Team:UNIPV-Pavia/Project/References

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<h2 class="art-postheader">References</h2>
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<li> Anderson JC, Voigt CA, Arkin AP (2007) <b>Environmental signal integration by a modular
<li> Anderson JC, Voigt CA, Arkin AP (2007) <b>Environmental signal integration by a modular
-
AND gate.</b> <i>Mol. Syst. Biol.</i> 2007;3:133.</li><br>
+
AND gate.</b> <i>Mol. Syst. Biol.</i>3:133.</li><br>
<li>Anderson JC, Dueber JE, Leguia M et al. (2010)
<li>Anderson JC, Dueber JE, Leguia M et al. (2010)
<b>BglBricks: A flexible standard for biological part assembly.</b> <i>J. Biol. Eng.</i> 20;4(1):1.
<b>BglBricks: A flexible standard for biological part assembly.</b> <i>J. Biol. Eng.</i> 20;4(1):1.
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<i>Mol. Syst. Biol.</i> 2:2006.0028.
<i>Mol. Syst. Biol.</i> 2:2006.0028.
</li> <br>
</li> <br>
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<li>Atkinson MR,Savageau MA, Myers JT et al. (2003) <b>Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli. </b> <i>Cell. </i> 113(5):597-607.
+
<li>Atkinson MR,Savageau MA, Myers JT et al. (2003) <b>Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli. </b> <i>Cell.</i> 113(5):597-607.
</li><br>
</li><br>
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<li>Bassler BL (2002) <b>Small Talk: Cell-to-Cell Communication in Bacteria. </b> <i>Cell. </i> 109(4):421-4.
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<li>Bassler BL (2002) <b>Small Talk: Cell-to-Cell Communication in Bacteria. </b> <i>Cell.</i> 109(4):421-4.
</li><br>
</li><br>
<li>Braun D, Basu S, Weiss R (2005) <b>Parameter estimation for two synthetic gene networks: a case study. </b> <i>Acoustics, Speech, and Signal Processing Proceedings.</i> IEEE International Conference. on vol.5, no., pp. v/769- v/772 Vol. 5, 18-23.  
<li>Braun D, Basu S, Weiss R (2005) <b>Parameter estimation for two synthetic gene networks: a case study. </b> <i>Acoustics, Speech, and Signal Processing Proceedings.</i> IEEE International Conference. on vol.5, no., pp. v/769- v/772 Vol. 5, 18-23.  
</li> <br>
</li> <br>
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<li>Canton B, Labno A, Endy D. (2008) <b>Refinement and standardization of synthetic biological parts and devices. </b> <i> Nat Biotechnol. </i>  26(7):787-93.  
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<li>Canton B, Labno A, Endy D (2008) <b>Refinement and standardization of synthetic biological parts and devices. </b> <i> Nat. Biotechnol. </i>  26(7):787-93.  
</li> <br>
</li> <br>
<li>Collins CH, Arnold FH, Leadbetter JR (2005)  
<li>Collins CH, Arnold FH, Leadbetter JR (2005)  
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</li> <br>  
</li> <br>  
<li>Garcia-Ojalvo J, Elowitz MB, Strogatz SH (2004) <b>Modeling a synthetic multicellular
<li>Garcia-Ojalvo J, Elowitz MB, Strogatz SH (2004) <b>Modeling a synthetic multicellular
-
clock: repressilators coupled by quorum sensing.</b> <i>Proc. Natl. Acad. Sci. U.S.A. 2004</i> 101(30):10955-60.
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clock: repressilators coupled by quorum sensing.</b> <i>Proc. Natl. Acad. Sci. U.S.A.</i> 101(30):10955-60.
</li> <br>
</li> <br>
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<li>Hanzelka BL, Stevens AM, Parsek MR et al. (1997)  
+
<li>Girotti S, Ferri EN, Furmo MG et al. (2008) <b>Monitoring of environmental pollutants by bioluminescent bacteria. </b> <i>Anal. Chim. Acta.</i> 608(1):2-2.
-
<b>Mutational analysis of the Vibrio fischeri LuxI polypeptide: critical regions of an autoinducer synthase.</b>  
+
</li><br>
-
<i>J. Bacteriol.</i> 179(15):4882-7.
+
<li>Guet CC, Elowitz MB, Hsing W et al. (2002) <b>Combinatorial Synthesis of Genetic Networks. </b> <i>Science.</i>  296(5572):1466-70.
 +
</li><br>
 +
<li>Hanzelka BL, Stevens AM, Parsek MR et al. (1997) <b>Mutational analysis of the Vibrio fischeri LuxI polypeptide: critical regions of an autoinducer synthase.</b> <i>J. Bacteriol.</i> 179(15):4882-7.
</li> <br>
</li> <br>
 +
<li>Hellinga HW, Marvin JS (1998) <b>Protein engineering and the development of generic biosensors.  </b> <i>Trends Biotechnol. </i>16(4):183-9.
 +
</li><br>
<li>Kelly JR, Rubin AJ, Davis JH et al. (2009) <b>Measuring the activity of BioBrick promoters using an in vivo reference standard.</b>  
<li>Kelly JR, Rubin AJ, Davis JH et al. (2009) <b>Measuring the activity of BioBrick promoters using an in vivo reference standard.</b>  
<i>J. Biol. Eng.</i> 3:4.
<i>J. Biol. Eng.</i> 3:4.
</li> <br>
</li> <br>
 +
<li>Looger LL, Dwyer MA, Smith JJ et al. (2003) <b>Computational design of receptor and sensor proteins with novel functions. </b> <i> Nature.</i>  423, 185-190.
 +
</li><br>
