Team:Heidelberg/Project References

From 2009.igem.org

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==References==
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=References=
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=== Introduction ===  
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== Introduction ==  
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<div style="text-align:justify;">
* "Synthetic Biology. Applying Engineering to Biology". Report of a NEST High-Level Expert Group. European Commission, Directorate-General for Research. Available online at http://www.synbiosafe.eu/uploads///pdf/EU-highlevel-syntheticbiology.pdf
* "Synthetic Biology. Applying Engineering to Biology". Report of a NEST High-Level Expert Group. European Commission, Directorate-General for Research. Available online at http://www.synbiosafe.eu/uploads///pdf/EU-highlevel-syntheticbiology.pdf
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* Endy, D. Foundations for engineering biology. Nature 438: 449-453 (2005)
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* Endy, D. Foundations for engineering biology. ''Nature'' 438: 449-453 (2005).
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* Endy, D. Deese I. Adventures in synthetic biology (comic).Nature 438: 449-453 (2005)Available online at [http://www.nature.com/nature/comics/syntheticbiologycomic/index.html nature.com]
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* Endy, D. & Deese I. Adventures in synthetic biology (comic). ''Nature'' 438: 449-453 (2005) Available online at [http://www.nature.com/nature/comics/syntheticbiologycomic/index.html nature.com]
* http://www.partsregistry.org/Assembly:Standard_assembly (Website, accessed 10/15/2009)
* http://www.partsregistry.org/Assembly:Standard_assembly (Website, accessed 10/15/2009)
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* Kelly, J. R., Rubin A. J., Davis J. H., Ajo-Franklin C. M., Cumbers J., Czar M. J., de Mora K., Glieberman A. L., Monie D. D., Endy D. Measuring the activity of BioBrick promoters using an in vivo reference standard. Journal of Biological Engineering 3 (2009)
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* Kelly J. R., Rubin A. J., Davis J. H., Ajo-Franklin C. M., Cumbers J., Czar M. J., de Mora K., Glieberman A. L., Monie D. D. & Endy D. Measuring the activity of BioBrick promoters using an ''in vivo'' reference standard. ''Journal of Biological Engineering'' 3:4 (2009).
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* Voigt, C. Genetic parts to program bacteria. Current Opinion in Biotechnology 17: 548–557
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* Voigt, C. Genetic parts to program bacteria. ''Current Opinion in Biotechnology'' 17 (5): 548–557 (2006).
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* Andrianantoandro E., Basu S., Karig D. K., Weiss R. Synthetic biology: new engineering rules for an emerging discipline. Molecular Systems Biology: 0028 (2006)
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* Andrianantoandro E., Basu S., Karig D. K. & Weiss R. Synthetic biology: new engineering rules for an emerging discipline. ''Molecular Systems Biology'' 2: article number 0028 (2006).
* https://2009.igem.org/About (Website, accessed 10/15/2009)
* https://2009.igem.org/About (Website, accessed 10/15/2009)
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* Goodman, C. Engineering ingenuity at iGEM. Nat Chem Biology 4:13. (2008)
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* Goodman, C. Engineering ingenuity at iGEM. ''Nat Chem Biology'' 4:13 (2008).
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* Basu, S. A synthetic multicellular system for programmed pattern formation. Nature 434:1130-1133
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* Basu, S. A synthetic multicellular system for programmed pattern formation. ''Nature'' 434: 1130-1133 (2005).
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* Ellis T., Wang X., Collins J.J. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nature Biotechnology 27: 465-471 (2009)
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* Ellis T., Wang X. & Collins J.J. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. ''Nature Biotechnology'' 27: 465-471 (2009).
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* Canton, B., Anna Labno A., Endy D. Refinement and standardization of synthetic biological parts and devices. Nature Biotechnology 26: 787-793 (2009)
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* Canton, B., Anna Labno A. & Endy D. Refinement and standardization of synthetic biological parts and devices. ''Nature Biotechnology'' 26: 787-793 (2009).
