulatory networks. Buchler NE (2008) J Mol Biol.
Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression. Nevozhay D (2009) Proc Natl Acad Sci U S A.
Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Shalem O (2008) Mol Syst Biol.
Wed 08 Apr
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.
Cell lineages and the logic of proliferative control. Lander AD (2009) PLoS Biol.
Wed 25 Feb
Synthetic Controller to tune fitness tradeoffs.
Or, following up on our "Endy" topic with "Smolke" :P -F
Synthetic control of a fitness tradeoff in yeast nitrogen metabolism. Bayer TS (2009) J Biol Eng.
Determination of cell fate selection during phage lambda infection. St-Pierre F (2008) Proc Natl Acad Sci U S A.
Survival of the sparsest: robust gene networks are parsimonious. Leclerc RD (2008) Mol Syst Biol.
Chromatin decouples promoter threshold from dynamic range. Lam FH (2008) Nature.
Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Gertz J (2009) Nature.
2008
A quantitative model of transcription factor-activated gene expression. Kim HD (2008) Nat Struct Mol Biol.
Wed 19 Nov
* Activity motifs
* principles of timing
* transcriptional control
* yeast
* metabolic networks
Comments:
Promising, but ultimately disappointing. The curve fitting to the mRNA data was not convincing (the shape of the data did not match the fit). Measurements (mRNA and ChIP-chip in particular) should probably have large error bars, bringing fine distinctions in timing or affinity into question. Time resolution was also questionable - the first measurement was taken at 15...
Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network. Chechik G (2008) Nat Biotechnol.
A fast, robust and tunable synthetic gene oscillator. Stricker J (2008) Nature.
A stochastic single-molecule event triggers phenotype switching of a bacterial cell. Choi PJ (2008) Science.
Higher-order cellular information processing with synthetic RNA devices. Win MN (2008) Science.
Design and construction of a double inversion recombination switch for heritable sequential genetic memory. Ham TS (2008) PLoS One.
A genetic timer through noise-induced stabilization of an unstable state. Turcotte M (2008) Proc Natl Acad Sci U S A.
Frequency-modulated nuclear localization bursts coordinate gene regulation. Cai L (2008) Nature.
Wed 01 Oct
Game theoretic approach to modeling DNA-protein binding
Game theoretic algorithms for protein-DNA binding (Perez-Breva, Ortiz, Yeang, Jaakkola)
Stimulus design for model selection and validation in cell signaling. Apgar JF (2008) PLoS Comput Biol.
Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Tsai TY (2008) Science.
Production of benzylisoquinoline alkaloids in Saccharomyces cerevisiae. Hawkins KM (2008) Nat Chem Biol.
Metabolic gene regulation in a dynamically changing environment. Bennett MR (2008) Nature.