Bibliography on gene and genome duplication (2006)

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  1. Jean-Marc Aury, Olivier Jaillon, Laurent Duret, Benjamin Noel, Claire Jubin, Betina M. Porcel, Béatrice Ségurens, Vincent Daubin, Véronique Anthouard, Nathalie Aiach, Olivier Arnaiz, Alain Billaut, Janine Beisson, Isabelle Blanc, Khaled Bouhouche, Francisco Câmara, Sandra Duharcourt, Roderic Guigo, Delphine Gogendeau, Michael Katinka, Anne-Marie Keller, Roland Kissmehl, Catherine Klotz, France Koll, Anne Le Mouël, Gersende Lepère, Sophie Malinsky, Mariusz Nowacki, Jacek K. Nowak, Helmut Plattner, Julie Poulain, Françoise Ruiz, Vincent Serrano, Marek Zagulski, Philippe Dessen, Mireille Bétermier, Jean Weissenbach, Claude Scarpelli, Vincent Schächter, Linda Sperling, Eric Meyer, Jean Cohen, and Patrick Wincker (2006), "Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia", Nature, 444:171-178.

  2. Jeffrey A. Bailey and Evan E. Eichler (2006) "Primate segmental duplications: crucibles of evolution, diversity and disease", Nature Reviews Genetics, 7(7):552-564.
    [abstract]

  3. T Blomme, K Vandepoele, S De Bodt, C Simillion, S Maere, Y Van de Peer (2006), "The gain and loss of genes during 600 million years of vertebrate evolution", Genome Biology, 7:R43.

  4. RJ Britten (2006), "Almost all human genes resulted from ancient duplication", Proceedings of National Academy of Sciences, 103(50):19027-19032.
    [abstract]

  5. Rémy Bruggmann, Arvind K. Bharti, Heidrun Gundlach, Jinsheng Lai, Sarah Young, Ana C. Pontaroli, Fusheng Wei, Georg Haberer, Galina Fuks, Chunguang Du, Christina Raymond, Matt C. Estep, Renyi Liu, Jeffrey L. Bennetzen, Agnes P. Chan, Pablo D. Rabinowicz, John Quackenbush, W. Brad Barbazuk, Rod A. Wing, Bruce Birren, Chad Nusbaum, Steve Rounsley, Klaus F.X. Mayer, and Joachim Messing (2006), "Uneven chromosome contraction and expansion in the maize genome", Genome Research, 16(10):1241-1251.
    [abstract]

  6. FG Brunet, HR Crollius, M Paris, J-M Aury, P Gibert, O Jaillon, V Laudet, and M Robinson-Rechavi (2007), "Gene loss and evolutionary rates following whole-genome duplication in Teleost fishes", Molecular Biology and Evolution, 23(9):1808-1816.
    [abstract]

  7. Xinjiang Cai, Yanhong Zhang (2006), "Molecular evolution of the Ankyrin gene family", Molecular Biology and Evolution, 23(3):550-558.
    [abstract]

  8. T Casneuf, S De Bodt, J Raes, S Maere, Y Van de Peer (2006), "Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana", Genome Biology, 7:R13.

  9. BA Chapman, JE Bowers, FA Feltus, AH Paterson (2006), "Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication", Proceedings of National Academy of Sciences, 103(8):2730-2735.
    [abstract]

  10. GC Conant, KH Wolfe (2006), "Functional partitioning of yeast co-expression networks after genome duplication", PLoS Biology, 4:e109.

  11. KD Crow, PF Stadler, VJ Lynch, C Amemiya, GP Wagner (2006), "The 'fish-specific' Hox cluster duplication is coincident with the origin of Teleosts", Molecular Biology and Evolution, 23(1):121-136.
    [abstract]

  12. KD Crow, GP Wagner (2006), "What is the role of genome duplication in the evolution of complexity and diversity?" Molecular Biology and Evolution, 23(5):887-892.
    [abstract]

  13. Miklos Csuros, Istvan Miklos (2006), "A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer", Proceedings of the Tenth International Conference on Research in Computational Molecular Biology , pp.?-?