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* Weber, W. & Fussenegger, M. Engineering of Synthetic Mammalian Gene Networks. Chemistry and Biology 16: 287-297 (2009)
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* Weber, W. & Fussenegger, M. Engineering of Synthetic Mammalian Gene Networks. ''Chemistry and Biology'' 16: 287-297 (2009).
* http://openwetware.org/wiki/The_BioBricks_Foundation:Standards/Technical/Formats (Website, accessed 10/19/2009)
* http://openwetware.org/wiki/The_BioBricks_Foundation:Standards/Technical/Formats (Website, accessed 10/19/2009)
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* Ducrest A-L., Amacker M., Lingner J., Nabholz M. Detection of promoter activity by flow cytometric analysis of GFP reporter expression. Nucleic Acids Res. 30, e65 (2002).  
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* Ducrest A-L., Amacker M., Lingner J. & Nabholz M. Detection of promoter activity by flow cytometric analysis of GFP reporter expression. ''Nucleic Acids Res.'' 30: e65 (2002).  
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* Venter, M. Synthetic promoters: genetic control through cis engineering. Trends in Plant Science 12, 118-124 (2007). (and the references cited therein)  
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* Venter M. Synthetic promoters: genetic control through cis engineering. ''Trends in Plant Science'' 12: 118-124 (2007). (and the references cited therein)  
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* Ogawa, R. Construction of strong mammalian promoters by random cis-acting element elongation. Biotechniques 42, 628-632 (2007).  
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* Ogawa R. Construction of strong mammalian promoters by random cis-acting element elongation. ''Biotechniques'' 42: 628-632 (2007).  
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* Tornoe, J. Generation of a synthetic mammalian promoter library by modification of sequences spacing transcription factor binding sites. Gene 297, 21-32 (2002).  
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* Tornoe J. Generation of a synthetic mammalian promoter library by modification of sequences spacing transcription factor binding sites. ''Gene'' 297: 21-32 (2002).  
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* Dorer, D. E., Nettelbeck, D. Targeting cancer by transcriptional control in cancer gene therapy and viral oncolysis. Advanced Drug Delivery Reviews 61, 554-557 (2009).  
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* Dorer D. E. & Nettelbeck D. Targeting cancer by transcriptional control in cancer gene therapy and viral oncolysis. ''Advanced Drug Delivery Reviews'' 61: 554-557 (2009).  
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* Weber W., Fussenegger M. The impact of synthetic biology on drug discovery. Drug Discovery Today 14, 956-963 (2009)
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* Weber W. & Fussenegger M. The impact of synthetic biology on drug discovery. ''Drug Discovery Today'' 14: 956-963 (2009).
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</div>
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===Natural Promoters===
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==Natural Promoters==
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<div style="text-align:justify;">
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* Alberts B., Johnson A., Walter P. & Lewis J. ''Molecular Biology of the Cell''. 4th edition, 2008. Garland Science, Chapter 6, p. 357-359. <br>
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* Alberts, B., Johnson A., Walter P., Lewis J. Molecular Biology of the Cell, 4th edition, 2008. Garland Science, Chapter 6, p. 357-359. <br>
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* Clarke N., Arenzana N., Hai T., Minden A. & Prywes R. Epidermal Growth Factor Induction of the c-jun Promoter by a Rac Pathway. ''Mol Cell Biol'' 18: 1065–1073 (1998).<br>
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* Clarke N., Arenzana N., Hai T., Minden A., Prywes R. Epidermal Growth Factor Induction of the c-jun Promoter by a Rac Pathway. Mol Cell Biol 18, 1065–1073 (1998).<br>
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* Hoffman L. M., Garcha K., Karamboulas K., Cowan M. F., Drysdale L. M., Horton W. A. & Underhill T. M. BMP action in skeletogenesis involves attenuation of retinoid signaling. ''J Cell Biol'' 174: 101–113 (2006). <br>
