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For: Stone EA. Joint genotyping on the fly: identifying variation among a sequenced panel of inbred lines. Genome Res 2012;22:966-74. [PMID: 22367192 PMCID: PMC3337441 DOI: 10.1101/gr.129122.111] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 02/21/2012] [Indexed: 02/03/2023]
Number Cited by Other Article(s)
1
Collins KM, Howansky E, Macon-Foley SC, Adonay ME, Shankar V, Lyman RF, Nazario-Yepiz NO, Brooks JK, Lyman RA, Mackay TFC, Anholt RRH. Drosophila Toxicogenomics: genetic variation and sexual dimorphism in susceptibility to 4-Methylimidazole. Hum Genomics 2024;18:119. [PMID: 39497218 PMCID: PMC11533318 DOI: 10.1186/s40246-024-00689-3] [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: 07/25/2024] [Accepted: 10/24/2024] [Indexed: 11/07/2024]  Open
2
Yamamoto A, Huang W, Carbone MA, Anholt RRH, Mackay TFC. The genetic basis of incipient sexual isolation in Drosophila melanogaster. Proc Biol Sci 2024;291:20240672. [PMID: 39045689 PMCID: PMC11267472 DOI: 10.1098/rspb.2024.0672] [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: 03/21/2024] [Revised: 05/15/2024] [Accepted: 06/05/2024] [Indexed: 07/25/2024]  Open
3
Lyman RF, Lyman RA, Yamamoto A, Huang W, Harbison ST, Zhou S, Anholt RRH, Mackay TFC. Natural genetic variation in a dopamine receptor is associated with variation in female fertility in Drosophila melanogaster. Proc Biol Sci 2023;290:20230375. [PMID: 37040806 PMCID: PMC10089713 DOI: 10.1098/rspb.2023.0375] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/15/2023] [Indexed: 04/13/2023]  Open
4
Winbush A, Singh ND. Variation in fine-scale recombination rate in temperature-evolved Drosophila melanogaster populations in response to selection. G3 GENES|GENOMES|GENETICS 2022;12:6663992. [PMID: 35961026 PMCID: PMC9526048 DOI: 10.1093/g3journal/jkac208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/05/2022] [Indexed: 11/16/2022]
5
Winbush A, Singh ND. Genomics of Recombination Rate Variation in Temperature-Evolved Drosophila melanogaster Populations. Genome Biol Evol 2020;13:6008691. [PMID: 33247719 PMCID: PMC7851596 DOI: 10.1093/gbe/evaa252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2020] [Indexed: 12/14/2022]  Open
6
Pannebakker BA, Cook N, van den Heuvel J, van de Zande L, Shuker DM. Genomics of sex allocation in the parasitoid wasp Nasonia vitripennis. BMC Genomics 2020;21:499. [PMID: 32689940 PMCID: PMC7372847 DOI: 10.1186/s12864-020-06904-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/10/2020] [Indexed: 12/25/2022]  Open
7
A Genomic Reference Panel for Drosophila serrata. G3-GENES GENOMES GENETICS 2018;8:1335-1346. [PMID: 29487184 PMCID: PMC5873922 DOI: 10.1534/g3.117.300487] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
8
Jackson BC, Campos JL, Haddrill PR, Charlesworth B, Zeng K. Variation in the Intensity of Selection on Codon Bias over Time Causes Contrasting Patterns of Base Composition Evolution in Drosophila. Genome Biol Evol 2017;9:102-123. [PMID: 28082609 PMCID: PMC5381600 DOI: 10.1093/gbe/evw291] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2016] [Indexed: 12/11/2022]  Open
9
Guo Y, Fudali S, Gimeno J, DiGennaro P, Chang S, Williamson VM, Bird DM, Nielsen DM. Networks Underpinning Symbiosis Revealed Through Cross-Species eQTL Mapping. Genetics 2017;206:2175-2184. [PMID: 28642272 PMCID: PMC5560814 DOI: 10.1534/genetics.117.202531] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 06/09/2017] [Indexed: 12/13/2022]  Open
10
