Bibliography on gene and genome duplication (2004)

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  1. C Alkan, EE Eichler, JA Bailey, SC Sahinalp, E Tuzun (2004), "The role of unequal crossover in alpha-satellite DNA evolution: a computational analysis", Journal of Computational Biology, 11(5):933-944.

  2. Angel Amores, Tohru Suzuki, Yi-Lin Yan, Jordan Pomeroy, Amy Singer, Chris Amemiya, John H. Postlethwait (2004), "Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish", Genome Research, 14:1-10.
    [abstract]

  3. Alex A Andalis, Zuzana Storchova, Cora Styles, Timothy Galitski, David Pellman, Gerald R Fink (2004), "Defects arising from whole-genome duplications in Saccharomyces cerevisiae", Genetics, 167:1109-1121.
    [PDF]

  4. Lars Arvestad, Ann-Charlotte Berglund, Jens Lagergren and Bengt Sennblad (2004), "Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution", Proceedings of the Eighth International Conference on Research in Computational Molecular Biology , pp.?-?

  5. Jeffrey A. Bailey, Deanna M. Church, Mario Ventura, Mariano Rocchi, and Evan E. Eichler (2004), "Analysis of segmental duplications and genome assembly in the mouse", Genome Research, 14:789-801.

  6. MJ Behe, DW Snoke (2004), "Simulating evolution by gene duplication of protein features that require multiple amino acid residues", Protein Science, 13(10):2651-2664.

  7. G Blanc, KH Wolfe (2004), "Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes", Plant Cell, 16:1667-1678.

  8. Katherine S Caldwell, Jan Dvorak, Evans S Lagudah, Eduard Akhunov, Ming-Cheng Luo, Petra Wolters, Wayne Powell (2004), "Sequence polymorphism in polyploid wheat and their D-genome diploid ancestor", Genetics, 167:941-947.
    [abstract]

  9. Cristian I Castillo-Davis, Daniel L Hartl, Guillaume Achaz (2004), "cis-regulatory and protein evolution in orthologous and duplicate genes", Genome Research, 14:1530-1536.
    [abstract]

  10. Brad A Chapman, John E Bowers, Stefan R Schulze, Andrew H Paterson (2004), "A comparative phylogenetic approach for dating whole genome duplication events", Bioinformatics, 20(2):180-185.
    [ abstract] [PDF]

  11. Daniel C Chen, Janna Saarela, Royden A Clark, Timo Miettinen, Anthony Chi, Evan E Eichler, Leena Peltonen, Aarno Palotie (2004), "Segmental duplications flank the multiple sclerosis locus on chromosome 17q", Genome Research, 14:1483-1492.

  12. A Christoffels, EG Koh, JM Chia, S Brenner, S Aparicio, B Venkatesh (2004), "Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes", Molecular Biology and Evolution, 21:1146-1151.

  13. GC Conant, A Wagner (2004), "Duplicate genes and robustness to transient gene knockouts in Caenorhabditis elegans", Proceedings of the Royal Society of London. Series B. Biological Sciences, 271:89-96.

  14. Etienne Danchin (2004), Reconstruction of Ancestral Genomic Regions by Comparative Analysis of Evolutionary Conserved Syntenies. Towards Reconstructing the Genome of the Ancestor of All Bilaterian Species (Urbilateria) , Ph.D Thesis, Universite de la Mediterranee, Aix-Marseille II.
    [PDF]

  15. EGJ Danchin, P Pontarotti (2004), "Towards the reconstruction of the bilaterian ancestral pre-MHC region", Trends in Genetics, 20(12):587-591.
    [ abstract]

  16. Renato D'Ovidio, Alessandro Raiola, Cristina Capodicasa, Alessandra Devoto, Daniela Pontiggia, Serena Roberti, Roberta Galletti, Eric Conti, Donal O'Sullivan, Giulia De Lorenzo (2004), "Characterization of the complex locus of bean encoding polygalacturonase-inhibiting proteins reveals subfunctionalization for defense against fungi and insects", Plant Physiology Preview, 135:2424-2435.
    [abstract]

  17. Bernard Dujon, et al. (2004), "Genome evolution in yeasts", Nature, 430:35-44.
    [PDF]

  18. David Fredman, Stefan J White, Susanna Potter, Evan E Eichler, Johan T Den Dunnen, Anthony J Brookes (2004), "Complex SNP-related sequence variation in segmental genome duplications", Nature Genetics, 36(8):861-866.