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* Hoffman L. M., Garcha K., Karamboulas K., Cowan M. F., Drysdale L. M., Horton W. A., Underhill T. M. BMP action in skeletogenesis involves attenuation of retinoid signaling. J Cell Biol 174, 101–113 (2006). <br>
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* Castoreno A. B., Wang Y., Stockinger W., Jarzylo L. A., Du H., Pagnon J. C., Shieh E. C. & Nohturfft A. Transcriptional regulation of phagocytosis-induced membrane biogenesis by sterol regulatory element binding proteins. ''Proc Natl Acad Sci U S A'' 102: 13129–13134 (2005). <br>
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* Castoreno A. B., Wang Y., Stockinger W., Jarzylo L. A., Du H., Pagnon J. C., Shieh E. C., Nohturfft A. Transcriptional regulation of phagocytosis-induced membrane biogenesis by sterol regulatory element binding proteins. Proc Natl Acad Sci U S A 102, 13129–13134 (2005). <br>
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* Schmidt M., Heimberger T., Gruensfelder P., Schler G. & Hoppe F. Inducible promoters for gene therapy of head and neck cancer: an in vitro study. ''Eur Arch Otorhinolaryngol'' 261: 208–215 (2004).<br>
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* Schmidt M., Heimberger T., Gruensfelder P., Schler G., Hoppe F. Inducible promoters for gene therapy of head and neck cancer: an in vitro study. Eur Arch Otorhinolaryngol 261, 208–215 (2004).<br>
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* Jorgensen E. C. B. & Autrup H. Autoregulation of human CYP1A1 gene promoter activity in HepG2 and MCF-7 cells. ''Carcinogenesis'' 17: 435-441 (1996). <br>
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* Jorgensen, E. C. B. and Autrup, H. Autoregulation of human CYP1A1 gene promoter activity in HepG2 and MCF-7 cells. Carcinogenesis 17, 435-441 (1996). <br>
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* Schreiber T. D., Köhle C., Buckler F., Schmohl S., Braeuning A., Schmiechen A., Schwarz M. & Münzel P.A. Regulation of CYP1A1 expression by the antioxidant Tert butylhydroquinone. ''Drug Metabolism And Disposition'' 43: 1096–1101 (2006).
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</div><br>
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* Schreiber T. D., Köhle C., Buckler F., Schmohl S., Braeuning A., Schmiechen A., Schwarz M., Münzel P.A. Regulation of CYP1A1 expression by the antioxidant Tert butylhydroquinone. Drug Metabolism And Disposition 43, 1096–1101 (2006).<br>
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==Synthetic Promoters==
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<div style="text-align:justify;">
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* Alberts B., Johnson A., Walter P. & Lewis J. ''Molecular Biology of the Cell''. 4th edition, 2008. Garland Science, p. 432-453
-
===Synthetic Promoters===
+
* Fussenegger M. & Weber, W. Engineering of Synthetic Mammalian Gene Networks. ''Chemistry and Biology'' 16: 287-297 (2009).
-
* Alberts, B., Johnson A., Walter P., Lewis J. Molecular Biology of the Cell, 5th edition, 2008. Garland Science, p. 432-453
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* Gossen M. & Bujard, L. Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. ''PNAS'' 89: 5547-5551 (1992).
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* Fussenegger M., Weber, W. Engineering of Synthetic Mammalian Gene Networks. Chemistry and Biology 16, 287-297 (2009).
+
* Dorer D. E. & Nettelbeck, D. Targeting cancer by transcriptional control in cancer gene therapy and viral oncolysis. ''Advanced Drug Delivery Reviews'' 61: 554-557 (2009).
-
* Gossen M., Bujard, L. Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. PNAS 89, 5547-5551 (1992).
+
* Venter M. Synthetic promoters: genetic control through cis engineering. ''Trends in Plant Science'' 12: 118-124 (2007). (and the references cited therein)
-
* Dorer D. E., Nettelbeck, D. Targeting cancer by transcriptional control in cancer gene therapy and viral oncolysis. Advanced Drug Delivery Reviews 61, 554-557 (2009).
+
* Rushton P. J., Reinstädler A., Lipka V., Lippok B. & Somssich I. E. Synthetic plant promoters containing defined regulatory elements provide novel insights into pathogen- and wound-induced signalling. ''Plant Cell'' 14: 749–762 (2002).
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* Venter M. Synthetic promoters: genetic control through cis engineering. Trends in Plant Science 12, 118-124 (2007). (and the references cited therein)
+
* Ogawa R. Construction of strong mammalian promoters by random cis-acting element elongation. ''Biotechniques'' 42: 628-632 (2007).  
-
