Selection in the evolution of gene duplications
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* Corresponding author: Fyodor A Kondrashov fkondras@ncbi.nlm.nih.gov
Genome Biology 2002, 3:research0008-research0008.9 doi:10.1186/gb-2002-3-2-research0008
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Guy Naamati, Menachem Fromer, Michal Linial BMC Genomics 2009, 10:593 (10 December 2009) |
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Does negative auto-regulation increase gene duplicability? Tobias Warnecke, Guang-Zhong Wang, Martin J Lercher, Laurence D Hurst BMC Evolutionary Biology 2009, 9:193 (7 August 2009) |
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Phylogeny and evolution of Rab7 and Rab9 proteins Paweł Mackiewicz, Elżbieta Wyroba BMC Evolutionary Biology 2009, 9:101 (14 May 2009) |
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Cinzia Di Pietro, Marco Ragusa, Davide Barbagallo, Laura R Duro, Maria R Guglielmino, Alessandra Majorana, Rosario Angelica, Marina Scalia, Luisa Statello, Loredana Salito, Luisa Tomasello, Salvo Pernagallo, Salvo Valenti, Vito D'Agostino, Patrizio Triberio, Igor Tandurella, Giuseppe A Palumbo, Piera La Cava, Viviana Cafiso, Taschia Bertuccio, Maria Santagati, Giovanni Li Destri, Salvatore Lanzafame, Francesco Di Raimondo, Stefania Stefani, Bud Mishra, Michele Purrello BMC Medical Genomics 2009, 2:20 (30 April 2009) |
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Emergence, development and diversification of the TGF-β signalling pathway within the animal kingdom Lukasz Huminiecki, Leon Goldovsky, Shiri Freilich, Aristidis Moustakas, Christos Ouzounis, Carl-Henrik Heldin BMC Evolutionary Biology 2009, 9:28 (3 February 2009) |
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Syntenator: Multiple gene order alignments with a gene-specific scoring function Christian Rödelsperger, Christoph Dieterich Algorithms for Molecular Biology 2008, 3:14 (6 November 2008) |
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Unique genes in plants: specificities and conserved features throughout evolution David Armisén, Alain Lecharny, Sébastien Aubourg BMC Evolutionary Biology 2008, 8:280 (10 October 2008) |
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Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids Claudia Münch, Stefan Kirsch, António MG Fernandes, Werner Schempp BMC Evolutionary Biology 2008, 8:269 (2 October 2008) |
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Commentary
MalVac: Database of malarial vaccine candidates Rupanjali Chaudhuri, Shakil Ahmed, Faraz Ansari, Harinder Singh, Srinivasan Ramachandran Malaria Journal 2008, 7:184 (23 September 2008) A web server has been developed to facilitate the identification of probable vaccine candidates: it can be freely accessed.
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Tomàs Marques-Bonet, Ze Cheng, Xinwei She, Evan E Eichler, Arcadi Navarro BMC Genomics 2008, 9:384 (12 August 2008) |
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Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization Frédéric JJ Chain, Dora Ilieva, Ben J Evans BMC Evolutionary Biology 2008, 8:43 (8 February 2008) In frog species that have undergone allopolyploidization, gene expression levels of duplicate genes often diverge quickly in spite of strong initial purifying selection, giving insight in to the evolutionary mechanisms that occur after genome duplication in vertebrates.
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Research article
Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene Maayan Amit, Noa Sela, Hadas Keren, Ze'ev Melamed, Inna Muler, Noam Shomron, Shai Izraeli, Gil Ast BMC Molecular Biology 2007, 8:109 (29 November 2007) Exonization of transposed elements is higher within duplicated genes, implying that duplicates of the transcription initiation factor gene TIF-1A, for example, are free from the evolutionary constraints on single-copy genes.
