Visualizing population structure with variational autoencoders

Autor: C J Battey, Gabrielle C Coffing, Andrew D Kern

Publikováno v: G3: Genes, Genomes, Genetics, Vol 11, Iss 1 (2021)

AbstractDimensionality reduction is a common tool for visualization and inference of population structure from genotypes, but popular methods either return too many dimensions for easy plotting (PCA) or fail to preserve global geometry (t-SNE and UMA

Externí odkaz: https://doaj.org/article/4f31357f702b496ea0ce3644fa390ec4

Discovery of ongoing selective sweeps within Anopheles mosquito populations using deep learning

Autor: Xue, Alexander T, Schrider, Daniel R, Kern, Andrew D, DELLA TORRE, Alessandra, Caputo, Beniamino, Bilali, Kabula, Bradley, White, Charles, Godfray, Constant, Edi, Craig, Wilding, Dan, Neafsey, David, Conway, David, Weetman, Diego, Ayala, Dominic, Kwiatkowski, Igor, Sharakhov, Janet, Midega, Jiannong John Xu, João, Pinto, John, Essandoh, Johnson, Matowo, Ken, Vernick, Luc, S Djogbenou, Mamadou, Coulibaly, Mara, Lawniczak, Martin, Donnelly, Matthew, Hahn, Michaël, Fontaine, Michelle, Riehle, Besansky, Nora Jessie, Omar, Cornejo, Robert, Mccann, Sam, O'Loughlin, Vincent, Robert, Alistair, Miles, Chris, Clarkson, J Battey, C, Cody, Champion, Frederic, Labbe, Giordano, Bottà, Jeffrey, Adrion, Joel, Nelson, Nick, Harding, Richard, Wang, Scott, T Small, Seth, Redmond, Tiago, Antão

Publikováno v: Repositório Científico de Acesso Aberto de Portugal
Repositório Científico de Acesso Aberto de Portugal (RCAAP)
instacron:RCAAP
Molecular Biology and Evolution
Molecular Biology and Evolution, Oxford University Press (OUP), 2021, 38 (3), pp.1168-1183. ⟨10.1093/molbev/msaa259⟩
Molecular Biology and Evolution, 38(3), 1168-1183. Oxford University Press
Molecular Biology and Evolution, 2021, 38 (3), pp.1168-1183. ⟨10.1093/molbev/msaa259⟩

Publisher Copyright: © 2020 The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. Identification of partial sweeps, which include both hard and soft sweeps that have not currently reac

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c3de8b954c821dd7e27cdac52aaead6d
https://hdl.handle.net/11370/159efe5c-42a1-4df2-a8d2-bea1a7fa10ec

Ecological Release of the Anna’s Hummingbird during a Northern Range Expansion

Autor: C. J. Battey

Publikováno v: The American Naturalist. 194:306-315

During range expansions, species can experience rapid population growth if changes in climate or interspecific interactions remove limits on growth rates in novel habitats. Here I document a century of range expansion in the Anna's hummingbird (Calyp

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b62c8786ca319f5394cb5ced4c588d87
https://doi.org/10.1086/704249

Visualizing Population Structure with Variational Autoencoders

Autor: Gabrielle C. Coffing, C. J. Battey, Andrew D. Kern

Publikováno v: G3: Genes, Genomes, Genetics, Vol 11, Iss 1 (2021)
G3: Genes|Genomes|Genetics

Dimensionality reduction is a common tool for visualization and inference of population structure from genotypes, but popular methods either return too many dimensions for easy plotting (PCA) or fail to preserve global geometry (t-SNE and UMAP). Here

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0d3bedea967e809f929cfaaa592b2bba
https://doi.org/10.1101/2020.08.12.248278

Supplemental Material for Battey, Coffing, and Kern, 2020

Autor: C. J. Battey, Coffing, Gabrielle C., Kern, Andrew D.

supplementary figures and tables for "Visualizing Population Structure with Variational Autoencoders"

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5078e5bfa176e39c690344f17e3f4860