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Team:Arizona State/Project/References
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| - | # D. Haft ''et al'', “A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes,” PLoS Computational Biology, vol. 1, no. 6, pp. 474-483, 1 | + | # <div id="ref1">M. Thomas ''et al'', “Hybridization of RNA to double-stranded DNA: formation of R-loops,” PNAS, vol. 73, no. 7, pp. 2294-2298, 1 July 1976.</div> |
| - | # R. Barrangou ''et al'', “CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes,” | + | # <div id="ref2">NB Vartak ''et al'', “A functional leuABCD operon is required for leucine synthesis by the tyrosine-repressible transaminase in Escherichia coli K-12,” J Bacteriol., vol. 173, no. 12, pp. 3864-3871, June 1991.</div> |
| - | # R. Sorek ''et al'', “CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea,” Nature Reviews Microbiology, | + | # <div id="ref3">E. Klauck ''et al'', “The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA,” Mol. Microbio, vol. 25, no. 3, pp. 559-569, August 1997.</div> |
| - | # S. Brouns ''et al'', “Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes,” Science, vol. 321, pp. 960-964, 15 | + | # <div id="ref4">L. Aravind and EV Koonin, “The HD domain defines a new superfamily of metaldependent phosphohydrolases,” Trends Biochem Sci., vol. 23, no. 12, pp. 469-472, December 1998.</div> |
| - | # S. Marraffini and E. Sontheimer, | + | # <div id="ref5">F. Hommais ''et al'', “Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS,” Mol. Microbio, vol. 40, no. 1, pp. 20-36, April 2001.</div> |
| - | # J. Heidelberg ''et al'', “Germ Warfare in a Microbial Mat Community: CRISPRs Provide Insights into the Co-Evolution of Host and Viral Genomes,” | + | # <div id="ref6">A. Majumder ''et al'', “LeuO expression in response to starvation for branched-chain amino acids,” J Biol Chem., vol. 276, no. 22, pp. 19046-19051, 1 June 2001.</div> |
| - | # C. Hale ''et al'', “RNA-Guided RNA Cleavage by a CRISPR RNA-Cas Protein Complex,” Cell, vol. 139, pp. 945-956, 25 | + | # <div id="ref7">K. S. Makarova ''et al'', “A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis,” Nucl. Acids Res., vol. 30, no. 2, 1 November 2001.</div> |
| - | # J. van der Oost and S. Brouns, “RnAi: Prokaryotes get in on the Act,” Cell, vol. 139, pp. 863-865, 25 | + | # <div id="ref8">R. Jansen ''et al'', “Identification of genes that are associated with DNA repeats in prokaryotes,” Mol Microbiol., vol. 43, no. 6, March 2002.</div> |
| - | # L. Marraffini and E. Sontheimer, “Self vs. non-self discrimination during CRISPR RNA-directed immunity,” Nature, vol. 463, pp. 568-571, 13 | + | # <div id="ref9">T.H. Tang ''et al'', “Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus,” PNAS, vol. 99, no. 11, pp. 7536-7541, 28 May 2002.</div> |
| - | # F. Karginov and G. Hannon, “The CRISPR system: small RNA-guided defense in bacteria and archaea,” Mol Cell, vol. 37, no. 1, pp. 7-19, 15 | + | # <div id="ref10">FJ Mojica ''et al'', “Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements,” J Mol Evol., vol. 60, no. 2, pp. 174-182, February 2005.</div> |
| - | # A. Stern ''et al'', “Self-targeting by CRISPR: gene regulation or autoimmunity?,” Trends in Genetics, vol. 26, no. 8, pp. 335-340, 1 | + | # <div id="ref11">R. Dame ''et al'', “DNA bridging: a property shared among H-NS-like proteins,” J. Bacteriol., vol. 187, no. 5, pp. 1845-1848, March 2005.</div> |
| - | # M. Aklujkar and D. Lovley, “Interference with histidyl-tRNA synthetase by a CRISPR spacer sequence as a factor in the evolution of ''Pelobacter carbinolicus | + | # <div id="ref12">C. Pourcel ''et al'', “CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies,” Microbiology, vol. 151, no. 3, pp. 653-663, March 2005.</div> |