<li>Lutz R, Bujard H (1997) <b> Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. </b> <i>Nucleic Acids Res.</i> 25(6):1203-10.
<li>Lutz R, Bujard H (1997) <b> Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. </b> <i>Nucleic Acids Res.</i> 25(6):1203-10.
</li><br>
</li><br>
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<li>Molina L, Constantinescu F, Micheal L et al. (2003) <b>Degradation of pathogen quorum-sensing molecules by soil bacteria: a preventive and curative biological control mechanism. </b> <i>FEMS Microbiology Ecology. </i>  45: 71-81.
<li>Molina L, Constantinescu F, Micheal L et al. (2003) <b>Degradation of pathogen quorum-sensing molecules by soil bacteria: a preventive and curative biological control mechanism. </b> <i>FEMS Microbiology Ecology. </i>  45: 71-81.
</li><br>
</li><br>
 +
<li>Miller MB, Bassler BL (2001) <b>Quorum Sensing in Bacteria. </b> <i> Annual Review of Microbiology.</i>  55: 165-199. </li><br>
<li>Pasotti L, Quattrocelli M, Galli D et al. (2011) <b>Multiplexing and demultiplexing logic functions for computing signal processing tasks in synthetic biology. </b> <i>Biotechnol. J. </i>6(7):784-95.  
<li>Pasotti L, Quattrocelli M, Galli D et al. (2011) <b>Multiplexing and demultiplexing logic functions for computing signal processing tasks in synthetic biology. </b> <i>Biotechnol. J. </i>6(7):784-95.  
</li><br>
</li><br>
-
<li>Salis H M, Mirsky E A, Voight C A (2009)<b>Automated design of synthetic ribosome binding sites to control protein expression. </b> <i>Nat. Biotechnol.</i>27:946-950.  
+
<li>Salis HM, Mirsky EA, Voight CA (2009)<b>Automated design of synthetic ribosome binding sites to control protein expression. </b> <i>Nat. Biotechnol.</i>27:946-950.  
</li><br>  
</li><br>  
-
<li>Shaefer AL, Hanzelka BL, Eberhard A et al. (1996) <b>Quorum Sensing in Vibrio fischeri: Probing Autoinducer-LuxR Interactions with Autoinducer Analogs. </b> <i>Journal Of Bacteriology. </i> 178 (10): 2897-2901.
+
<li>Schaefer AL, Hanzelka BL, Eberhard A et al. (1996) <b>Quorum Sensing in Vibrio fischeri: Probing Autoinducer-LuxR Interactions with Autoinducer Analogs. </b> <i>Journal Of Bacteriology. </i> 178 (10): 2897-2901.
</li><br>
</li><br>
<li>Sleight SC, Bartley BA, Lieviant JA et al. (2010) <b>Designing and engineering evolutionary robust genetic circuits. </b> <i>J. Biol. Eng. </i>4:12.
<li>Sleight SC, Bartley BA, Lieviant JA et al. (2010) <b>Designing and engineering evolutionary robust genetic circuits. </b> <i>J. Biol. Eng. </i>4:12.
 +
</li><br>
 +
<li>Stevenson AM, Dolan KM, Greenberg EP (1994) <b>Synergistic binding of the Vibriofischeri LuxR transcriptional activator domain and RNA polymerase to the lux promoter region. </b> <i>Proc. Natl. Acad. Sci. U.S.A. </i>  91(26):12619-23.
 +
</li><br>
 +
<li>Tagkopoulos I, Liu Y, Tavazoie S (2008) <b>Predictive Behavior Within Microbial Genetic Networks. </b> <i>Science.</i>  320(5881):1313-7.
</li><br>
</li><br>
<li>Tamsir A, Tabor JJ, Voigt CA (2011) <b>Robust multicellular computing using genetically
<li>Tamsir A, Tabor JJ, Voigt CA (2011) <b>Robust multicellular computing using genetically
-
encoded NOR gates and chemical 'wires'.</b> <i>Nature</i>  469(7329):212-5. </li><br>
+
encoded NOR gates and chemical 'wires'.</b> <i>Nature.</i>  469(7329):212-5.  
-
<li>Thomas PW, Stone EM, Costello AL et al. (2005) <b>The quorum-quenching lactonase from Bacillus thuringiensis is a metalloprotein.</b>  
+
</li><br>
-
<i>Biochemistry.</i> 44(20):7559-69.
+
<li>Thomas PW, Stone EM, Costello AL et al. (2005) <b>The quorum-quenching lactonase from Bacillus thuringiensis is a metalloprotein.</b> <i>Biochemistry.</i> 44(20):7559-69.
</li> <br>  
</li> <br>  
-
<li>Wang LH, Weng LX, Dong YH et al. (2004)  
+
<li>Wang LH, Weng LX, Dong YH et al. (2004) <b>Specificity and enzyme kinetics of the quorum-quenching N-Acyl homoserine lactone lactonase (AHL-lactonase).</b> <i>J. Biol. Chem.</i>279(14):13645-51.
-
<b>Specificity and enzyme kinetics of the quorum-quenching N-Acyl homoserine lactone lactonase (AHL-lactonase).</b>  
+
-
<i>J. Biol. Chem.</i>279(14):13645-51.
+
</li> <br>
</li> <br>
-
<li>Waters C.M., Bonnie L (2005) <b>Quorum Sensing: Cell-to-Cell Communication in Bacteria. </b> <i>Annu. Rev. Cell Dev. Biol. </i> 21:319–46.
+
<li>Waters CM, Bonnie L (2005) <b>Quorum Sensing: Cell-to-Cell Communication in Bacteria. </b> <i>Annu. Rev. Cell Dev. Biol. </i> 21:319–46.
</li><br>
</li><br>
-
<li>You L, Cox RS 3rd, Weiss R et al. (2004) <b>Programmed population control by cell-cell communication and regulated killing.</b>  
+
<li>You L, Cox RS 3rd, Weiss R et al. (2004) <b>Programmed population control by cell-cell communication and regulated killing.</b> <i>Nature.</i> 428(6985):868-71.  
-
<i>Nature.</i> 428(6985):868-71.  
+
</ol>
</ol>
<br>
<br>

