Team:ETH Zurich/Modeling/References

From 2011.igem.org

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== Single-Cell Model ==
== Single-Cell Model ==
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<span id="Ref1">[1] [http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold & Ron Weiss, '''A synthetic multicellular system for programmed pattern formation''', Nature Vol. 434, 2005]</span>
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<span id="Ref2">[2] [http://www.pnas.org/content/101/30/10955.fullJordi Garcia-Ojalvo, Michael B. Elowitz, and Steven H. Strogatz, '''Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing''', PNAS vol. 101 no. 30, 2004]</span>
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<span id="Ref3">[3] [https://2010.igem.org/Team:MIT_tmodel MIT igem 2010]</span>
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|style="text-align: center"|<span id="Ref1">[1]</span>
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|[http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold & Ron Weiss,<br> '''A synthetic multicellular system for programmed pattern formation''', <br>Nature Vol. 434, 2005]
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<span id="Ref4">[4] [http://onlinelibrary.wiley.com/doi/10.1002/cyto.a.20461/abstract;jsessionid=00173AFD03BE779CB9031A77277F1458.d01t01 Michael Halter,Alex Tona,Kiran Bhadriraju,Anne L. Plant,John T. Elliott,''' Automated Live Cell Imaging of Green Fluorescent Protein Degradation in Individual Fibroblasts''', Cytometry Part A, Volume 71A Issue 10, 2007]
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|style="text-align: center"|<span id="Ref2">[2]</span>
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|[http://www.pnas.org/content/101/30/10955.fullJordi Garcia-Ojalvo, Michael B. Elowitz, and Steven H. Strogatz, <br>'''Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing''', <br>PNAS vol. 101 no. 30, 2004]
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<span id="Ref5">[5] [http://www.nature.com/nbt/journal/v22/n11/full/nbt1021.html Weber W. et al, '''Gas-inducible transgene expression in mammalian cells and mice, Nature Biotechnology''', volume 22, number 11, November 2004]</span>
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|style="text-align: center"|<span id="Ref3">[3]</span>
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<span id="Ref6">[6] [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2010.02245.x/abstract Michalis Koutinas, Ming-Chi Lam, Alexandros Kiparissides, Rafael Silva-Rocha, Miguel Godinho, Andrew G. Livingston, Efstratios N. Pistikopoulos, Victor de Lorenzo, Vitor A. P. Martins dos Santos and Athanasios Mantalaris, '''The regulatory logic of m-xylene biodegradation by Pseudomonas putida mt-2 exposed by dynamic modelling of the principal node Ps/Pr of the TOL plasmid''', Environmental Microbiology vol. 12, Issue 6, 2010]</span>
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|[https://2010.igem.org/Team:MIT_tmodel MIT igem 2010]
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<span id="Ref7">[7] [http://aem.asm.org/cgi/reprint/64/3/1006 Development and Testing of a Bacterial Biosensor for Toluene-Based Environmental Contaminants]</span>
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|style="text-align: center"|<span id="Ref4">[4]</span>
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|[http://onlinelibrary.wiley.com/doi/10.1002/cyto.a.20461/abstract;jsessionid=00173AFD03BE779CB9031A77277F1458.d01t01 Michael Halter, Alex Tona, Kiran Bhadriraju, Anne L. Plant, John T. Elliott,<br>''' Automated Live Cell Imaging of Green Fluorescent Protein Degradation in Individual Fibroblasts''',<br>Cytometry Part A, Volume 71A Issue 10, 2007]
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|style="text-align: center"|<span id="Ref5">[5]</span>
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|[http://www.nature.com/nbt/journal/v22/n11/full/nbt1021.html Weber W. et al,<br>'''Gas-inducible transgene expression in mammalian cells and mice, Nature Biotechnology''',<br>volume 22, number 11, November 2004]
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|style="text-align: center"|<span id="Ref6">[6]</span>
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|[http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2010.02245.x/abstract Michalis Koutinas, Ming-Chi Lam, Alexandros Kiparissides, Rafael Silva-Rocha, Miguel Godinho, Andrew G. Livingston, Efstratios N. Pistikopoulos, Victor de Lorenzo, Vitor A. P. Martins dos Santos and Athanasios Mantalaris,<br>'''The regulatory logic of m-xylene biodegradation by Pseudomonas putida mt-2 exposed by dynamic modelling of the principal node Ps/Pr of the TOL plasmid''',<br>Environmental Microbiology vol. 12, Issue 6, 2010]
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|style="text-align: center"|<span id="Ref7">[7]</span>
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|[http://aem.asm.org/cgi/reprint/64/3/1006 Development and Testing of a Bacterial Biosensor for Toluene-Based Environmental Contaminants]
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Revision as of 13:35, 15 September 2011

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Modeling References
Single-Cell Model Microfluidics Model Combined Model
Of course, our models do not work without parameters, and in our case, there are quite a lot of them. In order to keep track of all of their respective values and units, we gathered them in a series of tables on this page.

Single-Cell Model

# Source
[1] [http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold & Ron Weiss,
A synthetic multicellular system for programmed pattern formation,
Nature Vol. 434, 2005]
[2] [http://www.pnas.org/content/101/30/10955.fullJordi Garcia-Ojalvo, Michael B. Elowitz, and Steven H. Strogatz,
Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing,
PNAS vol. 101 no. 30, 2004]
[3] MIT igem 2010
[4] [http://onlinelibrary.wiley.com/doi/10.1002/cyto.a.20461/abstract;jsessionid=00173AFD03BE779CB9031A77277F1458.d01t01 Michael Halter, Alex Tona, Kiran Bhadriraju, Anne L. Plant, John T. Elliott,
Automated Live Cell Imaging of Green Fluorescent Protein Degradation in Individual Fibroblasts,
Cytometry Part A, Volume 71A Issue 10, 2007]
[5] [http://www.nature.com/nbt/journal/v22/n11/full/nbt1021.html Weber W. et al,
Gas-inducible transgene expression in mammalian cells and mice, Nature Biotechnology,
volume 22, number 11, November 2004]
[6] [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2010.02245.x/abstract Michalis Koutinas, Ming-Chi Lam, Alexandros Kiparissides, Rafael Silva-Rocha, Miguel Godinho, Andrew G. Livingston, Efstratios N. Pistikopoulos, Victor de Lorenzo, Vitor A. P. Martins dos Santos and Athanasios Mantalaris,
The regulatory logic of m-xylene biodegradation by Pseudomonas putida mt-2 exposed by dynamic modelling of the principal node Ps/Pr of the TOL plasmid,
Environmental Microbiology vol. 12, Issue 6, 2010]
[7] [http://aem.asm.org/cgi/reprint/64/3/1006 Development and Testing of a Bacterial Biosensor for Toluene-Based Environmental Contaminants]

Microfluidics Model

[8] [http://www.gsi-net.com/en/publications/gsi-chemical-database/single/3.html GSI Environmental Inc, Acetaldehyde, GSI Chemical Database]

[9] [http://jb.asm.org/cgi/reprint/185/5/1485 FIX ME Diffusion in Biofilms]

Combined Model

[10] [http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.2.1.10&Suchword=&organism[]=Escherichia+coli&show_tm=0 FIX ME BRENDA Acetaldehyde Dehydrogenase]

[11] [http://pubs.acs.org/doi/abs/10.1021/bi00529a026 Clifford C. Shone, Herbert J. Fromm, Steady-state and pre-steady-state kinetics of coenzyme A-linked aldehyde dehydrogenase from Escherichia coli, Biochemistry, 1981, 20 (26), pp 7494–7501]

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