| - | # J. He and M. Deen, “Heterogeneous diversity of spacers within CRISPR,” arXiv, 16 | + | # <div id="ref13">CC Chen and HY Wu, “LeuO protein delimits the transcriptionally active and repressive domains on the bacterial chromosome,” J Biol Chem., vol. 280, no. 15, pp. 15111-15112, 15 April 2005.</div> |
| - | # E. Westra ''et al'', “H-NS-mediated repression of CRISPR-based immunity in ''Escherichia coli'' K12 can be relieved by the transcription activator LeuO,” Molecular Microbiology, vol. 77, no. 6, pp. 1380-1393, 18 | + | # <div id="ref14">A. Bolotin ''et al'', “Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin,” Microbiology, vol. 151, no. 8, pp. 2551-2561, August 2005.</div> |
| - | # N. Held ''et al'', “CRISPR Associated Diversity within a Population of ''Sulfolobus islandicus'',” | + | # <div id="ref15">D. Haft ''et al'', “A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes,” PLoS Computational Biology, vol. 1, no. 6, pp. 474-483, 1 November 2005.</div> |
| - | # K. Palmer and M. Gilmore, “Multidrug-Resistant Enterococci Lack CRISPR-''cas'',” mBio, vol. 1, no. 4, 12 | + | # <div id="ref16">W. Navarre ''et al'', “Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella,” Science, vol. 313, no. 5784, pp. 236-238, 14 July 2006.</div> |
| - | # E. Sontheimer and L. Marraffini, “Slicer for DNA,” Nature, vol. 468, pp. 45-46, 4 | + | # <div id="ref17">R. Barrangou ''et al'', “CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes,” Science, vol. 315, pp. 1709-1712, 23 March 2007.</div> |
| - | # D. Pride ''et al'', “Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time,” Genome Research, vol. 21, pp. 126-136, 13 | + | # <div id="ref18">V. Kunin ''et al'', “Evolutionary conservation of sequence and secondary structures in CRISPR repeats,” Genome Biology, vol. 8, 18 April 2007.</div> |
| - | # R. Garrett ''et al'', “CRISPR-based immune systems of the Sulfolobales: complexity and diversity,” Biochem. Soc. Trans., vol. 39, pp. 51-57, 19 | + | # <div id="ref19">V. Kunin ''et al'', “Evolutionary conservation of sequence and secondary structures in CRISPR repeats,” Genome Biology, vol. 8, 18 April 2007.</div> |
| - | # F. Rezzonico ''et al'', “Diversity, Evolution, and Functionality of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Regions in the Fire Blight Pathogen ''Erwinia amylovora'',” Applied and Environmental Microbiology, vol. 77, no. 11, pp. 3819-3829, 24 | + | # <div id="ref20">I. Grissa ''et al'', “The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeat,” BMC Bioinformatics, vol. 8, no. 172, 23 May 2007.</div> |
| - | # E. Deltcheva ''et al'', “CRISPR RNA maturation by ''trans''-encoded small RNA and host factor RNase III,” Nature, vol. 471, no. 7340, pp. 602-607, 30 | + | # <div id="ref21">H. Deveau ''et al'', “Phage response to CRISPR-encoded resistance in Streptococcus thermophilus,” J. Bacteriol., vol. 190, no. 4, pp. 1390-1400, February 2008.</div> |
| - | # M. Jore ''et al'', “Structural basis for CRISPR RNA-guided DNA recognition by Cascade,” Nature Structural & Molecular Biology, vol. 18, pp. 529-536, 3 | + | # <div id="ref22">P. Horvath ''et al'', “Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus,” J. Bacteriol., vol. 190, no. 4, pp. 1401-1412, February 2008.</div> |
| - | # T. Nozawa ''et al'', “CRISPR Inhibition of Prophage Acquisition in ''Streptococcus pyogenes'',” PLoS ONE, vol. 6, no. 5, 6 May 2011. | + | # <div id="ref23">R. Sorek ''et al'', “CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea,” Nature Reviews Microbiology, no. 6, pp. 181-186, March 2008.</div> |
| - | # K. S. | + | # <div id="ref24">N. Beloglazova ''et al'', “A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats.,” J Biol Chem., vol. 283, no. 29, pp. 20361-20371, 18 July 2008.</div> |
