TY - JOUR AU - Gogarten, J. P. AU - Townsend, J. P. PY - 2005 DA - 2005// TI - Horizontal gene transfer, genome innovation and evolution. JO - Nat Rev Microbiol VL - 3 UR - https://doi.org/10.1038/nrmicro1204 DO - 10.1038/nrmicro1204 ID - Gogarten2005 ER - TY - JOUR AU - Canchaya, C. AU - Fournous, G. AU - Chibani-Chennoufi, S. AU - Dillmann, M. L. AU - Brussow, H. PY - 2003 DA - 2003// TI - Phage as agents of lateral gene transfer. JO - Curr Opin Microbiol VL - 6 UR - https://doi.org/10.1016/S1369-5274(03)00086-9 DO - 10.1016/S1369-5274(03)00086-9 ID - Canchaya2003 ER - TY - JOUR AU - Frost, L. S. AU - Leplae, R. AU - Summers, A. O. AU - Toussaint, A. PY - 2005 DA - 2005// TI - Mobile genetic elements: the agents of open source evolution. JO - Nat Rev Microbiol VL - 3 UR - https://doi.org/10.1038/nrmicro1235 DO - 10.1038/nrmicro1235 ID - Frost2005 ER - TY - JOUR AU - Canchaya, C. AU - Fournous, G. AU - Brussow, H. PY - 2004 DA - 2004// TI - The impact of prophages on bacterial chromosomes. JO - Mol Microbiol VL - 53 UR - https://doi.org/10.1111/j.1365-2958.2004.04113.x DO - 10.1111/j.1365-2958.2004.04113.x ID - Canchaya2004 ER - TY - JOUR AU - Karlin, S. PY - 2001 DA - 2001// TI - Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. JO - Trends Microbiol VL - 9 UR - https://doi.org/10.1016/S0966-842X(01)02079-0 DO - 10.1016/S0966-842X(01)02079-0 ID - Karlin2001 ER - TY - JOUR AU - Hsiao, W. W. AU - Ung, K. AU - Aeschliman, D. AU - Bryan, J. AU - Finlay, B. B. AU - Brinkman, F. S. PY - 2005 DA - 2005// TI - Evidence of a large novel gene pool associated with prokaryotic genomic islands. JO - PLoS Genet VL - 1 UR - https://doi.org/10.1371/journal.pgen.0010062 DO - 10.1371/journal.pgen.0010062 ID - Hsiao2005 ER - TY - JOUR AU - Mantri, Y. AU - Williams, K. P. PY - 2004 DA - 2004// TI - Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities. JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh059 DO - 10.1093/nar/gkh059 ID - Mantri2004 ER - TY - JOUR AU - Hambly, E. AU - Suttle, C. A. PY - 2005 DA - 2005// TI - The viriosphere, diversity, and genetic exchange within phage communities. JO - Curr Opin Microbiol VL - 8 UR - https://doi.org/10.1016/j.mib.2005.06.005 DO - 10.1016/j.mib.2005.06.005 ID - Hambly2005 ER - TY - JOUR AU - Siew, N. AU - Azaria, Y. AU - Fischer, D. PY - 2004 DA - 2004// TI - The ORFanage: an ORFan database. JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh116 DO - 10.1093/nar/gkh116 ID - Siew2004 ER - TY - JOUR AU - Yin, Y. AU - Fischer, D. PY - 2006 DA - 2006// TI - On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer. JO - BMC Evol Biol VL - 6 UR - https://doi.org/10.1186/1471-2148-6-63 DO - 10.1186/1471-2148-6-63 ID - Yin2006 ER - TY - JOUR AU - Siew, N. AU - Fischer, D. PY - 2003 DA - 2003// TI - Analysis of singleton ORFans in fully sequenced microbial genomes. JO - Proteins VL - 53 UR - https://doi.org/10.1002/prot.10423 DO - 10.1002/prot.10423 ID - Siew2003 ER - TY - JOUR AU - Yin, Y. AU - Fischer, D. PY - 2008 DA - 2008// TI - Identification and investigation of ORFans in the viral world. JO - BMC Genomics VL - 9 UR - https://doi.org/10.1186/1471-2164-9-24 DO - 10.1186/1471-2164-9-24 ID - Yin2008 ER - TY - JOUR AU - Prangishvili, D. AU - Garrett, R. A. AU - Koonin, E. V. PY - 2006 DA - 2006// TI - Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. JO - Virus Res VL - 117 UR - https://doi.org/10.1016/j.virusres.2006.01.007 DO - 10.1016/j.virusres.2006.01.007 ID - Prangishvili2006 ER - TY - JOUR AU - Daubin, V. AU - Ochman, H. PY - 2004 DA - 2004// TI - Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli. JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.2231904 