TY - JOUR AU - Ragan, M. A. AU - Beiko, R. G. PY - 2009 DA - 2009// TI - Lateral genetic transfer: open issues JO - Philos Trans R Soc Lond B Biol Sci VL - 364 ID - Ragan2009 ER - TY - JOUR AU - Boto, L. PY - 2010 DA - 2010// TI - Horizontal gene transfer in evolution: facts and challenges JO - Proc Biol Sci VL - 277 UR - https://doi.org/10.1098/rspb.2009.1679 DO - 10.1098/rspb.2009.1679 ID - Boto2010 ER - TY - JOUR AU - Koonin, E. V. AU - Makarova, K. S. AU - Aravind, L. PY - 2001 DA - 2001// TI - Horizontal gene transfer in prokaryotes: quantification and classification JO - Annu Rev Microbiol VL - 55 UR - https://doi.org/10.1146/annurev.micro.55.1.709 DO - 10.1146/annurev.micro.55.1.709 ID - Koonin2001 ER - TY - JOUR AU - Gogarten, J. P. AU - Doolittle, W. F. AU - Lawrence, J. G. PY - 2002 DA - 2002// TI - Prokaryotic evolution in light of gene transfer JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a004046 DO - 10.1093/oxfordjournals.molbev.a004046 ID - Gogarten2002 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 - Pal, C. AU - Papp, B. AU - Lercher, M. J. PY - 2005 DA - 2005// TI - Adaptive evolution of bacterial metabolic networks by horizontal gene transfer JO - Nat Genet VL - 37 UR - https://doi.org/10.1038/ng1686 DO - 10.1038/ng1686 ID - Pal2005 ER - TY - JOUR AU - Koslowski, T. AU - Zehender, F. PY - 2005 DA - 2005// TI - Towards a quantitative understanding of horizontal gene transfer: a kinetic model JO - J Theor Biol VL - 237 UR - https://doi.org/10.1016/j.jtbi.2005.03.028 DO - 10.1016/j.jtbi.2005.03.028 ID - Koslowski2005 ER - TY - JOUR AU - Nielsen, K. M. AU - Townsend, J. P. PY - 2004 DA - 2004// TI - Monitoring and modeling horizontal gene transfer JO - Nat Biotechnol VL - 22 UR - https://doi.org/10.1038/nbt1006 DO - 10.1038/nbt1006 ID - Nielsen2004 ER - TY - JOUR AU - Novozhilov, A. S. AU - Karev, G. P. AU - Koonin, E. V. PY - 2005 DA - 2005// TI - Mathematical modeling of evolution of horizontally transferred genes JO - Mol Biol Evol VL - 22 UR - https://doi.org/10.1093/molbev/msi167 DO - 10.1093/molbev/msi167 ID - Novozhilov2005 ER - TY - JOUR AU - Levin, B. R. AU - Cornejo, O. E. PY - 2009 DA - 2009// TI - The population and evolutionary dynamics of homologous gene recombination in bacteria JO - PLoS Genet VL - 5 UR - https://doi.org/10.1371/journal.pgen.1000601 DO - 10.1371/journal.pgen.1000601 ID - Levin2009 ER - TY - JOUR AU - Philipsen, K. R. AU - Christiansen, L. E. AU - Hasman, H. AU - Madsen, H. PY - 2010 DA - 2010// TI - Modelling conjugation with stochastic differential equations JO - J Theor Biol VL - 263 UR - https://doi.org/10.1016/j.jtbi.2009.11.011 DO - 10.1016/j.jtbi.2009.11.011 ID - Philipsen2010 ER - TY - JOUR AU - Tagkopoulos, I. AU - Liu, Y. C. AU - Tavazoie, S. PY - 2008 DA - 2008// TI - Predictive behavior within microbial genetic networks JO - Science VL - 320 UR - https://doi.org/10.1126/science.1154456 DO - 10.1126/science.1154456 ID - Tagkopoulos2008 ER - TY - JOUR AU - Mozhayskiy, V. AU - Tagkopoulos, I. PY - 2011 DA - 2011// TI - In silico evolution of multi-scale microbial systems in the presence of mobile genetic elements and horizontal gene transfer JO - Lect Notes in Comput Sc VL - 6674 UR - https://doi.org/10.1007/978-3-642-21260-4_26 DO - 10.1007/978-3-642-21260-4_26 ID - Mozhayskiy2011 ER - TY - CHAP AU - Mozhayskiy, V. AU - Miller, R. AU - Ma, K. -. L. AU - Tagkopoulos, I. PY - 2011 DA - 2011// TI - A scalable multi-scale framework for parallel simulation and visualization of microbial evolution BT - TeraGrid'11; Salt Lake Sity, UT ID - Mozhayskiy2011 ER - TY - CHAP AU - Duda, R. O. AU - Hart, P. E. PY - 1973 DA - 1973// BT - Pattern classification and scene analysis ID - Duda1973 ER - TY - JOUR AU - Tago, Y. AU - Imai, M. AU - Ihara, M. AU - Atofuji, H. AU - Nagata, Y. AU - Yamamoto, K. PY - 2005 DA - 2005// TI - Escherichia coli mutator Delta polA is defective in base mismatch correction: the nature of in vivo DNA replication errors JO - J Mol Biol VL - 351 UR - https://doi.org/10.1016/j.jmb.2005.06.014 DO - 10.1016/j.jmb.2005.06.014 ID - Tago2005 ER - TY - JOUR AU - Drake, J. W. AU - Charlesworth, B. AU - Charlesworth, D. AU - Crow, J. F. PY - 1998 DA - 1998// TI - Rates of spontaneous mutation JO - Genetics VL - 148 ID - Drake1998 ER - TY - JOUR AU - Ochman, H. AU - Elwyn, S. AU - Moran, N. A. PY - 1999 DA - 1999// TI - Calibrating bacterial evolution JO - Proc Natl Acad Sci USA VL - 96 UR - https://doi.org/10.1073/pnas.96.22.12638 DO - 10.1073/pnas.96.22.12638 ID - Ochman1999 ER - TY - JOUR AU - Perfeito, L. AU - Fernandes, L. AU - Mota, C. AU - Gordo, I. PY - 2007 DA - 2007// TI - Adaptive mutations in bacteria: high rate and small effects JO - Science VL - 317 UR - https://doi.org/10.1126/science.1142284 DO - 10.1126/science.1142284 ID - Perfeito2007 ER - TY - JOUR AU - Lynch, M. AU - Sung, W. AU - Morris, K. AU - Coffey, N. AU - Landry, C. R. AU - Dopman, E. B. AU - Dickinson, W. J. AU - Okamoto, K. AU - Kulkarni, S. AU - Hartl, D. L. PY - 2008 DA - 2008// TI - A genome-wide view of the spectrum of spontaneous mutations in yeast JO - Proc Natl Acad Sci USA VL - 105 UR - https://doi.org/10.1073/pnas.0803466105 DO - 10.1073/pnas.0803466105 ID - Lynch2008 ER - TY - JOUR AU - Thomas, C. AU - Nielsen, K. PY - 2005 DA - 2005// TI - Mechanisms of, and barriers to, horizontal gene transfer between bacteria JO - Nat Rev Microbiol VL - 3 UR - https://doi.org/10.1038/nrmicro1234 DO - 10.1038/nrmicro1234 ID - Thomas2005 ER - TY - JOUR AU - Ando, T. AU - Itakura, S. AU - Uchii, K. AU - Sobue, R. AU - Maeda, S. PY - 2009 DA - 2009// TI - Horizontal transfer of non-conjugative plasmid in colony biofilm of Escherichia coli on food-based media JO - World Journal of Microbiology & Biotechnology VL - 25 UR - https://doi.org/10.1007/s11274-009-0070-y DO - 10.1007/s11274-009-0070-y ID - Ando2009 ER - TY - JOUR AU - Baur, B. AU - Hanselmann, K. AU - Schlimme, W. AU - Jenni, B. PY - 1996 DA - 