TY - JOUR AU - Lambowitz, A. M. AU - Zimmerly, S. PY - 2004 DA - 2004// TI - Mobile group II introns JO - Annu Rev Genet VL - 38 UR - https://doi.org/10.1146/annurev.genet.38.072902.091600 DO - 10.1146/annurev.genet.38.072902.091600 ID - Lambowitz2004 ER - TY - CHAP AU - Pyle, A. M. AU - Lambowitz, A. M. ED - Gesteland, R. F. ED - Cech, T. R. ED - Atkins, J. F. PY - 2006 DA - 2006// TI - Group II introns: ribozymes that splice RNA and invade DNA BT - The RNA world PB - Cold Spring Harbor Laboratory Press CY - Cold Spring Harbor, N.Y. ID - Pyle2006 ER - TY - JOUR AU - Robart, A. R. AU - Zimmerly, S. PY - 2005 DA - 2005// TI - Group II intron retroelements: function and diversity JO - Cytogenet Genome Res VL - 110 UR - https://doi.org/10.1159/000084992 DO - 10.1159/000084992 ID - Robart2005 ER - TY - JOUR AU - Toro, N. AU - Jimenez-Zurdo, J. I. AU - Garcia-Rodriguez, F. M. PY - 2007 DA - 2007// TI - Bacterial group II introns: not just splicing JO - FEMS Microbiol Rev VL - 31 UR - https://doi.org/10.1111/j.1574-6976.2007.00068.x DO - 10.1111/j.1574-6976.2007.00068.x ID - Toro2007 ER - TY - JOUR AU - Lehmann, K. AU - Schmidt, U. PY - 2003 DA - 2003// TI - Group II introns: structure and catalytic versatility of large natural ribozymes JO - Crit Rev Biochem Mol Biol VL - 38 UR - https://doi.org/10.1080/713609236 DO - 10.1080/713609236 ID - Lehmann2003 ER - TY - JOUR AU - Chin, K. AU - Pyle, A. M. PY - 1995 DA - 1995// TI - Branch-point attack in group II introns is a highly reversible transesterification, providing a potential proofreading mechanism for 5'-splice site selection JO - RNA VL - 1 ID - Chin1995 ER - TY - JOUR AU - Chu, V. T. AU - Liu, Q. AU - Podar, M. AU - Perlman, P. S. AU - Pyle, A. M. PY - 1998 DA - 1998// TI - More than one way to splice an RNA: branching without a bulge and splicing without branching in group II introns JO - RNA VL - 4 UR - https://doi.org/10.1017/S1355838298980724 DO - 10.1017/S1355838298980724 ID - Chu1998 ER - TY - JOUR AU - Daniels, D. L. AU - Michels, W. J. AU - Pyle, A. M. PY - 1996 DA - 1996// TI - Two competing pathways for self-splicing by group II introns: a quantitative analysis of in vitro reaction rates and products JO - J Mol Biol VL - 256 UR - https://doi.org/10.1006/jmbi.1996.0066 DO - 10.1006/jmbi.1996.0066 ID - Daniels1996 ER - TY - JOUR AU - Jarrell, K. A. AU - Peebles, C. L. AU - Dietrich, R. C. AU - Romiti, S. L. AU - Perlman, P. S. PY - 1988 DA - 1988// TI - Group II intron self-splicing. Alternative reaction conditions yield novel products JO - J Biol Chem VL - 263 ID - Jarrell1988 ER - TY - JOUR AU - Peebles, C. L. AU - Benatan, E. J. AU - Jarrell, K. A. AU - Perlman, P. S. PY - 1987 DA - 1987// TI - Group II intron self-splicing: development of alternative reaction conditions and identification of a predicted intermediate JO - Cold Spring Harb Symp Quant Biol VL - 52 UR - https://doi.org/10.1101/SQB.1987.052.01.027 DO - 10.1101/SQB.1987.052.01.027 ID - Peebles1987 ER - TY - JOUR AU - Dai, L. AU - Zimmerly, S. PY - 2002 DA - 2002// TI - Compilation and analysis of group II intron insertions in bacterial genomes: evidence for retroelement behavior JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.5.1091 DO - 10.1093/nar/30.5.1091 ID - Dai2002 ER - TY - JOUR AU - Klein, J. R. AU - Dunny, G. M. PY - 2002 DA - 2002// TI - Bacterial group II introns and their association with mobile genetic elements JO - Front Biosci VL - 7 UR - https://doi.org/10.2741/klein1 DO - 10.2741/klein1 ID - Klein2002 ER - TY - JOUR AU - Tourasse, N. J. AU - Kolstø, A. B. PY - 2008 DA - 2008// TI - Survey of group I and group II introns in 29 sequenced genomes of the Bacillus cereus group: insights into their spread and evolution JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkn372 DO - 10.1093/nar/gkn372 ID - Tourasse2008 ER - TY - JOUR AU - Dai, L. AU - Chai, D. AU - Gu, S. Q. AU - Gabel, J. AU - Noskov, S. Y. AU - Blocker, F. J. AU - Lambowitz, A. M. AU - Zimmerly, S. PY - 2008 DA - 2008// TI - A three-dimensional model of a group II intron RNA and its interaction with the intron-encoded reverse transcriptase JO - Mol Cell VL - 30 UR - https://doi.org/10.1016/j.molcel.2008.04.001 DO - 10.1016/j.molcel.2008.04.001 ID - Dai2008 ER - TY - JOUR AU - Toor, N. AU - Keating, K. S. AU - Taylor, S. D. AU - Pyle, A. M. PY - 2008 DA - 2008// TI - Crystal structure of a self-spliced group II intron JO - Science VL - 320 UR - https://doi.org/10.1126/science.1153803 DO - 10.1126/science.1153803 ID - Toor2008 ER - TY - JOUR AU - Pyle, A. M. PY - 2010 DA - 2010// TI - The tertiary structure of group II introns: implications for biological function and evolution JO - Crit Rev Biochem Mol Biol VL - 45 UR - https://doi.org/10.3109/10409231003796523 DO - 10.3109/10409231003796523 ID - Pyle2010 ER - TY - JOUR AU - Stabell, F. B. AU - Tourasse, N. J. AU - Kolstø, A. B. PY - 2009 DA - 2009// TI - A conserved 3' extension in unusual group II introns is important for efficient second-step splicing JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkp186 DO - 10.1093/nar/gkp186 ID - Stabell2009 ER - TY - JOUR AU - Tourasse, N. J. AU - Stabell, F. B. AU - Kolstø, A. B. PY - 2010 DA - 2010// TI - Structural and functional evolution of group II intron ribozymes: insights from unusual elements carrying a 3' extension JO - N Biotechnol VL - 27 UR - https://doi.org/10.1016/j.nbt.2010.02.014 DO - 10.1016/j.nbt.2010.02.014 ID - Tourasse2010 ER - TY - JOUR AU - Tourasse, N. J. AU - Stabell, F. B. AU - Reiter, L. AU - Kolstø, A. B. PY - 2005 DA - 2005// TI - Unusual group II introns in bacteria of the Bacillus cereus group JO - J Bacteriol VL - 187 UR - https://doi.org/10.1128/JB.187.15.5437-5451.2005 DO - 10.1128/JB.187.15.5437-5451.2005 ID - Tourasse2005 ER - TY - JOUR AU - Helgason, E. AU - Økstad, O. A. AU - Caugant, D. A. AU - Johansen, H. A. AU - Fouet, A. AU - Mock, M. AU - Hegna, I. AU - Kolsto, A. B. PY - 2000 DA - 2000// TI - Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis-one species on the basis of genetic evidence JO - Appl Environ Microbiol VL - 66 UR - https://doi.org/10.1128/AEM.66.6.2627-2630.2000 DO - 10.1128/AEM.66.6.2627-2630.2000 ID - Helgason2000 ER - TY - JOUR AU - Kolstø, A. B. AU - Tourasse, N. J. AU - Økstad, O. A. PY - 2009 DA - 2009// TI - What sets Bacillus anthracis apart from other Bacillus species? JO - Annu Rev Microbiol VL - 63 UR - https://doi.org/10.1146/annurev.micro.091208.073255 DO - 10.1146/annurev.micro.091208.073255 ID - Kolstø2009 ER - TY - JOUR AU - Rasko, D. A. AU - Altherr, M. R. AU - Han, C. S. AU - Ravel, J. PY - 2005 DA - 2005// TI - Genomics of the Bacillus cereus group of organisms JO - FEMS Microbiol Rev VL - 29 ID - Rasko2005 ER - TY - JOUR AU - Tourasse, N. J. AU - Helgason, E. AU - Økstad, O. A. AU - Hegna, I. K. AU - Kolstø, A. B. PY - 2006 DA - 2006// TI - The Bacillus cereus group: novel aspects of population structure and genome dynamics JO - J Appl Microbiol VL - 101 UR - https://doi.org/10.1111/j.1365-2672.2006.03087.x DO - 10.1111/j.1365-2672.2006.03087.x ID - Tourasse2006 ER - TY - JOUR AU - Stabell, F. B. AU - Tourasse, N. J. AU - Ravnum, S. AU - Kolstø, A. B. PY - 2007 DA - 