TY - CHAP AU - Li, W. -. H. PY - 1997 DA - 1997// BT - Molecular Evolution PB - Sinauer Associates CY - Sunderland, MA. ID - Li1997 ER - TY - JOUR AU - Brosius, J. PY - 1991 DA - 1991// TI - Retroposons--seeds of evolution JO - Science (New York, NY) VL - 251 UR - https://doi.org/10.1126/science.1990437 DO - 10.1126/science.1990437 ID - Brosius1991 ER - TY - JOUR AU - Long, M. AU - Wang, W. AU - Zhang, J. PY - 1999 DA - 1999// TI - Origin of new genes and source for N-terminal domain of the chimerical gene, jingwei, in Drosophila JO - Gene VL - 238 UR - https://doi.org/10.1016/S0378-1119(99)00229-2 DO - 10.1016/S0378-1119(99)00229-2 ID - Long1999 ER - TY - JOUR AU - Long, M. AU - Langley, C. H. PY - 1993 DA - 1993// TI - Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila JO - Science (New York, NY) VL - 260 UR - https://doi.org/10.1126/science.7682012 DO - 10.1126/science.7682012 ID - Long1993 ER - TY - JOUR AU - Wang, W. AU - Brunet, F. G. AU - Nevo, E. AU - Long, M. PY - 2002 DA - 2002// TI - Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster JO - Proceedings of the National Academy of Sciences of the United States of America VL - 99 UR - https://doi.org/10.1073/pnas.072066399 DO - 10.1073/pnas.072066399 ID - Wang2002 ER - TY - JOUR AU - Damert, A. AU - Raiz, J. AU - Horn, A. V. AU - Lower, J. AU - Wang, H. AU - Xing, J. AU - Batzer, M. A. AU - Lower, R. AU - Schumann, G. G. PY - 2009 DA - 2009// TI - 5'-Transducing SVA retrotransposon groups spread efficiently throughout the human genome JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.093435.109 DO - 10.1101/gr.093435.109 ID - Damert2009 ER - TY - JOUR AU - Buzdin, A. AU - Gogvadze, E. AU - Kovalskaya, E. AU - Volchkov, P. AU - Ustyugova, S. AU - Illarionova, A. AU - Fushan, A. AU - Vinogradova, T. AU - Sverdlov, E. PY - 2003 DA - 2003// TI - The human genome contains many types of chimeric retrogenes generated through in vivo RNA recombination JO - Nucleic acids research VL - 31 UR - https://doi.org/10.1093/nar/gkg496 DO - 10.1093/nar/gkg496 ID - Buzdin2003 ER - TY - JOUR AU - Buzdin, A. AU - Ustyugova, S. AU - Gogvadze, E. AU - Vinogradova, T. AU - Lebedev, Y. AU - Sverdlov, E. PY - 2002 DA - 2002// TI - A new family of chimeric retrotranscripts formed by a full copy of U6 small nuclear RNA fused to the 3' terminus of l1 JO - Genomics VL - 80 UR - https://doi.org/10.1006/geno.2002.6843 DO - 10.1006/geno.2002.6843 ID - Buzdin2002 ER - TY - JOUR AU - Bantysh, O. B. AU - Buzdin, A. A. PY - 2009 DA - 2009// TI - Novel family of human transposable elements formed due to fusion of the first exon of gene MAST2 with retrotransposon SVA JO - Biochemistry VL - 74 ID - Bantysh2009 ER - TY - JOUR AU - Hancks, D. C. AU - Ewing, A. D. AU - Chen, J. E. AU - Tokunaga, K. AU - Kazazian, H. H. PY - 2009 DA - 2009// TI - Exon-trapping mediated by the human retrotransposon SVA JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.093153.109 DO - 10.1101/gr.093153.109 ID - Hancks2009 ER - TY - JOUR AU - Betran, E. AU - Thornton, K. AU - Long, M. PY - 2002 DA - 2002// TI - Retroposed new genes out of the × in Drosophila JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.6049 DO - 10.1101/gr.6049 ID - Betran2002 ER - TY - JOUR AU - Nisole, S. AU - Lynch, C. AU - Stoye, J. P. AU - Yap, M. W. PY - 2004 DA - 2004// TI - A Trim5-cyclophilin A fusion protein found in owl monkey kidney cells can restrict