bib gene duplication (2008)

Bibliography on gene and genome duplication (2008)

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glossary
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2008
2007
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Steffen Beisswanger, Wolfgang Stephan and (2008), "Evidence that strong positive selection drives neofunctionalization in the tandemly duplicated polyhomeotic genes in Drosophila", Proceedings of National Academy of Sciences, 105:5447-5452.
[abstract]
Gavin C Conant, Kenneth H Wolfe (2008), "Turning a hobby into a job: How duplicated genes find new functions", Nature Reviews Genetics, 9:938-950.
[ abstract]
E Darai-Ramqvist, A Sandlund, S Müller, G Klein, S Imreh, M Kost-Alimova (2008), "Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions", Genome Research, 18(3):370-379.
interview by Jane Gitschier (2008), "Stable in a genome of instability: an interview with Evan Eichler", PLoS Genetics, 4(7):e1000124.
P Hallast, J Saarela, A Palotie, M Laan (2008), "High divergence in primate-specific duplicated regions: human and chimpanzee Chorionic Gonadotropin Beta genes", BMC Evolutionary Biology, 8(1):195.
Kristy Halverson, Stephen B. Heard, John D. Nason, John O. Stireman, III (2008), "Origins, distribution, and local co-occurrence of polyploid cytotypes in Solidago altissima (Asteraceae)", American Journal of Botany, 95:50-58.
[abstract]
Linda Z Holland, Ricard Albalat, Kaoru Azumi, Èlia Benito-Gutiérrez, Matthew J Blow, Marianne Bronner-Fraser, Frederic Brunet, Thomas Butts, Simona Candiani, Larry J Dishaw, David EK. Ferrier, Jordi Garcia-Fernàndez, Jeremy J Gibson-Brown, Carmela Gissi, Adam Godzik, Finn Hallböök, Dan Hirose, Kazuyoshi Hosomichi, Tetsuro Ikuta, Hidetoshi Inoko, Masanori Kasahara, Jun Kasamatsu, Takeshi Kawashima, Ayuko Kimura, Masaaki Kobayashi, Zbynek Kozmik, Kaoru Kubokawa, Vincent Laudet, Gary W Litman, Alice C McHardy, Daniel Meulemans, Masaru Nonaka, Robert P Olinski, Zeev Pancer, Len A Pennacchio, Mario Pestarino, Jonathan P Rast, Isidore Rigoutsos, Marc Robinson-Rechavi, Graeme Roch, Hidetoshi Saiga, Yasunori Sasakura, Masanobu Satake, Yutaka Satou, Michael Schubert, Nancy Sherwood, Takashi Shiina, Naohito Takatori, Javier Tello, Pavel Vopalensky, Shuichi Wada, Anlong Xu, Yuzhen Ye, Keita Yoshida, Fumiko Yoshizaki, Jr-Kai Yu, Qing Zhang, Christian M Zmasek, Pieter J de Jong, Kazutoyo Osoegawa, Nicholas H Putnam, Daniel S Rokhsar, Noriyuki Satoh and, Peter WH Holland (2008), "The amphioxus genome illuminates vertebrate origins and cephalochordate biology", Genome Research, 18(7):1100-1111.
[abstract]
, R Hovav, JA Udall, B Chaudhary, L Flagel, R Rapp, JF Wendel (2008), "Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant", Proceedings of National Academy of Sciences, to appear.
Zhaoshi Jiang, Robert Hubley, Arian Smit, Evan E Eichler (2008), "DupMasker: A tool for annotating primate segmental duplications", Genome Research, 18(8):1362-1368.
[ abstract ]
Rebecca Hufft Kao (2008), "Origins and widespread distribution of co-existing polyploids in Arnica cordifolia (Asteraceae)", Annals of Botany, 101(1):145-152.
[abstract]
Stefan Kirsch, Claudia Münch, Zhaoshi Jiang, Ze Cheng, Lin Chen, Christiane Batz, Evan E. Eichler, Werner Schempp (2008) "Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions", Genome Research, 18(7):1030-1042.
