Team:Paris Bettencourt/Bibliography

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<div id="grouptitle">Bibliography</div>
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<p style="text-align:center"><b>
 
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We collected here the main references used for building our project
 
-
</b></p>
 
</div>
</div>
<div class="leftparagraph">
<div class="leftparagraph">
<ul>
<ul>
-
   <li id="DiCarlo2013">James E. DiCarlo, Julie E. Norville, Prashant Mali, Xavier Rios, John Aach and George M. Church (2013). Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems.<i> Nucleic Acids Research.</i> 2013, 1–8.</li>
+
  <div id="Crane1997"></div>
-
   <li id="FernaÂndez de Henestrosa2000">Antonio R. FernaÂndez de Henestrosa, Tomoo Ogi, Sayura Aoyagi, David Chafin, Jeffrey J. Hayes, Haruo Ohmori and Roger Woodgate (2000). Identification of additional genes belonging to the LexA regulon in Escherichia coli.<i> Molecular Microbiology .</i> 2000 35(6), 1560±1572.</li>
+
   <li>Crane, B. R., Siegel, L. M., and Getzoff, E. D (1997).<i>  Probing the catalytic mechanism of sulfite reductase by X-ray crystallography: Structures of Escherichia coli hemoprotein.</i> Biochemistry 36, 12120-12137.</li>
-
   <li id="Higashitani1992">Higashitani N., Higashitani I.A., Roth A., Horiuchi A.K. (1992). SOS Induction in Escherichia coli by Infection with Mutant Filamentous Phage That Are Defective in Initiation of Complementary-Strand DNA Synthesis.<i> Journal of Bacteriology.</i> 174:1612-1618.</li>
+
  <div id="DiCarlo2013"></div>
-
    <li id="Jayachandran2007">Jayachandran R., Sundaramurthy V., Combaluzier B., Mueller P., Korf H., Huygen K., Miyazaki T., Albrecht I., Massner J., Pieters J. (2007). Survival of Mycobacteria in Macrophages Is Mediated by Coronin 1-Dependent Activation of Calcineurin. <i>Cell.</i> 130:12-14 </li>
+
  <li>James E. DiCarlo, Julie E. Norville, Prashant Mali, Xavier Rios, John Aach and George M. Church (2013).<i>  Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems.</i> Nucleic Acids Research. 2013, 1–8.</li>
-
<li id="Jiang2013">Wenyan Jiang, David Bikard, David Cox, Feng Zhang & Luciano A Marraffini (2013). RNA-guided editing of bacterial genomes using CRISPR-Cas systems.<i> Nature Biotechnology.</i> 31 (3), 233-2398.</li>
+
  <div id="Duflo2011"></div>
-
   <li id="Juers2012">Douglas H. Juers, Brian W. Matthews, and Reuben E. Huber (2012). LacZ b-galactosidase: Structure and function of an enzyme of historical and molecular biological importance.<i> PROTEIN SCIENCE.</i> 2012, 21,1792—1807.</li>
+
  <li id="">Esther Duflo and Abhjit Banerjee, <i>Poor Economics: A Radical Rethinking of the Way to Fight Global Poverty,</i> PublicAffairs, 2011</li>
-
    