  14. Liying Cui, P. Kerr Wall, James H. Leebens-Mack, Bruce G. Lindsay, Douglas E. Soltis, Jeff J. Doyle, Pamela S. Soltis, John E. Carlson, Kathiravetpilla Arumuganathan, Abdelali Barakat, Victor A. Albert, Hong Ma, and Claude W. dePamphilis (2006), "Widespread genome duplications throughout the history of flowering plants", Genome Research, 16(6):738-749.
    [abstract]

  15. SC Drea, NT Lao, KH Wolfe, TA Kavanagh (2006), "Gene duplication, exon gain and neofunctionalization of OEP16-related genes in land plants", Plant J. 46:723-735.

  16. Jill M Duarte, Liying Cui, P Kerr Wall, Qing Zhang, Xiaohong Zhang, Jim Leebens-Mack, Hong Ma, Naomi Altman, Claude W dePamphilis (2006), "Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis", Molecular Biology and Evolution, 23(2):469-478
    [abstract]

  17. Isabelle Dupanloup and Henrik Kaessmann (2006), "Evolutionary simulations to detect functional lineage-specific genes", Bioinformatics, 22(15):1815-1822.
    [abstract]

  18. D Durand, R Hoberman (2006), "Diagnosing duplications--can it be done?", Trends in Genetics, 22(3):156-164.

  19. MA Fares, KP Byrne, KH Wolfe (2006), "Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species", Molecular Biology and Evolution, 23:245-253.

  20. Michael Freeling and Brian C. Thomas (2006), "Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity", Genome Research, 16(7):805-814.
    [abstract]

  21. Jennifer L Freeman, George H Perry, Lars Feuk, Richard Redon, Steven A McCarroll, David M Altshuler, Hiroyuki Aburatani, Keith W Jones8, Chris Tyler-Smith, Matthew E Hurles, Nigel P Carter, Stephen W Scherer and Charles Lee (2006), "Copy number variation: new insights in genome diversity", Genome Research, 16:949-961.
    [abstract]

  22. D Gevers, Y Van de Peer (2006), "Gene duplicates in vibrio genomes", in The Biology of Vibrios, eds. FL Thompson, B Austin, J Swings . pp. 76-83 (ASM Press)

  23. Alexander A Gimelbrant and Andrew Chess (2006), "An epigenetic state associated with areas of gene duplication", Genome Research, 16(6): 723-729.
    [abstract]

  24. Julien Grassot, Manolo Gouy, Guy Perrière, Guy Mouchiroud (2006), "Origin and molecular evolution of receptor tyrosine kinases with immunoglobulin-like domains", Molecular Biology and Evolution, 23:1232-1241.
    [abstract]

  25. X He, and J Zhang (2006), "Higher duplicability of less important genes in yeast genomes", Molecular Biology and Evolution, 23:144-151.
    [abstract]

  26. X He, and J Zhang (2006), "Transcriptional reprogramming and backup between duplicate genes: is it a genome-wide phenomenon?", Genetics, 172:1363-1367.

  27. V Katju, M Lynch (2006), "On the formation of novel genes by duplication in the Caenorhabditis elegans genome", Molecular Biology and Evolution, 23:1056-1067.