* Rushton P. J., Reinstädler A., Lipka V., Lippok B., Somssich I. E. Synthetic plant promoters containing defined regulatory elements provide novel insights into pathogen- and wound-induced signalling.  Plant Cell 14, 749–762 (2002).
+
* Edelman G. M., Meech R., Owens G. C. & Jones F. S. Synthetic promoter elements obtained by nucleotide sequence variation and selection for activity. ''PNAS'' 97: 3038-43 (2000).
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* Ogawa R. Construction of strong mammalian promoters by random cis-acting element elongation. Biotechniques 42, 628-632 (2007).  
+
* Ellis T., Wang X. & Collins J. J. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. ''Nature Biotechnology'' 27: 465-471 (2009).
-
* Edelman G. M., Meech R., Owens G. C., Jones F. S. Synthetic promoter elements obtained by nucleotide sequence variation and selection for activity. PNAS 97, 3038-43 (2000).
+
* Tornoe J. Generation of a synthetic mammalian promoter library by modification of sequences spacing transcription factor binding sites. ''Gene'' 297: 21-32 (2002).
-
* Ellis T., Wang X., Collins J. J. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nature Biotechnology 27, 465-471 (2009).
+
* Heintzman N. D. & Ren B. The gateway to transcription: identifying, characterizing and understanding promoters in the eukaryotic genome. ''Cellular and Molecular Life Science'' 64: 386-400 (2007).
-
* Tornoe J. Generation of a synthetic mammalian promoter library by modification of sequences spacing transcription factor binding sites. Gene 297, 21-32 (2002).
+
* Stemmer W. P., Crameri A., Ha K. D., Brennan T. M. & Heyneker H. L. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. ''Gene'' 164: 49-53 (1995).
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* Heintzman N. D., Ren B. The gateway to transcription: identifying, characterizing and understanding promoters in the eukaryotic genome. Cellular and Molecular Life Science 64, 386-400 (2007).
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* Rattner A. NF-&kappa;B activates the HIV promoter in neurons. ''EMBO'' 12: 4261–4267 (1993).
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* Stemmer W. P., Crameri A., Ha K. D., Brennan T. M., Heyneker H. L. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene 164, 49-53 (1995).
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* Yokoyama D. K., Ohler U. & Wray G. A. Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships. ''Nuc Acids Res'': 1-21 (2009).
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* Rattner A. NF-&kappa; B activates the HIV promoter in neurons. EMBO 12, 4261–4267 (1993).
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* del Val C., Pelz O., Glatting K-H, Barta E. & Hotz-Wagenblatt A. PromoterSweep: a tool for identification of transcription factor binding site. ''Theor Chem Acc'' (in press)
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* Yokoyama D. K., Ohler U., Wray G. A. Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships. Nuc Acids Res, 1-21 (2009).
+
* Ghosh S., May M. J. & Kopp E. B. Rel/NF-&kappa;B and IKB proteins: an overview. ''Seminars in Cancer Biology'' 8: 63-73 (1997).  
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* del Val C., Pelz O., Glatting K-H, Barta E., Hotz-Wagenblatt A.  PromoterSweep: a tool for identification of transcription factor binding site. Theor Chem Acc (in press)
+
* Moyano P. & Rotwein P. Mini-review: estrogen action in the uterus and insulin-like growth factor-I. ''Growth Hormone & IGF Research'' 14: 431-435 (2009).
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</div>
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* Ghosh S., May M. J., Kopp E. B. Rel/NF-&kappa;B and IKB proteins: an overview. Seminars in Cancer Biology, 8, 63-73 (1997).  
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==Stable cell line==
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<div style="text-align:justify;">
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* Zhou H. Development of site-specific integration system to high-level expression recombinant proteins in CHO cells. ''Chinese journal of biotechnology'' 23: 756-62 (2007).  
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* Moyano P.& Rotwein P. Mini-review: estrogen action in the uterus and insulin-like growth factor-I. Growth Hormone & IGF Research, 14, 431-435 (2009).
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* Andrews B. J., Proteau G. A., Beatty L. G. & Sadowski P. D. The FLP Recombinase of the 2&mu; Circle DNA of Yeast: Interaction with Its Target Sequences. ''Cell'' 40: 795-803 (1985).  
