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For: Brewer BJ, Payen C, Raghuraman MK, Dunham MJ. Origin-dependent inverted-repeat amplification: a replication-based model for generating palindromic amplicons. PLoS Genet 2011;7:e1002016. [PMID: 21437266 PMCID: PMC3060070 DOI: 10.1371/journal.pgen.1002016] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
Number Cited by Other Article(s)
1
Eugen-Olsen RB, Hariprakash J, Oestergaard V, Regenberg B. Molecular mechanisms of extrachromosomal circular DNA formation. Nucleic Acids Res 2025;53:gkaf122. [PMID: 40037708 PMCID: PMC11879418 DOI: 10.1093/nar/gkaf122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 01/26/2025] [Accepted: 02/06/2025] [Indexed: 03/06/2025]  Open
2
Spealman P, de Santana C, De T, Gresham D. Multilevel Gene Expression Changes in Lineages Containing Adaptive Copy Number Variants. Mol Biol Evol 2025;42:msaf005. [PMID: 39847535 PMCID: PMC11789944 DOI: 10.1093/molbev/msaf005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 10/28/2024] [Accepted: 12/02/2024] [Indexed: 01/25/2025]  Open
3
Chuong JN, Ben Nun N, Suresh I, Matthews JC, De T, Avecilla G, Abdul-Rahman F, Brandt N, Ram Y, Gresham D. Template switching during DNA replication is a prevalent source of adaptive gene amplification. eLife 2025;13:RP98934. [PMID: 39899365 PMCID: PMC11790251 DOI: 10.7554/elife.98934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2025]  Open
4
Chuong JN, Nun NB, Suresh I, Matthews JC, De T, Avecilla G, Abdul-Rahman F, Brandt N, Ram Y, Gresham D. Template switching during DNA replication is a prevalent source of adaptive gene amplification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.589936. [PMID: 39464144 PMCID: PMC11507740 DOI: 10.1101/2024.05.03.589936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
5
Longan ER, Fay JC. The distribution of beneficial mutational effects between two sister yeast species poorly explains natural outcomes of vineyard adaptation. Genetics 2024;228:iyae160. [PMID: 39373582 PMCID: PMC11631397 DOI: 10.1093/genetics/iyae160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2024] [Revised: 09/21/2024] [Accepted: 10/03/2024] [Indexed: 10/08/2024]  Open
6
Longan ER, Fay JC. The distribution of beneficial mutational effects between two sister yeast species poorly explains natural outcomes of vineyard adaptation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597243. [PMID: 38895255 PMCID: PMC11185594 DOI: 10.1101/2024.06.03.597243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
7
Brewer BJ, Dunham MJ, Raghuraman MK. A unifying model that explains the origins of human inverted copy number variants. PLoS Genet 2024;20:e1011091. [PMID: 38175827 PMCID: PMC10766186 DOI: 10.1371/journal.pgen.1011091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]  Open
8
Martin R, Espinoza CY, Large CRL, Rosswork J, Van Bruinisse C, Miller AW, Sanchez JC, Miller M, Paskvan S, Alvino GM, Dunham MJ, Raghuraman MK, Brewer BJ. Template switching between the leading and lagging strands at replication forks generates inverted copy number variants through hairpin-capped extrachromosomal DNA. PLoS Genet 2024;20:e1010850. [PMID: 38175823 PMCID: PMC10766183 DOI: 10.1371/journal.pgen.1010850] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/23/2023] [Indexed: 01/06/2024]  Open
9
Selmecki A. Recurrent copy number variations in the human fungal pathogen Candida parapsilosis. mBio 2023;14:e0071323. [PMID: 37787545 PMCID: PMC10653803 DOI: 10.1128/mbio.00713-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]  Open
10
