TY - JOUR AU - Shoemaker, C. A. AU - Klesius, P. H. AU - Evans, J. J. AU - Arias, C. R. PY - 2009 DA - 2009// TI - Use of modified live vaccines in aquaculture JO - J World Aquacult Soc VL - 40 UR - https://doi.org/10.1111/j.1749-7345.2009.00279.x DO - 10.1111/j.1749-7345.2009.00279.x ID - Shoemaker2009 ER - TY - JOUR AU - Brussow, H. PY - 2005 DA - 2005// TI - Phage therapy: the Escherichia coli experience JO - Microbiology VL - 151 UR - https://doi.org/10.1099/mic.0.27849-0 DO - 10.1099/mic.0.27849-0 ID - Brussow2005 ER - TY - JOUR AU - Skurnik, M. AU - Strauch, E. PY - 2006 DA - 2006// TI - Phage therapy: facts and fiction JO - International Journal of Medical Microbiology VL - 296 UR - https://doi.org/10.1016/j.ijmm.2005.09.002 DO - 10.1016/j.ijmm.2005.09.002 ID - Skurnik2006 ER - TY - JOUR AU - Cairns, B. J. AU - Payne, R. J. H. PY - 2008 DA - 2008// TI - Bacteriophage therapy and the mutant selection window JO - Antimicrobial agents and chemotherapy VL - 52 UR - https://doi.org/10.1128/AAC.00574-08 DO - 10.1128/AAC.00574-08 ID - Cairns2008 ER - TY - CHAP AU - Merril, C. R. AU - Biswas, B. AU - Carlton, R. AU - Jensen, N. C. AU - Creed, G. J. AU - Zullo, S. AU - Adhya, S. PY - 1996 DA - 1996// BT - Long-Circulating Bacteriophage as Antibacterial Agents PB - JSTOR CY - JSTOR ID - Merril1996 ER - TY - JOUR AU - Carlton, R. M. PY - 1999 DA - 1999// TI - Phage therapy: past history and future prospects JO - Arch Immunol Ther Exp VL - 47 ID - Carlton1999 ER - TY - JOUR AU - Walakira, J. K. AU - Carrias, A. A. AU - Hossain, M. J. AU - Jones, E. AU - Terhune, J. S. AU - Liles, M. R. PY - 2008 DA - 2008// TI - Identification and characterization of bacteriophages specific to the catfish pathogen, Edwardsiella ictaluri JO - J Appl Microbiol VL - 105 UR - https://doi.org/10.1111/j.1365-2672.2008.03933.x DO - 10.1111/j.1365-2672.2008.03933.x ID - Walakira2008 ER - TY - JOUR AU - Rohwer, F. AU - Edwards, R. PY - 2002 DA - 2002// TI - The Phage Proteomic Tree: a genome-based taxonomy for phage JO - Journal of bacteriology VL - 184 UR - https://doi.org/10.1128/JB.184.16.4529-4535.2002 DO - 10.1128/JB.184.16.4529-4535.2002 ID - Rohwer2002 ER - TY - JOUR AU - Chibani-Chennoufi, S. AU - Canchaya, C. AU - Bruttin, A. AU - Brussow, H. PY - 2004 DA - 2004// TI - Comparative genomics of the T4-like Escherichia coli phage JS98: implications for the evolution of T4 phages JO - Journal of bacteriology VL - 186 UR - https://doi.org/10.1128/JB.186.24.8276-8286.2004 DO - 10.1128/JB.186.24.8276-8286.2004 ID - Chibani-Chennoufi2004 ER - TY - JOUR AU - Lima-Mendez, G. AU - Van Helden, J. AU - Toussaint, A. AU - Leplae, R. PY - 2008 DA - 2008// TI - Reticulate representation of evolutionary and functional relationships between phage genomes JO - Molecular biology and evolution VL - 25 UR - https://doi.org/10.1093/molbev/msn023 DO - 10.1093/molbev/msn023 ID - Lima-Mendez2008 ER - TY - JOUR AU - Serwer, P. AU - Hayes, S. J. AU - Thomas, J. A. AU - Hardies, S. C. PY - 2007 DA - 2007// TI - Propagating the missing bacteriophages: a large bacteriophage in a new class JO - Virology Journal VL - 4 UR - https://doi.org/10.1186/1743-422X-4-21 DO - 10.1186/1743-422X-4-21 ID - Serwer2007 ER - TY - JOUR AU - Kropinski, A. M. AU - Sibbald, M. J. PY - 1999 DA - 1999// TI - Transfer RNA genes and their significance to codon usage in the Pseudomonas aeruginosa lamboid bacteriophage D3 JO - Canadian journal of microbiology VL - 45 UR - https://doi.org/10.1139/w99-078 DO - 10.1139/w99-078 ID - Kropinski1999 ER - TY - JOUR AU - Bukovska, G. AU - Klucar, L. AU - Vlcek, C. AU - Adamovic, J. AU - Turna, J. AU - Timko, J. PY - 2006 DA - 2006// TI - Complete nucleotide sequence and genome analysis of bacteriophage BFK20--a lytic phage of the industrial producer Brevibacterium flavum JO - Virology VL - 348 UR - https://doi.org/10.1016/j.virol.2005.12.010 DO - 10.1016/j.virol.2005.12.010 ID - Bukovska2006 ER - TY - JOUR AU - Xu, J. AU - Hendrix, R. W. AU - Duda, R. L. PY - 2004 DA - 2004// TI - Conserved translational frameshift in dsDNA bacteriophage tail assembly genes JO - Molecular cell VL - 16 UR - https://doi.org/10.1016/j.molcel.2004.09.006 DO - 10.1016/j.molcel.2004.09.006 ID - Xu2004 ER - TY - JOUR AU - Levin, M. E. AU - Hendrix, R. W. AU - Casjens, S. R. PY - 1993 DA - 1993// TI - A programmed translational frameshift is required for the synthesis of a bacteriophage l tail assembly protein JO - J Mol Biol VL - 234 UR - https://doi.org/10.1006/jmbi.1993.1568 DO - 10.1006/jmbi.1993.1568 ID - Levin1993 ER - TY - JOUR AU - Brüssow, H. AU - Desiere, F. PY - 2001 DA - 2001// TI - Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages JO - Molecular Microbiology VL - 39 UR - https://doi.org/10.1046/j.1365-2958.2001.02228.x DO - 10.1046/j.1365-2958.2001.02228.x ID - Brüssow2001 ER - TY - STD TI - Timms AR, Cambray-Young J, Scott AE, Petty NK, Connerton PL, Clarke L, Seeger K, Quail M, Cummings N, Maskell DJ: Evidence for a lineage of virulent bacteriophages that target Campylobacter.BMC genomics11: 214. 10.1186/1471-2164-11-214 ID - ref17 ER - TY - JOUR AU - Denou, E. AU - Bruttin, A. AU - Barretto, C. AU - Ngom-Bru, C. AU - Brüssow, H. AU - Zuber, S. PY - 2009 DA - 2009// TI - T4 phages against Escherichia coli diarrhea: potential and problems JO - Virology VL - 388 UR - https://doi.org/10.1016/j.virol.2009.03.009 DO - 10.1016/j.virol.2009.03.009 ID - Denou2009 ER - TY - JOUR AU - Hatfull, G. F. AU - Jacobs-Sera, D. AU - Lawrence, J. G. AU - Pope, W. H. AU - Russell, D. A. AU - Ko, C. C. AU - Weber, R. J. AU - Patel, M. C. AU - Germane, K. L. AU - Edgar, R. H. PY - 2010 DA - 2010// TI - Comparative genomic analysis of sixty mycobacteriophage genomes: Genome clustering, gene acquisition and gene size JO - Journal of molecular biology VL - 397 UR - https://doi.org/10.1016/j.jmb.2010.01.011 DO - 10.1016/j.jmb.2010.01.011 ID - Hatfull2010 ER - TY - JOUR AU - Casjens, S. PY - 2003 DA - 2003// TI - Prophages and bacterial genomics: what have we learned so far? JO - Molecular microbiology VL - 49 UR - https://doi.org/10.1046/j.1365-2958.2003.03580.x DO - 10.1046/j.1365-2958.2003.03580.x ID - Casjens2003 ER - TY - JOUR AU - Lehman, S. M. AU - Kropinski, A. M. AU - Castle, A. J. AU - Svircev, A. M. PY - 2009 DA - 2009// TI - Complete Genome of the Broad-Host-Range Erwinia amylovora Phage {Phi} Ea21-4 and Its Relationship to Salmonella