[ abstract ]
Charles A Knight, Jeremy M Beaulieu (2008), "Genome size scaling through phenotype space", Annals of Botany, to appear.
Arthur S Lee, María Gutiérrez-Arcelus, George H Perry, Eric J Vallender, Welkin E Johnson, Gregory M Miller, Jan O Korbel, and Charles Lee (2008), "Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies", Human Molecular Genetics, to apper.
Anthony Levasseur, Pierre Pontarotti, Olivier Poch, Julie D Thompson (2008), "Strategies for reliable exploitation of evolutionary concepts in high throughput biology", Evolutionary Bioinformatics Online, 4:121-137.
[html]
T Marques-Bonet, Z Cheng, X She, EE Eichler, A Navarro (2008), "The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements", BMC Genomics, 9:384.
Sean Yu McLoughlin, Shelley D Copley (2008), "A compromise required by gene sharing enables survival: Implications for evolution of new enzyme activities", Proceedings of National Academy of Sciences, 105:13497-13502.
[abstract]
Gabriel Musso, Michael Costanzo, ManQin Huangfu, Andrew M Smith, Jadine Paw, Bryan-Joseph San Luis, Charles Boone, Guri Giaever, Corey Nislow, Andrew Emili, Zhaolei Zhang (2008) "The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast", Genome Research, 18(7):1092-1099.
[abstract]
Belinda J Norris, Vicki A Whan (2008), "A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sheep", Genome Research, 18(8):1282-1293.
[abstract]
A Prachumwat and WH Li (2008) "Gene number expansion and contraction in vertebrate genomes with respect to invertebrate genomes", Genome Research, 18(2):221-232.
[abstract]
Aviva Presser, Michael B. Elowitz, Manolis Kellis, Roy Kishony (2008) "The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication", Proceedings of National Academy of Sciences, 105:950-954.
[html]
Nicholas H Putnam, Thomas Butts, David E K Ferrier, Rebecca F Furlong, Uffe Hellsten, Takeshi Kawashima, Marc Robinson-Rechavi, Eiichi Shoguchi, Astrid Terry, Jr-Kai Yu, Elia Benito-Gutiérrez, Inna Dubchak, Jordi Garcia-Fernàndez, Jeremy J Gibson-Brown, Igor V Grigoriev, Amy C Horton, Pieter J de Jong, Jerzy Jurka, Vladimir V Kapitonov, Yuji Kohara, Yoko Kuroki, Erika Lindquist, Susan Lucas, Kazutoyo Osoegawa, Len A Pennacchio, Asaf A Salamov, Yutaka Satou, Tatjana Sauka-Spengler, Jeremy Schmutz, Tadasu Shin-I, Atsushi Toyoda, Marianne Bronner-Fraser, Asao Fujiyama, Linda Z Holland, Peter W H Holland, Nori Satoh, Daniel S Rokhsar (2008), "The amphioxus genome and the evolution of the chordate karyotype", Nature, 453:1064-1071.
[ abstract]
DR Scannell and KH Wolfe (2008) "A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast", Genome Research, 18(1):137-147.
[abstract]
Marie Sémon, Kenneth H. Wolfe (2008), "Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis", Proceedings of National Academy of Sciences, 105:8333-8338.
[abstract]
Zhen Wang, Guohui Ding, Zhonghao Yu, Lei Liu, Yixue Li (2008), "Modeling the age distribution of gene duplications in vertebrate genome using mixture density", Genomics, 93(2):146-151.
[ abstract]
Robert Warren, David Sankoff (2008), "Genome halving with double cut and join", in Proceedings of the 6th Asia-Pacific Bioinformatics Conference eds. A Brazma, S Miyano, T Akutsu, pp.231-240 (Imperial College Press).
Jian-Hong Xu, Joachim Messing (2008), "Organization of the prolamin gene family provides insight into the evolution of the maize genome and gene duplications in grass species", Proceedings of National Academy of Sciences, 105:14330-14335.
[abstract]
D Zheng (2008), "Asymmetric histone modifications between the original and derived loci of human segmental duplications", Genome Biology, 9(7):R105.