Hoerr RE, Eng A, Payen C, Di Rienzi SC, Raghuraman MK, Dunham MJ, Brewer BJ, Friedman KL. Hotspot of de novo telomere addition stabilizes linear amplicons in yeast grown in sulfate-limiting conditions. Genetics 2023;224:iyad010. [PMID: 36702776 PMCID: PMC10213492 DOI: 10.1093/genetics/iyad010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/10/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023]  Open
11
Nunn CJ, Goyal S. Contingency and selection in mitochondrial genome dynamics. eLife 2022;11:76557. [PMID: 35404229 PMCID: PMC9054137 DOI: 10.7554/elife.76557] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/08/2022] [Indexed: 11/22/2022]  Open
12
Gorkovskiy A, Verstrepen KJ. The Role of Structural Variation in Adaptation and Evolution of Yeast and Other Fungi. Genes (Basel) 2021;12:699. [PMID: 34066718 PMCID: PMC8150848 DOI: 10.3390/genes12050699] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 01/12/2023]  Open
13
Doi G, Okada S, Yasukawa T, Sugiyama Y, Bala S, Miyazaki S, Kang D, Ito T. Catalytically inactive Cas9 impairs DNA replication fork progression to induce focal genomic instability. Nucleic Acids Res 2021;49:954-968. [PMID: 33398345 PMCID: PMC7826275 DOI: 10.1093/nar/gkaa1241] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/05/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022]  Open
14
Liang X, Chen H, Li L, An R, Komiyama M. Ring-Structured DNA and RNA as Key PlayersIn VivoandIn Vitro. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
15
Spealman P, Burrell J, Gresham D. Inverted duplicate DNA sequences increase translocation rates through sequencing nanopores resulting in reduced base calling accuracy. Nucleic Acids Res 2020;48:4940-4945. [PMID: 32255181 PMCID: PMC7229812 DOI: 10.1093/nar/gkaa206] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 03/14/2020] [Accepted: 04/03/2020] [Indexed: 12/27/2022]  Open
16
Todd RT, Selmecki A. Expandable and reversible copy number amplification drives rapid adaptation to antifungal drugs. eLife 2020;9:e58349. [PMID: 32687060 PMCID: PMC7371428 DOI: 10.7554/elife.58349] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/09/2020] [Indexed: 12/13/2022]  Open
17
Todd RT, Wikoff TD, Forche A, Selmecki A. Genome plasticity in Candida albicans is driven by long repeat sequences. eLife 2019;8:45954. [PMID: 31172944 PMCID: PMC6591007 DOI: 10.7554/elife.45954] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 06/07/2019] [Indexed: 11/13/2022]  Open
18
Lauer S, Gresham D. An evolving view of copy number variants. Curr Genet 2019;65:1287-1295. [PMID: 31076843 DOI: 10.1007/s00294-019-00980-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/17/2019] [Accepted: 04/20/2019] [Indexed: 01/08/2023]
19
Palacios-Flores K, Castillo A, Uribe C, García Sotelo J, Boege M, Dávila G, Flores M, Palacios R, Morales L. Prediction and identification of recurrent genomic rearrangements that generate chimeric chromosomes in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2019;116:8445-8450. [PMID: 30962378 PMCID: PMC6486755 DOI: 10.1073/pnas.1819585116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]  Open
20
Lu S. De novo origination of MIRNAs through generation of short inverted repeats in target genes. RNA Biol 2019;16:846-859. [PMID: 30870071 DOI: 10.1080/15476286.2019.1593744] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]  Open
21
Lauer S, Avecilla G, Spealman P, Sethia G, Brandt N, Levy SF, Gresham D. Single-cell copy number variant detection reveals the dynamics and diversity of adaptation. PLoS Biol 2018;16:e3000069. [PMID: 30562346 PMCID: PMC6298651 DOI: 10.1371/journal.pbio.3000069] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/14/2018] [Indexed: 12/13/2022]  Open
22
Lavi B, Levy Karin E, Pupko T, Hazkani-Covo E. The Prevalence and Evolutionary Conservation of Inverted Repeats in Proteobacteria. Genome Biol Evol 2018;10:918-927. [PMID: 29608719 PMCID: PMC5941160 DOI: 10.1093/gbe/evy044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2018] [Indexed: 12/11/2022]  Open
