Template:Team:Waterloo/Modeling/Citations

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        <b id="Citation_Jia2009">[15]</b>Jianfang Jia and Hong Yue. “Sensitivity Analysis and Parameter Estimation of Signal Transduction Pathways Model”. In: <i>Proceedings of the 7th Asian Control Conference</i> (Aug. 2009), pp. 1357–1362.
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        <b id="Citation_Chang1992">[16]</b>Fi-John Chang and J. W. Delleur. “Systematic Parameter Estimation Of Watershed
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Acidification Model”. In: <i>Hydrological Processes</i> 6. (1992), pp. 29–44. doi: <a href="http://dx.doi.org/10.1002/hyp.3360060104">10.1002/hyp.3360060104</a>.
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        <b id="Citation_Aiba2007">[17]</b>Aiba, H. (2007). Mechanism of RNA silencing by Hfq-binding small RNAs. <i>Current opinion in microbiology, 10</i> (2), 134-139.
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        <b id="Citation_Horstmann2012">[18]</b>Horstmann, N., Orans, J., Valentin-Hansen, P., Shelburne, S. A., & Brennan, R. G. (2012). Structural mechanism of Staphylococcus aureus Hfq binding to an RNA A-tract. <i> Nucleic acids research,</i>  gks809.
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        <b id="Citation_Eyraud2014">[19]</b>Eyraud, A., Tattevin, P., Chabelskaya, S., & Felden, B. (2014). A small RNA controls a protein regulator involved in antibiotic resistance in Staphylococcus aureus.  <i> Nucleic acids research,</i>  gku149.
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        <b id="Citation_Shimoni2007">[20]</b>Shimoni, Y., Friedlander, G., Hetzroni, G., Niv, G., Altuvia, S., Biham, O., & Margalit, H. (2007). Regulation of gene expression by small non‐coding RNAs: a quantitative view.  <i> Molecular Systems Biology, 3</i> (1)
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        <b id="Citation_Fender2010">[21]</b>Fender, A., Elf, J., Hampel, K., Zimmermann, B., & Wagner, E. G. H. (2010). RNAs actively cycle on the Sm-like protein Hfq.  <i> Genes & Development, 24</i> (23),2621-2626.
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        <b id="Citation_Swain2004">[22]</b> Swain, P. S. (2004). Efficient attenuation of stochasticity in gene expression through post-transcriptional control. <i> Journal of molecular biology, 344</i> (4),965-976.
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        <b id="Citation_Hussein2012">[23]</b> Hussein, R., & Lim, H. N. (2012). Direct comparison of small RNA and transcription factor signaling. <i> Nucleic acids research, 40</i> (15), 7269-7279.
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        <b id="Citation_Levin1979">[24]</b> Levin, B.R., Stewart, F.M. and Rice, V.A. 1979. “The Kinetics of Conjugative Plasmid Transmission: Fit of a Simple Mass Action Model.” In: <i> Plasmid. 2. </i> pp. 247-260.
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        <b id="Citation_Projan1989">[25]</b>Projan, S.J. and Archer, G.L. 1989. “Mobilization of the Relaxable Staphylococcus aureus Plasmid pC221 by the Conjugative Plasmid pGO1 Involves Three pC221 Loci.” In:<i> Journal of Bacteriology.</i> pp. 1841-1845.
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        <b id="Citation_Phornphisutthimas2007">[26]</b>Phornphisutthimas, S., Thamchaipenet, A., and Panijpan, B. 2007. “Conjugation in Escherichia coli.” In:<i>  The International Union of Biochemistry and Molecular Biology. 35. 6.</i> pp. 440-445.
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        <b id="Citation_Phornphisutthimas2007">[27]</b>Phornphisutthimas, S., Thamchaipenet, A., and Panijpan, B. 2007. “Conjugation in Escherichia coli.” In:<i>  The International Union of Biochemistry and Molecular Biology. 35. 6.</i> pp. 440-445.
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        <b id="Citation_Chung2006">[28]</b>P Chung P., McNamara P.J., Campion J.J., Evans M.E. 2006. “Mechanism-based pharmacodynamic models of fluoroquinolone resistance in <i>Staphylococcus aureus.</i>” In:<i>  In:  Antimicrobial Agents Chemotherapy. 50.</i> pp. 2957-2965.
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        <b id="Citation_Chang2010">[29]</b> Chang H., Wang L. “A Simple Proof of Thue's Theorem on Circle Packing” In: arXiv:1009.4322v1.
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Latest revision as of 05:55, 13 December 2014