HIV-1 JO - Proceedings of the National Academy of Sciences of the United States of America VL - 101 UR - https://doi.org/10.1073/pnas.0404640101 DO - 10.1073/pnas.0404640101 ID - Nisole2004 ER - TY - JOUR AU - Zhang, J. AU - Dean, A. M. AU - Brunet, F. AU - Long, M. PY - 2004 DA - 2004// TI - Evolving protein functional diversity in new genes of Drosophila JO - Proceedings of the National Academy of Sciences of the United States of America VL - 101 UR - https://doi.org/10.1073/pnas.0407066101 DO - 10.1073/pnas.0407066101 ID - Zhang2004 ER - TY - JOUR AU - Long, M. AU - Betran, E. AU - Thornton, K. AU - Wang, W. PY - 2003 DA - 2003// TI - The origin of new genes: glimpses from the young and old JO - Nature reviews VL - 4 UR - https://doi.org/10.1038/nrg1204 DO - 10.1038/nrg1204 ID - Long2003 ER - TY - JOUR AU - Emerson, J. J. AU - Kaessmann, H. AU - Betran, E. AU - Long, M. PY - 2004 DA - 2004// TI - Extensive gene traffic on the mammalian × chromosome JO - Science (New York, NY) VL - 303 UR - https://doi.org/10.1126/science.1090042 DO - 10.1126/science.1090042 ID - Emerson2004 ER - TY - JOUR AU - Krasnov, A. N. AU - Kurshakova, M. M. AU - Ramensky, V. E. AU - Mardanov, P. V. AU - Nabirochkina, E. N. AU - Georgieva, S. G. PY - 2005 DA - 2005// TI - A retrocopy of a gene can functionally displace the source gene in evolution JO - Nucleic acids research VL - 33 UR - https://doi.org/10.1093/nar/gki969 DO - 10.1093/nar/gki969 ID - Krasnov2005 ER - TY - JOUR AU - Bai, Y. AU - Casola, C. AU - Feschotte, C. AU - Betran, E. PY - 2007 DA - 2007// TI - Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila JO - Genome biology VL - 8 UR - https://doi.org/10.1186/gb-2007-8-1-r11 DO - 10.1186/gb-2007-8-1-r11 ID - Bai2007 ER - TY - JOUR AU - Zhang, Y. AU - Wu, Y. AU - Liu, Y. AU - Han, B. PY - 2005 DA - 2005// TI - Computational identification of 69 retroposons in Arabidopsis JO - Plant physiology VL - 138 UR - https://doi.org/10.1104/pp.105.060244 DO - 10.1104/pp.105.060244 ID - Zhang2005 ER - TY - JOUR AU - Yu, Z. AU - Morais, D. AU - Ivanga, M. AU - Harrison, P. M. PY - 2007 DA - 2007// TI - Analysis of the role of retrotransposition in gene evolution in vertebrates JO - BMC bioinformatics VL - 8 UR - https://doi.org/10.1186/1471-2105-8-308 DO - 10.1186/1471-2105-8-308 ID - Yu2007 ER - TY - JOUR AU - Wang, W. AU - Zheng, H. AU - Fan, C. AU - Li, J. AU - Shi, J. AU - Cai, Z. AU - Zhang, G. AU - Liu, D. AU - Zhang, J. AU - Vang, S. PY - 2006 DA - 2006// TI - High rate of chimeric gene origination by retroposition in plant genomes JO - Plant Cell VL - 18 UR - https://doi.org/10.1105/tpc.106.041905 DO - 10.1105/tpc.106.041905 ID - Wang2006 ER - TY - JOUR AU - Bellingham, J. AU - Tarttelin, E. E. AU - Foster, R. G. AU - Wells, D. J. PY - 2003 DA - 2003// TI - Structure and evolution of the teleost extraretinal rod-like opsin (errlo) and ocular rod opsin (rho) genes: is teleost rho a retrogene? JO - Journal of experimental zoology Part B VL - 297 UR - https://doi.org/10.1002/jez.b.18 DO - 10.1002/jez.b.18 ID - Bellingham2003 ER - TY - JOUR AU - Esnault, C. AU - Maestre, J. AU - Heidmann, T. PY - 2000 DA - 2000// TI - Human LINE retrotransposons generate processed pseudogenes JO - Nature genetics VL - 24 UR - https://doi.org/10.1038/74184 DO - 10.1038/74184 ID - Esnault2000 ER - TY - JOUR AU - Furano, A. V. PY - 2000 DA - 2000// TI - The biological properties and evolutionary