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For: Liu GE, Alkan C, Jiang L, Zhao S, Eichler EE. Comparative analysis of Alu repeats in primate genomes. Genome Res 2009;19:876-85. [PMID: 19411604 DOI: 10.1101/gr.083972.108] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Number Cited by Other Article(s)
1
Du H, Diao C, Zhuo Y, Zheng X, Hu Z, Lu S, Jin W, Zhou L, Liu JF. Assembly of novel sequences for Chinese domestic pigs reveals new genes and regulatory variants providing new insights into their diversity. Genomics 2024;116:110782. [PMID: 38176574 DOI: 10.1016/j.ygeno.2024.110782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/27/2023] [Accepted: 01/01/2024] [Indexed: 01/06/2024]
2
Zhao P, Gu L, Gao Y, Pan Z, Liu L, Li X, Zhou H, Yu D, Han X, Qian L, Liu GE, Fang L, Wang Z. Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits. Commun Biol 2023;6:894. [PMID: 37652983 PMCID: PMC10471783 DOI: 10.1038/s42003-023-05234-x] [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: 03/02/2022] [Accepted: 08/09/2023] [Indexed: 09/02/2023]  Open
3
Blechter B, Wong JYY, Hu W, Cawthon R, Downward GS, Portengen L, Zhang Y, Ning B, Rahman ML, Ji BT, Li J, Yang K, Dean Hosgood H, Silverman DT, Huang Y, Rothman N, Vermeulen R, Lan Q. Exposure to smoky coal combustion emissions and leukocyte Alu retroelement copy number. Carcinogenesis 2023;44:404-410. [PMID: 37119119 PMCID: PMC10414142 DOI: 10.1093/carcin/bgad027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/09/2022] [Accepted: 04/28/2023] [Indexed: 04/30/2023]  Open
4
Zhao P, Peng C, Fang L, Wang Z, Liu GE. Taming transposable elements in livestock and poultry: a review of their roles and applications. Genet Sel Evol 2023;55:50. [PMID: 37479995 PMCID: PMC10362595 DOI: 10.1186/s12711-023-00821-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/30/2023] [Indexed: 07/23/2023]  Open
5
Shao Y, Zhou L, Li F, Zhao L, Zhang BL, Shao F, Chen JW, Chen CY, Bi X, Zhuang XL, Zhu HL, Hu J, Sun Z, Li X, Wang D, Rivas-González I, Wang S, Wang YM, Chen W, Li G, Lu HM, Liu Y, Kuderna LFK, Farh KKH, Fan PF, Yu L, Li M, Liu ZJ, Tiley GP, Yoder AD, Roos C, Hayakawa T, Marques-Bonet T, Rogers J, Stenson PD, Cooper DN, Schierup MH, Yao YG, Zhang YP, Wang W, Qi XG, Zhang G, Wu DD. Phylogenomic analyses provide insights into primate evolution. Science 2023;380:913-924. [PMID: 37262173 DOI: 10.1126/science.abn6919] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/26/2023] [Indexed: 06/03/2023]
6
Liu X, Zhang Y, Pu Y, Ma Y, Jiang L. Whole-genome identification of transposable elements reveals the equine repetitive element insertion polymorphism in Chinese horses. Anim Genet 2023;54:144-154. [PMID: 36464985 DOI: 10.1111/age.13277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/29/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022]
7
Storer JM, Walker JA, Baker JN, Hossain S, Roos C, Wheeler TJ, Batzer MA. Framework of the Alu Subfamily Evolution in the Platyrrhine Three-Family Clade of Cebidae, Callithrichidae, and Aotidae. Genes (Basel) 2023;14:249. [PMID: 36833175 PMCID: PMC9956951 DOI: 10.3390/genes14020249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/10/2023] [Accepted: 01/14/2023] [Indexed: 01/20/2023]  Open
8
Liu P, Cuerda-Gil D, Shahid S, Slotkin RK. The Epigenetic Control of the Transposable Element Life Cycle in Plant Genomes and Beyond. Annu Rev Genet 2022;56:63-87. [DOI: 10.1146/annurev-genet-072920-015534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
9