Latest revision as of 08:31, 19 September 2011

UNIPV TEAM 2011

References


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  2. Anderson JC, Voigt CA, Arkin AP (2007) Environmental signal integration by a modular AND gate. Mol. Syst. Biol.3:133.

  3. Anderson JC, Dueber JE, Leguia M et al. (2010) BglBricks: A flexible standard for biological part assembly. J. Biol. Eng. 20;4(1):1.

  4. Andrianantoandro E, Basu S, Karig DK et al. (2006) Synthetic biology: new engineering rules for an emerging discipline. Mol. Syst. Biol. 2:2006.0028.

  5. Atkinson MR,Savageau MA, Myers JT et al. (2003) Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli. Cell. 113(5):597-607.

  6. Bassler BL (2002) Small Talk: Cell-to-Cell Communication in Bacteria. Cell. 109(4):421-4.

  7. Braun D, Basu S, Weiss R (2005) Parameter estimation for two synthetic gene networks: a case study. Acoustics, Speech, and Signal Processing Proceedings. IEEE International Conference. on vol.5, no., pp. v/769- v/772 Vol. 5, 18-23.

  8. Canton B, Labno A, Endy D (2008) Refinement and standardization of synthetic biological parts and devices. Nat. Biotechnol. 26(7):787-93.

  9. Collins CH, Arnold FH, Leadbetter JR (2005) Directed evolution of Vibrio fischeri LuxR for increased sensitivity to a broad spectrum of acyl-homoserine lactones. Mol. Microbiol. 55(3):712-23.

  10. Cox RS 3rd, Surette MG, Elowitz MB (2007) Programming gene expression with combinatorial promoters. Mol. Syst. Biol. 3:145.

  11. Danino T, Mondragón-Palomino O, Tsimring L et al. (2010) A synchronized quorum of genetic clocks. Nature. 463(7279):326-30.

  12. De Lorimier RM, Smith JJ, Dwyer MA et al. (2002) Construction of a fluorescent biosensor family. Protein Science. 11:2655–2675.

  13. Dong YH, Gusti AR, Zhang Q et al. (2002) Identification ofquorum-quenching N-acyl homoserine lactonases from Bacillus species. Appl. Environ. Microbiol. 68(4):1754-9.

  14. Dong Y, Xu J, Li X et al. (2002) AiiA, an enzyme that inactivates the acylhomoserine lactone quorum-sensing signal and attenuates the virulence of Erwinia carotovora. Applied And Environmental Microbiology. 68: 1754–1759.

