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 A Rajeev K. Azad and Jeffrey G. Lawrence. Use of artificial geonmes in assessing methods for atypical gene detection. PLoS Comput Biol, 1(5), November 2005.
 Claire Balding, Stephen A. Bromley, Roger W. Pickup, and Jon R. Saunders. Diversity of phage integrases in enterobacteriaceae: development of markers for environmental analysis of temperate phages. Environmental Microbiology, 7(10):1558-1567, October 2005.
 Samuel Baron, editor. Medical Microbiology. The University of Texas Medical Branch at Galveston, fourth edition, 1996.
 Michael Bose and Robert D. Barber. Prophage finder: a prophage loci prediction tool for prokaryotic genome sequences. In Silico Biol, 6(3), April 2006.
 H. Brussow, C. Canchaya, and W.D. Hardt. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev, 68(3):560-602, September 2004.
 Frederic Bushman. Lateral DNA Transfer: Mechanisms and Consequences. Cold Spring Harbor Laboratory Press, November 2001.
 A. Campbell. Prophage insertion sites. Res Microbiol, 154(4):277-282, May 2003.
 A.M. Campbell. Chromosomal insertion sites for phages and plasmids. J Bacteriol, 174(23):7495-7499, December 1992.
 Carlos Canchaya, Ghislain Fournous, and Harald Brussow. The impact of prophages on bacterial chromosomes. Molecular Microbiology, 32(1):9-18, July 2004.
 Carlos Canchaya, Caroline Proux, Ghislain Fournous, Anne Bruttin, and Harald Brussow. Prophage genomics. Microbiology and Molecular Biology Reviews, 67(2):238-276, June 2003.
 S.R. Casjens. Comparative genomics and evolution of the tail-bacteriophages. Curr Opin Microbiol, 8(4):451-458, August 2005.
 Ines Chen, Peter J. Christie, and David Dubnau. The ins and outs of dna transfer in bacteria. Science, 310(5753):1456-1460, December 2005.
 S.R. Eddy and R. Durbin. Rna sequence analysis using covariance models. Nucleic Acids Res, 22(11):2079-2088, June 1994.
 Robert A. Edwards and Forest Rohwer. Opinion: Viral metagenomics. Nature Reviews Microbiology, 3(6):504-510, June 1994.
 Andrew E. Firth and Chris M. Brown. Detecting overlapping coding sequences in virus genomes. BMC Bioinformatics, 7(1), February 2006.
 Patrick Forterre. The origin of viruses and their possible roles in major evolutionary transitions. Virus Research, 117(1):5-16, April 2006.
 Derrick E. Fouts. Phage_finder: Automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res, October 2006.
 Amy C. Groth and Michele P. Calos. Phage integrases: Biology and applications. Journal of Molecular Biology, 335(3):667-678, January 2004.
 M.A. Hauser and J.J. Scocca. Site-specific integration of the haemophilus influenzae bacteriophage hp1: location of the boundaries of the phage attachment site. J Bacteriol, 174(20):6674-6677, October 1992.
 T. Hayashi, K. Makino, M. Ohnishi, K. Kurokawa, K. Ishii, K. Yokoyama, C.G. Han, E. Ohtsubo, K. Nakayama, T. Murata, M. Tanaka, T. Tobe, T. Iida, H. Takami, T. Honda, C. Sasakawa, N. Ogasawara, T. Yasunaga, S. Kuhara, T. Shiba, M. Hattori, and H. Shinagawa. Complete genome sequence of enterohemorrhagic escherichia coli o157:h7 and genomic comparison with a laboratory strain k-12. DNA Res, 8(1):11-22, February 2001.
 A.P. Hermans, A.M. Beuling, A.H. van Hoek, H.J. Aarts, T. Abee, and M.H. Zwietering. Distribution of prophages and sgi-1 antibiotic-resistance genes among different salmonella enterica serovar typhimurium isolates. Microbiology, 152(Pt 7):2137-2147, July 2006.
 W. Hsiao, I. Wan, S.J. Jones, and F.S. Brinkman. Islandpath: aiding detection of genomic islands in prokaryotes. Bioinformatics, 19(3):418-420, February 2003.
 P. Lauer, M.Y. Chow, M.J. Loessner, D.A. Portnoy, and R. Calendar. Construction, characterization, and use of two listeria monocytogenes site-specific phage integration vectors. J Bacteriol, 184(15):4177-4186, August 2002.
 R. Leplae, A. Hebrant, S.J. Wodak, and A. Toussaint. Aclame: a classification of mobile genetic elements. Nucleic Acids Res, 32(Database issue), January 2004.
