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For: Teshima KM, Innan H. The coalescent with selection on copy number variants. Genetics 2012;190:1077-86. [PMID: 22174068 DOI: 10.1534/genetics.111.135343] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Porubsky D, Dashnow H, Sasani TA, Logsdon GA, Hallast P, Noyes MD, Kronenberg ZN, Mokveld T, Koundinya N, Nolan C, Steely CJ, Guarracino A, Dolzhenko E, Harvey WT, Rowell WJ, Grigorev K, Nicholas TJ, Goldberg ME, Oshima KK, Lin J, Ebert P, Watkins WS, Leung TY, Hanlon VCT, McGee S, Pedersen BS, Happ HC, Jeong H, Munson KM, Hoekzema K, Chan DD, Wang Y, Knuth J, Garcia GH, Fanslow C, Lambert C, Lee C, Smith JD, Levy S, Mason CE, Garrison E, Lansdorp PM, Neklason DW, Jorde LB, Quinlan AR, Eberle MA, Eichler EE. Human de novo mutation rates from a four-generation pedigree reference. Nature 2025:10.1038/s41586-025-08922-2. [PMID: 40269156 DOI: 10.1038/s41586-025-08922-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 03/20/2025] [Indexed: 04/25/2025]
2
Porubsky D, Dashnow H, Sasani TA, Logsdon GA, Hallast P, Noyes MD, Kronenberg ZN, Mokveld T, Koundinya N, Nolan C, Steely CJ, Guarracino A, Dolzhenko E, Harvey WT, Rowell WJ, Grigorev K, Nicholas TJ, Oshima KK, Lin J, Ebert P, Watkins WS, Leung TY, Hanlon VCT, McGee S, Pedersen BS, Goldberg ME, Happ HC, Jeong H, Munson KM, Hoekzema K, Chan DD, Wang Y, Knuth J, Garcia GH, Fanslow C, Lambert C, Lee C, Smith JD, Levy S, Mason CE, Garrison E, Lansdorp PM, Neklason DW, Jorde LB, Quinlan AR, Eberle MA, Eichler EE. A familial, telomere-to-telomere reference for human de novo mutation and recombination from a four-generation pedigree. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.05.606142. [PMID: 39149261 PMCID: PMC11326147 DOI: 10.1101/2024.08.05.606142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
3
Vollger MR, Dishuck PC, Harvey WT, DeWitt WS, Guitart X, Goldberg ME, Rozanski AN, Lucas J, Asri M, Munson KM, Lewis AP, Hoekzema K, Logsdon GA, Porubsky D, Paten B, Harris K, Hsieh P, Eichler EE. Increased mutation and gene conversion within human segmental duplications. Nature 2023;617:325-334. [PMID: 37165237 PMCID: PMC10172114 DOI: 10.1038/s41586-023-05895-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 02/28/2023] [Indexed: 05/12/2023]
4
Hollox EJ, Zuccherato LW, Tucci S. Genome structural variation in human evolution. Trends Genet 2021;38:45-58. [PMID: 34284881 DOI: 10.1016/j.tig.2021.06.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 01/01/2023]
5
Esoh KK, Apinjoh TO, Nyanjom SG, Wonkam A, Chimusa ER, Amenga-Etego L, Amambua-Ngwa A, Achidi EA. Fine scale human genetic structure in three regions of Cameroon reveals episodic diversifying selection. Sci Rep 2021;11:1039. [PMID: 33441574 PMCID: PMC7807043 DOI: 10.1038/s41598-020-79124-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/28/2020] [Indexed: 01/29/2023]  Open
6
MacQueen A, Tian D, Chang W, Holub E, Kreitman M, Bergelson J. Population Genetics of the Highly Polymorphic RPP8 Gene Family. Genes (Basel) 2019;10:E691. [PMID: 31500388 PMCID: PMC6771003 DOI: 10.3390/genes10090691] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/31/2019] [Accepted: 09/03/2019] [Indexed: 02/06/2023]  Open
7
Hartasánchez DA, Brasó-Vives M, Heredia-Genestar JM, Pybus M, Navarro A. Effect of Collapsed Duplications on Diversity Estimates: What to Expect. Genome Biol Evol 2018;10:2899-2905. [PMID: 30364947 PMCID: PMC6239678 DOI: 10.1093/gbe/evy223] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2018] [Indexed: 12/19/2022]  Open
8
Steenwyk JL, Soghigian JS, Perfect JR, Gibbons JG. Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii from the North American Pacific Northwest. BMC Genomics 2016;17:700. [PMID: 27590805 PMCID: PMC5009542 DOI: 10.1186/s12864-016-3044-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/24/2016] [Indexed: 12/13/2022]  Open
9
Bickhart DM, Xu L, Hutchison JL, Cole JB, Null DJ, Schroeder SG, Song J, Garcia JF, Sonstegard TS, Van Tassell CP, Schnabel RD, Taylor JF, Lewin HA, Liu GE. Diversity and population-genetic properties of copy number variations and multicopy genes in cattle. DNA Res 2016;23:253-62. [PMID: 27085184 PMCID: PMC4909312 DOI: 10.1093/dnares/dsw013] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/29/2016] [Indexed: 11/14/2022]  Open
10
Hartasánchez DA, Brasó-Vives M, Fuentes-Díaz J, Vallès-Codina O, Navarro A. SeDuS: segmental duplication simulator. Bioinformatics 2015;32:148-50. [PMID: 26358728 DOI: 10.1093/bioinformatics/btv481] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 08/12/2015] [Indexed: 11/12/2022]  Open
11
Estimating copy numbers of alleles from population-scale high-throughput sequencing data. BMC Bioinformatics 2015;16 Suppl 1:S4. [PMID: 25707811 PMCID: PMC4331703 DOI: 10.1186/1471-2105-16-s1-s4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]  Open
12
Interplay of interlocus gene conversion and crossover in segmental duplications under a neutral scenario. G3-GENES GENOMES GENETICS 2014;4:1479-89. [PMID: 24906640 PMCID: PMC4132178 DOI: 10.1534/g3.114.012435] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
13
Human gene copy number variation and infectious disease. Hum Genet 2014;133:1217-33. [PMID: 25110110 DOI: 10.1007/s00439-014-1457-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 05/20/2014] [Indexed: 01/05/2023]
14
Both positive and negative selection pressures contribute to the polymorphism pattern of the duplicated human CYP21A2 gene. PLoS One 2013;8:e81977. [PMID: 24312389 PMCID: PMC3843699 DOI: 10.1371/journal.pone.0081977] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Accepted: 10/20/2013] [Indexed: 11/19/2022]  Open
15
Hanikenne M, Kroymann J, Trampczynska A, Bernal M, Motte P, Clemens S, Krämer U. Hard selective sweep and ectopic gene conversion in a gene cluster affording environmental adaptation. PLoS Genet 2013;9:e1003707. [PMID: 23990800 PMCID: PMC3749932 DOI: 10.1371/journal.pgen.1003707] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 06/22/2013] [Indexed: 12/27/2022]  Open
16
Bánlaki Z, Szabó JA, Szilágyi Á, Patócs A, Prohászka Z, Füst G, Doleschall M. Intraspecific evolution of human RCCX copy number variation traced by haplotypes of the CYP21A2 gene. Genome Biol Evol 2013;5:98-112. [PMID: 23241443 PMCID: PMC3595039 DOI: 10.1093/gbe/evs121] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
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