		Bibliography on gene and genome duplication (2008)
	front page glossary 2009 2008 2007 2006 2005 2004 2003 2002 2001 2000 1999 1998 1997 1996 1995 1994 1993 1992 1991 1990 80s 70s 60s 50s 40s 30s 20s 10s	Steffen Beisswanger, Wolfgang Stephan and (2008), "Evidence that strong positive selection drives neofunctionalization in the tandemly duplicated polyhomeotic genes in Drosophila", Proceedings of National Academy of Sciences, 105:5447-5452. [abstract] Gavin C Conant, Kenneth H Wolfe (2008), "Turning a hobby into a job: How duplicated genes find new functions", Nature Reviews Genetics, 9:938-950. [ abstract] E Darai-Ramqvist, A Sandlund, S Müller, G Klein, S Imreh, M Kost-Alimova (2008), "Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions", Genome Research, 18(3):370-379. interview by Jane Gitschier (2008), "Stable in a genome of instability: an interview with Evan Eichler", PLoS Genetics, 4(7):e1000124. P Hallast, J Saarela, A Palotie, M Laan (2008), "High divergence in primate-specific duplicated regions: human and chimpanzee Chorionic Gonadotropin Beta genes", BMC Evolutionary Biology, 8(1):195. Kristy Halverson, Stephen B. Heard, John D. Nason, John O. Stireman, III (2008), "Origins, distribution, and local co-occurrence of polyploid cytotypes in Solidago altissima (Asteraceae)", American Journal of Botany, 95:50-58. [abstract] Linda Z Holland, Ricard Albalat, Kaoru Azumi, Èlia Benito-Gutiérrez, Matthew J Blow, Marianne Bronner-Fraser, Frederic Brunet, Thomas Butts, Simona Candiani, Larry J Dishaw, David EK. Ferrier, Jordi Garcia-Fernàndez, Jeremy J Gibson-Brown, Carmela Gissi, Adam Godzik, Finn Hallböök, Dan Hirose, Kazuyoshi Hosomichi, Tetsuro Ikuta, Hidetoshi Inoko, Masanori Kasahara, Jun Kasamatsu, Takeshi Kawashima, Ayuko Kimura, Masaaki Kobayashi, Zbynek Kozmik, Kaoru Kubokawa, Vincent Laudet, Gary W Litman, Alice C McHardy, Daniel Meulemans, Masaru Nonaka, Robert P Olinski, Zeev Pancer, Len A Pennacchio, Mario Pestarino, Jonathan P Rast, Isidore Rigoutsos, Marc Robinson-Rechavi, Graeme Roch, Hidetoshi Saiga, Yasunori Sasakura, Masanobu Satake, Yutaka Satou, Michael Schubert, Nancy Sherwood, Takashi Shiina, Naohito Takatori, Javier Tello, Pavel Vopalensky, Shuichi Wada, Anlong Xu, Yuzhen Ye, Keita Yoshida, Fumiko Yoshizaki, Jr-Kai Yu, Qing Zhang, Christian M Zmasek, Pieter J de Jong, Kazutoyo Osoegawa, Nicholas H Putnam, Daniel S Rokhsar, Noriyuki Satoh and, Peter WH Holland (2008), "The amphioxus genome illuminates vertebrate origins and cephalochordate biology", Genome Research, 18(7):1100-1111. [abstract] , R Hovav, JA Udall, B Chaudhary, L Flagel, R Rapp, JF Wendel (2008), "Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant", Proceedings of National Academy of Sciences, to appear. Zhaoshi Jiang, Robert Hubley, Arian Smit, Evan E Eichler (2008), "DupMasker: A tool for annotating primate segmental duplications", Genome Research, 18(8):1362-1368. [ abstract ] Rebecca Hufft Kao (2008), "Origins and widespread distribution of co-existing polyploids in Arnica cordifolia (Asteraceae)", Annals of Botany, 101(1):145-152. [abstract] Stefan Kirsch, Claudia Münch, Zhaoshi Jiang, Ze Cheng, Lin Chen, Christiane Batz, Evan E. Eichler, Werner Schempp (2008) "Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions", Genome Research, 18(7):1030-1042. [ abstract ] Charles A Knight, Jeremy M Beaulieu (2008), "Genome size scaling through phenotype space", Annals of Botany, to appear. Arthur S Lee, María