Team:NTU-Singapore/Project/References

From 2009.igem.org

(Difference between revisions)
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<div class="ref">
* MayoClinic.com. (2008). "'''Definition of Arterioscleriosis.'''" from http://www.mayoclinic.com/health/arteriosclerosis-atherosclerosis/DS00525.
* MayoClinic.com. (2008). "'''Definition of Arterioscleriosis.'''" from http://www.mayoclinic.com/health/arteriosclerosis-atherosclerosis/DS00525.
 +
* E. Galkina, K. Ley, “'''Immune and Inflammatory Mechanisms of Atherosclerosis'''” Annu. Rev. Immunol., vol 27, 165-97, 2009.
* E. Galkina, K. Ley, “'''Immune and Inflammatory Mechanisms of Atherosclerosis'''” Annu. Rev. Immunol., vol 27, 165-97, 2009.
 +
* G. K. Hansson, Anna-Karin L. Robertson, C. Soderberg-Naucler, “'''Inflammation and Atherosclerosis'''” Annu. Rev. Pathol. Mech. Dis., vol 1, 297-329, 2006.
* G. K. Hansson, Anna-Karin L. Robertson, C. Soderberg-Naucler, “'''Inflammation and Atherosclerosis'''” Annu. Rev. Pathol. Mech. Dis., vol 1, 297-329, 2006.
 +
* NIH. "'''How is Atherosclerosis Diagnosed?'''", from http://www.nhlbi.nih.gov/health/dci/Diseases/Atherosclerosis/Atherosclerosis_Diagnosis.html.
* NIH. "'''How is Atherosclerosis Diagnosed?'''", from http://www.nhlbi.nih.gov/health/dci/Diseases/Atherosclerosis/Atherosclerosis_Diagnosis.html.
 +
* Anderson, T. J. M. (2003). "'''Nitric Oxide, Atherosclerosis and clinical relevance of endothelial dysfunction.'''" Heart Failure Reviews 8: 71 - 86.
* Anderson, T. J. M. (2003). "'''Nitric Oxide, Atherosclerosis and clinical relevance of endothelial dysfunction.'''" Heart Failure Reviews 8: 71 - 86.
</div>
</div>
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<div class="ref">
* S. Verma, M. R. Buchanan, T. J. Anderson, “'''Endothelial Function Testing as a Biomarker of Vascular Disease'''” Circulation, vol 108, 2054-2059, 2003.
* S. Verma, M. R. Buchanan, T. J. Anderson, “'''Endothelial Function Testing as a Biomarker of Vascular Disease'''” Circulation, vol 108, 2054-2059, 2003.
 +
* W. Thomas, “'''Catch Bonds in Adhesion'''” Annu. Rev. Biomed. Eng., vol 10, 39-57, 2008.
* W. Thomas, “'''Catch Bonds in Adhesion'''” Annu. Rev. Biomed. Eng., vol 10, 39-57, 2008.
 +
* L. M. Nilsson, W. E. Thomas, E. V. Sokurenko, V. Vogel, “'''Elevated Shear Stress Protects Escherichia Coli Cells Adhering to Surfaces via Catch Bonds from Detachment by Soluble Inhibitors'''” Applied and Environmental Microbiology, vol 72 no. 4, 3005-3010, 2006.
* L. M. Nilsson, W. E. Thomas, E. V. Sokurenko, V. Vogel, “'''Elevated Shear Stress Protects Escherichia Coli Cells Adhering to Surfaces via Catch Bonds from Detachment by Soluble Inhibitors'''” Applied and Environmental Microbiology, vol 72 no. 4, 3005-3010, 2006.
 +
* Eric Borges, W. T., Martin Steegmaier,* Thomas Moll,* Rupert Hallmann,§ Alf Hamann, and Dietmar Vestweber* (1997). "'''P-Selectin Glycoprotein Ligand-1 (PSGL-1) on T Helper 1 but Not on T Helper 2 Cells Binds to P-Selectin and Supports Migration into Inflamed Skin'''" Journal of Experimental Medicine 185.
* Eric Borges, W. T., Martin Steegmaier,* Thomas Moll,* Rupert Hallmann,§ Alf Hamann, and Dietmar Vestweber* (1997). "'''P-Selectin Glycoprotein Ligand-1 (PSGL-1) on T Helper 1 but Not on T Helper 2 Cells Binds to P-Selectin and Supports Migration into Inflamed Skin'''" Journal of Experimental Medicine 185.
</div>
</div>
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<div class="ref">
<div class="ref">
* Wilkinson, D. J. (2006). '''Stochastic modelling for systems biology'''. Boca Raton, FL, Taylor & Francis.
* Wilkinson, D. J. (2006). '''Stochastic modelling for systems biology'''. Boca Raton, FL, Taylor & Francis.
 +
* Dunn, I. J. (2003). '''Biological reaction engineering : dynamic modelling fundamentals with simulation examples.''' [Great Britain], Wiley-VCH.
* Dunn, I. J. (2003). '''Biological reaction engineering : dynamic modelling fundamentals with simulation examples.''' [Great Britain], Wiley-VCH.
 +
