Difference between revisions of "Logic Gates - Emma Garren"

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====References====
 
====References====
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*Anderson JC, Voigt CA, Arkin AP (2007) Environmental signal integration by a modular AND gate. ''Molecular Systems Biology'' 3:133. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17700541&ordinalpos=6&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Anderson, J. C., Voigt, C. A., Arkin, A. P. (2007). Environmental signal integration by a modular AND gate. Mol Syst Biol. 3:133. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17700541&ordinalpos=4&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Andrianantoandro E, Basu S, Karig DK, Weiss R (2006) Synthetic biology: new engineering principles for an emerging discipline. ''Molecular Systems Biology'' 2:2006.0028. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16738572&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Andrianantoandro, E., Subhayu, B., Karig, D. K., Weiss, R. (2006). Synthetic biology: new engineering rules for an emerging discipline. Mol Syst. Biol. 2:2006.0028. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16738572&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Greber D, Fussenegger M (2007) Mammalian synthetic biology: engineering of sophisticated gene networks. J Biotechnol 130(4):329-345. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17602777&ordinalpos=12&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Ashkenasy, G., Ghadiri, M. R. (2004). Boolean Logic Functions of a Synthetic Peptide Network. J Am Chem Soc. 126(36):11140-1. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=15355081&ordinalpos=13&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Kramer BP, Fischer C, Fussenegger M (2004) BioLogic Gates Enable Logical Trascription Control in Mammalian Cells. ''Biotechnology and Bioengineering'' 87:4, 478-484. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=15286985&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Baron, R., Lioubashevski, O., Katz, E., Niazov, T., Willner, I. (2006). Two coupled enzymes perform in parallel the “AND” and “InhibAND” logic gate operations. Org Biomol Chem. 4(6): 989-91. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16525539&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Voigt CA (2006) Genetic parts to program bacteria. ''Curr Opin Biotechnol''. 17(5): 548-557. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16978856&query_hl=1&itool=pubmed_docsum Abstract]
+
*Baron, R., Lioubashevski, O., Katz, E., Niazov, T., Willner, I. (2006). Logic gates and elementary computing by enzymes. J Phys Chem A. 110(27):8548-53. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16821840&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Wall ME, Hlavacek WS, Savageau MA (2004) Design of gene circuits: lessons from bacteria. 5(1): 34-42. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=14708014&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus Abstract]
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*Boczko, E., Gedeon, T., Mischaikow, K. (2007). Dynamics of a simple regulatory switch. J Math Biol. 55(5-6):679-719. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17622532&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
 +
*Chen, X., Wang, Y., Liu, Q., Zhang, Z., Fan, C., He, L. (2006). Construction of molecular logic gates with a DNA-cleaving deoxyribozyme. Angew Chem Int Ed Engl. 45(11):1759-62. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16470893&ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Davidson, E.A., Ellington, A.D. (2007). Synthetic RNA circuits. Nat Chem Biol. 3(1):23-8. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17173026&ordinalpos=4&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Drubin, D. A., Way, J. C., Silver, P. A. (2007). Designing biological systems. Genes Dev. 21(3):242-54. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17289915&ordinalpos=4&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Elowitz, M. B., & Leibler, S. (2000). A synthetic oscillatory network of transcriptional regulators. Nature. 403(6767):335-8. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=10659856&ordinalpos=10&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
 +
*Farfel, J., Stefanovic, D. (2005). Towards practical biomolecular computers using microfluidic deoxyribozyme logic gate networks.  University of New Mexico.
 +
*Frezza, B.M., Cockroft, S. L., Ghadiri, M.R. (2007). Modular Multi-level Circuits from Immobilized DNA-Based Logic Gates. J Am Chem Soc. (Epub ahead of print) [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17994734&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Gardner, T.S., Cantor, C.R., Collins, J.J. (2000). Construction of a genetic toggle switch in Escherichia coli. Nature. 403(6767):338-42. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=10659857&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Heinemann, M., Panke, S. (2006). Synthetic biology—putting engineering into biology. Bioinformatics. 22(22):2790-9. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16954140&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Kaznessis, Y. N. (2007). Models for synthetic biology. BMC Syst Biol. 1(1):47. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17986347&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
 +
*Kramer, B. P., Fischer, C., Fussenegger, M. (2004). BioLogic Gates Enable Transcription Control in Mammalian Cells. Biotechnol Bioeng. 87(4):478-84. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=15286985&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Lederman, H., Macdonald, J., Stefanovic, D., Stojanovic, M. N. (2006). Deoxyribozyme-based three-input logic gates and construction of a molecular full adder. Biochemistry. 45(4):1194-9. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16430215&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Narayanaswamy, R., Ellington, A.D. (2006). Engineering RNA-based circuits. Handb Exp Pharmacol. (173):423-45. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16594629&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus Abstract]
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*Rackham, O., Chin, J. W. (2005). Cellular logic with orthogonal ribosomes. JACS 1227:17584-85. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16351070&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Sayut, D.J., Kambam, P.K., Sun, L. (2007). Engineering and applications of genetic circuits. Mol Biosyst. 3(12):835-840. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=18000560&ordinalpos=4&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Seelig G., Soloveichik, D., Zhang, D. Y., Winfree, E., (2006). Enzyme-free nucleic acid logic circuits. Science. 314(5805): 1585-8. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17158324&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Stojanovic, M. N., Semova, S., Kolpashchikov, D., Macdonald, J., Morgan, C., Stefanovic, D. (2005). Deoxyribozyme-based ligase logic gates and their initial circuits. J Am Chem Soc. 127(19):6914-5.  [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=15884910&ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Voigt, C. A. (2006). Genetic parts to program bacteria. Curr Opin Biotechnol. 17:548-557. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16978856&ordinalpos=9&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
 +
*Wall, M. E., Hlavacek, W. S., Savageau, M. A. (2004). Design of gene circuits: lessons from bacteria. Nat Rev Genet. 5(1):34-42. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=14708014&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]
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*Yoshida, W., Yokobayashi, Y. (2007). Photon Boolean logic gates based on DNA aptamers. Chem Commun (Camb). (2):195-7. [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17180244&ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract]