+
  <div id="Easterly2002"></div>
 +
  <li id="">William Easterly, <i>The Elusive Quest for Growth,</i> MIT University Press, 2002</li>
 +
  <div id="Fernandez_de_Henestrosa2000"></div>
 +
   <li id="">Antonio R. Fernandez de Henestrosa, Tomoo Ogi, Sayura Aoyagi, David Chafin, Jeffrey J. Hayes, Haruo Ohmori and Roger Woodgate (2000). <i>Identification of additional genes belonging to the LexA regulon in Escherichia coli.</i> Molecular Microbiology .2000 35(6), 1560-1572.</li>
 +
  <div id="Grown2005"></div>
 +
   <li id="">Caren Grown, Geeta Rao Gupta, Aslihan Kes, <i>Taking action: Achieving Gender Equality and Empowering Women,</i> <i>Earthscan</i>, 2005</li>
 +
  <div id="Higashitani1992"></div>
 +
  <li id="">Higashitani N., Higashitani I.A., Roth A., Horiuchi A.K. (1992). <i>SOS Induction in Escherichia coli by Infection with Mutant Filamentous Phage That Are Defective in Initiation of Complementary-Strand DNA Synthesis.</i> Journal of Bacteriology. 174:1612-1618.</li>
 +
  <div id="Jayachandran2007"></div>
 +
  <li id="">Jayachandran R., Sundaramurthy V., Combaluzier B., Mueller P., Korf H., Huygen K., Miyazaki T., Albrecht I., Massner J., Pieters J. (2007). <i>Survival of Mycobacteria in Macrophages Is Mediated by Coronin 1-Dependent Activation of Calcineurin. </i>Cell. 130:12-14 </li>
 +
  <div id="Jiang2013"></div>
 +
  <li id="">Wenyan Jiang, David Bikard, David Cox, Feng Zhang & Luciano A Marraffini (2013). <i>RNA-guided editing of bacterial genomes using CRISPR-Cas systems.</i> Nature Biotechnology. 31 (3), 233-2398.</li>
 +
   <div id="Juers2012"></div>
 +
  <li id="">Douglas H. Juers, Brian W. Matthews, and Reuben E. Huber (2012). <i>LacZ b-galactosidase: Structure and function of an enzyme of historical and molecular biological importance.</i> Protein Science. 2012, 21,1792—1807.</li>
 +
   <div id="Karlsson2005"></div>
 +
  <li id="">Karlsson F., Malmborg-Hager A.C., Albrekt A.S., Borrebaeck C.A.K. (2005). <i>Genome-wide comparison of phage M13-infected vs. uninfected Escherichia coli. </i> Can. J. Microbiol. 51:29-35.</li>
 +
  <div id="Keller2001"></div>
 +
  <li id="">Kimberly L. Keller, Terri L. Overbeck-Carrick, Doris J. Beck (2001). <i>Survival and induction of SOS in Escherichia coli treated with cisplatin, UV irradiation, or mitomycin C are dependent on the function of the RecBC and RecFOR pathways of homologous recombination. </i> Mutation Research. 486, 2001, 21–29.</li>
 +
<div id="KhalidCh2004"></div>
 +
<li id="">Khalid Ch M, Rasul S, Khan SU, Saeed MS, Imran MN (2004).  Gender Differences in Delays to Tuberculosis Diagnosis and Treatment Outcome. <i>pjcm.net/pdf_v10_n4_a2.pdf‎</i> 10:4
   </li>
   </li>
-
</ul>
+
  <div id="Kobayashi2009"></div>
 +
  <li id="">Kobayashi, Ichizo; and Handa, Naofumi (2009). <i>DNA Doublestrand Breaks and Their Consequences in Bacteria. </i> Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd: Chichester.</li>
 +
  </li>
 +
  <div id="Lu2013"></div>
 +
<li id=""> Timothy K. Lu, Jayson Bowers, and Michael S. Koeris (2013). <i> Advancing bacteriophage-based microbial diagnostics with synthetic biology. </i>Trends in Biotechnology. April 2013, 31 (6), 325-227.</li>
 +
  <div id="MinYoo2013"></div>
 +
  <li id="">Seung Min Yoo, Dokyun Na and Sang Yup Lee. <i>Design and use of synthetic regulatory small RNAs to control gene expression in Escherichia coli</i>. Nature Protocols 8, 1694–1707 (2013)</li>
 +
  <div id="Murphy2003"></div>
 +
<li id="">Murphy BM, Singer BH, Kirschner D (2003).  On treatment of tuberculosis in heterogeneous populations. <i>J of Theoretical Biology</i> 223:391-404
 +
  </li>
 +
  <div id="Na2013"></div>
 +
  <li id="">Na D, Yoo SM, Chung H, Park H, Park JH, Lee SY. <i>Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs.</i> Nature Biotechnology (2013).</li>
 +
 +
  </div>
 +
 