* Linkens, D. A. (1979). '''Biological systems, modelling, and control'''. Stevenage [Eng.] ; New York, P. Peregrinus on behalf of the Institution of Electrical Engineers.
* Linkens, D. A. (1979). '''Biological systems, modelling, and control'''. Stevenage [Eng.] ; New York, P. Peregrinus on behalf of the Institution of Electrical Engineers.
 +
* Drubin, D. A., J. C. Way, et al. (2007). "'''Designing biological systems'''" Genes & Development 21(1): 242 - 254.
* Drubin, D. A., J. C. Way, et al. (2007). "'''Designing biological systems'''" Genes & Development 21(1): 242 - 254.
 +
* Murthy, D. N. P., N. W. Page, et al. (1990). '''Mathematical modelling : a tool for problem solving in engineering, physical, biological, and social sciences.''' Oxford ; New York, Pergamon Press.
* Murthy, D. N. P., N. W. Page, et al. (1990). '''Mathematical modelling : a tool for problem solving in engineering, physical, biological, and social sciences.''' Oxford ; New York, Pergamon Press.
 +
* Murphy, K., G. Balazsi, et al. (2007). "'''Combinatorial promoter design for engineering noisy gene expression.'''" Proc Natl Acad Sci USA 104: 12726 - 12731.
* Murphy, K., G. Balazsi, et al. (2007). "'''Combinatorial promoter design for engineering noisy gene expression.'''" Proc Natl Acad Sci USA 104: 12726 - 12731.
 +
* Naidoo, K. J. and Royal Society of Chemistry (Great Britain) (2006). '''Modelling molecular structure and reactivity in biological systems.''' Cambridge, Royal Society of Chemistry.
* Naidoo, K. J. and Royal Society of Chemistry (Great Britain) (2006). '''Modelling molecular structure and reactivity in biological systems.''' Cambridge, Royal Society of Chemistry.
 +
* Garcia-Martinez, J., A. Aranda, et al. (2004). "'''Genomic run-on evaluates transcription rates for all yeast gens and identifies gene regulatory mechanisms.'''" Mol Cell 15: 303 - 313.
* Garcia-Martinez, J., A. Aranda, et al. (2004). "'''Genomic run-on evaluates transcription rates for all yeast gens and identifies gene regulatory mechanisms.'''" Mol Cell 15: 303 - 313.
 +
* Ullner, E., A. Koseska, et al. (2008). "'''Multistability of synthetic genetic networks with repressive cell-to-cell communication.'''" Physical Review 78: 03904-1 - 03904-8.
* Ullner, E., A. Koseska, et al. (2008). "'''Multistability of synthetic genetic networks with repressive cell-to-cell communication.'''" Physical Review 78: 03904-1 - 03904-8.
</div>
</div>
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<div class="ref">
<div class="ref">
* D’Autre´aux, B., N. P. Tucker, et al. (2005). "'''A non-haem iron centre in the transcription factor NorR senses nitric oxide.'''" Nature 437(29): 769 -772.
* D’Autre´aux, B., N. P. Tucker, et al. (2005). "'''A non-haem iron centre in the transcription factor NorR senses nitric oxide.'''" Nature 437(29): 769 -772.
 +
* Hutchings, M. I., N. Mandhana, et al. (2002). "'''The NorR protein of Escherichia coli activates expression of the Flavorbredoxin gene NorV in response to reactive nitrogen species.'''" Journal of bacteriology 184(16): 4640 - 4643.
* Hutchings, M. I., N. Mandhana, et al. (2002). "'''The NorR protein of Escherichia coli activates expression of the Flavorbredoxin gene NorV in response to reactive nitrogen species.'''" Journal of bacteriology 184(16): 4640 - 4643.
 +
* Tucker, N. P., B. D. Autreaux, et al. (2006). "'''Mechanism of transcriptional regulation by Escherichia Coli nitric oxide sensor NorR.'''" Biochemical Society Transactions 34(1): 191 - 194.
* Tucker, N. P., B. D. Autreaux, et al. (2006). "'''Mechanism of transcriptional regulation by Escherichia Coli nitric oxide sensor NorR.'''" Biochemical Society Transactions 34(1): 191 - 194.
</div>
</div>
Line 79: Line 96:
<div class="ref">
<div class="ref">
* S. Ghosh, et al., "'''Molecular cloning and expression of rat hepatic neutral cholesteryl ester hydrolase,'''" Biochimica Et Biophysica Acta-Lipids and Lipid Metabolism, vol. 1259, pp. 305-312, Dec 1995.
* S. Ghosh, et al., "'''Molecular cloning and expression of rat hepatic neutral cholesteryl ester hydrolase,'''" Biochimica Et Biophysica Acta-Lipids and Lipid Metabolism, vol. 1259, pp. 305-312, Dec 1995.