  15. Endler L, Rodriguez N, Juty N et al. (2009) Designing and encoding models for synthetic biology. J. R. Soc. Interface. 6:S405-S417.

  16. Engebrecht J, Nealson K, Silverman M (1983) Bacterial bioluminescence: isolation and genetic analysis of functions from Vibrio fischeri. Cell. 32:773–81.

  17. Fuqua C, Greenberg EP (2002) Listening in on bacteria: acyl- homoserine lactone signalling. Nat. Rev. Mol. Cell Biol. 3: 685–695.

  18. Fussenegger M (2010) Synthetic biology: Synchronized bacterial clocks. Nature. 463(7279):301-2.

  19. Garcia-Ojalvo J, Elowitz MB, Strogatz SH (2004) Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing. Proc. Natl. Acad. Sci. U.S.A. 101(30):10955-60.

  20. Girotti S, Ferri EN, Furmo MG et al. (2008) Monitoring of environmental pollutants by bioluminescent bacteria. Anal. Chim. Acta. 608(1):2-2.

  21. Guet CC, Elowitz MB, Hsing W et al. (2002) Combinatorial Synthesis of Genetic Networks. Science. 296(5572):1466-70.

  22. Hanzelka BL, Stevens AM, Parsek MR et al. (1997) Mutational analysis of the Vibrio fischeri LuxI polypeptide: critical regions of an autoinducer synthase. J. Bacteriol. 179(15):4882-7.

  23. Hellinga HW, Marvin JS (1998) Protein engineering and the development of generic biosensors. Trends Biotechnol. 16(4):183-9.

  24. Kelly JR, Rubin AJ, Davis JH et al. (2009) Measuring the activity of BioBrick promoters using an in vivo reference standard. J. Biol. Eng. 3:4.

  25. Looger LL, Dwyer MA, Smith JJ et al. (2003) Computational design of receptor and sensor proteins with novel functions. Nature. 423, 185-190.

  26. Lutz R, Bujard H (1997) Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res. 25(6):1203-10.

  27. McMillen D, Kopell N, Hasty J et al. (2002) Synchronizing genetic relaxation oscillators by intercell signaling. Proc. Natl. Acad. Sci. U.S.A. 99(2):679-84.

  28. Molina L, Constantinescu F, Micheal L et al. (2003) Degradation of pathogen quorum-sensing molecules by soil bacteria: a preventive and curative biological control mechanism. FEMS Microbiology Ecology. 45: 71-81.

  29. Miller MB, Bassler BL (2001) Quorum Sensing in Bacteria. Annual Review of Microbiology. 55: 165-199.

  30. Pasotti L, Quattrocelli M, Galli D et al. (2011) Multiplexing and demultiplexing logic functions for computing signal processing tasks in synthetic biology. Biotechnol. J. 6(7):784-95.

  31. Salis HM, Mirsky EA, Voight CA (2009)Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol.27:946-950.

  32. Schaefer AL, Hanzelka BL, Eberhard A et al. (1996) Quorum Sensing in Vibrio fischeri: Probing Autoinducer-LuxR Interactions with Autoinducer Analogs. Journal Of Bacteriology. 178 (10): 2897-2901.

  33. Sleight SC, Bartley BA, Lieviant JA et al. (2010) Designing and engineering evolutionary robust genetic circuits. J. Biol. Eng. 4:12.

  34. Stevenson AM, Dolan KM, Greenberg EP (1994) Synergistic binding of the Vibriofischeri LuxR transcriptional activator domain and RNA polymerase to the lux promoter region. Proc. Natl. Acad. Sci. U.S.A. 91(26):12619-23.

  35. Tagkopoulos I, Liu Y, Tavazoie S (2008) Predictive Behavior Within Microbial Genetic Networks. Science. 320(5881):1313-7.

  36. Tamsir A, Tabor JJ, Voigt CA (2011) Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'. Nature. 469(7329):212-5.

  37. Thomas PW, Stone EM, Costello AL et al. (2005) The quorum-quenching lactonase from Bacillus thuringiensis is a metalloprotein. Biochemistry. 44(20):7559-69.

  38. Wang LH, Weng LX, Dong YH et al. (2004) Specificity and enzyme kinetics of the quorum-quenching N-Acyl homoserine lactone lactonase (AHL-lactonase). J. Biol. Chem.279(14):13645-51.

  39. Waters CM, Bonnie L (2005) Quorum Sensing: Cell-to-Cell Communication in Bacteria. Annu. Rev. Cell Dev. Biol. 21:319–46.

  40. You L, Cox RS 3rd, Weiss R et al. (2004) Programmed population control by cell-cell communication and regulated killing. Nature. 428(6985):868-71.

Laboratory for Biomedical Informatics | Centre of Tissutal Engineering

University of Pavia
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