23
Whole Genome Sequence Analysis of Mutations Accumulated in rad27Δ Yeast Strains with Defects in the Processing of Okazaki Fragments Indicates Template-Switching Events. G3-GENES GENOMES GENETICS 2017;7:3775-3787. [PMID: 28974572 PMCID: PMC5677150 DOI: 10.1534/g3.117.300262] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
24
Ohsaki K, Ohgaki Y, Shimizu N. Amplification of a transgene within a long array of replication origins favors higher gene expression in animal cells. PLoS One 2017;12:e0175585. [PMID: 28403180 PMCID: PMC5389822 DOI: 10.1371/journal.pone.0175585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/28/2017] [Indexed: 11/27/2022]  Open
25
Chen ZX, Oliver B, Zhang YE, Gao G, Long M. Expressed Structurally Stable Inverted Duplicates in Mammalian Genomes as Functional Noncoding Elements. Genome Biol Evol 2017;9:981-992. [PMID: 28338961 PMCID: PMC5398296 DOI: 10.1093/gbe/evx054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2017] [Indexed: 12/24/2022]  Open
26
Differential paralog divergence modulates genome evolution across yeast species. PLoS Genet 2017;13:e1006585. [PMID: 28196070 PMCID: PMC5308817 DOI: 10.1371/journal.pgen.1006585] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/13/2017] [Indexed: 11/24/2022]  Open
27
Beyer T, Weinert T. Ontogeny of Unstable Chromosomes Generated by Telomere Error in Budding Yeast. PLoS Genet 2016;12:e1006345. [PMID: 27716774 PMCID: PMC5065131 DOI: 10.1371/journal.pgen.1006345] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 09/07/2016] [Indexed: 11/19/2022]  Open
28
Kuzminov A. Chromosomal Replication Complexity: A Novel DNA Metrics and Genome Instability Factor. PLoS Genet 2016;12:e1006229. [PMID: 27711112 PMCID: PMC5053440 DOI: 10.1371/journal.pgen.1006229] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]  Open
29
Telomere Dysfunction Triggers Palindrome Formation Independently of Double-Strand Break Repair Mechanisms. Genetics 2016;203:1659-68. [PMID: 27334270 PMCID: PMC4981268 DOI: 10.1534/genetics.115.183020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 06/06/2016] [Indexed: 11/18/2022]  Open
30
Thierry A, Khanna V, Dujon B. Massive Amplification at an Unselected Locus Accompanies Complex Chromosomal Rearrangements in Yeast. G3 (BETHESDA, MD.) 2016;6:1201-15. [PMID: 26945028 PMCID: PMC4856073 DOI: 10.1534/g3.115.024547] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 02/20/2016] [Indexed: 12/13/2022]
31
Deng SK, Yin Y, Petes TD, Symington LS. Mre11-Sae2 and RPA Collaborate to Prevent Palindromic Gene Amplification. Mol Cell 2016;60:500-8. [PMID: 26545079 DOI: 10.1016/j.molcel.2015.09.027] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 08/20/2015] [Accepted: 09/28/2015] [Indexed: 12/17/2022]
32
Brewer BJ, Payen C, Di Rienzi SC, Higgins MM, Ong G, Dunham MJ, Raghuraman MK. Origin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification. PLoS Genet 2015;11:e1005699. [PMID: 26700858 PMCID: PMC4689423 DOI: 10.1371/journal.pgen.1005699] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/03/2015] [Indexed: 01/20/2023]  Open
33
Extrachromosomal circular DNA is common in yeast. Proc Natl Acad Sci U S A 2015;112:E3114-22. [PMID: 26038577 DOI: 10.1073/pnas.1508825112] [Citation(s) in RCA: 185] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
34
Sunshine AB, Payen C, Ong GT, Liachko I, Tan KM, Dunham MJ. The fitness consequences of aneuploidy are driven by condition-dependent gene effects. PLoS Biol 2015;13:e1002155. [PMID: 26011532 PMCID: PMC4444335 DOI: 10.1371/journal.pbio.1002155] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 04/15/2015] [Indexed: 11/30/2022]  Open