dynamics of mammalian LINE-1 retrotransposons JO - Progress in nucleic acid research and molecular biology VL - 64 UR - https://doi.org/10.1016/S0079-6603(00)64007-2 DO - 10.1016/S0079-6603(00)64007-2 ID - Furano2000 ER - TY - JOUR AU - Furano, A. V. AU - Duvernell, D. D. AU - Boissinot, S. PY - 2004 DA - 2004// TI - L1 (LINE-1) retrotransposon diversity differs dramatically between mammals and fish JO - Trends Genet VL - 20 UR - https://doi.org/10.1016/j.tig.2003.11.006 DO - 10.1016/j.tig.2003.11.006 ID - Furano2004 ER - TY - JOUR AU - Volff, J. N. AU - Bouneau, L. AU - Ozouf-Costaz, C. AU - Fischer, C. PY - 2003 DA - 2003// TI - Diversity of retrotransposable elements in compact pufferfish genomes JO - Trends Genet VL - 19 UR - https://doi.org/10.1016/j.tig.2003.10.006 DO - 10.1016/j.tig.2003.10.006 ID - Volff2003 ER - TY - JOUR AU - Betran, E. AU - Long, M. PY - 2003 DA - 2003// TI - Dntf-2r, a young Drosophila retroposed gene with specific male expression under positive Darwinian selection JO - Genetics VL - 164 ID - Betran2003 ER - TY - JOUR AU - Betran, E. AU - Wang, W. AU - Jin, L. AU - Long, M. PY - 2002 DA - 2002// TI - Evolution of the phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene JO - Molecular biology and evolution VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a004124 DO - 10.1093/oxfordjournals.molbev.a004124 ID - Betran2002 ER - TY - JOUR AU - Burki, F. AU - Kaessmann, H. PY - 2004 DA - 2004// TI - Birth and adaptive evolution of a hominoid gene that supports high neurotransmitter flux JO - Nature genetics VL - 36 UR - https://doi.org/10.1038/ng1431 DO - 10.1038/ng1431 ID - Burki2004 ER - TY - JOUR AU - Marques, A. C. AU - Dupanloup, I. AU - Vinckenbosch, N. AU - Reymond, A. AU - Kaessmann, H. PY - 2005 DA - 2005// TI - Emergence of young human genes after a burst of retroposition in primates JO - PLoS biology VL - 3 UR - https://doi.org/10.1371/journal.pbio.0030357 DO - 10.1371/journal.pbio.0030357 ID - Marques2005 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 research VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 ER - TY - JOUR AU - Birney, E. AU - Clamp, M. AU - Durbin, R. PY - 2004 DA - 2004// TI - GeneWise and Genomewise JO - Genome research VL - 14 UR - https://doi.org/10.1101/gr.1865504 DO - 10.1101/gr.1865504 ID - Birney2004 ER - TY - JOUR AU - Pearson, W. R. PY - 1990 DA - 1990// TI - Rapid and sensitive sequence comparison with FASTP and FASTA JO - Methods in enzymology VL - 183 UR - https://doi.org/10.1016/0076-6879(90)83007-V DO - 10.1016/0076-6879(90)83007-V ID - Pearson1990 ER - TY - JOUR AU - Yeo, G. AU - Hoon, S. AU - Venkatesh, B. AU - Burge, C. B. PY - 2004 DA - 2004// TI - Variation in sequence and organization of splicing regulatory elements in vertebrate genes JO - Proceedings of the National Academy of Sciences of the United States of America VL - 101 UR - https://doi.org/10.1073/pnas.0404901101 DO - 10.1073/pnas.0404901101 ID - Yeo2004 ER - TY - JOUR AU - Kruiswijk, C. P. AU - Hermsen, T. T. AU - Westphal, A. H. AU - Savelkoul, H. F. AU - Stet, R. J. PY - 2002 DA - 2002// TI - A novel functional class I lineage in zebrafish (Danio rerio), carp (Cyprinus carpio), and large barbus (Barbus intermedius) showing an unusual conservation of the peptide binding domains JO - J Immunol VL - 169 UR - https://doi.org/10.4049/jimmunol.169.4.1936 DO - 10.4049/jimmunol.169.4.1936 ID - Kruiswijk2002 