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Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence
Joseph Cheung, Xavier Estivill, Razi Khaja, Jeffrey R MacDonald, Ken Lau, Lap-Chee Tsui, Stephen W Scherer
Genome Biol. 2003; 4(4): R25. Published online 2003 March 17. doi: 10.1186/gb-2003-4-4-r25
PMCID:
PMC154576
Abstract Full Text PDF–836K Supplementary Material
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 Is Cited by the Following 60 Articles in this Archive:
RAF gene fusion breakpoints in pediatric brain tumors are characterized by significant enrichment of sequence microhomology
Andrew R.J. Lawson, Guy F.L. Hindley, Tim Forshew, Ruth G. Tatevossian, Gabriel A. Jamie, Gavin P. Kelly, Geoffrey A. Neale, Jing Ma, Tania A. Jones, David W. Ellison, Denise Sheer
Genome Res. 2011 April; 21(4): 505–514. doi: 10.1101/gr.115782.110
PMCID:
PMC3065698
Abstract Full Text PDF–1.0M
Segmental duplication as one of the driving forces underlying the diversity of the human immunoglobulin heavy chain variable gene region
Sreemanta Pramanik, Xiangfeng Cui, Hui-Yun Wang, Nyam-Osor Chimge, Guohong Hu, Li Shen, Richeng Gao, Honghua Li
BMC Genomics. 2011; 12: 78. Published online 2011 January 27. doi: 10.1186/1471-2164-12-78
PMCID:
PMC3042411
Abstract Full Text PDF–379K
The evolution and expression of the snaR family of small non-coding RNAs
Andrew M. Parrott, Michael Tsai, Priyanka Batchu, Karen Ryan, Harvey L. Ozer, Bin Tian, Michael B. Mathews
Nucleic Acids Res. 2011 March; 39(4): 1485–1500. Published online 2010 October 8. doi: 10.1093/nar/gkq856
PMCID:
PMC3045588
Abstract Full Text PDF–2.8M Supplementary Material
A large, complex structural polymorphism at 16p12.1 underlies microdeletion disease risk
Francesca Antonacci, Jeffrey M. Kidd, Tomas Marques-Bonet, Brian Teague, Mario Ventura, Santhosh Girirajan, Can Alkan, Catarina D. Campbell, Laura Vives, Maika Malig, Jill A. Rosenfeld, Blake C. Ballif, Lisa G. Shaffer, Tina A. Graves, Richard K. Wilson, David C. Schwartz, Evan E. Eichler
Nat Genet. Author manuscript; available in PMC 2011 March 1.
Published in final edited form as: Nat Genet. 2010 September; 42(9): 745–750. Published online 2010 August 22. doi: 10.1038/ng.643
PMCID:
PMC2930074
Abstract Full Text PDF–546K Supplementary Material
Mosaic Uniparental Disomies and Aneuploidies as Large Structural Variants of the Human Genome
Benjamín Rodríguez-Santiago, Núria Malats, Nathaniel Rothman, Lluís Armengol, Montse Garcia-Closas, Manolis Kogevinas, Olaya Villa, Amy Hutchinson, Julie Earl, Gaëlle Marenne, Kevin Jacobs, Daniel Rico, Adonina Tardón, Alfredo Carrato, Gilles Thomas, Alfonso Valencia, Debra Silverman, Francisco X. Real, Stephen J. Chanock, Luis A. Pérez-Jurado
Am J Hum Genet. 2010 July 9; 87(1): 129–138. doi: 10.1016/j.ajhg.2010.06.002
PMCID:
PMC2896781
Abstract Full Text PDF–1.9M Supplementary Material
Detection and correction of false segmental duplications caused by genome mis-assembly
David R Kelley, Steven L Salzberg
Genome Biol. 2010; 11(3): R28. Published online 2010 March 10. doi: 10.1186/gb-2010-11-3-r28
PMCID:
PMC2864568
Abstract Full Text PDF–1.2M Supplementary Material
Population-genetic nature of copy number variations in the human genome
Mamoru Kato, Takahisa Kawaguchi, Shumpei Ishikawa, Takayoshi Umeda, Reiichiro Nakamichi, Michael H. Shapero, Keith W. Jones, Yusuke Nakamura, Hiroyuki Aburatani, Tatsuhiko Tsunoda
Hum Mol Genet. 2010 March 1; 19(5): 761–773. Published online 2009 December 5. doi: 10.1093/hmg/ddp541
PMCID:
PMC2816609
Abstract Full Text PDF–452K Supplementary Material
Analysis of recent segmental duplications in the bovine genome
George E Liu, Mario Ventura, Angelo Cellamare, Lin Chen, Ze Cheng, Bin Zhu, Congjun Li, Jiuzhou Song, Evan E Eichler
BMC Genomics. 2009; 10: 571. Published online 2009 December 1. doi: 10.1186/1471-2164-10-571
PMCID:
PMC2796684
Abstract Full Text PDF–1.3M Supplementary Material
