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For: Horscroft C, Ennis S, Pengelly RJ, Sluckin TJ, Collins A. Sequencing era methods for identifying signatures of selection in the genome. Brief Bioinform 2020;20:1997-2008. [PMID: 30053138 DOI: 10.1093/bib/bby064] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/16/2018] [Indexed: 12/12/2022]  Open
Number Cited by Other Article(s)
1
Liu H, Zhu B, Wang T, Dong Y, Ju Y, Li Y, Su W, Zhang R, Dong S, Wang H, Zhou Y, Zhu Y, Wang L, Zhang Z, Zhao P, Zhang S, Guo R, A E, Zhang Y, Liu X, Tamate HB, Liang Q, Ma D, Xing X. Population genomics of sika deer reveals recent speciation and genetic selective signatures during evolution and domestication. BMC Genomics 2025;26:364. [PMID: 40217144 PMCID: PMC11987376 DOI: 10.1186/s12864-025-11541-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Accepted: 03/28/2025] [Indexed: 04/15/2025]  Open
2
Miron-Toruno MF, Morett E, Aguilar-Ordonez I, Reynolds AW. Genome-Wide Selection Scans in Mexican Indigenous Populations Reveal Recent Signatures of Pathogen and Diet Adaptation. Genome Biol Evol 2025;17:evaf043. [PMID: 40070201 PMCID: PMC11954594 DOI: 10.1093/gbe/evaf043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2025] [Indexed: 04/01/2025]  Open
3
Carvajal-Rodríguez A. iHDSel software: The price equation and the population stability index to detect genomic patterns compatible with selective sweeps. An example with SARS-CoV-2. Biol Methods Protoc 2024;9:bpae089. [PMID: 39679303 PMCID: PMC11646571 DOI: 10.1093/biomethods/bpae089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2024] [Revised: 11/19/2024] [Accepted: 11/25/2024] [Indexed: 12/17/2024]  Open
4
Yang H, Zhu M, Wang M, Zhou H, Zheng J, Qiu L, Fan W, Yang J, Yu Q, Yang Y, Zhang W. Genome-wide comparative analysis reveals selection signatures for reproduction traits in prolific Suffolk sheep. Front Genet 2024;15:1404031. [PMID: 38911299 PMCID: PMC11193351 DOI: 10.3389/fgene.2024.1404031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/20/2024] [Indexed: 06/25/2024]  Open
5
Panigrahi M, Rajawat D, Nayak SS, Ghildiyal K, Sharma A, Jain K, Lei C, Bhushan B, Mishra BP, Dutt T. Landmarks in the history of selective sweeps. Anim Genet 2023;54:667-688. [PMID: 37710403 DOI: 10.1111/age.13355] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/28/2023] [Indexed: 09/16/2023]
6
Matthews DG, Dial TR, Lauder GV. Genes, Morphology, Performance, and Fitness: Quantifying Organismal Performance to Understand Adaptive Evolution. Integr Comp Biol 2023;63:843-859. [PMID: 37422435 DOI: 10.1093/icb/icad096] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/06/2023] [Accepted: 06/22/2023] [Indexed: 07/10/2023]  Open
7
The study of selection signature and its applications on identification of candidate genes using whole genome sequencing data in chicken - a review. Poult Sci 2023;102:102657. [PMID: 37054499 PMCID: PMC10123265 DOI: 10.1016/j.psj.2023.102657] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023]  Open
8
Strandén I, Kantanen J, Lidauer MH, Mehtiö T, Negussie E. Animal board invited review: Genomic-based improvement of cattle in response to climate change. Animal 2022;16:100673. [PMID: 36402112 DOI: 10.1016/j.animal.2022.100673] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 12/24/2022]  Open
9
Gu X. A Simple Evolutionary Model of Genetic Robustness After Gene Duplication. J Mol Evol 2022;90:352-361. [PMID: 35913597 DOI: 10.1007/s00239-022-10065-1] [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: 03/01/2022] [Accepted: 06/23/2022] [Indexed: 10/16/2022]
10
Gabián M, Morán P, Saura M, Carvajal-Rodríguez A. Detecting Local Adaptation between North and South European Atlantic Salmon Populations. BIOLOGY 2022;11:933. [PMID: 35741456 PMCID: PMC9219887 DOI: 10.3390/biology11060933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/09/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
11
Kumar H, Panigrahi M, Panwar A, Rajawat D, Nayak SS, Saravanan KA, Kaisa K, Parida S, Bhushan B, Dutt T. Machine-Learning Prospects for Detecting Selection Signatures Using Population Genomics Data. J Comput Biol 2022;29:943-960. [PMID: 35639362 DOI: 10.1089/cmb.2021.0447] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
12
Silver LW, Cheng Y, Quigley BL, Robbins A, Timms P, Hogg CJ, Belov K. A targeted approach to investigating immune genes of an iconic Australian marsupial. Mol Ecol 2022;31:3286-3303. [PMID: 35510793 PMCID: PMC9325493 DOI: 10.1111/mec.16493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 03/02/2022] [Accepted: 04/05/2022] [Indexed: 11/30/2022]
13
Nguembang Fadja A, Riguzzi F, Bertorelle G, Trucchi E. Identification of natural selection in genomic data with deep convolutional neural network. BioData Min 2021;14:51. [PMID: 34863217 PMCID: PMC8642854 DOI: 10.1186/s13040-021-00280-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/25/2021] [Indexed: 11/10/2022]  Open
14
Luqman H, Widmer A, Fior S, Wegmann D. Identifying loci under selection via explicit demographic models. Mol Ecol Resour 2021;21:2719-2737. [PMID: 33964107 PMCID: PMC8596768 DOI: 10.1111/1755-0998.13415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 04/03/2021] [Accepted: 04/28/2021] [Indexed: 01/28/2023]
15
Meeks KAC, Bentley AR, Adeyemo AA, Rotimi CN. Evolutionary forces in diabetes and hypertension pathogenesis in Africans. Hum Mol Genet 2021;30:R110-R118. [PMID: 33734377 DOI: 10.1093/hmg/ddaa238] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/16/2020] [Accepted: 10/22/2020] [Indexed: 11/12/2022]  Open
16
Genetic Signatures of Selection for Cashmere Traits in Chinese Goats. Animals (Basel) 2020;10:ani10101905. [PMID: 33080940 PMCID: PMC7603090 DOI: 10.3390/ani10101905] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/12/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022]  Open
17
Torada L, Lorenzon L, Beddis A, Isildak U, Pattini L, Mathieson S, Fumagalli M. ImaGene: a convolutional neural network to quantify natural selection from genomic data. BMC Bioinformatics 2019;20:337. [PMID: 31757205 PMCID: PMC6873651 DOI: 10.1186/s12859-019-2927-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 05/31/2019] [Indexed: 12/25/2022]  Open
18
Vergara-Lope A, Jabalameli MR, Horscroft C, Ennis S, Collins A, Pengelly RJ. Linkage disequilibrium maps for European and African populations constructed from whole genome sequence data. Sci Data 2019;6:208. [PMID: 31624256 PMCID: PMC6797713 DOI: 10.1038/s41597-019-0227-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/29/2019] [Indexed: 11/08/2022]  Open
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