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For: Kern AD, Haussler D. A population genetic hidden Markov model for detecting genomic regions under selection. Mol Biol Evol 2010;27:1673-85. [PMID: 20185453 DOI: 10.1093/molbev/msq053] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
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
2
Galimberti M, Leuenberger C, Wolf B, Szilágyi SM, Foll M, Wegmann D. Detecting Selection from Linked Sites Using an F-Model. Genetics 2020;216:1205-1215. [PMID: 33067324 PMCID: PMC7768260 DOI: 10.1534/genetics.120.303780] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 10/03/2020] [Indexed: 11/18/2022]  Open
3
Flagel L, Brandvain Y, Schrider DR. The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference. Mol Biol Evol 2019;36:220-238. [PMID: 30517664 PMCID: PMC6367976 DOI: 10.1093/molbev/msy224] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
4
Schrider DR, Kern AD. Supervised Machine Learning for Population Genetics: A New Paradigm. Trends Genet 2018;34:301-312. [PMID: 29331490 PMCID: PMC5905713 DOI: 10.1016/j.tig.2017.12.005] [Citation(s) in RCA: 210] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/29/2017] [Accepted: 12/08/2017] [Indexed: 01/21/2023]
5
Sand A, Kristiansen M, Pedersen CNS, Mailund T. zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm. BMC Bioinformatics 2013;14:339. [PMID: 24266924 PMCID: PMC4222747 DOI: 10.1186/1471-2105-14-339] [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: 06/18/2013] [Accepted: 11/14/2013] [Indexed: 11/10/2022]  Open
6
Gompert Z, Buerkle CA. Analyses of genetic ancestry enable key insights for molecular ecology. Mol Ecol 2013;22:5278-94. [DOI: 10.1111/mec.12488] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 08/05/2013] [Accepted: 08/08/2013] [Indexed: 12/15/2022]
7
Schoville SD, Bonin A, François O, Lobreaux S, Melodelima C, Manel S. Adaptive Genetic Variation on the Landscape: Methods and Cases. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2012. [DOI: 10.1146/annurev-ecolsys-110411-160248] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
8
Gompert Z, Parchman TL, Buerkle CA. Genomics of isolation in hybrids. Philos Trans R Soc Lond B Biol Sci 2012;367:439-50. [PMID: 22201173 DOI: 10.1098/rstb.2011.0196] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
9
Hofer T, Foll M, Excoffier L. Evolutionary forces shaping genomic islands of population differentiation in humans. BMC Genomics 2012;13:107. [PMID: 22439654 PMCID: PMC3317871 DOI: 10.1186/1471-2164-13-107] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 03/22/2012] [Indexed: 12/19/2022]  Open
10
HAUDRY ANNABELLE, ZHA HONGGUANG, STIFT MARC, MABLE BARBARAK. Disentangling the effects of breakdown of self-incompatibility and transition to selfing in North AmericanArabidopsis lyrata. Mol Ecol 2012;21:1130-42. [DOI: 10.1111/j.1365-294x.2011.05435.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
11
Zhen Y, Andolfatto P. Methods to detect selection on noncoding DNA. Methods Mol Biol 2012;856:141-59. [PMID: 22399458 DOI: 10.1007/978-1-61779-585-5_6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
12
Wilson DJ, Hernandez RD, Andolfatto P, Przeworski M. A population genetics-phylogenetics approach to inferring natural selection in coding sequences. PLoS Genet 2011;7:e1002395. [PMID: 22144911 PMCID: PMC3228810 DOI: 10.1371/journal.pgen.1002395] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 10/08/2011] [Indexed: 01/23/2023]  Open
13
Kolaczkowski B, Hupalo DN, Kern AD. Recurrent adaptation in RNA interference genes across the Drosophila phylogeny. Mol Biol Evol 2010;28:1033-42. [PMID: 20971974 DOI: 10.1093/molbev/msq284] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
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