  19. Dirk Gevers, Klaas Vandepoele, Cedric Similion, Yves van de Peer (2004), "Gene duplication and biased functional retention of paralogs in bacterial genomes", Trends in Microbiology, 12(4):148-154.
    [PDF]

  20. Pawel Gorecki (2004), "Reconciliation problems for duplication, loss and horizontal gene transfer", Proceedings of the Eighth International Conference on Research in Computational Molecular Biology , pp.?-?

  21. Z Gu, SA Rifkin, KP White, WH Li (2004), "Duplicate genes increase expression diversity within and between species", Nature Genetics, 36:577-579.
    [PDF]

  22. R Guyot, B Keller (2004), "Ancestral genome duplication in rice", Genome Research, 47:610-614.

  23. M. Hallett, J. Lagergren, A. Tofigh (2004), "Simultaneous identification of duplications and lateral transfers", Proceedings of the Eighth International Conference on Research in Computational Molecular Biology , pp.?-?

  24. Brian J. Haas, Arthur L. Delcher, Jennifer R. Wortman, and Steven L. Salzberg (2004), "DAGchainer: a tool for mining segmental genome duplications and synteny", Bioinformatics, 20:3643-3646.

  25. S Hoegg, H Brinkmann, JS Taylor, A Meyer (2004), "Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish", Journal of Molecular Evolution, 59:190-203.

  26. Peter WH Holland (2004), " More genes in vertebrates?", Journal of Structural and Functional Genomics, 3:75-84.
    [ abstract]

  27. Austin L Hughes (2005), "Gene duplication and the origin of novel proteins", Proceedings of the National Academy of Sciences, 102:8791-8792.

  28. Lukasz Huminiecki and Kenneth H. Wolfe (2004), "Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse", Genome Research, 14:1870-1879.

  29. M Hurles (2004), "Gene duplication: the genomic trade in spare parts", PLoS Biology, 2:e206.

  30. AJ Iafrate, L Feuk, MN Rivera, ML Listewnik, PK Donahoe, Y Qi, SW Scherer, C Lee (2004), "Detection of large-scale variation in the human genome", Nature Genetics, 36(9):949-951.

  31. O Jaillon, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, Segurens B, Dasilva C, Salanoubat M, Levy M, Boudet N, Castellano S, Anthouard V, Jubin C, Castelli V, Katinka M, Vacherie B, Biemont C, Skalli Z, Cattolico L, Poulain J, De Berardinis V, Cruaud C, Duprat S, Brottier P, Coutanceau JP, Gouzy J, Parra G, Lardier G, Chapple C, McKernan KJ, McEwan P, Bosak S, Kellis M, Volff JN, Guigo R, Zody MC, Mesirov J, Lindblad-Toh K, Birren B, Nusbaum C, Kahn D, Robinson-Rechavi M, Laudet V, Schachter V, Quetier F, Saurin W, Scarpelli C, Wincker P, Lander ES, Weissenbach J, Roest Crollius H (2004), "Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype", Nature, 431(7011):946-957.

  32. M Kasahara, T Suzuki, LD Pasquier (2004), "On the origins of the adaptive immune system: novel insights from invertebrates and cold-blooded vertebrates", Trends in Immunology, 25(2):105-111.

  33. I King Jordan,Yuri I Wolf,Eugene V Koonin (2004), "Duplicated genes evolve slower than singletons despite the initial rate increase", BMC Evolutionary Biology, 4:22.
    [abstract]

  34. M Kellis, BW Birren, ES Lander (2004), "Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae", Nature, 428:617-624.

  35. H Kitano (2004), "Biological robustness", Nature Reviews Genetics, 5(11):826-837.

  36. Eugene V Koonin, Natalie D Fedorova, John D Jackson, Aviva R Jacobs, Dmitri M Krylov, Kira S Makarova, Raja Mazumder, Sergei L Mekhedov, Anastasia N Nikolskaya, B Sridhar Rao, Igor B Rogozin, Sergei Smirnov, Alexander V Sorokin, Alexander V Sverdlov, Sona Vasudevan, Yuri I Wolf, Jodie J Yin and Darren A Natale (2004), "A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes", Genome Biology, 5:R6.
    [abstract]

  37. Elena M Kramer, M Alejandra Jaramillo, Verónica S Di Stilio (2004), "Patterns of gene duplication and functional evolution during the diversification of the AGAMOUS subfamily of MADS box genes in angiosperms", Genetics, 166:1011-1023.
    [abstract]

  38. Kiyoshi Naruse, Minoru Tanaka, Kazuei Mita, Akihiro Shima, John Postlethwait, Hiroshi Mitani (2004), "A Medaka gene map: the trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping", Genome Research, 14:820-828.
    [abstract]

  39. AH Paterson, JE Bowers, BA Chapman (2004), "Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics", Proceedings of National Academy of Sciences, 101:9903-9908.

