Bibliography on gene and genome duplication (2007)

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  1. Sébastien Angibaud, Guillaume Fertin, Irena Rusu, Stéphane Vialette (2007), "A pseudo-Boolean framework for computing rearrangement distances between genomes with duplicates", Journal of Computational Biology, 14(4):379-393.
    [abstract ]

  2. U Bergthorsson, DI Andersson, JR Roth (2007), "Ohno's dilemma: Evolution of new genes under continuous selection", Proceedings of National Academy of Sciences, 104(43):17004-17009.
    [abstract]

  3. James A. Birchler (2007), "The gene balance hypothesis: from classical genetics to modern genomics", Plant Cell, 19:395-402.
    [html]

  4. KP Byrne, KH Wolfe (2007), "Consistent patterns of rate asymmetry and gene loss indicate widespread neofunctionalization of yeast genes sfter whole-genome duplication", Genetics, 175(3):1341-1350.
    [abstract]

  5. Jon Cohen (2007), "Genomics: DNA duplications and deletions help determine health" (news focus), Science, 317(5843):1315-1317.
    [ html]

  6. GC Conant, KH Wolfe (2007), "Increased glycolytic flux as an outcome of whole-genome duplication in yeast", Molecular Systems Biology, 3:129.

  7. B Conrad, SE Antonarakis (2007), "Gene Duplication: a drive for phenotypic diversity and cause of human disease", Annual Review of Genomics and Human Genetics, 8:17-35.

  8. BP Cusack, KH Wolfe (2007), "When gene marriages don't work out: divorce by subfunctionalization", Trends in Genetics, 23:270-272.

  9. BP Cusack, KH Wolfe (2007), "Not born equal: increased rate asymmetry in relocated and retrotransposed rodent gene duplicates", Molecular Biology and Evolution, 24:679-86.

  10. D Duboule (2007) "The rise and fall of Hox gene clusters", Development, 134(14):2549-2560.
    [abstract]

  11. L Dumas, YH Kim, A Karimpour-Fard, M Cox, J Hopkins, JR Pollack, JM Sikela (2007), "Gene copy number variation spanning 60 million years of human and primate evo lution", Genome Research, 17(9):1266-1277.
    [abstract]

  12. EW Ganko, BC Meyers, TJ Vision (2007), "Divergence in expression between duplicated genes in Arabidopsis", Molecular Biology and Evolution, 24(10):2298-2309.
    [abstract]

  13. Y Guan, MJ Dunham, OG Troyanskaya (2007), "Functional analysis of gene duplications in Saccharomyces cerevisiae", Genetics, 175(2):933-943.
    [abstract]

  14. IA Hurley, JL Scemama, VE Prince (2007), "Consequences of hoxb1 duplication in teleost fish", Evolution and Development, 9:540-554.

  15. Olivier Jaillon, Jean-Marc Aury, Benjamin Noel, Alberto Policriti, Christian Clepet, Alberto Casagrande, Nathalie Choisne, Sébastien Aubourg, Nicola Vitulo, Claire Jubin, Alessandro Vezzi, Fabrice Legeai, Philippe Hugueney, Corinne Dasilva, David Horner, Erica Mica, Delphine Jublot, Julie Poulain, Clémence Bruyère, Alain Billault, Béatrice Segurens, Michel Gouyvenoux, Edgardo Ugarte, Federica Cattonaro, Véronique Anthouard, Virginie Vico, Cristian Del Fabbro, Michaël Alaux, Gabriele Di Gaspero, Vincent Dumas, Nicoletta Felice, Sophie Paillard, Irena Juman, Marco Moroldo, Simone Scalabrin, Aurélie Canaguier, Isabelle Le Clainche, Giorgio Malacrida, Eléonore Durand, Graziano Pesole, Valérie Laucou, Philippe Chatelet, Didier Merdinoglu, Massimo Delledonne, Mario Pezzotti, Alain Lecharny, Claude Scarpelli, François Artiguenave, M. Enrico Pè, Giorgio Valle, Michele Morgante, Michel Caboche, Anne-Françoise Adam-Blondon, Jean Weissenbach, Francis Quétier, Patrick Wincker, for The French-Italian Public Consortium for Grapevine Genome Characterization (2007), "The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla", Nature, 449:463-467. [PDF]

  16. Prem P. Jauhar (2007), "Meiotic restitution in wheat polyhaploids (Amphihaploids): a potent evolutionary force", Journal of Heredity, 98(2):188-193.
    [abstract]

  17. CR Johnston, C O'Dushlaine, DA Fitzpatrick, RJ Edwards, DC Shields (2007), "Evaluation of whether accelerated protein evolution in chordates has occurred before, after, or simultaneously with gene duplication", Molecular Biology and Evolution, 24(1):315-323.
    [abstract]

  18. M Kasahara (2007), "The 2R hypothesis: an update", Current Opinion in Immunology, 19(5):547-552.

  19. Thomas MacCarthy, Aviv Bergman (2007), "The limits of subfunctionalization", BMC Evolutionary Biology, 7:213.
    [abstract]