Phage Felix O1 JO - Applied and environmental microbiology VL - 75 UR - https://doi.org/10.1128/AEM.02352-08 DO - 10.1128/AEM.02352-08 ID - Lehman2009 ER - TY - JOUR AU - Duffy, C. AU - Feiss, M. PY - 2002 DA - 2002// TI - The large subunit of bacteriophage [lambda]'s terminase plays a role in DNA translocation and packaging termination1 JO - Journal of molecular biology VL - 316 UR - https://doi.org/10.1006/jmbi.2001.5368 DO - 10.1006/jmbi.2001.5368 ID - Duffy2002 ER - TY - JOUR AU - Maluf, N. K. AU - Yang, Q. AU - Catalano, C. E. PY - 2005 DA - 2005// TI - Self-association Properties of the Bacteriophage [lambda] Terminase Holoenzyme: Implications for the DNA Packaging Motor JO - Journal of molecular biology VL - 347 UR - https://doi.org/10.1016/j.jmb.2005.01.016 DO - 10.1016/j.jmb.2005.01.016 ID - Maluf2005 ER - TY - JOUR AU - Wang, I. N. AU - Smith, D. L. AU - Young, R. PY - 2000 DA - 2000// TI - H OLINS: The Protein Clocks of Bacteriophage Infections JO - Annu Rev Microbiol VL - 54 UR - https://doi.org/10.1146/annurev.micro.54.1.799 DO - 10.1146/annurev.micro.54.1.799 ID - Wang2000 ER - TY - JOUR AU - Summer, E. J. AU - Berry, J. AU - Tran, T. A. T. AU - Niu, L. AU - Struck, D. K. AU - Young, R. PY - 2007 DA - 2007// TI - Rz/Rz1 lysis gene equivalents in phages of Gram-negative hosts JO - Journal of molecular biology VL - 373 UR - https://doi.org/10.1016/j.jmb.2007.08.045 DO - 10.1016/j.jmb.2007.08.045 ID - Summer2007 ER - TY - JOUR AU - Borysowski, J. AU - Weber-Dabrowska, B. AU - Gorski, A. PY - 2006 DA - 2006// TI - Bacteriophage endolysins as a novel class of antibacterial agents JO - Experimental Biology and Medicine VL - 231 ID - Borysowski2006 ER - TY - JOUR AU - Egelman, E. H. AU - Yu, X. AU - Wild, R. AU - Hingorani, M. M. AU - Patel, S. S. PY - 1995 DA - 1995// TI - Bacteriophage T7 helicase/primase proteins form rings around single-stranded DNA that suggest a general structure for hexameric helicases JO - Proc Natl Acad Sci USA VL - 92 UR - https://doi.org/10.1073/pnas.92.9.3869 DO - 10.1073/pnas.92.9.3869 ID - Egelman1995 ER - TY - JOUR AU - Clarke, S. PY - 1993 DA - 1993// TI - Protein methylation JO - Current opinion in cell biology VL - 5 UR - https://doi.org/10.1016/0955-0674(93)90080-A DO - 10.1016/0955-0674(93)90080-A ID - Clarke1993 ER - TY - JOUR AU - Eisen, J. A. AU - Sweder, K. S. AU - Hanawalt, P. C. PY - 1995 DA - 1995// TI - Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions JO - Nucleic acids research VL - 23 UR - https://doi.org/10.1093/nar/23.14.2715 DO - 10.1093/nar/23.14.2715 ID - Eisen1995 ER - TY - JOUR AU - Schneider-Scherzer, E. AU - Auer, B. AU - de Groot, E. J. AU - Schweiger, M. PY - 1990 DA - 1990// TI - Primary structure of a DNA (N6-adenine)-methyltransferase from Escherichia coli virus T1. DNA sequence, genomic organization, and comparative analysis JO - Journal of Biological Chemistry VL - 265 ID - Schneider-Scherzer1990 ER - TY - JOUR AU - Oakey, H. J. AU - Cullen, B. R. AU - Owens, L. PY - 2002 DA - 2002// TI - The complete nucleotide sequence of the Vibrio harveyi bacteriophage VHML JO - Journal of applied microbiology VL - 93 UR - https://doi.org/10.1046/j.1365-2672.2002.01776.x