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===Stable cell line===
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* Senecoff J. F., Bruckner R. C. & Cox M. M. The FLP recombinase of the yeast 2-&mu; plasmid: Characterization of its recombination site. ''Proc. Nati. Acad. Sci. USA'' 82: 7270-7274 (1985).
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* Zhou, H. Development of site-specific integration system to high-level expression recombinant proteins in CHO cells. Chinese journal of biotechnology 23: 756-62 (2007)  
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* Holmberg A., Blomstergren A., Nord O., Lukacs M., Lundeberg J. & Uhlén M. The biotin-streptavidin interaction can be eversibly broken using water at elevated temperatures. ''Electrophoresis'' 26(3): 501-10 (2005).
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* Andrews, B. J., Proteau, G. A., Beatty, L. G. & Sadowski, P. D. The FLP Recombinase of the 2&mu; Circle DNA of Yeast: Interaction with Its Target Sequences. Cell 40: 795-803 (1985)  
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* Schmidt M., Schwarzwaelder K., Bartholomae C., Zaoui K., Ball B., Pilz I., Braun S., Glimm H., von Kalle C., High-resolution insertion-site analysis by linear amplification–mediated PCR (LAM-PCR). ''Nature Methods'' 4 (12): 1051-1057 (2005).
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</div>
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* Senecoff, J. F., Bruckner, R. C. & COX, M. M. The FLP recombinase of the yeast 2-&mu; plasmid: Characterization of its recombination site. Proc. Nati. Acad. Sci. USA 82: 7270-7274 (1985)  
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==Outlook and Summary==
 +
<div style="text-align:justify;">
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* Venter M. Synthetic promoters: genetic control through cis engineering. ''Trends in Plant Science'' 12: 118-24 (2007).
 +
* Carey M., Smale S. T. & Hughes H., Transcriptional Regulation in Eukaryotes: Concepts, Strategies and Techniques. ''New York: CSHL'': p. 18-25 (2000).
 +
</div>
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* Holmberg A., Blomstergren A., Nord O., Lukacs M., Lundeberg J., Uhlén M. The biotin-streptavidin interaction can be eversibly broken using water at elevated temperatures. Electrophoresis 26(3):501-10. (2005)
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==HEARTBEAT Database & Fuzzy Modeling==
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<div style="text-align:justify;">
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== References ==
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* Schmidt M., Schwarzwaelder K., Bartholomae C., Zaoui K., Ball B., Pilz I., Braun S., Glimm H., von Kalle C., High-resolution insertion-site analysis by linear amplification–mediated PCR (LAM-PCR) Nature Methods 4:12, 1051-1057 (2005)
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* Harbison C. T., Gordon D. B., Lee T. I., Rinaldi N. J., Macisaac K. D., Danford T. W., Hannett N. M., Tagne J. B., Reynolds D. B., Yoo J., Jennings E. G., Zeitlinger J., Pokholok D. K., Kellis M., Rolfe P. A., Takusagawa K. T., Lander E. S., Gifford D. K., Fraenkel E., Young R. A. Transcriptional regulatory code of a eukaryotic genome. ''Nature'' 431: 99-104 (2004).<br>
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* Hu Z., Killion P. J., Iyer, V. R. Genetic reconstruction of a functional transcriptional regulatory network. ''Nature Genet.'' 39: 683-687 (2007).<br>
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* Gertz J., Siggia E. D., Cohen B. A. Analysis of combinatorial ''cis''-regulation in synthetic and genomic promoters. ''Nature'' 457: 215-218 (2009)<br>
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===Outlook and summary===
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* Roider H. G., Kanhere A., Manke T., Vingron M. Predicting transcription factor affinities to DNA from a biophysical model.'' Bioinformatics'' 23: 134-141 (2006)<br>
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* Venter M., Synthetic promoters: genetic control through cis engineering, Trends in Plant Science, 12:118-12
+
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* Carey M., Smale S. T., Hughes H., Transcriptional Regulation in Eukaryotes: Concepts, Strategies and Techniques. New York:CSHL, p. 18-25 (2000)
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===Modeling===
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* Carrera J., Rodrigo G., Jaramillo A. Towards the automated engineering of a synthetic genome. ''Mol. Biosyst.'' 5: 733-43 (2009).<br>