 +
* S. Ghosh, "'''Cholesteryl ester hydrolase in human monocyte/macrophage: cloning, sequencing, and expression of full-length cDNA'''" Physiological Genomics, vol. 2, pp. 1-8, Jan 2000.
* S. Ghosh, "'''Cholesteryl ester hydrolase in human monocyte/macrophage: cloning, sequencing, and expression of full-length cDNA'''" Physiological Genomics, vol. 2, pp. 1-8, Jan 2000.
 +
* B. Zhao, et al., "'''Macrophage-specific transgenic expression of cholesteryl ester hydrolase significantly reduces atherosclerosis and lesion necrosis in Ldlr(-)/(-) mice'''" Journal of Clinical Investigation, vol. 117, pp. 2983-2992, Oct 2007.
* B. Zhao, et al., "'''Macrophage-specific transgenic expression of cholesteryl ester hydrolase significantly reduces atherosclerosis and lesion necrosis in Ldlr(-)/(-) mice'''" Journal of Clinical Investigation, vol. 117, pp. 2983-2992, Oct 2007.
 +
* H. Okazaki, et al., "'''Elimination of cholesterol ester from macrophage foam cells by adenovirus-mediated gene transfer of hormone-sensitive lipase'''" Journal of Biological Chemistry, vol. 277, pp. 31893-31899, Aug 2002.
* H. Okazaki, et al., "'''Elimination of cholesterol ester from macrophage foam cells by adenovirus-mediated gene transfer of hormone-sensitive lipase'''" Journal of Biological Chemistry, vol. 277, pp. 31893-31899, Aug 2002.
 +
* A. Sugihara, et al., "'''Purification and characterization of a novel cholesterol esterase from Pseudomonas aeruginosa, with its application to cleaning lipid-stained contact lenses'''" Bioscience Biotechnology and Biochemistry, vol. 66, pp. 2347-2355, Nov 2002.
* A. Sugihara, et al., "'''Purification and characterization of a novel cholesterol esterase from Pseudomonas aeruginosa, with its application to cleaning lipid-stained contact lenses'''" Bioscience Biotechnology and Biochemistry, vol. 66, pp. 2347-2355, Nov 2002.
</div>  
</div>  
Line 90: Line 111:
<div class="ref">
<div class="ref">
* Kein, B. (2009). "'''Infrared Proteins Give Deep View Inside Living Animals.'''" from http://www.wired.com/wiredscience/2009/05/infraredcells/.
* Kein, B. (2009). "'''Infrared Proteins Give Deep View Inside Living Animals.'''" from http://www.wired.com/wiredscience/2009/05/infraredcells/.
 +
* S. Xiaokun, A. Royant, M.Z. Lin, T.A. Aguilera, V. Lev-Ram, P.A. Steinbach and R.Y Tsien, “'''Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome'''” Science, vol 324, 804, 2009.
* S. Xiaokun, A. Royant, M.Z. Lin, T.A. Aguilera, V. Lev-Ram, P.A. Steinbach and R.Y Tsien, “'''Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome'''” Science, vol 324, 804, 2009.
 +
* S. Xiaokun, A. Royant, M.Z. Lin, T.A. Aguilera, V. Lev-Ram, P.A. Steinbach and R.Y Tsien, “'''Supporting Online Material for Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome'''" Science, vol 324, 804, 2009.
* S. Xiaokun, A. Royant, M.Z. Lin, T.A. Aguilera, V. Lev-Ram, P.A. Steinbach and R.Y Tsien, “'''Supporting Online Material for Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome'''" Science, vol 324, 804, 2009.
 +
* N. C. Shaner, R. E. Campbell, P. A. Steinbach, B.N.G Giepmans, A.E. Palmer and R.Y. Tsien, “'''Improved Monomeric Red, Orange and Yellow Fluorescent Proteins derived from Discosoma sp. red fluorescent protein'''” Nature Biotechnology, vol 22, number 12, 2004.
* N. C. Shaner, R. E. Campbell, P. A. Steinbach, B.N.G Giepmans, A.E. Palmer and R.Y. Tsien, “'''Improved Monomeric Red, Orange and Yellow Fluorescent Proteins derived from Discosoma sp. red fluorescent protein'''” Nature Biotechnology, vol 22, number 12, 2004.
 +
* C.T. Migita, X. Zhang, T. Yoshida, “'''Expression and Characterization of cyanobacterium heme oxygenase, a key enzyme in the phycobilin synthesis'''” Eur J Biochem, vol 270, 687-698, 2003.  
* C.T. Migita, X. Zhang, T. Yoshida, “'''Expression and Characterization of cyanobacterium heme oxygenase, a key enzyme in the phycobilin synthesis'''” Eur J Biochem, vol 270, 687-698, 2003.  
</div>
</div>