1996// TI - Genetic transformation in freshwater: Escherichia coli is able to develop natural competence JO - Appl Environ Microbiol VL - 62 ID - Baur1996 ER - TY - JOUR AU - Jiang, S. C. AU - Paul, J. H. PY - 1998 DA - 1998// TI - Gene transfer by transduction in the marine environment JO - Appl Environ Microbiol VL - 64 ID - Jiang1998 ER - TY - JOUR AU - McDaniel, L. AU - Young, E. AU - Delaney, J. AU - Ruhnau, F. AU - Ritchie, K. AU - Paul, J. PY - 2010 DA - 2010// TI - High frequency of horizontal gene transfer in the oceans JO - Nature VL - 330 ID - McDaniel2010 ER - TY - JOUR AU - Kashtan, N. AU - Noor, E. AU - Alon, U. PY - 2007 DA - 2007// TI - Varying environments can speed up evolution JO - Proc Natl Acad Sci USA VL - 104 UR - https://doi.org/10.1073/pnas.0611630104 DO - 10.1073/pnas.0611630104 ID - Kashtan2007 ER - TY - JOUR AU - Parter, M. AU - Kashtan, N. AU - Alon, U. PY - 2008 DA - 2008// TI - Facilitated variation: how evolution learns from past environments to generalize to new environments JO - PloS Comput Biol VL - 4 UR - https://doi.org/10.1371/journal.pcbi.1000206 DO - 10.1371/journal.pcbi.1000206 ID - Parter2008 ER - TY - JOUR AU - Park, S. C. AU - Simon, D. AU - Krug, J. PY - 2010 DA - 2010// TI - The speed of evolution in large asexual populations JO - J Stat Phys VL - 138 UR - https://doi.org/10.1007/s10955-009-9915-x DO - 10.1007/s10955-009-9915-x ID - Park2010 ER - TY - JOUR AU - Gerrish, P. J. AU - Lenski, R. E. PY - 1998 DA - 1998// TI - The fate of competing beneficial mutations in an asexual population JO - Genetica VL - 102-3 UR - https://doi.org/10.1023/A:1017067816551 DO - 10.1023/A:1017067816551 ID - Gerrish1998 ER - TY - JOUR AU - Eigen, M. PY - 1971 DA - 1971// TI - Selforganization of matter and the evolution of biological macromolecules JO - Naturwissenschaften VL - 58 ID - Eigen1971 ER - TY - JOUR AU - Elena, S. F. AU - Ekunwe, L. AU - Hajela, N. AU - Oden, S. A. AU - Lenski, R. E. PY - 1998 DA - 1998// TI - Distribution of fitness effects caused by random insertion mutations in Escherichia coli JO - Genetica VL - 102-3 UR - https://doi.org/10.1023/A:1017031008316 DO - 10.1023/A:1017031008316 ID - Elena1998 ER - TY - JOUR AU - Kibota, T. T. AU - Lynch, M. PY - 1996 DA - 1996// TI - Estimate of the genomic mutation rate deleterious to overall fitness in E-coli JO - Nature VL - 381 UR - https://doi.org/10.1038/381694a0 DO - 10.1038/381694a0 ID - Kibota1996 ER - TY - JOUR AU - Domingo-Calap, P. AU - Cuevas, J. M. AU - Sanjuan, R. PY - 2009 DA - 2009// TI - The fitness effects of random mutations in single-stranded DNA and RNA bacteriophages JO - PloS Genet VL - 5 UR - https://doi.org/10.1371/journal.pgen.1000742 DO - 10.1371/journal.pgen.1000742 ID - Domingo-Calap2009 ER - TY - JOUR AU - Peris, J. B. AU - Davis, P. AU - Cuevas, J. M. AU - Nebot, M. R. AU - Sanjuan, R. PY - 2010 DA - 2010// TI - Distribution of fitness effects caused by single-nucleotidesubstitutions in bacteriophage f1 JO - Genetics