Wang J, Weatheritt R, Voineagu I. Alu-minating the Mechanisms Underlying Primate Cortex Evolution. Biol Psychiatry 2022;92:760-771. [PMID: 35981906 DOI: 10.1016/j.biopsych.2022.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 04/04/2022] [Accepted: 04/28/2022] [Indexed: 11/02/2022]
10
Billon V, Sanchez-Luque FJ, Rasmussen J, Bodea GO, Gerhardt DJ, Gerdes P, Cheetham SW, Schauer SN, Ajjikuttira P, Meyer TJ, Layman CE, Nevonen KA, Jansz N, Garcia-Perez JL, Richardson SR, Ewing AD, Carbone L, Faulkner GJ. Somatic retrotransposition in the developing rhesus macaque brain. Genome Res 2022;32:1298-1314. [PMID: 35728967 PMCID: PMC9341517 DOI: 10.1101/gr.276451.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/14/2022] [Indexed: 12/03/2022]
11
Palmada-Flores M, Orkin JD, Haase B, Mountcastle J, Bertelsen MF, Fedrigo O, Kuderna LFK, Jarvis ED, Marques-Bonet T. A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta). Gigascience 2022;11:6562532. [PMID: 35365833 PMCID: PMC8975718 DOI: 10.1093/gigascience/giac026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/14/2022] [Accepted: 02/19/2022] [Indexed: 01/31/2023]  Open
12
Recently Integrated Alu Elements in Capuchin Monkeys: A Resource for Cebus/Sapajus Genomics. Genes (Basel) 2022;13:genes13040572. [PMID: 35456378 PMCID: PMC9030454 DOI: 10.3390/genes13040572] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022]  Open
13
Li Y, Jiang N, Sun Y. AnnoSINE: a short interspersed nuclear elements annotation tool for plant genomes. PLANT PHYSIOLOGY 2022;188:955-970. [PMID: 34792587 PMCID: PMC8825457 DOI: 10.1093/plphys/kiab524] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
14
Zhao P, Du H, Jiang L, Zheng X, Feng W, Diao C, Zhou L, Liu GE, Zhang H, Chamba Y, Zhang Q, Li B, Liu JF. PRE-1 Revealed Previous Unknown Introgression Events in Eurasian Boars during the Middle Pleistocene. Genome Biol Evol 2021;12:1751-1764. [PMID: 33151306 PMCID: PMC7643367 DOI: 10.1093/gbe/evaa142] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 12/22/2022]  Open
15
Wong JYY, Cawthon R, Dai Y, Vermeulen R, Bassig BA, Hu W, Duan H, Niu Y, Downward GS, Leng S, Ji BT, Fu W, Xu J, Meliefste K, Zhou B, Yang J, Ren D, Ye M, Jia X, Meng T, Bin P, Hosgood Iii HD, Silverman DT, Rothman N, Zheng Y, Lan Q. Elevated Alu retroelement copy number among workers exposed to diesel engine exhaust. Occup Environ Med 2021;78:823-828. [PMID: 34039759 DOI: 10.1136/oemed-2021-107462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/03/2021] [Accepted: 05/07/2021] [Indexed: 11/04/2022]
16
Long X, Xue H. Genetic-variant hotspots and hotspot clusters in the human genome facilitating adaptation while increasing instability. Hum Genomics 2021;15:19. [PMID: 33741065 PMCID: PMC7976700 DOI: 10.1186/s40246-021-00318-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 03/04/2021] [Indexed: 12/25/2022]  Open
17
Casanova EL, Konkel MK. The Developmental Gene Hypothesis for Punctuated Equilibrium: Combined Roles of Developmental Regulatory Genes and Transposable Elements. Bioessays 2020;42:e1900173. [PMID: 31943266 DOI: 10.1002/bies.201900173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/30/2019] [Indexed: 12/13/2022]
18
Lee W, Choi M, Kim S, Tang W, Kim DH, Kim HS, Liang P, Han K. A comprehensive analysis of the Baboon-specific full-length LINE-1 retrotransposons. Genes Genomics 2019;41:831-837. [PMID: 30887304 DOI: 10.1007/s13258-019-00794-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 02/08/2019] [Indexed: 11/26/2022]
19