Revision as of 07:06, 19 October 2009

Literature & References


Atherosclerosis resources

  • MayoClinic.com. (2008). "Definition of Arterioscleriosis." from http://www.mayoclinic.com/health/arteriosclerosis-atherosclerosis/DS00525.
  • E. Galkina, K. Ley, “Immune and Inflammatory Mechanisms of Atherosclerosis” Annu. Rev. Immunol., vol 27, 165-97, 2009.
  • G. K. Hansson, Anna-Karin L. Robertson, C. Soderberg-Naucler, “Inflammation and Atherosclerosis” Annu. Rev. Pathol. Mech. Dis., vol 1, 297-329, 2006.
  • NIH. "How is Atherosclerosis Diagnosed?", from http://www.nhlbi.nih.gov/health/dci/Diseases/Atherosclerosis/Atherosclerosis_Diagnosis.html.
  • Anderson, T. J. M. (2003). "Nitric Oxide, Atherosclerosis and clinical relevance of endothelial dysfunction." Heart Failure Reviews 8: 71 - 86.


Catch-bonds resources

  • S. Verma, M. R. Buchanan, T. J. Anderson, “Endothelial Function Testing as a Biomarker of Vascular Disease” Circulation, vol 108, 2054-2059, 2003.
  • W. Thomas, “Catch Bonds in Adhesion” Annu. Rev. Biomed. Eng., vol 10, 39-57, 2008.
  • L. M. Nilsson, W. E. Thomas, E. V. Sokurenko, V. Vogel, “Elevated Shear Stress Protects Escherichia Coli Cells Adhering to Surfaces via Catch Bonds from Detachment by Soluble Inhibitors” Applied and Environmental Microbiology, vol 72 no. 4, 3005-3010, 2006.
  • Eric Borges, W. T., Martin Steegmaier,* Thomas Moll,* Rupert Hallmann,§ Alf Hamann, and Dietmar Vestweber* (1997). "P-Selectin Glycoprotein Ligand-1 (PSGL-1) on T Helper 1 but Not on T Helper 2 Cells Binds to P-Selectin and Supports Migration into Inflamed Skin" Journal of Experimental Medicine 185.