  28. SH Kim, SV Yi (2006), "Correlated ssymmetry of sequence and functional divergence between duplicate proteins of Saccharomyces cerevisiae", Molecular Biology and Evolution, 23(5):1068-1075.
    [abstract]

  29. DG Knowles, A McLysaght (2006), "High rate of recent intron gain and loss in simultaneously duplicated Arabidopsis genes", Molecular Biology and Evolution, 23(8):1548-1557.
    [abstract]

  30. Fyodor A Kondrashov and Alexey S. Kondrashov (2006), "Role of selection in fixation of gene duplications", Journal of Theoretical Biology, 239(2):141-151.
    [ abstract]

  31. L Li, Y Huang, X Xia, Z Sun (2006), "Preferential duplication in the sparse part of yeast protein interaction network", Molecular Biology and Evolution, 23(12):2467-2473.
    [abstract]

  32. Jianxin Ma and Scott A. Jackson (2006), "Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice", Genome Reseach, 16(2):251-259.
    [abstract]

  33. Gayle K. McEwen, Adam Woolfe, Debbie Goode, Tanya Vavouri, Heather Callaway, and Greg Elgar (2006), "Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis", Genome Research, 16(4):451-465.
    [abstract]

  34. Jennifer A. Lee and James R. Lupski (2006), "Genomic rearrangements and gene copy-number alterations as a cause of nervous system disorders", Neuron, 52:103-121.

  35. George H Perry, Joelle Tchinda, Sean D McGrath, Junjun Zhang, Simon R Picker, Angela M Cáceres, A John Iafrate, Chris Tyler-Smith, Stephen W Scherer, Evan E Eichler, Anne C Stone, Charles Lee (2006), "Hotspots for copy number variation in chimpanzees and humans", Proceedings of National Academy of Sciences, 103(21):8006-8011.
    [abstract]

  36. Benoit Piegu, Romain Guyot, Nathalie Picault, Anne Roulin, Abhijit Saniyal, Hyeran Kim, Kristi Collura, Darshan S. Brar, Scott Jackson, Rod A. Wing, and Olivier Panaud (2006), "Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice", Genome Research, 16(10):1262-1269.
    [abstract]

  37. Richard Redon, Shumpei Ishikawa, Karen R Fitch, Lars Feuk, George H Perry, T Daniel Andrews, Heike Fiegler, Michael H Shapero, Andrew R Carson, Wenwei Chen, Eun Kyung Cho, Stephanie Dallaire, Jennifer L Freeman, Juan R Gonzalez, Monica Gratacos, Jing Huang, Dimitrios Kalaitzopoulos, Daisuke Komura, Jeffrey R MacDonald, Christian R Marshall, Rui Mei, Lyndal Montgomery, Kunihiro Nishimura, Kohji Okamura, Fan Shen, Martin J Somerville, Joelle Tchinda, Armand Valsesia, Cara Woodwark, Fengtang Yang, Junjun Zhang, Tatiana Zerjal, Jane Zhang, Lluis Armengol, Donald F Conrad, Xavier Estivill, Chris Tyler-Smith, Nigel P Carter, Hiroyuki Aburatani, Charles Lee, Keith W Jones, Stephen W Scherer and Matthew E Hurles (2006), "Global variation in copy number in the human genome", Nature, 444(7118):444-454.
    [abstract]

  38. DR Scannell, KP Byrne, JL Gordon, S Wong, KH Wolfe (2006), "Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts", Nature, 440:341-345.

  39. ME Schranz, T Mitchell-Olds (2006), "Independent ancient polyploidy events in the sister families Brassicaceae and Cleomaceae", Plant Cell, 18(5):1152-1165.
    [abstract]

  40. Boris E. Shakhnovich, Eugene V. Koonin (2006) "Origins and impact of constraints in evolution of gene families", Genome Research, 16:1529-1536.
    [abstract]

  41. Andrew J Sharp, Sierra Hansen, Rebecca R Selzer, Ze Cheng, Regina Regan, Jane A Hurst, Helen Stewart, Sue M Price, Edward Blair, Raoul C Hennekam, Carrie A Fitzpatrick, Rick Segraves, Todd A Richmond, Cheryl Guiver, Donna G Albertson, Daniel Pinkel, Peggy S Eis, Stuart Schwartz, Samantha J L Knight, Evan E Eichler (2006), "Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome", Nature Genetics, 38:1038-1042.
    [abstract]

  42. Xinwei She, Ge Liu, Mario Ventura, Shaying Zhao, Doriana Misceo, Roberta Roberto, Maria Francesca Cardone, Mariano Rocchi, NISC Comparative Sequencing Program, Eric D. Green, Nicoletta Archidiacano, and Evan E. Eichler (2006), "A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications", Genome Research, 16(5):576-583.
    [abstract]

  43. RC Shoemaker, J Schlueter, JJ Doyle (2006), "Paleopolyploidy and gene duplication in soybean and other legumes", Current Opinion in Plant Biology, 9(2):104-109.