Xu S, Feng Y, Zhao S. Proteins with Evolutionarily Hypervariable Domains are Associated with Immune Response and Better Survival of Basal-like Breast Cancer Patients. Comput Struct Biotechnol J 2019;17:430-440. [PMID: 30996822 PMCID: PMC6451114 DOI: 10.1016/j.csbj.2019.03.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/21/2019] [Accepted: 03/16/2019] [Indexed: 10/27/2022]  Open
20
Moshiri N, Mirarab S. A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition. Syst Biol 2018;67:475-489. [PMID: 29165679 DOI: 10.1093/sysbio/syx088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 11/15/2017] [Indexed: 11/14/2022]  Open
21
Buena-Atienza E, Nasser F, Kohl S, Wissinger B. A 73,128 bp de novo deletion encompassing the OPN1LW/OPN1MW gene cluster in sporadic Blue Cone Monochromacy: a case report. BMC MEDICAL GENETICS 2018;19:107. [PMID: 29940872 PMCID: PMC6019650 DOI: 10.1186/s12881-018-0623-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/12/2018] [Indexed: 01/04/2023]
22
Mao H, Wang H. Distribution, Diversity, and Long-Term Retention of Grass Short Interspersed Nuclear Elements (SINEs). Genome Biol Evol 2018;9:2048-2056. [PMID: 28903462 PMCID: PMC5585668 DOI: 10.1093/gbe/evx145] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2017] [Indexed: 02/06/2023]  Open
23
Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin AA, Karn RC, Laukaitis CM, Jingtao L, Martin F, Muffato M, Nachtweide S, Quail MA, Sisu C, Stanke M, Stefflova K, Van Oosterhout C, Veyrunes F, Ward B, Yang F, Yazdanifar G, Zadissa A, Adams DJ, Brazma A, Gerstein M, Paten B, Pham S, Keane TM, Odom DT, Flicek P. Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes. Genome Res 2018;28:448-459. [PMID: 29563166 PMCID: PMC5880236 DOI: 10.1101/gr.234096.117] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 03/05/2018] [Indexed: 12/31/2022]
24
Disease onset in X-linked dystonia-parkinsonism correlates with expansion of a hexameric repeat within an SVA retrotransposon in TAF1. Proc Natl Acad Sci U S A 2017;114:E11020-E11028. [PMID: 29229810 PMCID: PMC5754783 DOI: 10.1073/pnas.1712526114] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
25
Hoad G, Harrison K. The Design and Optimization of DNA Methylation Pyrosequencing Assays Targeting Region-Specific Repeat Elements. Methods Mol Biol 2017;1589:17-27. [PMID: 26246355 DOI: 10.1007/7651_2015_285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
26
Turner TN, Coe BP, Dickel DE, Hoekzema K, Nelson BJ, Zody MC, Kronenberg ZN, Hormozdiari F, Raja A, Pennacchio LA, Darnell RB, Eichler EE. Genomic Patterns of De Novo Mutation in Simplex Autism. Cell 2017;171:710-722.e12. [PMID: 28965761 PMCID: PMC5679715 DOI: 10.1016/j.cell.2017.08.047] [Citation(s) in RCA: 224] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/03/2017] [Accepted: 08/25/2017] [Indexed: 12/22/2022]
27
Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions. Nat Commun 2016;7:12997. [PMID: 27708261 PMCID: PMC5059674 DOI: 10.1038/ncomms12997] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 08/17/2016] [Indexed: 12/28/2022]  Open
28
Sheinman M, Ramisch A, Massip F, Arndt PF. Evolutionary dynamics of selfish DNA explains the abundance distribution of genomic subsequences. Sci Rep 2016;6:30851. [PMID: 27488939 PMCID: PMC4973250 DOI: 10.1038/srep30851] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/08/2016] [Indexed: 12/26/2022]  Open
29
Bailey J. Monkey-based research on human disease: the implications of genetic differences. Altern Lab Anim 2016;42:287-317. [PMID: 25413291 DOI: 10.1177/026119291404200504] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