2007// TI - Group II intron in Bacillus cereus has an unusual 3' extension and splices 56 nucleotides downstream of the predicted site JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkm031 DO - 10.1093/nar/gkm031 ID - Stabell2007 ER - TY - JOUR AU - Takami, H. AU - Krulwich, T. A. PY - 2000 DA - 2000// TI - Reidentification of facultatively alkaliphilic Bacillus firmus OF4 as Bacillus pseudofirmus OF4 JO - Extremophiles VL - 4 UR - https://doi.org/10.1007/s007920050003 DO - 10.1007/s007920050003 ID - Takami2000 ER - TY - JOUR AU - Goto, K. AU - Omura, T. AU - Hara, Y. AU - Sadaie, Y. PY - 2005 DA - 2005// TI - Application of the partial 16S rDNA sequence as an index for rapid identification of species in the genus Bacillus JO - J Gen Appl Microbiol VL - 46 UR - https://doi.org/10.2323/jgam.46.1 DO - 10.2323/jgam.46.1 ID - Goto2005 ER - TY - JOUR AU - Grynberg, M. AU - Li, Z. AU - Szczurek, E. AU - Godzik, A. PY - 2007 DA - 2007// TI - Putative type IV secretion genes in Bacillus anthracis JO - Trends Microbiol VL - 15 UR - https://doi.org/10.1016/j.tim.2007.03.002 DO - 10.1016/j.tim.2007.03.002 ID - Grynberg2007 ER - TY - JOUR AU - Rasko, D. A. AU - Rosovitz, M. J. AU - Økstad, O. A. AU - Fouts, D. E. AU - Jiang, L. AU - Cer, R. Z. AU - Kolstø, A. B. AU - Gill, S. R. AU - Ravel, J. PY - 2007 DA - 2007// TI - Complete sequence analysis of novel plasmids from emetic and periodontal Bacillus cereus isolates reveals a common evolutionary history among the B. cereus-group plasmids, including Bacillus anthracis pXO1 JO - J Bacteriol VL - 189 UR - https://doi.org/10.1128/JB.01313-06 DO - 10.1128/JB.01313-06 ID - Rasko2007 ER - TY - CHAP AU - Tourasse, N. J. AU - Økstad, O. A. AU - Kolstø, A. B. PY - 2010 DA - 2010// TI - HyperCAT: an extension of the SuperCAT database for global multi-scheme and multi-datatype phylogenetic analysis of the Bacillus cereus group population BT - Database (Oxford) ID - Tourasse2010 ER - TY - JOUR AU - Dai, L. AU - Toor, N. AU - Olson, R. AU - Keeping, A. AU - Zimmerly, S. PY - 2003 DA - 2003// TI - Database for mobile group II introns JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg049 DO - 10.1093/nar/gkg049 ID - Dai2003 ER - TY - STD TI - Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW: GenBank. Nucleic Acids Res. 2011, D32-D37. 39 Database ID - ref31 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schaffer, A. A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. AU - Lipman, D. J. PY - 1997 DA - 1997// TI - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 ER - TY - STD TI - Tourasse NJ, Kolstø AB: SuperCAT: a supertree database for combined and integrative multilocus sequence typing analysis of the Bacillus cereus group of bacteria (including B. cereus, B. anthracis and B. thuringiensis). Nucleic Acids Res. 2008, D461-D468. 36 Database ID - ref33 ER - TY - JOUR AU - Zuker, M. PY - 2003 DA - 2003// TI - Mfold web server for nucleic acid folding and hybridization prediction JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg595 DO - 10.1093/nar/gkg595 ID - Zuker2003 ER - TY - JOUR AU - Markham, N. R. AU - Zuker, M. PY - 2008 DA - 2008// TI - UNAFold: software for nucleic acid folding and hybridization JO - Methods Mol Biol VL - 453 UR - https://doi.org/10.1007/978-1-60327-429-6_1 DO - 10.1007/978-1-60327-429-6_1 ID - Markham2008 ER - TY - JOUR AU - Toor, N. AU - Hausner, G. AU - Zimmerly, S. PY - 2001 DA - 2001// TI - Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases JO - RNA VL - 7 UR - https://doi.org/10.1017/S1355838201010251 DO - 10.1017/S1355838201010251 ID - Toor2001 ER - TY - JOUR AU - Larkin, M. A. AU - Blackshields, G. AU - Brown, N. P. AU - Chenna, R. AU - McGettigan, P. A. AU - McWilliam, H. AU - Valentin, F. AU - Wallace, I. M. AU - Wilm, A. AU - Lopez, R. PY - 2007 DA - 2007// TI - Clustal W and Clustal × version 2.0 JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm404 DO - 10.1093/bioinformatics/btm404 ID - Larkin2007 ER - TY - JOUR AU - Thompson, J. D. AU - Higgins, D. G. AU - Gibson, T. J. PY - 1994 DA - 1994// TI - CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice JO - Nucleic Acids Res VL - 22 UR - https://doi.org/10.1093/nar/22.22.4673 DO - 10.1093/nar/22.22.4673 ID - Thompson1994 ER - TY - JOUR AU - Gouy, M. AU - Guindon, S. AU - Gascuel, O. PY - 2010 DA - 2010// TI - SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building JO - Mol Biol Evol VL - 27 UR - https://doi.org/10.1093/molbev/msp259 DO - 10.1093/molbev/msp259 ID - Gouy2010 ER - TY - JOUR AU - Galtier, N. AU - Gouy, M. AU - Gautier, C. PY - 1996 DA - 1996// TI - SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny JO - Comput Appl Biosci VL - 12 ID - Galtier1996 ER - TY - JOUR AU - Saitou, N. AU - Nei, M. PY - 1987 DA - 1987// TI - The neighbor-joining method: a new method for reconstructing phylogenetic trees JO - Mol Biol Evol VL - 4 ID - Saitou1987 ER - TY - JOUR AU - Tamura, K. PY - 1992 DA - 1992// TI - Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases JO - Mol Biol Evol VL - 9 ID - Tamura1992 ER - TY - JOUR AU - Felsenstein, J. PY - 1985 DA - 1985// TI - Confidence limits on phylogenies: an approach using the bootstrap JO - Evolution VL - 39 UR - https://doi.org/10.2307/2408678 DO - 10.2307/2408678 ID - Felsenstein1985 ER - TY - JOUR AU - Tamura, K. AU - Dudley, J. AU - Nei, M. AU - Kumar, S. PY - 2007 DA - 2007// TI - MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0 JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msm092 DO - 10.1093/molbev/msm092 ID - Tamura2007 ER - TY - JOUR AU - Hill, K. K. AU - Ticknor, L. O. AU - Okinaka, R. T. AU - Asay, M. AU - Blair, H. AU - Bliss, K. A. AU - Laker, M. AU - Pardington, P. E. AU - Richardson, A. P. AU - Tonks, M. PY - 2004 DA - 2004// TI - Fluorescent amplified fragment length polymorphism analysis of Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis isolates JO - Appl Environ Microbiol VL - 70 UR - https://doi.org/10.1128/AEM.70.2.1068-1080.2004 DO - 10.1128/AEM.70.2.1068-1080.2004 ID - Hill2004 ER - TY - JOUR AU - Guindon, S. AU - Dufayard, J. F. AU - Lefort, V. AU - Anisimova, M. AU - Hordijk, W. AU - Gascuel, O. PY - 2010 DA - 2010// TI - New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0 JO - Syst Biol VL - 59 UR - https://doi.org/10.1093/sysbio/syq010 DO - 10.1093/sysbio/syq010 ID - Guindon2010 ER - TY - JOUR AU - Guindon, S. AU - Gascuel, O. PY - 2003 DA - 2003// TI - A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood JO - Syst Biol VL - 52 UR - https://doi.org/10.1080/10635150390235520 DO - 10.1080/10635150390235520 ID - Guindon2003 ER - TY - JOUR AU - Felsenstein, J. AU - Churchill, G. A. PY - 1996 DA - 1996// TI - A hidden markov model approach to variation among sites in rate of evolution JO - Mol Biol Evol VL - 13 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025575 DO - 10.1093/oxfordjournals.molbev.a025575 ID - Felsenstein1996 ER - TY - JOUR AU - Anisimova, M. AU - Gascuel, O. PY - 2006 DA - 2006// TI - Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative JO - Syst Biol VL - 55 UR - https://doi.org/10.1080/10635150600755453 DO - 10.1080/10635150600755453 ID - Anisimova2006 ER -