User:Jarle Pahr/Genetic circuits

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Notes on designs for genetic circuits:

Regulatory motifs

Published circuits

A genetic bistable switch utilizing nonlinear protein degradation.: http://www.ncbi.nlm.nih.gov/pubmed/22776405

Oscillators

Elowitz & Leiber 2000. A synthetic oscillatory network of transcriptional regulators.: http://www.ncbi.nlm.nih.gov/pubmed/10659856?dopt=Abstract&holding=npg

Toggle switches

Gardner et al. 2000. Construction of a genetic toggle switch in Escherichia coli: http://www.nature.com/nature/journal/v403/n6767/full/403339a0.html


Hypothetical/proposed circuits

Discrete-Time Signal Processing with DNA: http://pubs.acs.org/doi/abs/10.1021/sb300087n


Tools

Tools for the design of genetic circuits:


Bibliography

Positive feedback circuits and memory.: http://www.ncbi.nlm.nih.gov/pubmed/10742912

Emergence of complex behaviour from simple circuit structures.: http://www.ncbi.nlm.nih.gov/pubmed/12754938


Engineering prokaryotic gene circuits: http://www.ncbi.nlm.nih.gov/pubmed/19016883

Gene regulation: Towards a circuit engineering discipline. Harley H. McAdams and Adam Arkin: http://www.chemengr.ucsb.edu/~ceweb/courses/che154/pdf/McAdams_and_Arkin_CurrBiol_2000.pdf


Foundations for engineering biology. Hasty, J. , McMillen, D. & Collins, J. J. Engineered gene circuits. Nature 420, 224–230 (2002)


Reconstruction of genetic circuits: http://www.nature.com/nature/journal/v438/n7067/full/nature04335.html

A coherent feedforward loop design principle to sustain robustness of biological networks: http://bioinformatics.oxfordjournals.org/content/29/5/630.full


Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0022490


Automatic Design of Synthetic Gene Circuits through Mixed Integer Non-linear Programming: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035529

Foundations for the design and implementation of synthetic genetic circuits: http://cs.brynmawr.edu/Courses/cs380/fall2012/nrg3227.pdf


Combining Genetic Circuit and Microbial Growth Kinetic Models: A Challenge for Biological Modelling : http://www.aidic.it/escape20/webpapers/257Koutinas.pdf