Biological modelling resources

  • Wilkinson, D. J. (2006). Stochastic modelling for systems biology. Boca Raton, FL, Taylor & Francis.
  • Dunn, I. J. (2003). Biological reaction engineering : dynamic modelling fundamentals with simulation examples. [Great Britain], Wiley-VCH.
  • Linkens, D. A. (1979). Biological systems, modelling, and control. Stevenage [Eng.] ; New York, P. Peregrinus on behalf of the Institution of Electrical Engineers.
  • Drubin, D. A., J. C. Way, et al. (2007). "Designing biological systems" Genes & Development 21(1): 242 - 254.
  • Murthy, D. N. P., N. W. Page, et al. (1990). Mathematical modelling : a tool for problem solving in engineering, physical, biological, and social sciences. Oxford ; New York, Pergamon Press.
  • Murphy, K., G. Balazsi, et al. (2007). "Combinatorial promoter design for engineering noisy gene expression." Proc Natl Acad Sci USA 104: 12726 - 12731.
  • Naidoo, K. J. and Royal Society of Chemistry (Great Britain) (2006). Modelling molecular structure and reactivity in biological systems. Cambridge, Royal Society of Chemistry.
  • Garcia-Martinez, J., A. Aranda, et al. (2004). "Genomic run-on evaluates transcription rates for all yeast gens and identifies gene regulatory mechanisms." Mol Cell 15: 303 - 313.
  • Ullner, E., A. Koseska, et al. (2008). "Multistability of synthetic genetic networks with repressive cell-to-cell communication." Physical Review 78: 03904-1 - 03904-8.


Sense Device Resources

  • D’Autre´aux, B., N. P. Tucker, et al. (2005). "A non-haem iron centre in the transcription factor NorR senses nitric oxide." Nature 437(29): 769 -772.
  • Hutchings, M. I., N. Mandhana, et al. (2002). "The NorR protein of Escherichia coli activates expression of the Flavorbredoxin gene NorV in response to reactive nitrogen species." Journal of bacteriology 184(16): 4640 - 4643.
  • Tucker, N. P., B. D. Autreaux, et al. (2006). "Mechanism of transcriptional regulation by Escherichia Coli nitric oxide sensor NorR." Biochemical Society Transactions 34(1): 191 - 194.


Degradation Device Resources

  • S. Ghosh, et al., "Molecular cloning and expression of rat hepatic neutral cholesteryl ester hydrolase," Biochimica Et Biophysica Acta-Lipids and Lipid Metabolism, vol. 1259, pp. 305-312, Dec 1995.
  • S. Ghosh, "Cholesteryl ester hydrolase in human monocyte/macrophage: cloning, sequencing, and expression of full-length cDNA" Physiological Genomics, vol. 2, pp. 1-8, Jan 2000.
  • B. Zhao, et al., "Macrophage-specific transgenic expression of cholesteryl ester hydrolase significantly reduces atherosclerosis and lesion necrosis in Ldlr(-)/(-) mice" Journal of Clinical Investigation, vol. 117, pp. 2983-2992, Oct 2007.
  • H. Okazaki, et al., "Elimination of cholesterol ester from macrophage foam cells by adenovirus-mediated gene transfer of hormone-sensitive lipase" Journal of Biological Chemistry, vol. 277, pp. 31893-31899, Aug 2002.
  • A. Sugihara, et al., "Purification and characterization of a novel cholesterol esterase from Pseudomonas aeruginosa, with its application to cleaning lipid-stained contact lenses" Bioscience Biotechnology and Biochemistry, vol. 66, pp. 2347-2355, Nov 2002.


Imaging Device Resources

  • Kein, B. (2009). "Infrared Proteins Give Deep View Inside Living Animals." from http://www.wired.com/wiredscience/2009/05/infraredcells/.
  • S. Xiaokun, A. Royant, M.Z. Lin, T.A. Aguilera, V. Lev-Ram, P.A. Steinbach and R.Y Tsien, “Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome” Science, vol 324, 804, 2009.
  • S. Xiaokun, A. Royant, M.Z. Lin, T.A. Aguilera, V. Lev-Ram, P.A. Steinbach and R.Y Tsien, “Supporting Online Material for Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome" Science, vol 324, 804, 2009.
  • N. C. Shaner, R. E. Campbell, P. A. Steinbach, B.N.G Giepmans, A.E. Palmer and R.Y. Tsien, “Improved Monomeric Red, Orange and Yellow Fluorescent Proteins derived from Discosoma sp. red fluorescent protein” Nature Biotechnology, vol 22, number 12, 2004.
  • C.T. Migita, X. Zhang, T. Yoshida, “Expression and Characterization of cyanobacterium heme oxygenase, a key enzyme in the phycobilin synthesis” Eur J Biochem, vol 270, 687-698, 2003.



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