  44. SH Shiu, JK Byrnes, R Pan, P Zhang, WH Li (2005), "Role of positive selection in the retention of duplicate genes in mammalian genomes", Proceedings of National Academy of Sciences, 103:2232-2236

  45. Zhixi Su, Jianmin Wang, Jun Yu, Xiaoqiu Huang, and Xun Gu (2006), "Evolution of alternative splicing after gene duplication", Genome Research, 16(2):182-189.
    [abstract]

  46. Petr Tvrdik, Mario R. Capecchi (2006), "Reversal of Hox1 gene subfunctionalization in the mouse", Developmental Cell, 11(2):239-250.
    [ abstract]

  47. JA Udall, JF Wendel (2006), "Polyploidy and crop improvement", Crop Science, 46(Suppl 1): S3-S14. [abstract]

  48. Y Van de Peer (2006), "When duplicated genes don't stick to the rules", Heredity, 96:204-205.

  49. Xiyin Wang, Xiaoli Shi, Zhe Li, Qihui Zhu, Lei Kong, Wen Tang, Song Ge, Jingchu Luo (2006), "Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice", BMC Bioinformatics, 7:447.
    [ abstract]

  50. S Wong, KH Wolfe (2006), "Duplication of genes and genomes in yeasts", in Comparative genomics, Vol 15, eds. P Sunnerhagen, J Piskur, pp.78-99 (Springer-Verlag, Heidelberg).

  51. Chunfang Zheng, Qian Zhum David Sankoff (2006), "Genome halving with an outgroup", Evolutionary Bioinformatics, 2:319-326.

  52. Michael C. Zody, Manuel Garber, Ted Sharpe, Sarah K. Young, Lee Rowen, Keith O'Neill, Charles A. Whittaker, Michael Kamal, Jean L. Chang, Christina A. Cuomo, Ken Dewar, Michael G. FitzGerald, Chinnappa D. Kodira, Anup Madan, Shizhen Qin, Xiaoping Yang, Nissa Abbasi, Amr Abouelleil, Harindra M. Arachchi, Lida Baradarani, Brian Birditt, Scott Bloom, Toby Bloom, Mark L. Borowsky, Jeremy Burke, Jonathan Butler, April Cook, Kurt DeArellano, David DeCaprio, Lester Dorris, III, Monica Dors, Evan E. Eichler, Reinhard Engels, Jessica Fahey, Peter Fleetwood, Cynthia Friedman, Gary Gearin, Jennifer L. Hall, Grace Hensley, Ericka Johnson, Charlien Jones, Asha Kamat, Amardeep Kaur, Devin P. Locke, Anuradha Madan, Glen Munson, David B. Jaffe, Annie Lui, Pendexter Macdonald, Evan Mauceli, Jerome W. Naylor, Ryan Nesbitt, Robert Nicol, Sinéad B. O'Leary, Amber Ratcliffe, Steven Rounsley, Xinwei She, Katherine M. B. Sneddon, Sandra Stewart, Carrie Sougnez, Sabrina M. Stone, Kerri Topham, Dascena Vincent, Shunguang Wang, Andrew R. Zimmer, Bruce W. Birren, Leroy Hood, Eric S. Lander and Chad Nusbaum (2006), "Analysis of the DNA sequence and duplication history of human chromosome 15", Nature, 440:671-675.