DO - 10.1101/gr.2231904 ID - Daubin2004 ER - TY - JOUR AU - Cortez, D. Q. AU - Lazcano, A. AU - Becerra, A. PY - 2005 DA - 2005// TI - Comparative analysis of methodologies for the detection of horizontally transferred genes: a reassessment of first-order Markov models. JO - In Silico Biol VL - 5 ID - Cortez2005 ER - TY - JOUR AU - Nakamura, Y. AU - Itoh, T. AU - Matsuda, H. AU - Gojobori, T. PY - 2004 DA - 2004// TI - Biased biological functions of horizontally transferred genes in prokaryotic genomes. JO - Nat Genet VL - 36 UR - https://doi.org/10.1038/ng1381 DO - 10.1038/ng1381 ID - Nakamura2004 ER - TY - JOUR AU - Ochman, H. AU - Lawrence, J. G. AU - Groisman, E. A. PY - 2000 DA - 2000// TI - Lateral gene transfer and the nature of bacterial innovation. JO - Nature VL - 405 UR - https://doi.org/10.1038/35012500 DO - 10.1038/35012500 ID - Ochman2000 ER - TY - JOUR AU - Garcia-Vallve, S. AU - Romeu, A. AU - Palau, J. PY - 2000 DA - 2000// TI - Horizontal gene transfer in bacterial and archaeal complete genomes. JO - Genome Res VL - 10 UR - https://doi.org/10.1101/gr.130000 DO - 10.1101/gr.130000 ID - Garcia-Vallve2000 ER - TY - JOUR AU - Ou, H. Y. AU - Chen, L. L. AU - Lonnen, J. AU - Chaudhuri, R. R. AU - Thani, A. B. AU - Smith, R. AU - Garton, N. J. AU - Hinton, J. AU - Pallen, M. AU - Barer, M. R. AU - Rajakumar, K. PY - 2006 DA - 2006// TI - A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria. JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gnj005 DO - 10.1093/nar/gnj005 ID - Ou2006 ER - TY - JOUR AU - Lawrence, J. G. AU - Ochman, H. PY - 1997 DA - 1997// TI - Amelioration of bacterial genomes: rates of change and exchange. JO - J Mol Evol VL - 44 UR - https://doi.org/10.1007/PL00006158 DO - 10.1007/PL00006158 ID - Lawrence1997 ER - TY - JOUR AU - Hayes, W. S. AU - Borodovsky, M. PY - 1998 DA - 1998// TI - How to interpret an anonymous bacterial genome: machine learning approach to gene identification. JO - Genome Res VL - 8 ID - Hayes1998 ER - TY - JOUR AU - van Passel, M. W. AU - Bart, A. AU - Thygesen, H. H. AU - Luyf, A. C. AU - van Kampen, A. H. AU - Ende, A. v. a. n. d. e. r. PY - 2005 DA - 2005// TI - An acquisition account of genomic islands based on genome signature comparisons. JO - BMC Genomics VL - 6 UR - https://doi.org/10.1186/1471-2164-6-163 DO - 10.1186/1471-2164-6-163 ID - van Passel2005 ER - TY - JOUR AU - Campbell, A. AU - Mrazek, J. AU - Karlin, S. PY - 1999 DA - 1999// TI - Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA. JO - Proc Natl Acad Sci USA VL - 96 UR - https://doi.org/10.1073/pnas.96.16.9184 DO - 10.1073/pnas.96.16.9184 ID - Campbell1999 ER - TY - JOUR AU - van Passel, M. W. AU - Bart, A. AU - Luyf, A. C. AU - van Kampen, A. H. AU - Ende, A. v. a. n. d. e. r. PY - 2006 DA - 2006// TI - Compositional discordance between prokaryotic plasmids and host chromosomes. JO - BMC Genomics VL - 7 UR - https://doi.org/10.1186/1471-2164-7-26 DO - 10.1186/1471-2164-7-26 ID - van Passel2006 ER - TY - JOUR AU - Monier, A. AU - Claverie, J. M. AU - Ogata, H. PY - 2007 DA - 2007// TI - Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses. JO - BMC Genomics VL - 8 UR - https://doi.org/10.1186/1471-2164-8-456 DO - 10.1186/1471-2164-8-456 ID - Monier2007 ER - TY - JOUR AU - Mrazek, J. AU - Karlin, S. PY - 2007 DA - 2007// TI - Distinctive features of large complex virus genomes and proteomes. JO - Proc Natl Acad Sci USA VL - 104 UR - https://doi.org/10.1073/pnas.0700429104 DO - 10.1073/pnas.0700429104 ID - Mrazek2007 ER - TY - JOUR AU - Lerat, E. AU - Daubin, V. AU - Moran, N. A. PY - 2003 DA - 2003// TI - From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria. JO - PLoS Biol VL - 1 UR - https://doi.org/10.1371/journal.pbio.0000019 DO - 10.1371/journal.pbio.0000019 ID - Lerat2003 ER - TY - JOUR AU - van Passel, M. W. AU - Smillie, C. S. AU - Ochman, H. PY - 2007 DA - 2007// TI - Gene decay in archaea. JO - Archaea VL - 2 UR - https://doi.org/10.1155/2007/165723 DO - 10.1155/2007/165723 ID - van Passel2007 ER - TY - JOUR AU - She, Q. AU - Peng, X. AU - Zillig, W. AU - Garrett, R. A. PY - 2001 DA - 2001// TI - Gene capture in archaeal chromosomes. JO - Nature VL - 409 UR - https://doi.org/10.1038/35054138 DO - 10.1038/35054138 ID - She2001 ER - TY - JOUR AU - Williams, K. P. PY - 2002 DA - 2002// TI - Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies. JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.4.866 DO - 10.1093/nar/30.4.866 ID - Williams2002 ER - TY - JOUR AU - Keller, J. AU - Leulliot, N. AU - Cambillau, C. AU - Campanacci, V. AU - Porciero, S. AU - Prangishvilli, D. AU - Forterre, P. AU - Cortez, D. AU - Quevillon-Cheruel, S. AU - van Tilbeurgh, H. PY - 2007 DA - 2007// TI - Crystal structure of AFV3-109, a highly conserved protein from crenarchaeal viruses. JO - Virol J VL - 4 UR - https://doi.org/10.1186/1743-422X-4-12 DO - 10.1186/1743-422X-4-12 ID - Keller2007 ER - TY - JOUR AU - Auchtung, J. M. AU - Lee, C. A. AU - Monson, R. E. AU - Lehman, A. P. AU - Grossman, A. D. PY - 2005 DA - 2005// TI - Regulation of a Bacillus subtilismobile genetic element by intercellular signaling and the global DNA damage response. JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0505835102 DO - 10.1073/pnas.0505835102 ID - Auchtung2005 ER - TY - JOUR AU - Sobecky, P. A. AU - Coombs, J. M. PY - 2009 DA - 2009// TI - Horizontal gene transfer in metal and radionuclide contaminated soils. JO - Methods Mol Biol VL - 532 UR - https://doi.org/10.1007/978-1-60327-853-9_26 DO - 10.1007/978-1-60327-853-9_26 ID - Sobecky2009 ER - TY - JOUR AU - Coleman, M. L. AU - Sullivan, M. B. AU - Martiny, A. C. AU - Steglich, C. AU - Barry, K. AU - Delong, E. F. AU - Chisholm, S. W. PY - 2006 DA - 2006// TI - Genomic islands and the ecology and evolution of Prochlorococcus. JO - Science VL - 311 UR - https://doi.org/10.1126/science.1122050 DO - 10.1126/science.1122050 ID - Coleman2006 ER - TY - JOUR AU - Angly, F. E. AU - Felts, B. AU - Breitbart, M. AU - Salamon, P. AU - Edwards, R. A. AU - Carlson, C. AU - Chan, A. M. AU - Haynes, M. AU - Kelley, S. AU - Liu, H. AU - Mahaffy, J. M. AU - Mueller, J. E. AU - Nulton, J. AU - Olson, R. AU - Parsons, R. AU - Rayhawk, S. AU - Suttle, C. A. AU - Rohwer, F. PY - 2006 DA - 2006// TI - The marine viromes of four oceanic regions. JO - PLoS Biol VL - 4 UR - https://doi.org/10.1371/journal.pbio.0040368 DO - 10.1371/journal.pbio.0040368 ID - Angly2006 ER - TY - JOUR AU - Weinbauer, M. G. AU - Rassoulzadegan, F. PY - 2004 DA - 2004// TI - Are viruses driving microbial diversification and diversity? JO - Environ Microbiol VL - 6 UR - https://doi.org/10.1046/j.1462-2920.2003.00539.x DO - 10.1046/j.1462-2920.2003.00539.x ID - Weinbauer2004 ER - TY - STD TI - NCBI Database. [http://www.ncbi.nlm.nih.gov/] UR - http://www.ncbi.nlm.nih.gov/ ID - ref37 ER - TY - BOOK AU - Durbin, R. PY - 1998 DA - 1998// TI - Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids PB - Cambridge University Press CY - Cambridge UR - https://doi.org/10.1017/CBO9780511790492 DO - 10.1017/CBO9780511790492 ID - Durbin1998 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 - R Project. [http://www.r-project.org/] UR - http://www.r-project.org/ ID - ref40 ER -