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===HEARTBEAT Fuzzy Modeling===
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* Agapakis C. M., Silver P. A. Synthetic biology: exploring and exploiting genetic modularity through the design of novel biological networks. ''Mol. Biosyst.'' 5: 704-13 (2009)<br>
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* Harbison C. T., Gordon D. B., Lee T. I., Rinaldi N. J., Macisaac K. D., Danford T. W., Hannett N. M., Tagne J. B., Reynolds D. B., Yoo J., Jennings E. G., Zeitlinger J., Pokholok D. K., Kellis M., Rolfe P. A., Takusagawa K. T., Lander E. S., Gifford D. K., Fraenkel E., Young R. A. Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99-104 (2004).<br>
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* Purnick P. E., Weiss R. The second wave of synthetic biology: from modules to systems. ''Nat Rev Mol Cell Biol.'' 10: 410-22 (2009).<br>
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* Hu, Z., Killion, P. J. & Iyer, V. R. Genetic reconstruction of a functional transcriptional regulatory network. Nature Genet. 39, 683-687 (2007).<br>
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* Bhalerao K. D. Synthetic gene networks: the next wave in biotechnology? ''Trends Biotechnol''. 27: 368-74 (2009).<br>
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* Gertz, J., Siggia E. D. & Cohen, B. A. Analysis of combinatorial ''cis''-regulation in synthetic and genomic promoters. Nature 457. 215-218 (2009)<br>
+
* Andrianantoandro E., Basu S., Karig D. K., Weiss R. Synthetic biology: new engineering rules for an emerging discipline. ''Mol Sys Biol'' (2006)<br>
-
* Roider H. G., Kanhere A., Manke T., Vingron M. Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics 23, 134-141 (2006)<br>
+
* Alberts B., Johnson A., Walter P., Lewis J. Molecular Biology of the Cell, 5th edition, 2008. Garland Science, Chapter 6<br>
-
* ref to come<br>
+
* Vardhanabhuti S., Wang J., Hannenhalli S. Position and distance specificity are important determinants of ''cis''-regulatory motifs in addition to evolutionary conservation. ''Nucl Acid Res'' 35: 3203-3213 (2007).<br>
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* Andrianantoandro E., Basu S., Karig D. K., Weiss R. Synthetic biology: new engineering rules for an emerging discipline. Mol Sys Biol (2006)<br>
+
* Yokoyama K. D., Ohler U., Wray G. A. Measuring spatial preferences at fine-scale resolution identifies known and novel ''cis''-regulatory element candidates and functional motif-pair relationships. ''Nucl Acid Res'' 37: e92 (2009)<br>
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* Alberts, B., Johnson A., Walter P., Lewis J. Molecular Biology of the Cell, 5th edition, 2008. Garland Science, Chapter 6<br>
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* Nelles O. ''Nonlinear System Identification'' Springer Verlag GmbH & Co., Berlin, 2000. <br>
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* Vardhanabhuti, S., Wang, J. & Hannenhalli, S. Position and distance specificity are important determinants of ''cis''-regulatory motifs in addition to evolutionary conservation. Nucl Acid Res 35, 3203-3213 (2007).<br>
+
* Bosl W. J. Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery.  
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''BMC Systems Biology''1:13 (2007).<br>
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* Yokoyama, K. D., Ohler, U. & Wray, G. A. Measuring spatial preferences at fine-scale resolution identifies known and novel ''cis''-regulatory element candidates and functional motif-pair relationships. Nucl Acid Res, 1-21 (2009)<br>
+
* Laschov D., Margaliot M. Mathematical modeling of the lambda switch:a fuzzy logic approach. ''J Theor Biol.''   21:475-89 (2009) <br>
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* Nelles, O. Nonlinear System Identification. Springer, 2000. <br>
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* Aldridge B. B., Saez-Rodriguez J., Muhlich  J. L., Sorger P. K., Lauffenburger D. A. Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling ''PLoS Comput Biol.''5:e1000340 (2009).
 +
<br>
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* Bosl, W. J. BMC systems biology 1, 13 (2007).<br>
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* Roider H. G., Kanhere A., Manke T., Vingron M. Predicting transcription factor affinities to DNA from a biophysical model. ''Bioinformatics'' 23: 134-141 (2007).
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* Mathematical modeling of the lambda switch:a fuzzy logic approach.<br>
 