Gutiérrez-Arcelus, George H Perry, Eric J Vallender, Welkin E Johnson, Gregory M Miller, Jan O Korbel, and Charles Lee (2008), "Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies", Human Molecular Genetics, to apper. Anthony Levasseur, Pierre Pontarotti, Olivier Poch, Julie D Thompson (2008), "Strategies for reliable exploitation of evolutionary concepts in high throughput biology", Evolutionary Bioinformatics Online, 4:121-137. [html] T Marques-Bonet, Z Cheng, X She, EE Eichler, A Navarro (2008), "The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements", BMC Genomics, 9:384. Sean Yu McLoughlin, Shelley D Copley (2008), "A compromise required by gene sharing enables survival: Implications for evolution of new enzyme activities", Proceedings of National Academy of Sciences, 105:13497-13502. [abstract] Gabriel Musso, Michael Costanzo, ManQin Huangfu, Andrew M Smith, Jadine Paw, Bryan-Joseph San Luis, Charles Boone, Guri Giaever, Corey Nislow, Andrew Emili, Zhaolei Zhang (2008) "The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast", Genome Research, 18(7):1092-1099. [abstract] Belinda J Norris, Vicki A Whan (2008), "A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sheep", Genome Research, 18(8):1282-1293. [abstract] A Prachumwat and WH Li (2008) "Gene number expansion and contraction in vertebrate genomes with respect to invertebrate genomes", Genome Research, 18(2):221-232. [abstract] Aviva Presser, Michael B. Elowitz, Manolis Kellis, Roy Kishony (2008) "The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication", Proceedings of National Academy of Sciences, 105:950-954. [html] Nicholas H Putnam, Thomas Butts, David E K Ferrier, Rebecca F Furlong, Uffe Hellsten, Takeshi Kawashima, Marc Robinson-Rechavi, Eiichi Shoguchi, Astrid Terry, Jr-Kai Yu, Elia Benito-Gutiérrez, Inna Dubchak, Jordi Garcia-Fernàndez, Jeremy J Gibson-Brown, Igor V Grigoriev, Amy C Horton, Pieter J de Jong, Jerzy Jurka, Vladimir V Kapitonov, Yuji Kohara, Yoko Kuroki, Erika Lindquist, Susan Lucas, Kazutoyo Osoegawa, Len A Pennacchio, Asaf A Salamov, Yutaka Satou, Tatjana Sauka-Spengler, Jeremy Schmutz, Tadasu Shin-I, Atsushi Toyoda, Marianne Bronner-Fraser, Asao Fujiyama, Linda Z Holland, Peter W H Holland, Nori Satoh, Daniel S Rokhsar (2008), "The amphioxus genome and the evolution of the chordate karyotype", Nature, 453:1064-1071. [ abstract] DR Scannell and KH Wolfe (2008) "A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast", Genome Research, 18(1):137-147. [abstract] Marie Sémon, Kenneth H. Wolfe (2008), "Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis", Proceedings of National Academy of Sciences, 105:8333-8338. [abstract] Zhen Wang, Guohui Ding, Zhonghao Yu, Lei Liu, Yixue Li (2008), "Modeling the age distribution of gene duplications in vertebrate genome using mixture density", Genomics, 93(2):146-151. [ abstract] Robert Warren, David Sankoff (2008), "Genome halving with double cut and join", in Proceedings of the 6th Asia-Pacific Bioinformatics Conference eds. A Brazma, S Miyano, T Akutsu, pp.231-240 (Imperial College Press). Jian-Hong Xu, Joachim Messing (2008), "Organization of the prolamin gene family provides insight into the evolution of the maize genome and gene duplications in grass species", Proceedings of National Academy of Sciences, 105:14330-14335. [abstract] D Zheng (2008), "Asymmetric histone modifications between the original and derived loci of human segmental duplications", Genome Biology, 9(7):R105.