 +
<div style="margin-top:30px">
</div>
</div>
 +
<ul>
<div class="rightparagraph">
<div class="rightparagraph">
-
   <li id="Karlsson2005">Karlsson F., Malmborg-Hager A.C., Albrekt A.S., Borrebaeck C.A.K. (2005). Genome-wide comparison of phage M13-infected vs. uninfected Escherichia coli. <i> Can. J. Microbiol.</i> 51:29-35.</li>
+
<div id="Norman2004"></div>
-
  <li id="Keller2001">Kimberly L. Keller, Terri L. Overbeck-Carrick, Doris J. Beck (2001). Survival and induction of SOS in Escherichia coli treated with cisplatin, UV irradiation, or mitomycin C are dependent on the function of the RecBC and RecFOR pathways of homologous recombination. <i> Mutation Research.</i> 486, 2001, 21–29.</li>
+
   <li id="">Anders Norman, Lars Hestbjerg Hansen, and Søren J. Sørensen (2004). <i>Construction of a ColD cda Promoter-Based SOS-Green Fluorescent Protein Whole-Cell Biosensor with Higher Sensitivity toward Genotoxic Compounds than Constructs Based on recA, umuDC, or sulA Promoters. </i> APPLIED AND ENVIRONMENTAL MICROBIOLOGY. May 2005, p. 2338–2346.</li>
-
   <li id="Kobayashi2009">Kobayashi, Ichizo; and Handa, Naofumi (2009). DNA Doublestrand Breaks and Their Consequences in Bacteria. <i> Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd: Chichester.</li>
+
  <div id="Nussbaum2000"></div>
-
   <li id="Norman2004">Anders Norman, Lars Hestbjerg Hansen, and Søren J. Sørensen (2004). Construction of a ColD cda Promoter-Based SOS-Green Fluorescent Protein Whole-Cell Biosensor with Higher Sensitivity toward Genotoxic Compounds than Constructs Based on recA, umuDC, or sulA Promoters. <i> APPLIED AND ENVIRONMENTAL MICROBIOLOGY.</i> May 2005, p. 2338–2346.</li>
+
<li id="">Martha C. Nussbaum, <i>Women and Human Development, </i> Cambridge University Press, 2000</li>
-
   <li id="Sommer2007">Sommer S., Leitao A., Bernardi A., Bailone A., Devoret R. (1991). Introduction of a UV-damaged replicon into a recipient cell is not a sufficient condition to produce an SOS-inducing signal. <i>Mutation Research/DNA Repair.</i> 254:107-17.</li>
+
  <div id="Ortiz2012"></div>
-
   <li id="Yang2012">Yang Y, Bhatti A, Ke D, Gonzalez-Juarrero M, Lenaerts A, Kremer L, Guerardel Y, Zhang P, Ojha AK (2012). Exposure to a cutinase-like serine esterase triggers rapid lysis of multiple mycobacterial species. <i>J Biol Chem.</i> 288:382-92.
+
  <li id="">Monica E Ortiz and Drew Endy.<i> Engineered cell-cell communication via DNA messaging</i>. Journal of Biological Engineering (2012).</li>
 +
   <div id="Rhines2013"></div>
 +
<li id="">Rhines, Allison S. (2013). <i>The role of sex differences in the prevalence and transmission of tuberculosis, in </i>Tuberculosis 93. pages 104-105</li>
 +
  <div id="Sachs2005"></div>
 +
<li id="">Jeffrey Sachs, <i>The End of Poverty: Economic Possibilities for Our Time, </i>The Penguin Press, New York, 2005</li>
 +
   <div id="Schnell2005"></div>
 +
  <li>Schnell,R., Sandalova, T., Hellman, U., Lindqvist, Y., and Schneider, G. (1997).<i>  Siroheme and the [Fe4-S4]-dependent NirA from Mycobacterium tuberculosis is a sulfite reducatase with a covalent Cys-Tyr bond in the active site.</i> J.Biol.Chem. 280: 27319-27328. </li>
 +
   <div id="Sommer2007"></div>
 +
<li id="">Sommer S., Leitao A., Bernardi A., Bailone A., Devoret R. (1991). Introduction of a UV-damaged replicon into a recipient cell is not a sufficient condition to produce an SOS-inducing signal. <i>Mutation Research/DNA Repair.</i> 254:107-17.</li>
 +
   <div id="Woodford2009"></div>
 +
<li id="">Woodford N, Wareham DW; UK Antibacterial Antisense Study Group. <i>Tackling antibiotic resistance: a dose of common antisense?</i> The Journal of Antimicrobial Chemotherapy. 2009 Feb;63(2):225-9.</li>
 +
  <div id="Yang2012"></div>
 +
  <li id="">Yang Y, Bhatti A, Ke D, Gonzalez-Juarrero M, Lenaerts A, Kremer L, Guerardel Y, Zhang P, Ojha AK (2012). Exposure to a cutinase-like serine esterase triggers rapid lysis of multiple mycobacterial species. <i>J Biol Chem.</i> 288:382-92.
 +
  </li>
 +
  <div id="Rhines2013"></div>
 +
<li id="">Rhines AS (2013). The role of sex differences in the prevalence and transmission of tuberculosis. <i>Tuberculosis.</i> 93:104-107
 +
  </li>
 +
  <div id="Uplekar2001"></div>
 +
<li id="">Uplekar MW, Rangan S, Weiss MG, Ogden J, Borgdorff MW, Hudelson P (2001).  Attention to gender issues in tuberculosis control. <i>Int J Tuberc Lung Dis.‎</i> 5(3):220-224
 +
  </li>
 +
  <div id="Allotey2008"></div>
 +
<li id="">Allotey P, Gyapong M (2008).  Gender in tuberculosis research. <i>Int J Tuberc Lung Dis.‎</i> 12(7):831-836
 +
  </li>
 +
  <div id="Martinez2000"></div>
 +
<li id="">Martinez AN, Rhee JT, Small PM, Behr MA (2000).  Sex differences in the epidemiology of tuberculosis in San Francisco. <i>Int J Tuberc Lung Dis.‎</i> 4(1):26-31
 +
  </li>
 +
  <div id="Holmes1998"></div>
 +
<li id="">Holmes CB, Hausler H, Nunn P (1998).  A review of sex differences in the epidemiolog of tuberculosis. <i>Int J Tuberc Lung Dis.‎</i> 2(2):96-104
 +
  </li>
 +
  <div id="Neyrolles2009"></div>
 +
<li id="">Neyrolles O, Quintana-Murci L (2009).  Sexual Inequality in Tuberculosis. <i>PLoS Medicine</i> 6:12
 +
  </li>
 +
  <div id="Schellenberger2011"></div>
 +
<li id="">Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson B (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. <i>Nature Protocols</i> 6:1290-1307
 +
  </li>
 +
  <div id="Schellenberger2010"></div>
 +
<li id="">Schellenberger J, Park JO, Conrad TC, Palsson B (2010).  BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions <i>BMC Bioinformatics</i> 11:213
 +
  </li>
 +
  <div id="Daniel2006"></div>
 +
<li id="">Daniel, Thomas M. "The history of tuberculosis." <i>Respiratory Medicine</i> 100.11 (2006): 1862-1870.
 +
  </li>
 +
</ul>
 +
 