  20. P Labbe, A Berthomieu, C Berticat, H Alout, M Raymond, T Lenormand, M Weill (2007), "Independent duplications of the acetylcholinesterase gene conferring insecticide resistance in the mosquito Culex pipiens", Molecular Biology and Evolution, 24(4):1056-1067.
    [abstract]

  21. Mathieu Lajoie, Denis Bertrand, Nadia El-Mabrouk, Olivier Gascuel (2007), "Duplication and inversion history of a tandemly repeated genes family", Journal of Computational Biology, 14(4):462-478.
    [abstract ]

  22. LJ Leach, Z Zhang, C Lu, MJ Kearsey, Z Luo (2007), "The role of cis-regulatory motifs and genetical control of expression in the divergence of yeast duplicate genes", Molecular Biology and Evolution, 24(11):2556-2565.
    [abstract]

  23. BY Liao and J Zhang (2007), "Mouse duplicate genes are as essential as singleton genes", Trends in Genetics, to appear.

  24. James R Lupski (2007), "An evolution revolution provides further revelation", Bioessays, 29(12):1182-1184.
    abstract: The extent of copy-number variation (CNV) in the human genome has been appreciated only recently. Nevertheless, for almost four decades, gene duplication has been a prevailing hypothesis for evolutionary change. Recently, gene CNV spanning 60 million years of human and primate evolution has been determined enabling lineage-specific gene CNV to be identified. Primate lineage-specific gene CNV studies reveal that almost one third of all human genes exhibit a copy-number change in one or more primate species. Intriguingly, human lineage-specific gene amplification can be correlated to the emergence of human-specific traits such as cognition and endurance running.

  25. James R Lupski (2007), "Genomic rearrangements and sporadic disease", Nature Genetics, 39(7 suppl):S43-S47.

  26. Martin A Lysak, Kwok Cheung, Michaela Kitschke, Petr Bure (2007), "Ancestral chromosomal blocks are triplicated in Brassiceae species with varying chromosome number and genome size", Plant Physiology, 145:402-410.
    [abstract]

  27. Jian Ma, Aakrosh Ratan, Louxin Zhang, Webb Miller, David Haussler (2007), in Comparative Genomics, ed. G Tesler, D Durand, Lecture Notes in Computer Science, Vol.4751, pp.122-135 (Springer). ISBN 9783540749592

  28. PW Messer, PF Arndt (2007), "The majority of recent short DNA insertions in the human genome are tandem duplications", Molecular Biology and Evolution, 24(5):1190-1197

  29. Yoichiro Nakatani, Hiroyuki Takeda, Yuji Kohara, and Shinichi Morishita (2007), "Reconstruction of the vertebrate ancestral genome reveals dynamic genome reor ganization in early vertebrates", Genome Research, 17:1254-1265.
    [abstract]

  30. V Negron-Ortiz (2007) "Chromosome numbers, nuclear DNA content, and polyploidy in Consolea (Cactaceae), an endemic cactus of the Caribbean Islands", American Journal of Botany, 94:1360-1370.
    [abstract]

  31. Martin O'Hely, Leesa Wockner (2007), "Models for loosely linked gene duplicates suggest lengthy persistence of both copies", Journal of Theoretical Biology, 246:636-645.

  32. George H Perry, Nathaniel J Dominy, Katrina G Claw, Arthur S Lee, Heike Fiegler, Richard Redon, John Werner, Fernando A Villanea, Joanna L Mountain, Rajeev Misra, Nigel P Carter, Charles Lee, Anne C Stone (2007), "Diet and the evolution of human amylase gene copy number variation", Nature Genetics, 39:1256-1260.
    [abstract] [story on Science magazine on this article: Science, 317(5844):1483. DOI: 10.1126/science.317.5844.1483a ]

  33. Magnus Popp, Bengt Oxelman (2007), "Origin and evolution of North American polyploid Silene (Caryophyllaceae)", American Journal of Botany, 94:330-349.
    [abstract]

  34. SA Rensing, J Ick, J Fawcett, D Lang, A Zimmer, Y Van de Peer, R Reski (2007), "An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens", BMC Evolutionary Biology, 7:130.

  35. D Sankoff, C Zheng, Q Zhu (2007), "Polyploids, genome halving and phylogeny", Bioinformatics, 23(13):i433-i439.
    [abstract]

  36. M Semon and KH Wolfe (2007), "Reciprocal gene loss between Tetraodon and zebrafish after whole genome duplication in their ancestor", Trends in Genetics, 23:108-12.

  37. M Semon and KH Wolfe (2007), "Rearrangement rate following the whole-genome duplication in Teleosts", Molecular Biology and Evolution, 24(3):860-867.
    [abstract]

  38. M Semon and KH Wolfe (2007), "Consequences of genome duplication", Current Opinion in Genetics & Genelopment, 17(6):505-512.
    [ abstract]

  39. DR Scannell, G Butler, KH Wolfe (2007), "Yeast genome evolution-the origin of the species", Yeast, 24(11):929-942.
    [ abstract]

  40. DR Scannell, AC Frank, GC Conant, KP Byrne, M Woolfit, KH Wolfe (2007), "Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication", Proceedings of National Academy of Sciences, 104:8397-8402.