  40. David Sankoff, Phil Trinh (2004), "Chromosomal breakpoint re-use in the inference of genome sequence rearrangement", Proceedings of the Eighth International Conference on Research in Computational Molecular Biology , pp.?-?

  41. Joseph Schacherer, Yves Tourrette, Jean-Luc Souciet, Serge Potier, and Jacky de Montigny (2004), "Recovery of a function involving gene duplication by retroposition in Saccharomyces cerevisiae", Genome Research, 14:1291-1297.

  42. Jonathan Sebat, B Lakshmi, Jennifer Troge, Joan Alexander, Janet Young, Pär Lundin, Susanne Mĺnér, Hillary Massa, Megan Walker, Maoyen Chi, Nicholas Navin, Robert Lucito, John Healy, James Hicks, Kenny Ye, Andrew Reiner, T Conrad Gilliam, Barbara Trask, Nick Patterson, Anders Zetterberg, Michael Wigler (2004), "Large-scale copy number polymorphism in the human genome" Science, 305(5683):525-528.
    [abstract]
    abstract: The extent to which large duplications and deletions contribute to human genetic variation and diversity is unknown. Here, we show that large-scale copy number polymorphisms (CNPs) (about 100 kilobases and greater) contribute substantially to genomic variation between normal humans. Representational oligonucleotide microarray analysis of 20 individuals revealed a total of 221 copy number differences representing 76 unique CNPs. On average, individuals differed by 11 CNPs, and the average length of a CNP interval was 465 kilobases. We observed copy number variation of 70 different genes within CNP intervals, including genes involved in neurological function, regulation of cell growth, regulation of metabolism, and several genes known to be associated with disease.

  43. C Seoighe, C Gehring (2004), "Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome", Trends in Genetics, 20(10):461-464.

  44. Douglas E Soltis, Pamela S Soltis, Jennifer A Tate (2004), "Advances in the study of polyploidy since plant speciation", New Phytologist, 161(1):173-191.
    [ abstract]

  45. Pawel Stankiewicz, Christine J. Shaw, Marjorie Withers, Ken Inoue, James R. Lupski (2004), "Serial segmental duplications during primate evolution result in complex human genome architecture", Genome Research, 14: 2209-2220.

  46. John S Taylor, Jeroen Raes (2004), "Duplication and divergence: the evolution of new genes and old ideas", Annual Review of Genetics, 38:615-643.

  47. EE Thomas, N Srebro, J Sebat, N Navin, J Healy, B Mishra, M Wigler (2004), "Distribution of short paired duplications in mammalian genomes", Proceedings of National Academy of Sciences, 101(28):10349-10354.

  48. Eray Tuzun, Jeffrey A. Bailey and Evan E. Eichler (2004), "Recent segmental duplications in the working draft assembly of the brown Norway rat", Genome Research, 14:493-506.

  49. Yves van de Peer (2004), "Computational approaches to unveiling ancient genome duplications", Nature Reviews Genetics, 5:752-763.
    [ abstract]

  50. Klaas Vandepoele, Wouter De Vos, John S Taylor, Axel Meyer, Yves Van de Peer (2004), "Major events in the genome evolution of vertebrates: paranome age and size differs considerably between ray-finned fishes and land vertebrates. Proceedings of National Academy of Sciences, 101(6):1638-1643.
    [abstract]

  51. W Wang, H Yu, M Long (2004), "Duplication-degeneration as a mechanism of gene fission and origin of new genes in Drosophila", Nature Genetics, 36:523-527.

  52. Rachel Ward, Richard Durrett (2004), "Subfunctionalization: How often does it occur? How long does it take?", Theoretical Population Biology, 66(2):93-100.
    [ abstract]

  53. J Zhang (2004), "The infancy of duplicate genes", Heredity, 92:479-480.

  54. Z Zhang, H Kishino (2004), "Genomic background predicts the fate of duplicated genes: evidence from the yeast genome", Genetics, 166(4):1995-1999.
    [abstract]

  55. Shaying Zhao, Jyoti Shetty, Lihua Hou, Arthur Delcher, Baoli Zhu, Kazutoyo Osoegawa, Pieter de Jong, William C. Nierman, Robert L. Strausberg, and Claire M. Fraser (2004), "Human, mouse, and rat genome large-scale rearrangements: stability versus speciation", Genome Research, 14:1851-1860.