Targets of Balancing Selection in the Human Genome
Aida M. Andrés, Melissa J. Hubisz, Amit Indap, Dara G. Torgerson, Jeremiah D. Degenhardt, Adam R. Boyko, Ryan N. Gutenkunst, Thomas J. White, Eric D. Green, Carlos D. Bustamante, Andrew G. Clark, Rasmus Nielsen
Mol Biol Evol. 2009 December; 26(12): 2755–2764. Published online 2009 August 27. doi: 10.1093/molbev/msp190
PMCID:
PMC2782326
Abstract Full Text PDF–365K Supplementary Material
DDX11L: a novel transcript family emerging from human subtelomeric regions
Valerio Costa, Amelia Casamassimi, Roberta Roberto, Fernando Gianfrancesco, Maria R Matarazzo, Michele D'Urso, Maurizio D'Esposito, Mariano Rocchi, Alfredo Ciccodicola
BMC Genomics. 2009; 10: 250. Published online 2009 May 28. doi: 10.1186/1471-2164-10-250
PMCID:
PMC2705379
Abstract Full Text PDF–1.9M Supplementary Material
Genetic Structures of Copy Number Variants Revealed by Genotyping Single Sperm
Minjie Luo, Xiangfeng Cui, David Fredman, Anthony J. Brookes, Marco A. Azaro, Danielle M. Greenawalt, Guohong Hu, Hui-Yun Wang, Irina V. Tereshchenko, Yong Lin, Yue Shentu, Richeng Gao, Li Shen, Honghua Li
PLoS ONE. 2009; 4(4): e5236. Published online 2009 April 22. doi: 10.1371/journal.pone.0005236
PMCID:
PMC2668179
Abstract Full Text PDF–371K
SNP discovery and haplotype analysis in the segmentally duplicated DRD5 coding region
D. J. E. HOUSLEY, M. NIKOLAS, P. J. VENTA, K. A. JERNIGAN, I. D. WALDMAN, J. T. NIGG, K. H. FRIDERICI
Ann Hum Genet. Author manuscript; available in PMC 2009 September 23.
Published in final edited form as: Ann Hum Genet. 2009 May; 73(Pt 3): 274–282. Published online 2009 March 30. doi: 10.1111/j.1469-1809.2009.00513.x
PMCID:
PMC2749463
Abstract Full Text PDF–455K Supplementary Material
Large-scale inference of the point mutational spectrum in human segmental duplications
Sigve Nakken, Einar A Rødland, Torbjørn Rognes, Eivind Hovig
BMC Genomics. 2009; 10: 43. Published online 2009 January 22. doi: 10.1186/1471-2164-10-43
PMCID:
PMC2640414
Abstract Full Text PDF–623K
Severe Combined Immunodeficiency (SCID) and Attention Deficit Hyperactivity Disorder (ADHD) Associated with a Coronin-1A Mutation and a Chromosome 16p11.2 Deletion
Lawrence R. Shiow, Kenneth Paris, Matthew C. Akana, Jason G. Cyster, Ricardo U. Sorensen, Jennifer M. Puck
Clin Immunol. Author manuscript; available in PMC 2010 April 1.
Published in final edited form as: Clin Immunol. 2009 April; 131(1): 24–30. Published online 2008 December 20. doi: 10.1016/j.clim.2008.11.002
PMCID:
PMC2692687
Abstract Full Text PDF–746K
Ultraconserved Elements: Analyses of Dosage Sensitivity, Motifs and Boundaries
Charleston W. K. Chiang, Adnan Derti, Daniel Schwartz, Michael F. Chou, Joel N. Hirschhorn, C.-ting Wu
Genetics. 2008 December; 180(4): 2277–2293. doi: 10.1534/genetics.108.096537
PMCID:
PMC2600958
Abstract Full Text PDF–1.2M
Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids
Claudia Münch, Stefan Kirsch, António MG Fernandes, Werner Schempp
BMC Evol Biol. 2008; 8: 269. Published online 2008 October 2. doi: 10.1186/1471-2148-8-269
PMCID:
PMC2566985
Abstract Full Text PDF–1.5M Supplementary Material
The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements
Tomàs Marques-Bonet, Ze Cheng, Xinwei She, Evan E Eichler, Arcadi Navarro
BMC Genomics. 2008; 9: 384. Published online 2008 August 12. doi: 10.1186/1471-2164-9-384
PMCID:
PMC2542386
Abstract Full Text PDF–427K Supplementary Material
DupMasker: A tool for annotating primate segmental duplications
Zhaoshi Jiang, Robert Hubley, Arian Smit, Evan E. Eichler
Genome Res. 2008 August; 18(8): 1362–1368. doi: 10.1101/gr.078477.108
PMCID:
PMC2493431
Abstract Full Text PDF–940K
Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions
Stefan Kirsch, Claudia Münch, Zhaoshi Jiang, Ze Cheng, Lin Chen, Christiane Batz, Evan E. Eichler, Werner Schempp