Yassin A, Delaney EK, Reddiex AJ, Seher TD, Bastide H, Appleton NC, Lack JB, David JR, Chenoweth SF, Pool JE, Kopp A. The pdm3 Locus Is a Hotspot for Recurrent Evolution of Female-Limited Color Dimorphism in Drosophila. Curr Biol 2016;26:2412-2422. [PMID: 27546577 DOI: 10.1016/j.cub.2016.07.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/24/2016] [Accepted: 07/08/2016] [Indexed: 12/30/2022]
11
Najarro MA, Hackett JL, Smith BR, Highfill CA, King EG, Long AD, Macdonald SJ. Identifying Loci Contributing to Natural Variation in Xenobiotic Resistance in Drosophila. PLoS Genet 2015;11:e1005663. [PMID: 26619284 PMCID: PMC4664282 DOI: 10.1371/journal.pgen.1005663] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/21/2015] [Indexed: 12/12/2022]  Open
12
Accounting for genetic architecture improves sequence based genomic prediction for a Drosophila fitness trait. PLoS One 2015;10:e0126880. [PMID: 25950439 PMCID: PMC4423967 DOI: 10.1371/journal.pone.0126880] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 04/08/2015] [Indexed: 12/01/2022]  Open
13
Huang W, Massouras A, Inoue Y, Peiffer J, Ràmia M, Tarone AM, Turlapati L, Zichner T, Zhu D, Lyman RF, Magwire MM, Blankenburg K, Carbone MA, Chang K, Ellis LL, Fernandez S, Han Y, Highnam G, Hjelmen CE, Jack JR, Javaid M, Jayaseelan J, Kalra D, Lee S, Lewis L, Munidasa M, Ongeri F, Patel S, Perales L, Perez A, Pu L, Rollmann SM, Ruth R, Saada N, Warner C, Williams A, Wu YQ, Yamamoto A, Zhang Y, Zhu Y, Anholt RR, Korbel JO, Mittelman D, Muzny DM, Gibbs RA, Barbadilla A, Johnston JS, Stone EA, Richards S, Deplancke B, Mackay TF. Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines. Genome Res 2014;24:1193-208. [PMID: 24714809 PMCID: PMC4079974 DOI: 10.1101/gr.171546.113] [Citation(s) in RCA: 434] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 04/01/2014] [Indexed: 12/30/2022]
14
A conserved suppressor mutation in a tryptophan auxotroph results in dysregulation of Pseudomonas quinolone signal synthesis. J Bacteriol 2014;196:2413-22. [PMID: 24748618 DOI: 10.1128/jb.01635-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
15
Robinson MC, Stone EA, Singh ND. Population genomic analysis reveals no evidence for GC-biased gene conversion in Drosophila melanogaster. Mol Biol Evol 2013;31:425-33. [PMID: 24214536 DOI: 10.1093/molbev/mst220] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
16
Kenigsberg E, Tanay A. Drosophila functional elements are embedded in structurally constrained sequences. PLoS Genet 2013;9:e1003512. [PMID: 23750124 PMCID: PMC3671938 DOI: 10.1371/journal.pgen.1003512] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 03/04/2013] [Indexed: 12/22/2022]  Open
17
Haerty W, Ponting CP. Mutations within lncRNAs are effectively selected against in fruitfly but not in human. Genome Biol 2013;14:R49. [PMID: 23710818 PMCID: PMC4053968 DOI: 10.1186/gb-2013-14-5-r49] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 05/27/2013] [Indexed: 02/07/2023]  Open
18
Zichner T, Garfield DA, Rausch T, Stütz AM, Cannavó E, Braun M, Furlong EEM, Korbel JO. Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing. Genome Res 2012;23:568-79. [PMID: 23222910 PMCID: PMC3589545 DOI: 10.1101/gr.142646.112] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
19
Inferences of demography and selection in an African population of Drosophila melanogaster. Genetics 2012;193:215-28. [PMID: 23105013 DOI: 10.1534/genetics.112.145318] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
20
The Drosophila melanogaster Genetic Reference Panel. Nature 2012;482:173-8. [PMID: 22318601 PMCID: PMC3683990 DOI: 10.1038/nature10811] [Citation(s) in RCA: 1181] [Impact Index Per Article: 90.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 12/21/2011] [Indexed: 01/03/2023]
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