| - | # D. Sashital ''et al'', “An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3,” Nature Structural & Molecular Biology, vol. 18, pp. 680-687, 15 May 2011. | + | # <div id="ref25">S. Brouns ''et al'', “Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes,” Science, vol. 321, pp. 960-964, 15 August 2008.</div> |
| - | # E. Gesner ''et al'', “Recognition and maturation of effector RNAs in a CRISPR interference pathway,” Nature Structural & Molecular Biology, vol. 18, no. 6, pp. 688-692, 15 May 2011. | + | # <div id="ref26">D. Stoebel ''et al'', “Antisilencing: overcoming H-NS-mediated repression of transcription in Gram-negative enteric bacteria.,” Microbiology, vol. 154, no. 9, pp. 2533-2545, September 2008.</div> |
| - | # C. Skennerton ''et al'', “Phage Encoded H-NS: A Potential Achilles Heel in the Bacterial Defence System,” PLoS ONE, vol. 6, no. 5, 18 May 2011. | + | # <div id="ref27">C. Hale ''et al'', “Prokaryotic silencing (psi)RNAs in Pyrococcus furiosus,” RNA, vol. 14, pp. 2572-2579, 29 October 2008.</div> |
| - | # W. Fricke ''et al'', “Comparative Genomics of 28 ''Salmonella enterica'' Isolates: Evidence for CRISPR-mediated Adaptive Sublineage Evolution,” J. Bacteriology, 20 May 2011. | + | # <div id="ref28">S. Marraffini and E. Sontheimer, ““CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA,” Science, no. 322, pp. 1843-1845, 19 December 2008.</div> |
| - | # E. Semenova ''et al'', “Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence,” PNAS, 6 | + | # <div id="ref29">J. Heidelberg ''et al'', “Germ Warfare in a Microbial Mat Community: CRISPRs Provide Insights into the Co-Evolution of Host and Viral Genomes,” PloS ONE, vol. 4, no. 1, 9 January 2009.</div> |
| + | # <div id="ref30">F. J. M. Mojica ''et al'', “Short motif sequences determine the targets of the prokaryotic CRISPR defence system,” Microbiology, vol. 155, no. 3, pp. 733-740, March 2009.</div> | ||
| + | # <div id="ref31">RK Lillestøl ''et al'', “CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties.,” Mol. Microbio, vol. 72, no. 1, pp. 259-272, April 2009.</div> | ||
| + | # <div id="ref32">B. Wiedenheft ''et al'', “Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense,” Structure, vol. 17, pp. 904-912, 10 June 2009.</div> | ||
| + | # <div id="ref33">T. Shimada ''et al'', “Involvement of the leucine response transcription factor LeuO in regulation of the genes for sulfa drug efflux,” J Bacteriol., vol. 191, no. 14, pp. 4562-4571, July 2009.</div> | ||
| + | # <div id="ref34">J. van der Oost ''et al'', “CRISPR based adaptive and heritable immunity in prokaryotes,” Trends in Biochemical Sciences, vol. 34, no. 8, pp. 401-407, 30 July 2009.</div> | ||
| + | # <div id="ref35">C. Hale ''et al'', “RNA-Guided RNA Cleavage by a CRISPR RNA-Cas Protein Complex,” Cell, vol. 139, pp. 945-956, 25 November 2009.</div> | ||
| + | # <div id="ref36">J. van der Oost and S. Brouns, “RnAi: Prokaryotes get in on the Act,” Cell, vol. 139, pp. 863-865, 25 November 2009.</div> | ||
| + | # <div id="ref37">Y. Liu ''et al'', “A divalent switch drives H-NS/DNA-binding conformations between stiffening and bridging modes,” Genes & Dev., vol. 24, pp. 339-344, 18 December 2009.</div> | ||
| + | # <div id="ref38">P. Horvath and R. Barrangou, “CRISPR/Cas, the immune system of bacteria and Archaea.,” Science, vol. 327, no. 5962, pp. 167-170, 8 January 2010.</div> | ||
| + | # <div id="ref39">L. Marraffini and E. Sontheimer, “Self vs. non-self discrimination during CRISPR RNA-directed immunity,” Nature, vol. 463, pp. 568-571, 13 January 2010.</div> | ||
| + | # <div id="ref40">F. Karginov and G. Hannon, “The CRISPR system: small RNA-guided defense in bacteria and archaea,” Mol. Cell, vol. 37, no. 1, pp. 7-19, 15 January 2010.</div> | ||