30
Seibt KM, Wenke T, Muders K, Truberg B, Schmidt T. Short interspersed nuclear elements (SINEs) are abundant in Solanaceae and have a family-specific impact on gene structure and genome organization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016;86:268-285. [PMID: 26996788 DOI: 10.1111/tpj.13170] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 03/11/2016] [Accepted: 03/14/2016] [Indexed: 06/05/2023]
31
Zhang Y, Peng X, Tang Y, Gan X, Wang C, Xie L, Xie X, Gan R, Wu Y. Identification of IgH gene rearrangement and immunophenotype in an animal model of Epstein-Barr virus-associated lymphomas. J Med Virol 2016;88:1804-13. [PMID: 26991077 DOI: 10.1002/jmv.24526] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2016] [Indexed: 11/10/2022]
32
Caudron-Herger M, Pankert T, Seiler J, Németh A, Voit R, Grummt I, Rippe K. Alu element-containing RNAs maintain nucleolar structure and function. EMBO J 2015;34:2758-74. [PMID: 26464461 DOI: 10.15252/embj.201591458] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 08/31/2015] [Indexed: 01/05/2023]  Open
33
Pizzato M, McCauley SM, Neagu MR, Pertel T, Firrito C, Ziglio S, Dauphin A, Zufferey M, Berthoux L, Luban J. Lv4 Is a Capsid-Specific Antiviral Activity in Human Blood Cells That Restricts Viruses of the SIVMAC/SIVSM/HIV-2 Lineage Prior to Integration. PLoS Pathog 2015;11:e1005050. [PMID: 26181333 PMCID: PMC4504712 DOI: 10.1371/journal.ppat.1005050] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 06/25/2015] [Indexed: 12/24/2022]  Open
34
Lee HE, Ayarpadikannan S, Kim HS. Role of transposable elements in genomic rearrangement, evolution, gene regulation and epigenetics in primates. Genes Genet Syst 2015;90:245-57. [DOI: 10.1266/ggs.15-00016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
35
Lee HE, Eo J, Kim HS. Composition and evolutionary importance of transposable elements in humans and primates. Genes Genomics 2014. [DOI: 10.1007/s13258-014-0249-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
36
Ottolini B, Hornsby MJ, Abujaber R, MacArthur JAL, Badge RM, Schwarzacher T, Albertson DG, Bevins CL, Solnick JV, Hollox EJ. Evidence of convergent evolution in humans and macaques supports an adaptive role for copy number variation of the β-defensin-2 gene. Genome Biol Evol 2014;6:3025-38. [PMID: 25349268 PMCID: PMC4255768 DOI: 10.1093/gbe/evu236] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
37
Dynamic Alu methylation during normal development, aging, and tumorigenesis. BIOMED RESEARCH INTERNATIONAL 2014;2014:784706. [PMID: 25243180 PMCID: PMC4163490 DOI: 10.1155/2014/784706] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 08/16/2014] [Indexed: 12/15/2022]
38
Inference of transposable element ancestry. PLoS Genet 2014;10:e1004482. [PMID: 25121584 PMCID: PMC4133154 DOI: 10.1371/journal.pgen.1004482] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 05/16/2014] [Indexed: 01/11/2023]  Open
39
Criscione SW, Zhang Y, Thompson W, Sedivy JM, Neretti N. Transcriptional landscape of repetitive elements in normal and cancer human cells. BMC Genomics 2014;15:583. [PMID: 25012247 PMCID: PMC4122776 DOI: 10.1186/1471-2164-15-583] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 07/03/2014] [Indexed: 12/11/2022]  Open
40
Maumus F, Quesneville H. Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana. Nat Commun 2014;5:4104. [PMID: 24954583 PMCID: PMC4090718 DOI: 10.1038/ncomms5104] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Accepted: 05/13/2014] [Indexed: 12/19/2022]  Open