 T.M. Lowe and S.R. Eddy. trnascan-se: a program for improved detection of transfer rna genes in genomic sequence. Nucleic Acids Res, 25(5):955-964, March 1997.
 Y. Mantri and K.P. Williams. Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their dna site specificites. Nucleic Acids Res, 32(Database issue), January 2004.
 Ian J. Molineux. Fifty-three years since hershey and chase; much ado about pressure but which pressure is it? Virology, 344(1):221-229, January 2006.
 Daniel Nelson. Phage taxonomy: We agree to disagree. J Bacteriol, 186(21):7029-7031, November 2004.
 H.Y. Ou, L.L. Chen, J. Lonnen, R.R. Chaudhuri, A.B. Thani, R. Smith, N.J. Garton, J. Hinton, M. Pallen, M.R. Barer, and K. Rajakumar. A novel strategry for the indentification of genomic islands by comparative analysis of the contents and contexts of trna sites in closely related bacteria. Nucleic Acids Res, 34(1), 2006.
 R. Ravatn, S. Studer, A.J. Zehnder, and J.R. van der Meer. Int-b13, an unusual site-specific recombinase of the bacteriophage p4 integrase family, is responsible for chromosomal insertion of the 105-kilobase clc element of pseudomonas sp. strain b13. J Bacteriol, 180(21):5505-5514, November 1998.
 W.D. Reiter, P.Palm, and S. Yeats. Transfer rna genes frequently serve as integration sites for prokaryotic genetic elements. Nucleic Acids Res, 17(5):1907-1914, March 1989.
 Edit Rutkai, Andrea Gyorgy, Laszlo Dorgai, and Robert A. Weisberg. Role of secondary attachment sites in changing the specificity of site-specific recombination. J Bacteriol, 188(9):3409-3411, May 2006.
 Soren J. Sorensen, Mark Bailey, Lars H. Hansen, Niels Kroer, and Stefan Wuertz. Studying plasmid horizontal transfer in situ: A critical review. Nat Rev Micro, 3(9):700-710, 2005.
 M. Sprinzl and K.W. Vassilenko. Compilation of trna sequences and sequences of trna genes. Nucleic Acids Res, 33(Database issue), January 2005.
 Christopher M. Thomas and Kaare M. Nielsen. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nature Reviews Microbiology, 3(9):711-721, September 2005.
 C.R. Tinsley, E. Bille, and X. Nassif. Bacteriophages and pathogenicity: more than just providing a toxin? Microbes Infect, 8(5):1365-1371, April 2006.
 M.H. Van Regenmortel, International and C.M. Fauquet. Virus Taxonomy: Classification and Nomenclature of Viruses: Seventh Report of the International Committee on Taxonomy of Viruses. Academic Press, October 2000.
 M. Ventura, C. Canchaya, D. Pridmore, B. Berger, and H. Brussow. Integration and distribution of lactobacillus johnsonii prophages. J Bacteriol, 185(15):4603-4608, August, 2003.
 S. Waack, O. Keller, R. Asper, T. Brodag, C. Damm, W.F. Fricke, K. Surovcik, P. Meinicke, and R. Merkl. Score-based prediction of genomic islands in prokaryotic genomes using hidden markov models. BMC Bioinformatics, 7, 2006.
 K.P. Williams. Integration sites for genetic elements in prokaryotic trna and tmran genes: sublocation preference of integrase subfamilies. Nucleic Acids Res, 30(4):866-875, February 2002.
 R.M. Woodsmall and D.A. Benson. Information resources at the national center for biotechnology information. Bull Med Libr Assoc, 81(3):282-284, July 1993.
 K. Yokoyama, K. Makino, Y. Kubota, M. Watanabe, S. Kimura, C.H. Yutsudo, K. Kurokawa, K. Ishii, M. Hattori, I. Tatsuno, H. Abe, M. Yoh, T. Iida, M. Ohnishi, T. Hayashi, T. Yasunaga, T. Honda, C. Sasakawa, and H. Shinagawa. Complete nucleotide sequence of the prophage vt1-sakai carrying the shiga toxin 1 genes of the enterohemorrhagic escherichia coli o157:h7 strain derived from the sakai outbreak. Gene, 258(1-2):127-139, November 2000.
 S.H. Yoon, C.G. Hur, H.Y. Kang, Y.H. Kim, T.K. Oh, and J.F. Kim. A computational approach for identifying pathogenicity islands in prokaryotic genomes. BMC Bioinformatics, 6, 2005.
 M. Zuker. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res, 31(13):3406-3415, July 2003.