Genome Res. 2008 July; 18(7): 1030–1042. doi: 10.1101/gr.076711.108
PMCID:
PMC2493392
Abstract Full Text PDF–1.0M
Retrotransposition as a Source of New Promoters
Kohji Okamura, Kenta Nakai
Mol Biol Evol. 2008 June; 25(6): 1231–1238. Published online 2008 March 25. doi: 10.1093/molbev/msn071
PMCID:
PMC2386082
Abstract Full Text PDF–652K Supplementary Material
Genome assembly forensics: finding the elusive mis-assembly
Adam M Phillippy, Michael C Schatz, Mihai Pop
Genome Biol. 2008; 9(3): R55. Published online 2008 March 14. doi: 10.1186/gb-2008-9-3-r55
PMCID:
PMC2397507
Abstract Full Text PDF–639K Supplementary Material
Invertebrate 7SK snRNAs
Andreas R. Gruber, Dorota Koper-Emde, Manja Marz, Hakim Tafer, Stephan Bernhart, Gregor Obernosterer, Axel Mosig, Ivo L. Hofacker, Peter F. Stadler, Bernd-Joachim Benecke
J Mol Evol. 2008 February; 66(2): 107–115. Published online 2008 January 12. doi: 10.1007/s00239-007-9052-6
PMCID:
PMC2755741
Abstract Full Text PDF–1.2M
Analysis of Drosophila Species Genome Size and Satellite DNA Content Reveals Significant Differences Among Strains as Well as Between Species
Giovanni Bosco, Paula Campbell, Joao T. Leiva-Neto, Therese A. Markow
Genetics. 2007 November; 177(3): 1277–1290. doi: 10.1534/genetics.107.075069
PMCID:
PMC2147996
Abstract Full Text PDF–1.0M
Database of Trypanosoma cruzi repeated genes: 20 000 additional gene variants
Erik Arner, Ellen Kindlund, Daniel Nilsson, Fatima Farzana, Marcela Ferella, Martti T Tammi, Björn Andersson
BMC Genomics. 2007; 8: 391. Published online 2007 October 26. doi: 10.1186/1471-2164-8-391
PMCID:
PMC2204015
Abstract Full Text PDF–398K
Copy Number Variants and Common Disorders: Filling the Gaps and Exploring Complexity in Genome-Wide Association Studies
Xavier Estivill, Lluís Armengol
PLoS Genet. 2007 October; 3(10): e190. Published online 2007 October 19. doi: 10.1371/journal.pgen.0030190
PMCID:
PMC2039766
Abstract Full Text PDF–1.9M
The Neutral Coalescent Process for Recent Gene Duplications and Copy-Number Variants
Kevin R. Thornton
Genetics. 2007 October; 177(2): 987–1000. doi: 10.1534/genetics.107.074948
PMCID:
PMC2034660
Abstract Full Text PDF–549K
The Diploid Genome Sequence of an Individual Human
Samuel Levy, Granger Sutton, Pauline C Ng, Lars Feuk, Aaron L Halpern, Brian P Walenz, Nelson Axelrod, Jiaqi Huang, Ewen F Kirkness, Gennady Denisov, Yuan Lin, Jeffrey R MacDonald, Andy Wing Chun Pang, Mary Shago, Timothy B Stockwell, Alexia Tsiamouri, Vineet Bafna, Vikas Bansal, Saul A Kravitz, Dana A Busam, Karen Y Beeson, Tina C McIntosh, Karin A Remington, Josep F Abril, John Gill, Jon Borman, Yu-Hui Rogers, Marvin E Frazier, Stephen W Scherer, Robert L Strausberg, J. Craig Venter
PLoS Biol. 2007 October; 5(10): e254. Published online 2007 September 4. doi: 10.1371/journal.pbio.0050254
PMCID:
PMC1964779
Abstract Full Text PDF–2.2M Supplementary Material
Gene copy number variation spanning 60 million years of human and primate evolution
Laura Dumas, Young H. Kim, Anis Karimpour-Fard, Michael Cox, Janet Hopkins, Jonathan R. Pollack, James M. Sikela
Genome Res. 2007 September; 17(9): 1266–1277. doi: 10.1101/gr.6557307
PMCID:
PMC1950895
Abstract Full Text PDF–1.0M
Challenges and standards in integrating surveys of structural variation
Stephen W Scherer, Charles Lee, Ewan Birney, David M Altshuler, Evan E Eichler, Nigel P Carter, Matthew E Hurles, Lars Feuk
Nat Genet. Author manuscript; available in PMC 2009 June 18.
Published in final edited form as: Nat Genet. 2007 July; 39(7 Suppl): S7–15. doi: 10.1038/ng2093
PMCID:
PMC2698291
Abstract Full Text PDF–174K Supplementary Material
Evolutionary implications of inversions that have caused intra-strand parity in DNA
Kohji Okamura, John Wei, Stephen W Scherer
BMC Genomics. 2007; 8: 160. Published online 2007 June 11. doi: 10.1186/1471-2164-8-160
PMCID:
PMC1913523
Abstract Full Text PDF–537K
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