VL - 185 UR - https://doi.org/10.1534/genetics.110.115162 DO - 10.1534/genetics.110.115162 ID - Peris2010 ER - TY - JOUR AU - Sanjuan, R. AU - Moya, A. AU - Elena, S. F. PY - 2004 DA - 2004// TI - The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus JO - Proc Natl Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.0400146101 DO - 10.1073/pnas.0400146101 ID - Sanjuan2004 ER - TY - JOUR AU - Sanjuan, R. PY - 2010 DA - 2010// TI - Mutational fitness effects in RNA and single-stranded DNA viruses: common patterns revealed by site-directed mutagenesis studies JO - Philos Trans R Soc Lond B Biol Sci VL - 365 UR - https://doi.org/10.1098/rstb.2010.0063 DO - 10.1098/rstb.2010.0063 ID - Sanjuan2010 ER - TY - JOUR AU - Lind, P. A. AU - Berg, O. G. AU - Andersson, D. I. PY - 2010 DA - 2010// TI - Mutational robustness of ribosomal protein genes JO - Science VL - 330 UR - https://doi.org/10.1126/science.1194617 DO - 10.1126/science.1194617 ID - Lind2010 ER - TY - JOUR AU - Eyre-Walker, A. AU - Keightley, P. D. PY - 2007 DA - 2007// TI - The distribution of fitness effects of new mutations JO - Nat Rev Genet VL - 8 UR - https://doi.org/10.1038/nrg2146 DO - 10.1038/nrg2146 ID - Eyre-Walker2007 ER - TY - JOUR AU - Eyre-Walker, A. AU - Keightley, P. D. AU - Smith, N. G. C. AU - Gaffney, D. PY - 2002 DA - 2002// TI - Quantifying the slightly deleterious mutation model of molecular evolution JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a004039 DO - 10.1093/oxfordjournals.molbev.a004039 ID - Eyre-Walker2002 ER - TY - JOUR AU - Kimura, M. PY - 1968 DA - 1968// TI - Evolutionary rate at molecular level JO - Nature VL - 217 UR - https://doi.org/10.1038/217624a0 DO - 10.1038/217624a0 ID - Kimura1968 ER - TY - JOUR AU - Welch, J. J. AU - Waxman, D. PY - 2003 DA - 2003// TI - Modularity and the cost of complexity JO - Evolution VL - 57 UR - https://doi.org/10.1111/j.0014-3820.2003.tb00581.x DO - 10.1111/j.0014-3820.2003.tb00581.x ID - Welch2003 ER - TY - JOUR AU - Martin, G. AU - Lenormand, T. PY - 2006 DA - 2006// TI - A general multivariate extension of Fisher's geometrical model and the distribution of mutation fitness effects across species JO - Evolution VL - 60 UR - https://doi.org/10.1111/j.0014-3820.2006.tb01169.x DO - 10.1111/j.0014-3820.2006.tb01169.x ID - Martin2006 ER - TY - JOUR AU - Orr, H. A. PY - 2005 DA - 2005// TI - Theories of adaptation: what they do and don't say JO - Genetica VL - 123 UR - https://doi.org/10.1007/s10709-004-2702-3 DO - 10.1007/s10709-004-2702-3 ID - Orr2005 ER - TY - JOUR AU - Orr, H. A. PY - 2003 DA - 2003// TI - The distribution of fitness effects among beneficial mutations JO - Genetics VL - 163 ID - Orr2003 ER - TY - JOUR AU - Cowperthwaite, M. C. AU - Bull, J. J. AU - Meyers, L. A. PY - 2005 DA - 2005// TI - Distiributions of beneficial fitness effects in RNA JO - Genetics VL - 170 UR - https://doi.org/10.1534/genetics.104.039248 DO - 10.1534/genetics.104.039248 ID - Cowperthwaite2005 ER -