| + | # <div id="ref41">Y. Agari ''et al'', “Transcription profile of Thermus thermophilus CRISPR systems after phage infection.,” Journal of Molecular Biology, vol. 395, no. 2, pp. 270-281, 15 January 2010.</div> | ||
| + | # <div id="ref42">L. Marraffini and E. Sontheimer, “CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea.,” Nature Reviews Genetics, vol. 11, pp. 181-190, 2 February 2010.</div> | ||
| + | # <div id="ref43">Ü. Pul ''et al'', “Identification and characterization of E. coli CRISPR-cas promoters and their silencing by H-NS,“ Mol. Microbio, vol. 75, no. 6, 17 February 2010.</div> | ||
| + | # <div id="ref44">U. Pul ''et al'', “Identification and characterization of E.coli CRISPR-cas promoters and their silencing by H-NS,” Mol. Microbio, vol. 75, no. 6, pp. 1495-1512, March 2010.</div> | ||
| + | # <div id="ref45">A. Stern ''et al'', “Self-targeting by CRISPR: gene regulation or autoimmunity?,” Trends in Genetics, vol. 26, no. 8, pp. 335-340, 1 July 2010.</div> | ||
| + | # <div id="ref46">M. Aklujkar and D. Lovley, “Interference with histidyl-tRNA synthetase by a CRISPR spacer sequence as a factor in the evolution of ''Pelobacter carbinolicus,” BMC Evolutionary Biology, vol. 10, 28 July 2010.</div> | ||
| + | # <div id="ref47">J. He and M. Deen, “Heterogeneous diversity of spacers within CRISPR,” arXiv, 16 August 2010.</div> | ||
| + | # <div id="ref48">E. Westra ''et al'', “H-NS-mediated repression of CRISPR-based immunity in ''Escherichia coli'' K12 can be relieved by the transcription activator LeuO,” Molecular Microbiology, vol. 77, no. 6, pp. 1380-1393, 18 August 2010.</div> | ||
| + | # <div id="ref49">N. Held ''et al'', “CRISPR Associated Diversity within a Population of ''Sulfolobus islandicus'',” PloS ONE, vol. 5, no. 9, 28 September 2010.</div> | ||
| + | # <div id="ref50">J. Carte ''et al'', “Binding and cleavage of CRISPR RNA by Cas6,” RNA, 30 September 2010.</div> | ||
| + | # <div id="ref51">R. Edgar and U. Qimron, “The Escherichia coli CRISPR system protects from lambda lysogenisation, lysogens and prophage induction,” J. bact., vol. 192, pp. 6291-6294, 1 October 2010.</div> | ||
| + | # <div id="ref52">K. Palmer and M. Gilmore, “Multidrug-Resistant Enterococci Lack CRISPR-''cas'',” mBio, vol. 1, no. 4, 12 October 2010.</div> | ||
| + | # <div id="ref53">H. Deveau ''et a'', “CRISPR/Cas System and Its Role in Phage-Bacteria Interactions,” Annu. Rev. Microbiol., 13 October 2010.</div> | ||
| + | # <div id="ref54">J. Garneau ''et al'', “The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA,” Nature, vol. 468, pp. 67-71, 3 November 2010.</div> | ||
| + | # <div id="ref55">E. Sontheimer and L. Marraffini, “Slicer for DNA,” Nature, vol. 468, pp. 45-46, 4 November 2010.</div> | ||
| + | # <div id="ref56">D. Pride ''et al'', “Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time,” Genome Research, vol. 21, pp. 126-136, 13 December 2010.</div> | ||
| + | # <div id="ref57">R. Perez-Rodriguez ''et al'', “Envelope stress is a trigger of CRISPR RNA-mediated DNA silencing in Escheria Coli,” Mol. Microbio, vol. 79, pp. 584-599, 13 December 2010.</div> | ||
| + | # <div id="ref58">M. Babu ''et al'', “A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair,” Mol. Microbio, vol. 79, no. 2, pp. 484-502, January 2011.</div> | ||
| + | # <div id="ref59">K. Pougach ''et al'', “Transcription, processing and function of CRISPR cassettes in Escherichia coli.,” Mol. Microbio, vol. 77, pp. 1367-1379, 1 January 2011.</div> | ||
| + | # <div id="ref60">R. Garrett ''et al'', “CRISPR-based immune systems of the Sulfolobales: complexity and diversity,” Biochem. Soc. Trans., vol. 39, pp. 51-57, 19 January 2011.</div> | ||
| + | # <div id="ref61">F. Rezzonico ''et al'', “Diversity, Evolution, and Functionality of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Regions in the Fire Blight Pathogen ''Erwinia amylovora'',” Applied and Environmental Microbiology, vol. 77, no. 11, pp. 3819-3829, 24 March 2011.</div> | ||