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* B. B. Aldridge, J. Saez-Rodriguez, J. L. Muhlich et al., PLoS computational biology 5 (4), e1000340 (2009).
 
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<br>
 
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* [https://2008.igem.org/Team:BCCS-Bristol/Modeling BCCS-Bristol: Best Model 2008]
 +
 +
* Heintzman N. D. & Ren B. The gateway to transcription: identifying, characterizing and understanding promoters in the eukaryotic genome. ''Cellular and Molecular Life Science'' 64: 386-400 (2007).
 +
 +
* Vardhanabhuti, S., Wang, J. & Hannenhalli, S. Position and distance specificity are important determinants of ''cis''-regulatory motifs in addition to evolutionary conservation. ''Nucl Acid Res'' 35(10): 3203-3213 (2007).<br>
 +
 +
* Yokoyama, K. D., Ohler, U. & Wray, G. A. Measuring spatial preferences at fine-scale resolution identifies known and novel ''cis''-regulatory element candidates and functional motif-pair relationships. ''Nucl Acid Res'' 37(13): e92 (2009)<br>
 +
 +
* Ellis T., Wang X. & Collins J. J. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. ''Nature Biotechnology'' 27: 465-471 (2009).
 +
 +
* Kent W. J., Sugnet C. W., Furey T. S., Roskin K. M., Pringle T. H., Zahler A. M. & Haussler D. The human genome browser at UCSC. ''Genome Res.'' 12(6): 996-1006 (2002).
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* Kuhn R. M., Karolchik D., Zweig A. S., Wang T., Smith K. E., Rosenbloom K. R., Rhead B., Raney B. J., Pohl A., Pheasant M., Meyer L., Hsu F., Hinrichs A. S., Harte R. A., Giardine B., Fujita P., Diekhans M., Dreszer T., Clawson H., Barber G. P., Haussler D. & Kent W. J. The UCSC Genome Browser Database: update 2009. ''Nucleic Acids Res.'' 37(Database issue): D755-61 (2009).
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* Kanehisa M., Araki M., Goto S., Hattori M., Hirakawa M., Itoh M., Katayama T., Kawashima S., Okuda S., Tokimatsu T. & Yamanishi, Y. KEGG for linking genomes to life and the environment. ''Nucleic Acids Res.'' 36 (Database issue): D480-4 (2008).
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* Kanehisa M., Goto S., Hattori M., Aoki-Kinoshita K.F., Itoh M., Kawashima S., Katayama T., Araki M. & Hirakawa M. From genomics to chemical genomics: new developments in KEGG. ''Nucleic Acids Res.'' 34 (Database issue): D354-7 (2006).
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* Kanehisa M. & Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. ''Nucleic Acids Res.'' 28(1): 27-30 (2000).
 +
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Eils, R. Breakthrough in the field of synthetic biology, iGEM team Heidelberg presents the results. science 180, 469–480 (2010).
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Eils, R. Breakthrough in the field of synthetic biology, iGEM team Heidelberg presents the results. Online publication, http://simonisdoof.co.uk, 13.10.2009
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Eils, R. Breakthrough in the field of synthetic biology, iGEM team Heidelberg presents the results. Heidelberg: Bioquant-Publishing, 2010, p. 1-1000.
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===Material and Methods===
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==Material and Methods==
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</div>

Latest revision as of 23:47, 21 October 2009

References

Introduction

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Natural Promoters

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Synthetic Promoters

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Stable cell line

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Outlook and Summary

  • Venter M. Synthetic promoters: genetic control through cis engineering. Trends in Plant Science 12: 118-24 (2007).
  • Carey M., Smale S. T. & Hughes H., Transcriptional Regulation in Eukaryotes: Concepts, Strategies and Techniques. New York: CSHL: p. 18-25 (2000).

HEARTBEAT Database & Fuzzy Modeling

References

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