35
Reams AB, Roth JR. Mechanisms of gene duplication and amplification. Cold Spring Harb Perspect Biol 2015;7:a016592. [PMID: 25646380 DOI: 10.1101/cshperspect.a016592] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
36
Thierry A, Khanna V, Créno S, Lafontaine I, Ma L, Bouchier C, Dujon B. Macrotene chromosomes provide insights to a new mechanism of high-order gene amplification in eukaryotes. Nat Commun 2015;6:6154. [PMID: 25635677 PMCID: PMC4317496 DOI: 10.1038/ncomms7154] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 12/15/2014] [Indexed: 12/30/2022]  Open
37
Laffitte MCN, Genois MM, Mukherjee A, Légaré D, Masson JY, Ouellette M. Formation of linear amplicons with inverted duplications in Leishmania requires the MRE11 nuclease. PLoS Genet 2014;10:e1004805. [PMID: 25474106 PMCID: PMC4256157 DOI: 10.1371/journal.pgen.1004805] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 10/06/2014] [Indexed: 11/22/2022]  Open
38
Rizvi AZ, Bhattacharya C. Detection of Replication Origin Sites in Herpesvirus Genomes by Clustering and Scoring of Palindromes with Quadratic Entropy Measures. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2014;11:1108-1118. [PMID: 26357048 DOI: 10.1109/tcbb.2014.2330622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
39
The dynamics of diverse segmental amplifications in populations of Saccharomyces cerevisiae adapting to strong selection. G3-GENES GENOMES GENETICS 2014;4:399-409. [PMID: 24368781 PMCID: PMC3962480 DOI: 10.1534/g3.113.009365] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
40
Darmon E, Leach DRF. Bacterial genome instability. Microbiol Mol Biol Rev 2014;78:1-39. [PMID: 24600039 PMCID: PMC3957733 DOI: 10.1128/mmbr.00035-13] [Citation(s) in RCA: 266] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
41
Beri S, Bonaglia MC, Giorda R. Low-copy repeats at the human VIPR2 gene predispose to recurrent and nonrecurrent rearrangements. Eur J Hum Genet 2013;21:757-61. [PMID: 23073313 PMCID: PMC3722940 DOI: 10.1038/ejhg.2012.235] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 08/07/2012] [Accepted: 09/12/2012] [Indexed: 01/30/2023]  Open
42
Gene copy-number variation in haploid and diploid strains of the yeast Saccharomyces cerevisiae. Genetics 2013;193:785-801. [PMID: 23307895 DOI: 10.1534/genetics.112.146522] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]  Open
43
Marotta M, Chen X, Inoshita A, Stephens R, Budd GT, Crowe JP, Lyons J, Kondratova A, Tubbs R, Tanaka H. A common copy-number breakpoint of ERBB2 amplification in breast cancer colocalizes with a complex block of segmental duplications. Breast Cancer Res 2012. [PMID: 23181561 PMCID: PMC4053137 DOI: 10.1186/bcr3362] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
44
Reams AB, Kofoid E, Kugelberg E, Roth JR. Multiple pathways of duplication formation with and without recombination (RecA) in Salmonella enterica. Genetics 2012;192:397-415. [PMID: 22865732 PMCID: PMC3454872 DOI: 10.1534/genetics.112.142570] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Accepted: 07/24/2012] [Indexed: 12/11/2022]  Open
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Di Rienzi SC, Lindstrom KC, Mann T, Noble WS, Raghuraman MK, Brewer BJ. Maintaining replication origins in the face of genomic change. Genome Res 2012;22:1940-52. [PMID: 22665441 PMCID: PMC3460189 DOI: 10.1101/gr.138248.112] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Carr AM, Paek AL, Weinert T. DNA replication: failures and inverted fusions. Semin Cell Dev Biol 2011;22:866-74. [PMID: 22020070 DOI: 10.1016/j.semcdb.2011.10.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 10/12/2011] [Indexed: 11/16/2022]
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