Revision as of 03:41, 17 November 2007

Paper Discussion 10/30/2007

Background Information

Information on logic gates:

Papers:

Project Topic: Logic Gates

References

  • Anderson, J. C., Voigt, C. A., Arkin, A. P. (2007). Environmental signal integration by a modular AND gate. Mol Syst Biol. 3:133. Abstract
  • Andrianantoandro, E., Subhayu, B., Karig, D. K., Weiss, R. (2006). Synthetic biology: new engineering rules for an emerging discipline. Mol Syst. Biol. 2:2006.0028. Abstract
  • Ashkenasy, G., Ghadiri, M. R. (2004). Boolean Logic Functions of a Synthetic Peptide Network. J Am Chem Soc. 126(36):11140-1. Abstract
  • Baron, R., Lioubashevski, O., Katz, E., Niazov, T., Willner, I. (2006). Two coupled enzymes perform in parallel the “AND” and “InhibAND” logic gate operations. Org Biomol Chem. 4(6): 989-91. Abstract
  • Baron, R., Lioubashevski, O., Katz, E., Niazov, T., Willner, I. (2006). Logic gates and elementary computing by enzymes. J Phys Chem A. 110(27):8548-53. Abstract
  • Boczko, E., Gedeon, T., Mischaikow, K. (2007). Dynamics of a simple regulatory switch. J Math Biol. 55(5-6):679-719. Abstract
  • Chen, X., Wang, Y., Liu, Q., Zhang, Z., Fan, C., He, L. (2006). Construction of molecular logic gates with a DNA-cleaving deoxyribozyme. Angew Chem Int Ed Engl. 45(11):1759-62. Abstract
  • Davidson, E.A., Ellington, A.D. (2007). Synthetic RNA circuits. Nat Chem Biol. 3(1):23-8. Abstract
  • Drubin, D. A., Way, J. C., Silver, P. A. (2007). Designing biological systems. Genes Dev. 21(3):242-54. Abstract
  • Elowitz, M. B., & Leibler, S. (2000). A synthetic oscillatory network of transcriptional regulators. Nature. 403(6767):335-8. Abstract
  • Farfel, J., Stefanovic, D. (2005). Towards practical biomolecular computers using microfluidic deoxyribozyme logic gate networks. University of New Mexico.
  • Frezza, B.M., Cockroft, S. L., Ghadiri, M.R. (2007). Modular Multi-level Circuits from Immobilized DNA-Based Logic Gates. J Am Chem Soc. (Epub ahead of print) Abstract
  • Gardner, T.S., Cantor, C.R., Collins, J.J. (2000). Construction of a genetic toggle switch in Escherichia coli. Nature. 403(6767):338-42. Abstract
  • Heinemann, M., Panke, S. (2006). Synthetic biology—putting engineering into biology. Bioinformatics. 22(22):2790-9. Abstract
  • Kaznessis, Y. N. (2007). Models for synthetic biology. BMC Syst Biol. 1(1):47. Abstract
  • Kramer, B. P., Fischer, C., Fussenegger, M. (2004). BioLogic Gates Enable Transcription Control in Mammalian Cells. Biotechnol Bioeng. 87(4):478-84. Abstract
  • Lederman, H., Macdonald, J., Stefanovic, D., Stojanovic, M. N. (2006). Deoxyribozyme-based three-input logic gates and construction of a molecular full adder. Biochemistry. 45(4):1194-9. Abstract
  • Narayanaswamy, R., Ellington, A.D. (2006). Engineering RNA-based circuits. Handb Exp Pharmacol. (173):423-45. Abstract
  • Rackham, O., Chin, J. W. (2005). Cellular logic with orthogonal ribosomes. JACS 1227:17584-85. Abstract
  • Sayut, D.J., Kambam, P.K., Sun, L. (2007). Engineering and applications of genetic circuits. Mol Biosyst. 3(12):835-840. Abstract
  • Seelig G., Soloveichik, D., Zhang, D. Y., Winfree, E., (2006). Enzyme-free nucleic acid logic circuits. Science. 314(5805): 1585-8. Abstract
  • Stojanovic, M. N., Semova, S., Kolpashchikov, D., Macdonald, J., Morgan, C., Stefanovic, D. (2005). Deoxyribozyme-based ligase logic gates and their initial circuits. J Am Chem Soc. 127(19):6914-5. Abstract
  • Voigt, C. A. (2006). Genetic parts to program bacteria. Curr Opin Biotechnol. 17:548-557. Abstract
  • Wall, M. E., Hlavacek, W. S., Savageau, M. A. (2004). Design of gene circuits: lessons from bacteria. Nat Rev Genet. 5(1):34-42. Abstract
  • Yoshida, W., Yokobayashi, Y. (2007). Photon Boolean logic gates based on DNA aptamers. Chem Commun (Camb). (2):195-7. Abstract
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