ER - TY - JOUR AU - Pan, D. AU - Zhang, L. PY - 2009 DA - 2009// TI - Burst of young retrogenes and independent retrogene formation in mammals JO - PloS one VL - 4 UR - https://doi.org/10.1371/journal.pone.0005040 DO - 10.1371/journal.pone.0005040 ID - Pan2009 ER - TY - JOUR AU - Reinartz, J. AU - Bruyns, E. AU - Lin, J. Z. AU - Burcham, T. AU - Brenner, S. AU - Bowen, B. AU - Kramer, M. AU - Woychik, R. PY - 2002 DA - 2002// TI - Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms JO - Briefings in functional genomics & proteomics VL - 1 UR - https://doi.org/10.1093/bfgp/1.1.95 DO - 10.1093/bfgp/1.1.95 ID - Reinartz2002 ER - TY - JOUR AU - Harbers, M. AU - Carninci, P. PY - 2005 DA - 2005// TI - Tag-based approaches for transcriptome research and genome annotation JO - Nature methods VL - 2 UR - https://doi.org/10.1038/nmeth768 DO - 10.1038/nmeth768 ID - Harbers2005 ER - TY - JOUR AU - Vinckenbosch, N. AU - Dupanloup, I. AU - Kaessmann, H. PY - 2006 DA - 2006// TI - Evolutionary fate of retroposed gene copies in the human genome JO - Proceedings of the National Academy of Sciences of the United States of America VL - 103 UR - https://doi.org/10.1073/pnas.0511307103 DO - 10.1073/pnas.0511307103 ID - Vinckenbosch2006 ER - TY - JOUR AU - Harrison, P. M. AU - Zheng, D. AU - Zhang, Z. AU - Carriero, N. AU - Gerstein, M. PY - 2005 DA - 2005// TI - Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability JO - Nucleic acids research VL - 33 UR - https://doi.org/10.1093/nar/gki531 DO - 10.1093/nar/gki531 ID - Harrison2005 ER - TY - JOUR AU - Wang, W. AU - Yu, H. AU - Long, M. PY - 2004 DA - 2004// TI - Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species JO - Nature genetics VL - 36 UR - https://doi.org/10.1038/ng1338 DO - 10.1038/ng1338 ID - Wang2004 ER - TY - JOUR AU - Zhu, Z. AU - Zhang, Y. AU - Long, M. PY - 2009 DA - 2009// TI - Extensive structural renovation of retrogenes in the evolution of the Populus genome JO - Plant physiology VL - 151 UR - https://doi.org/10.1104/pp.109.142984 DO - 10.1104/pp.109.142984 ID - Zhu2009 ER - TY - JOUR AU - Torrents, D. AU - Suyama, M. AU - Zdobnov, E. AU - Bork, P. PY - 2003 DA - 2003// TI - A genome-wide survey of human pseudogenes JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1455503 DO - 10.1101/gr.1455503 ID - Torrents2003 ER - TY - JOUR AU - Nekrutenko, A. AU - Makova, K. D. AU - Li, W. H. PY - 2002 DA - 2002// TI - The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.200901 DO - 10.1101/gr.200901 ID - Nekrutenko2002 ER - TY - JOUR AU - Moore, R. C. AU - Purugganan, M. D. PY - 2003 DA - 2003// TI - The early stages of duplicate gene evolution JO - Proceedings of the National Academy of Sciences of the United States of America VL - 100 UR - https://doi.org/10.1073/pnas.2535513100 DO - 10.1073/pnas.2535513100 ID - Moore2003 ER - TY - JOUR AU - Kazazian, H. H. PY - 2004 DA - 2004// TI - Mobile elements: drivers of genome evolution JO - Science (New York, NY) VL - 303 UR - https://doi.org/10.1126/science.1089670 DO - 10.1126/science.1089670 ID - Kazazian2004 ER - TY - JOUR AU - Sayah, D. M. AU - Sokolskaja, E. AU - Berthoux, L. AU - Luban, J. PY - 2004 DA - 2004// TI - Cyclophilin A retrotransposition into TRIM5 explains owl monkey resistance to HIV-1 JO - Nature VL - 430 UR - https://doi.org/10.1038/nature02777 DO - 10.1038/nature02777 ID - Sayah2004 ER - TY - JOUR AU - Brosius, J. AU - Gould, S. J. PY - 1992 DA - 1992// TI - On "genomenclature": a comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA" JO - Proceedings of the National Academy of Sciences of the United States of America VL - 89 UR - https://doi.org/10.1073/pnas.89.22.10706 DO - 10.1073/pnas.89.22.10706 ID - Brosius1992 ER - TY - JOUR AU - Brosius, J. PY - 1999 DA - 1999// TI - Many G-protein-coupled receptors are encoded by retrogenes JO - Trends Genet VL - 15 UR - https://doi.org/10.1016/S0168-9525(99)01783-7 DO - 10.1016/S0168-9525(99)01783-7 ID - Brosius1999 ER - TY - CHAP AU - Robinson, R. PY - 2005 DA - 2005// TI - Retrocopied Genes May Enhance Male Fitness BT - PLoS biology ID - Robinson2005 ER - TY - JOUR AU - Baertsch, R. AU - Diekhans, M. AU - Kent, W. J. AU - Haussler, D. AU - Brosius, J. PY - 2008 DA - 2008// TI - Retrocopy contributions to the evolution of the human genome JO - BMC genomics VL - 9 UR - https://doi.org/10.1186/1471-2164-9-466 DO - 10.1186/1471-2164-9-466 ID - Baertsch2008 ER - TY - JOUR AU - Ravi, V. AU - Venkatesh, B. PY - 2008 DA - 2008// TI - Rapidly evolving fish genomes and teleost diversity JO - Current opinion in genetics & development VL - 18 UR - https://doi.org/10.1016/j.gde.2008.11.001 DO - 10.1016/j.gde.2008.11.001 ID - Ravi2008 ER - TY - JOUR AU - Jaillon, O. AU - Aury, J. M. AU - Brunet, F. AU - Petit, J. L. AU - Stange-Thomann, N. AU - Mauceli, E. AU - Bouneau, L. AU - Fischer, C. AU - Ozouf-Costaz, C. AU - Bernot, A. PY - 2004 DA - 2004// TI - Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype JO - Nature VL - 431 UR - https://doi.org/10.1038/nature03025 DO - 10.1038/nature03025 ID - Jaillon2004 ER - TY - JOUR AU - Patthy, L. PY - 1999 DA - 1999// TI - Genome evolution and the evolution of exon-shuffling--a review JO - Gene VL - 238 UR - https://doi.org/10.1016/S0378-1119(99)00228-0 DO - 10.1016/S0378-1119(99)00228-0 ID - Patthy1999 ER - TY - JOUR AU - Long, M. AU - Deutsch, M. AU - Wang, W. AU - Betran, E. AU - Brunet, F. G. AU - Zhang, J. PY - 2003 DA - 2003// TI - Origin of new genes: evidence from experimental and computational analyses JO - Genetica VL - 118 UR - https://doi.org/10.1023/A:1024153609285 DO - 10.1023/A:1024153609285 ID - Long2003 ER - TY - JOUR AU - Podlaha, O. AU - Zhang, J. PY - 2004 DA - 2004// TI - Nonneutral evolution of the transcribed pseudogene Makorin1-p1 in mice JO - Molecular biology and evolution VL - 21 UR - https://doi.org/10.1093/molbev/msh230 DO - 10.1093/molbev/msh230 ID - Podlaha2004 ER - TY - JOUR AU - Hirotsune, S. AU - Yoshida, N. AU - Chen, A. AU - Garrett, L. AU - Sugiyama, F. AU - Takahashi, S. AU - Yagami, K. AU - Wynshaw-Boris, A. AU - Yoshiki, A. PY - 2003 DA - 2003// TI - An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene JO - Nature VL - 423 UR - https://doi.org/10.1038/nature01535 DO - 10.1038/nature01535 ID - Hirotsune2003 ER - TY - JOUR AU - Li, W. H. PY - 1993 DA - 1993// TI - Unbiased estimation of the rates of synonymous and nonsynonymous substitution JO - Journal of molecular evolution VL - 36 UR - https://doi.org/10.1007/BF02407308 DO - 10.1007/BF02407308 ID - Li1993 ER - TY - JOUR AU - Kent, W. J. PY - 2002 DA - 2002// TI - BLAT--the BLAST-like alignment tool JO - Genome research VL - 12 UR - https://doi.org/10.1101/gr.229202. Article published online before March 2002 DO - 10.1101/gr.229202. Article published online before March 2002 ID - Kent2002 ER -