  41. Jessica A Schlueter, Iryna F Vasylenko-Sanders, Shweta Deshpande, Jing Yi, Majesta Siegfried, Bruce A Roe, Shannon D Schlueter, Brian E Scheffler and Randy C Shoemaker (2007), "The FAD2 gene family of soybean: insights into the structural and functional divergence of a paleopolyploid genome", Crop Science, 37:S14-S26.
    [abstract]

  42. L Sterck, S Rombauts, K Vandepoele, P Rouze, Y Van de Peer (2007), "How many genes are there in plants (... and why are they there)?", Current Opinion in Plant Biology, 10(2):199-203.

  43. Barbara E Stranger, Matthew S Forrest, Mark Dunning, Catherine E Ingle, Claude Beazley, Natalie Thorne, Richard Redon, Christine P Bird, Anna de Grassi, Charles Lee, Chris Tyler-Smith, Nigel Carter, Stephen W Scherer, Simon Tavaré, Panagiotis Deloukas, Matthew E Hurles, Emmanouil T Dermitzakis (2007), "Relative impact of nucleotide and copy number variation on gene expression phenotypes", Science, 315(5813):848-853.
    [abstract]

  44. Robert M Stupar, Pudota B Bhaskar, Brian S Yandell, Willem A Rensink, Amy L Hart, Shu Ouyang, Richard E Veilleux, James S Busse, Robert J Erhardt, C Robin Buell, Jiming Jiang (2007), "Phenotypic and transcriptomic changes associated with potato autopolyploidization", Genetics, 176:2055-2067.
    [abstract]

  45. D Talavera, C Vogel, M Orozco, SA Teichmann, X de la Cruz (2007), "The (in)dependence of alternative splicing and gene duplication", PLoS Computational Biology, 3(3):e33.

  46. Helena B. Thomaides, Ella J. Davison, Lisa Burston, Hazel Johnson, David R Brown, Alison C Hunt, Jeffery Errington, Lloyd Czaplewski (2007), "Essential bacterial functions encoded by gene pairs", Journal of Bacteriology, 189(2):591-602.
    [abstract]

  47. Milan JA van Hoek and Paulien Hogeweg (2007), "The role of mutational dynamics in genome shrinkage", Molecular Biology and Evolution, 24(11):2485-2494.
    [abstract]

  48. KR Thornton (2007), "The neutral coalescent process for recent gene duplications and copy-number variants", ", Genetics, 177:987-1000.
    [abstract]

  49. Riccardo Velasco, Andrey Zharkikh, Michela Troggio, Dustin A Cartwright, Alessandro Cestaro, Dmitry Pruss, Massimo Pindo, Lisa M FitzGerald, Silvia Vezzulli, Julia Reid, Giulia Malacarne, Diana Iliev, Giuseppina Coppola, Bryan Wardell, Diego Micheletti, Teresita Macalma, Marco Facci, Jeff T Mitchell, Michele Perazzolli, Glenn Eldredge, Pamela Gatto, Rozan Oyzerski, Marco Moretto, Natalia Gutin, Marco Stefanini, Yang Chen, Cinzia Segala, Christine Davenport, Lorenzo Demattè, Amy Mraz, Juri Battilana, Keith Stormo, Fabrizio Costa, Quanzhou Tao, Azeddine Si-Ammour, Tim Harkins, Angie Lackey, Clotilde Perbost, Bruce Taillon, Alessandra Stella, Victor Solovyev, Jeffrey A Fawcett, Lieven Sterck, Klaas Vandepoele, Stella M Grando, Stefano Toppo, Claudio Moser, Jerry Lanchbury, Robert Bogden, Mark Skolnick, Vittorio Sgaramella, Satish K Bhatnagar, Paolo Fontana, Alexander Gutin, Yves Van de Peer, Francesco Salamini, Roberto Viola (2007), "A high quality draft consensus sequence of the genome of a heterozygous grapevine variety", PLoS One, 2(12):e1326.
    [ abstract] [PDF]

  50. Xiyin Wang, Haibao Tang, John E Bowers, Frank A Feltus, Andrew H Paterson (2007), "Extensive concerted evolution of rice paralogs and the road to regaining independence", Genetics, 177(3):1753-1763.
    [ abstract]

  51. Damian Wójtowicz, Jerzy Tiuryn (2007), "Evolution of gene families based on gene duplication, loss, accumulated chang e, and innovation", Journal of Computational Biology, 14(4):479-495.
    [abstract ]

  52. KK Wong, RJ deLeeuw, NS Dosanjh, LR Kimm, Z Cheng, DE Horsman, C MacAulay, RT Ng, CJ Brown, EE Eichler (2007), "A comprehensive analysis of common copy-number variations in the human genome", American Journal of Human Genetics, 80(1):91-104.

  53. Chunfang Zheng, Qian Zhu, David Sankoff (2007), "Parts of the problem of polyploids in rearrangement phylogeny", in Comparative Genomics, ed. G Tesler, D Durand, Lecture Notes in Computer Science, Vol.4751, pp.162-176 (Springer). ISBN 9783540749592