| + | # <div id="ref62">E. Deltcheva ''et al'', “CRISPR RNA maturation by ''trans''-encoded small RNA and host factor RNase III,” Nature, vol. 471, no. 7340, pp. 602-607, 30 March 2011.</div> | ||
| + | # <div id="ref63">M. Jore ''et al'', “Structural basis for CRISPR RNA-guided DNA recognition by Cascade,” Nature Structural & Molecular Biology, vol. 18, pp. 529-536, 3 April 2011.</div> | ||
| + | # <div id="ref64">T. Nozawa ''et al'', “CRISPR Inhibition of Prophage Acquisition in ''Streptococcus pyogenes'',” PLoS ONE, vol. 6, no. 5, 6 May 2011.</div> | ||
| + | # <div id="ref65">K. S. Makarova ''et al'', “Evolution and classification of the CRISPR–Cas systems,” Nature Reviews Microbiology, vol. 9, pp. 467-477, 9 May 2011.</div> | ||
| + | # <div id="ref66">D. Sashital ''et al'', “An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3,” Nature Structural & Molecular Biology, vol. 18, pp. 680-687, 15 May 2011.</div> | ||
| + | # <div id="ref67">E. Gesner ''et al'', “Recognition and maturation of effector RNAs in a CRISPR interference pathway,” Nature Structural & Molecular Biology, vol. 18, no. 6, pp. 688-692, 15 May 2011.</div> | ||
| + | # <div id="ref68">C. Skennerton ''et al'', “Phage Encoded H-NS: A Potential Achilles Heel in the Bacterial Defence System,” PLoS ONE, vol. 6, no. 5, 18 May 2011.</div> | ||
| + | # <div id="ref69">W. Fricke ''et al'', “Comparative Genomics of 28 ''Salmonella enterica'' Isolates: Evidence for CRISPR-mediated Adaptive Sublineage Evolution,” J. Bacteriology, 20 May 2011.</div> | ||
| + | # <div id="ref70">E. Semenova ''et al'', “Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence,” PNAS, 6 June 2011.</div> | ||
| + | # <div id="ref71">K. Phok ''el al'', “Identification of CRISPR and riboswitch related RNAs among novel non-coding RNAs of the euryarchaeon Pyrococcus abyss,” BMC Genomics, 13 June 2011.</div> | ||
| + | # <div id="ref72">K. Kyun ''et al'', “Crystal Structure of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Csn2 Protein Revealed Ca<sup>2+</sup>-dependent Double-stranded DNA-binding Activity,” J Biol Chem., 21 June 2011.</div> | ||
| + | # <div id="ref73">J. Howard ''et al'', “Helicase dissociation and annealing of RNA-DNA hybrids by ''Escherichia coli'' Cas3 protein,” Biochem. J., 23 June 2011.</div> | ||
| + | # <div id="ref74">R. Sapranauskas ''et al'', “The ''Streptococcus thermophilus'' CRISPR/Cas system provides immunity in ''Escherichia coli'',” Nucl. Acids Res., 8 July 2011.</div> | ||
| + | # <div id="ref75">K. S. Makarova ''et al'', “Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems,” Biol. Direct, vol. 6, no. 1, 14 July 2011.</div> | ||
| + | # <div id="ref76">B. Wiedenheft ''et al'', “Structures of the RNA-guided surveillance complex from a bacterial immune system,” Nature, vol. 477, 22 September 2011.</div> | ||
| + | # <div id="ref77">T. Blomqvist ''et al'', “Natural Genetic Transformation: a novel tool for efficient genetic engineering of the dairy bacterium Streptococcus thermophilus,” Applied and Environmental Microbiology, vol. 72, pp. 6751-6756, October 2006.</div> | ||
| + | # <div id="ref78">Salis ''et al'', “Automated design of synthetic ribosome binding sites to control protein expression,” Nature Biotechnology, vol. 27, pp. 946-950, 4 October 2009.</div> | ||
| + | # <div id="ref79">Esvelt ''et al'', “A system for the continuous directed evolution of biomolecules,” Nature, vol. 462, pp. 499-503, 11 February 2011.</div> | ||
| + | # <div id="ref80">Makarova ''et al'', “A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action,” Biology Direct, vol. 1 no. 7, 16 March 2006.</div> | ||
| + | }} | ||
Latest revision as of 02:44, 29 September 2011
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