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A call for benchmarking transposable element annotation methods.
Hoen DR, Hickey G, Bourque G, Casacuberta J, Cordaux R, Feschotte C, Fiston-Lavier AS, Hua-Van A, Hubley R, Kapusta A, Lerat E, Maumus F, Pollock DD, Quesneville H, Smit A, Wheeler TJ, Bureau TE, Blanchette M. Hoen DR, et al. Among authors: casacuberta j. Mob DNA. 2015 Aug 4;6:13. doi: 10.1186/s13100-015-0044-6. eCollection 2015. Mob DNA. 2015. PMID: 26244060 Free PMC article.
T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data.
Bogaerts-Márquez M, Barrón MG, Fiston-Lavier AS, Vendrell-Mir P, Castanera R, Casacuberta JM, González J. Bogaerts-Márquez M, et al. Among authors: casacuberta jm. Bioinformatics. 2020 Feb 15;36(4):1191-1197. doi: 10.1093/bioinformatics/btz727. Bioinformatics. 2020. PMID: 31580402 Free PMC article.
Plant transposable elements.
Deragon JM, Casacuberta JM, Panaud O. Deragon JM, et al. Among authors: casacuberta jm. Genome Dyn. 2008;4:69-82. doi: 10.1159/000126007. Genome Dyn. 2008. PMID: 18756078
Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence.
Alioto T, Alexiou KG, Bardil A, Barteri F, Castanera R, Cruz F, Dhingra A, Duval H, Fernández I Martí Á, Frias L, Galán B, García JL, Howad W, Gómez-Garrido J, Gut M, Julca I, Morata J, Puigdomènech P, Ribeca P, Rubio Cabetas MJ, Vlasova A, Wirthensohn M, Garcia-Mas J, Gabaldón T, Casacuberta JM, Arús P. Alioto T, et al. Among authors: casacuberta jm. Plant J. 2020 Jan;101(2):455-472. doi: 10.1111/tpj.14538. Epub 2019 Oct 22. Plant J. 2020. PMID: 31529539 Free PMC article.
121 results