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Research article
Persistence of duplicated PAC1 receptors in the teleost, Sparus auratus João CR Cardoso, Edwin CJM de Vet, Bruno Louro, Greg Elgar, Melody S Clark, Deborah M Power BMC Evolutionary Biology 2007, 7:221 (12 November 2007) |
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Research
All duplicates are not equal: the difference between small-scale and genome duplication Luke Hakes, John W Pinney, Simon C Lovell, Stephen G Oliver, David L Robertson Genome Biology 2007, 8:R209 (4 October 2007) The comparison of pairs of gene duplications generated by small-scale duplications with those created by large-scale duplications shows that they differ in quantifiable ways. It is suggested that this is directly due to biases on the paths to gene retention rather than association with different functional categories. |
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Research article
Yoshihiro Kawahara, Tadashi Imanishi BMC Evolutionary Biology 2007, 7:9 (29 January 2007) |
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Research
Shiri Freilich, Tim Massingham, Eric Blanc, Leon Goldovsky, Janet M Thornton Genome Biology 2006, 7:R89 (9 October 2006) An analysis of the relationship between duplication events, the time they took place and the expression breadth of the duplicated genes supports the subfunctionalization model, in which expression divergence following gene duplication promotes the retention of a gene in multicellular species. |
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Research
Julia Tischler, Ben Lehner, Nansheng Chen, Andrew G Fraser Genome Biology 2006, 7:R69 (2 August 2006) High-throughput combinatorial RNAi demonstrates that many duplicated genes in |
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Research article
Fast rate of evolution in alternatively spliced coding regions of mammalian genes Ekaterina O Ermakova, Ramil N Nurtdinov, Mikhail S Gelfand BMC Genomics 2006, 7:84 (18 April 2006) A comparison of orthologous human and mouse genes indicates that alternatively spliced exons tend to have a faster rate of evolution than constitutive exons, with the rate of both synonymous and nonsynonymous substitutions increased.
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Research
Tineke Casneuf, Stefanie De Bodt, Jeroen Raes, Steven Maere, Yves Van de Peer Genome Biology 2006, 7:R13 (20 February 2006) Analysis of expression data of duplicated genes in |
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Research article
Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network Wen-Yu Chung, Reka Albert, Istvan Albert, Anton Nekrutenko, Kateryna D Makova BMC Bioinformatics 2006, 7:46 (27 January 2006) When genes duplicate, they quickly diverge, losing shared coexpressed partners and acquiring different new partners according to a human coexpression network analysis that utilized tissue-specific microarray data.
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Research article
Duplicated genes evolve slower than singletons despite the initial rate increase I King Jordan, Yuri I Wolf, Eugene V Koonin BMC Evolutionary Biology 2004, 4:22 (6 July 2004) Following gene duplication there is a period of rapid evolution, which then slows down in cases where the original gene has an important biological function and the duplicate is retained.
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Software
FRAGS: estimation of coding sequence substitution rates from fragmentary data Estienne C Swart, Winston A Hide, Cathal Seoighe BMC Bioinformatics 2004, 5:8 (29 January 2004) |
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Research
Different evolutionary patterns between young duplicate genes in the human genome Peng Zhang, Zhenglong Gu, Wen-Hsiung Li Genome Biology 2003, 4:R56 (1 September 2003) Duplicate genes tend to evolve in different patterns following the duplication event. One copy evolves faster than the other and accumulates amino-acid substitutions evenly across the sequence, whereas the other copy evolves more slowly and accumulates amino-acid substitutions unevenly across the sequence. |
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Research
Duplication is more common among laterally transferred genes than among indigenous genes Sean D Hooper, Otto G Berg Genome Biology 2003, 4:R48 (11 July 2003) Using both a compositional method and a gene-tree approach, a number of proposed laterally transferred genes have been identified and their nucleotide composition and frequency of duplication studied. |
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Research
Recent segmental and gene duplications in the mouse genome Joseph Cheung, Michael D Wilson, Junjun Zhang, Razi Khaja, Jeffrey R MacDonald, Henry HQ Heng, Ben F Koop, Stephen W Scherer Genome Biology 2003, 4:R47 (9 July 2003) BLAST-based computational heuristics were used to identify large and recent segmental duplications in the mouse genome sequence. Here a database of recently duplicated regions of the mouse genome is presented. |
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Minireview
Tracking adaptive evolutionary events in genomic sequences David A Liberles, Marta L Wayne Genome Biology 2002, 3:reviews1018-reviews1018.4 (29 May 2002) |
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Minireview
Selection and gene duplication: a view from the genome Andreas Wagner Genome Biology 2002, 3:reviews1012-reviews1012.3 (15 April 2002) |