References

[1]D. Bikard et al. “Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system”. In: Nucleic Acids Res. 41.15 (Aug. 2013), pp. 7429–7437.
[2]Florian Brandt et al. “The Native 3D Organization of Bacterial Polysomes”. In: Cell 136.2 (2009), pp. 261 –271. issn: 0092-8674. doi: 10.1016/j.cell.2008.11.016.
[3]A. G. Cheng, D. Missiakas, and O. Schneewind. “The giant protein Ebh is a determinant of Staphylococcus aureus cell size and complement resistance”. In: J. Bacteriol. 196.5 (2014), pp. 971–981.
[4]A. L. Cheung, K. Nishina, and A. C. Manna. “SarA of Staphylococcus aureus binds to the sarA promoter to regulate gene expression”. In: J. Bacteriol. 190.6 (Mar. 2008), pp. 2239–2243.
[5]G. Domingue, J. W. Costerton, and M. R. Brown. “Bacterial doubling time modulates the effects of opsonisation and available iron upon interactions between Staphylococcus aureus and human neutrophils”. In: FEMS Immunol. Med. Microbiol. 16.3-4 (Dec. 1996), pp. 223–228.
[6]S. Michalik et al. “Life and death of proteins: a case study of glucose-starved Staphylococcus aureus”. In: Mol. Cell Proteomics 11.9 (Sept. 2012), pp. 558–570.
[7]R. Milo et al. “BioNumbers-the database of key numbers in molecular and cell biology”. In: Nucleic Acids Res. 30 (Jan. 2010), pp. D750–D753. url: http://bionumbers.hms.harvard.edu/bionumber.aspx?id=107869}.
[8]L. S. Qi et al. “Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression”. In: Cell 152.5 (Feb. 2013), pp. 1173–1183.
[9]C. Roberts et al. “Characterizing the effect of the Staphylococcus aureus virulence factor regulator, SarA, on log-phase mRNA half-lives”. In: J. Bacteriol. 188.7 (Apr. 2006), pp. 2593–2603. doi: 10.1128/JB.188.7.2593-2603.2006
[10]Marlena Siwiak and Piotr Zielenkiewicz. “Transimulation - Protein Biosynthesis Web Service”. In: PLoS ONE 8.9 (Sept. 2013), e73943. doi: 10.1371/journal.pone.0073943.
[11]S.H. Sternberg et al. “DNA interrogation by the CRISPR RNA-guided endonuclease Cas9”. In: Nature 7490 (2014), 6267. doi: 10.1038/nature13011. url: http://www.nature.com/nature/journal/v507/n7490/full/nature13011.html.
[12]Freiburg iGEM Team. dCas9. BBa K1150000 Standard Biological Part. 2013. url: http://parts.igem.org/Part:BBa_K1150000.
[13]UCSF iGEM Team. Operation CRISPR: Decision Making Circuit Model. 2013. url: https://2013.igem.org/Team:UCSF/Modeling.
[14]Jian-Qiu Wu and Thomas D. Pollard. “Counting Cytokinesis Proteins Globally and Locally in Fission Yeast”. In: Science 310.5746 (2005), pp. 310–314. doi: 10.1126/science.1113230.
[15]Jianfang Jia and Hong Yue. “Sensitivity Analysis and Parameter Estimation of Signal Transduction Pathways Model”. In: Proceedings of the 7th Asian Control Conference (Aug. 2009), pp. 1357–1362.
[16]Fi-John Chang and J. W. Delleur. “Systematic Parameter Estimation Of Watershed Acidification Model”. In: Hydrological Processes 6. (1992), pp. 29–44. doi: 10.1002/hyp.3360060104.
[17]Aiba, H. (2007). Mechanism of RNA silencing by Hfq-binding small RNAs. Current opinion in microbiology, 10 (2), 134-139.
[18]Horstmann, N., Orans, J., Valentin-Hansen, P., Shelburne, S. A., & Brennan, R. G. (2012). Structural mechanism of Staphylococcus aureus Hfq binding to an RNA A-tract. Nucleic acids research, gks809.
[19]Eyraud, A., Tattevin, P., Chabelskaya, S., & Felden, B. (2014). A small RNA controls a protein regulator involved in antibiotic resistance in Staphylococcus aureus. Nucleic acids research, gku149.
[20]Shimoni, Y., Friedlander, G., Hetzroni, G., Niv, G., Altuvia, S., Biham, O., & Margalit, H. (2007). Regulation of gene expression by small non‐coding RNAs: a quantitative view. Molecular Systems Biology, 3 (1)
[21]Fender, A., Elf, J., Hampel, K., Zimmermann, B., & Wagner, E. G. H. (2010). RNAs actively cycle on the Sm-like protein Hfq. Genes & Development, 24 (23),2621-2626.
[22] Swain, P. S. (2004). Efficient attenuation of stochasticity in gene expression through post-transcriptional control. Journal of molecular biology, 344 (4),965-976.
[23] Hussein, R., & Lim, H. N. (2012). Direct comparison of small RNA and transcription factor signaling. Nucleic acids research, 40 (15), 7269-7279.
[24] Levin, B.R., Stewart, F.M. and Rice, V.A. 1979. “The Kinetics of Conjugative Plasmid Transmission: Fit of a Simple Mass Action Model.” In: Plasmid. 2. pp. 247-260.
[25]Projan, S.J. and Archer, G.L. 1989. “Mobilization of the Relaxable Staphylococcus aureus Plasmid pC221 by the Conjugative Plasmid pGO1 Involves Three pC221 Loci.” In: Journal of Bacteriology. pp. 1841-1845.
[26]Phornphisutthimas, S., Thamchaipenet, A., and Panijpan, B. 2007. “Conjugation in Escherichia coli.” In: The International Union of Biochemistry and Molecular Biology. 35. 6. pp. 440-445.
[27]Phornphisutthimas, S., Thamchaipenet, A., and Panijpan, B. 2007. “Conjugation in Escherichia coli.” In: The International Union of Biochemistry and Molecular Biology. 35. 6. pp. 440-445.
[28]P Chung P., McNamara P.J., Campion J.J., Evans M.E. 2006. “Mechanism-based pharmacodynamic models of fluoroquinolone resistance in Staphylococcus aureus.” In: In: Antimicrobial Agents Chemotherapy. 50. pp. 2957-2965.
[29] Chang H., Wang L. “A Simple Proof of Thue's Theorem on Circle Packing” In: arXiv:1009.4322v1.

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