41
Walters-Conte KB, Johnson DLE, Johnson WE, O’Brien SJ, Pecon-Slattery J. The dynamic proliferation of CanSINEs mirrors the complex evolution of Feliforms. BMC Evol Biol 2014;14:137. [PMID: 24947429 PMCID: PMC4084570 DOI: 10.1186/1471-2148-14-137] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 06/11/2014] [Indexed: 01/22/2023]  Open
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McLain AT, Carman GW, Fullerton ML, Beckstrom TO, Gensler W, Meyer TJ, Faulk C, Batzer MA. Analysis of western lowland gorilla (Gorilla gorilla gorilla) specific Alu repeats. Mob DNA 2013;4:26. [PMID: 24262036 PMCID: PMC4177385 DOI: 10.1186/1759-8753-4-26] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 10/23/2013] [Indexed: 02/07/2023]  Open
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Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013;10:563-9. [PMID: 23644548 DOI: 10.1038/nmeth.2474] [Citation(s) in RCA: 3121] [Impact Index Per Article: 283.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 04/04/2013] [Indexed: 02/08/2023]
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Xu H, Luo X, Qian J, Pang X, Song J, Qian G, Chen J, Chen S. FastUniq: a fast de novo duplicates removal tool for paired short reads. PLoS One 2012;7:e52249. [PMID: 23284954 PMCID: PMC3527383 DOI: 10.1371/journal.pone.0052249] [Citation(s) in RCA: 357] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Accepted: 11/16/2012] [Indexed: 11/19/2022]  Open
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The lemur revolution starts now: the genomic coming of age for a non-model organism. Mol Phylogenet Evol 2012;66:442-52. [PMID: 22982436 DOI: 10.1016/j.ympev.2012.08.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 08/24/2012] [Accepted: 08/27/2012] [Indexed: 12/25/2022]
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McLain AT, Meyer TJ, Faulk C, Herke SW, Oldenburg JM, Bourgeois MG, Abshire CF, Roos C, Batzer MA. An alu-based phylogeny of lemurs (infraorder: Lemuriformes). PLoS One 2012;7:e44035. [PMID: 22937148 PMCID: PMC3429421 DOI: 10.1371/journal.pone.0044035] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 07/31/2012] [Indexed: 11/30/2022]  Open
47
Rawal K, Priya A, Malik A, Bahl R, Ramaswamy R. Distribution of MGEs and their insertion sites in the Macaca mulatta genome. Mob Genet Elements 2012;2:133-141. [PMID: 23061019 PMCID: PMC3463469 DOI: 10.4161/mge.21074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
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Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers. Mob DNA 2012;3:8. [PMID: 22541534 PMCID: PMC3357318 DOI: 10.1186/1759-8753-3-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 04/30/2012] [Indexed: 01/25/2023]  Open
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Deininger P. Alu elements: know the SINEs. Genome Biol 2011;12:236. [PMID: 22204421 PMCID: PMC3334610 DOI: 10.1186/gb-2011-12-12-236] [Citation(s) in RCA: 394] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 12/16/2011] [Indexed: 12/21/2022]  Open
50
de Andrade A, Wang M, Bonaldo MF, Xie H, Soares MB. Genetic and epigenetic variations contributed by Alu retrotransposition. BMC Genomics 2011;12:617. [PMID: 22185517 PMCID: PMC3272032 DOI: 10.1186/1471-2164-12-617] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 12/20/2011] [Indexed: 12/16/2022]  Open
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