DO - 10.1046/j.1365-2672.2002.01776.x ID - Oakey2002 ER - TY - JOUR AU - Nelson, D. PY - 2004 DA - 2004// TI - Phage taxonomy: we agree to disagree JO - Journal of bacteriology VL - 186 UR - https://doi.org/10.1128/JB.186.21.7029-7031.2004 DO - 10.1128/JB.186.21.7029-7031.2004 ID - Nelson2004 ER - TY - JOUR AU - Proux, C. AU - Van Sinderen, D. AU - Suarez, J. AU - Garcia, P. AU - Ladero, V. AU - Fitzgerald, G. F. AU - Desiere, F. AU - Brussow, H. PY - 2002 DA - 2002// TI - The dilemma of phage taxonomy illustrated by comparative genomics of Sfi21-like Siphoviridae in lactic acid bacteria JO - Journal of bacteriology VL - 184 UR - https://doi.org/10.1128/JB.184.21.6026-6036.2002 DO - 10.1128/JB.184.21.6026-6036.2002 ID - Proux2002 ER - TY - CHAP AU - Adams, M. H. PY - 1959 DA - 1959// BT - Bacteriophages PB - Interscience Pub- lishers, Inc CY - New York ID - Adams1959 ER - TY - JOUR AU - Schoenfeld, T. AU - Patterson, M. AU - Richardson, P. M. AU - Wommack, K. E. AU - Young, M. AU - Mead, D. PY - 2008 DA - 2008// TI - Assembly of viral metagenomes from yellowstone hot springs JO - Applied and environmental microbiology VL - 74 UR - https://doi.org/10.1128/AEM.02598-07 DO - 10.1128/AEM.02598-07 ID - Schoenfeld2008 ER - TY - STD TI - GeneMark Gene Prediction[http://opal.biology.gatech.edu/GeneMark/] UR - http://opal.biology.gatech.edu/GeneMark/ ID - ref36 ER - TY - STD TI - ORF Finder (Open Reading Frame Finder)[http://www.ncbi.nlm.nih.gov/gorf/gorf.html] UR - http://www.ncbi.nlm.nih.gov/gorf/gorf.html ID - ref37 ER - TY - STD TI - Calculating fractional GC content[http://inn-temp.weizmann.ac.il/cgi-bin/emboss/geecee] UR - http://inn-temp.weizmann.ac.il/cgi-bin/emboss/geecee ID - ref38 ER - TY - JOUR AU - Lowe, T. M. AU - Eddy, S. R. PY - 1997 DA - 1997// TI - tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence JO - Nucleic acids research VL - 25 UR - https://doi.org/10.1093/nar/25.5.0955 DO - 10.1093/nar/25.5.0955 ID - Lowe1997 ER - TY - STD TI - tRNAscan-SE Search Server[http://lowelab.ucsc.edu/tRNAscan-SE/] UR - http://lowelab.ucsc.edu/tRNAscan-SE/ ID - ref40 ER - TY - JOUR AU - Altschul, S. F. AU - Gish, W. AU - Miller, W. AU - Myers, E. W. AU - Lipman, D. J. PY - 1990 DA - 1990// TI - Basic local alignment search tool JO - Journal of molecular biology VL - 215 UR - https://doi.org/10.1016/S0022-2836(05)80360-2 DO - 10.1016/S0022-2836(05)80360-2 ID - Altschul1990 ER - TY - STD TI - Motif Search Server[http://motif.genome.jp/] UR - http://motif.genome.jp/ ID - ref42 ER - TY - STD TI - FrameD[http://tata.toulouse.inra.fr/apps/FrameD/FD] UR - http://tata.toulouse.inra.fr/apps/FrameD/FD ID - ref43 ER - TY - JOUR AU - Stothard, P. AU - Wishart, D. S. PY - 2005 DA - 2005// TI - Circular genome visualization and exploration using CGView JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti054 DO - 10.1093/bioinformatics/bti054 ID - Stothard2005 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 X 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 - 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 - Molecular biology and evolution VL - 24 UR - https://doi.org/10.1093/molbev/msm092 DO - 10.1093/molbev/msm092 ID - Tamura2007 ER -