</div>
</div>

Latest revision as of 12:39, 28 October 2013

  • Crane, B. R., Siegel, L. M., and Getzoff, E. D (1997). Probing the catalytic mechanism of sulfite reductase by X-ray crystallography: Structures of Escherichia coli hemoprotein. Biochemistry 36, 12120-12137.
  • James E. DiCarlo, Julie E. Norville, Prashant Mali, Xavier Rios, John Aach and George M. Church (2013). Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Research. 2013, 1–8.
  • Esther Duflo and Abhjit Banerjee, Poor Economics: A Radical Rethinking of the Way to Fight Global Poverty, PublicAffairs, 2011
  • William Easterly, The Elusive Quest for Growth, MIT University Press, 2002
  • Antonio R. Fernandez de Henestrosa, Tomoo Ogi, Sayura Aoyagi, David Chafin, Jeffrey J. Hayes, Haruo Ohmori and Roger Woodgate (2000). Identification of additional genes belonging to the LexA regulon in Escherichia coli. Molecular Microbiology .2000 35(6), 1560-1572.
  • Caren Grown, Geeta Rao Gupta, Aslihan Kes, Taking action: Achieving Gender Equality and Empowering Women, Earthscan, 2005
  • Higashitani N., Higashitani I.A., Roth A., Horiuchi A.K. (1992). SOS Induction in Escherichia coli by Infection with Mutant Filamentous Phage That Are Defective in Initiation of Complementary-Strand DNA Synthesis. Journal of Bacteriology. 174:1612-1618.
  • Jayachandran R., Sundaramurthy V., Combaluzier B., Mueller P., Korf H., Huygen K., Miyazaki T., Albrecht I., Massner J., Pieters J. (2007). Survival of Mycobacteria in Macrophages Is Mediated by Coronin 1-Dependent Activation of Calcineurin. Cell. 130:12-14
  • Wenyan Jiang, David Bikard, David Cox, Feng Zhang & Luciano A Marraffini (2013). RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nature Biotechnology. 31 (3), 233-2398.
  • Douglas H. Juers, Brian W. Matthews, and Reuben E. Huber (2012). LacZ b-galactosidase: Structure and function of an enzyme of historical and molecular biological importance. Protein Science. 2012, 21,1792—1807.
  • Karlsson F., Malmborg-Hager A.C., Albrekt A.S., Borrebaeck C.A.K. (2005). Genome-wide comparison of phage M13-infected vs. uninfected Escherichia coli. Can. J. Microbiol. 51:29-35.
  • Kimberly L. Keller, Terri L. Overbeck-Carrick, Doris J. Beck (2001). Survival and induction of SOS in Escherichia coli treated with cisplatin, UV irradiation, or mitomycin C are dependent on the function of the RecBC and RecFOR pathways of homologous recombination. Mutation Research. 486, 2001, 21–29.
  • Khalid Ch M, Rasul S, Khan SU, Saeed MS, Imran MN (2004). Gender Differences in Delays to Tuberculosis Diagnosis and Treatment Outcome. pjcm.net/pdf_v10_n4_a2.pdf‎ 10:4
  • Kobayashi, Ichizo; and Handa, Naofumi (2009). DNA Doublestrand Breaks and Their Consequences in Bacteria. Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd: Chichester.
  • Timothy K. Lu, Jayson Bowers, and Michael S. Koeris (2013). Advancing bacteriophage-based microbial diagnostics with synthetic biology. Trends in Biotechnology. April 2013, 31 (6), 325-227.
  • Seung Min Yoo, Dokyun Na and Sang Yup Lee. Design and use of synthetic regulatory small RNAs to control gene expression in Escherichia coli. Nature Protocols 8, 1694–1707 (2013)
  • Murphy BM, Singer BH, Kirschner D (2003). On treatment of tuberculosis in heterogeneous populations. J of Theoretical Biology 223:391-404
  • Na D, Yoo SM, Chung H, Park H, Park JH, Lee SY. Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nature Biotechnology (2013).
  • Anders Norman, Lars Hestbjerg Hansen, and Søren J. Sørensen (2004). Construction of a ColD cda Promoter-Based SOS-Green Fluorescent Protein Whole-Cell Biosensor with Higher Sensitivity toward Genotoxic Compounds than Constructs Based on recA, umuDC, or sulA Promoters. APPLIED AND ENVIRONMENTAL MICROBIOLOGY. May 2005, p. 2338–2346.
  • Martha C. Nussbaum, Women and Human Development, Cambridge University Press, 2000
  • Monica E Ortiz and Drew Endy. Engineered cell-cell communication via DNA messaging. Journal of Biological Engineering (2012).
  • Rhines, Allison S. (2013). The role of sex differences in the prevalence and transmission of tuberculosis, in Tuberculosis 93. pages 104-105
  • Jeffrey Sachs, The End of Poverty: Economic Possibilities for Our Time, The Penguin Press, New York, 2005
  • Schnell,R., Sandalova, T., Hellman, U., Lindqvist, Y., and Schneider, G. (1997). Siroheme and the [Fe4-S4]-dependent NirA from Mycobacterium tuberculosis is a sulfite reducatase with a covalent Cys-Tyr bond in the active site. J.Biol.Chem. 280: 27319-27328.
  • Sommer S., Leitao A., Bernardi A., Bailone A., Devoret R. (1991). Introduction of a UV-damaged replicon into a recipient cell is not a sufficient condition to produce an SOS-inducing signal. Mutation Research/DNA Repair. 254:107-17.
  • Woodford N, Wareham DW; UK Antibacterial Antisense Study Group. Tackling antibiotic resistance: a dose of common antisense? The Journal of Antimicrobial Chemotherapy. 2009 Feb;63(2):225-9.
  • Yang Y, Bhatti A, Ke D, Gonzalez-Juarrero M, Lenaerts A, Kremer L, Guerardel Y, Zhang P, Ojha AK (2012). Exposure to a cutinase-like serine esterase triggers rapid lysis of multiple mycobacterial species. J Biol Chem. 288:382-92.
  • Rhines AS (2013). The role of sex differences in the prevalence and transmission of tuberculosis. Tuberculosis. 93:104-107
  • Uplekar MW, Rangan S, Weiss MG, Ogden J, Borgdorff MW, Hudelson P (2001). Attention to gender issues in tuberculosis control. Int J Tuberc Lung Dis.‎ 5(3):220-224
  • Allotey P, Gyapong M (2008). Gender in tuberculosis research. Int J Tuberc Lung Dis.‎ 12(7):831-836
  • Martinez AN, Rhee JT, Small PM, Behr MA (2000). Sex differences in the epidemiology of tuberculosis in San Francisco. Int J Tuberc Lung Dis.‎ 4(1):26-31
  • Holmes CB, Hausler H, Nunn P (1998). A review of sex differences in the epidemiolog of tuberculosis. Int J Tuberc Lung Dis.‎ 2(2):96-104
  • Neyrolles O, Quintana-Murci L (2009). Sexual Inequality in Tuberculosis. PLoS Medicine 6:12
  • Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson B (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nature Protocols 6:1290-1307
  • Schellenberger J, Park JO, Conrad TC, Palsson B (2010). BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions BMC Bioinformatics 11:213
  • Daniel, Thomas M. "The history of tuberculosis." Respiratory Medicine 100.11 (2006): 1862-1870.

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