[HTML][HTML] Retrotransposons in plant genomes: structure, identification, and classification through bioinformatics and machine learning

S Orozco-Arias, G Isaza, R Guyot - International journal of molecular …, 2019 - mdpi.com
Transposable elements (TEs) are genomic units able to move within the genome of virtually
all organisms. Due to their natural repetitive numbers and their high structural diversity, the …

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

J Salojärvi, A Rambani, Z Yu, R Guyot, S Strickler… - Nature …, 2024 - nature.com
Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the
source of approximately 60% of coffee products worldwide, and its cultivated accessions …

The apricot (Prunus armeniaca L.) genome elucidates Rosaceae evolution and beta-carotenoid synthesis

F Jiang, J Zhang, S Wang, L Yang, Y Luo… - Horticulture …, 2019 - academic.oup.com
Apricots, scientifically known as Prunus armeniaca L, are drupes that resemble and are
closely related to peaches or plums. As one of the top consumed fruits, apricots are widely …

A systematic review of the application of machine learning in the detection and classification of transposable elements

S Orozco-Arias, G Isaza, R Guyot, R Tabares-Soto - PeerJ, 2019 - peerj.com
Background Transposable elements (TEs) constitute the most common repeated sequences
in eukaryotic genomes. Recent studies demonstrated their deep impact on species diversity …

[HTML][HTML] Measuring performance metrics of machine learning algorithms for detecting and classifying transposable elements

S Orozco-Arias, JS Piña, R Tabares-Soto… - Processes, 2020 - mdpi.com
Because of the promising results obtained by machine learning (ML) approaches in several
fields, every day is more common, the utilization of ML to solve problems in bioinformatics. In …

The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago

N Raharimalala, S Rombauts, A McCarthy… - Scientific reports, 2021 - nature.com
Caffeine is the most consumed alkaloid stimulant in the world. It is synthesized through the
activity of three known N-methyltransferase proteins. Here we are reporting on the 422-Mb …

Inpactor2: a software based on deep learning to identify and classify LTR-retrotransposons in plant genomes

S Orozco-Arias… - Briefings in …, 2023 - academic.oup.com
LTR-retrotransposons are the most abundant repeat sequences in plant genomes and play
an important role in evolution and biodiversity. Their characterization is of great importance …

InpactorDB: a classified lineage-level plant LTR retrotransposon reference library for free-alignment methods based on machine learning

S Orozco-Arias, PA Jaimes, MS Candamil… - Genes, 2021 - mdpi.com
Long terminal repeat (LTR) retrotransposons are mobile elements that constitute the major
fraction of most plant genomes. The identification and annotation of these elements via …

LtrDetector: a tool-suite for detecting long terminal repeat retrotransposons de-novo

JD Valencia, HZ Girgis - BMC genomics, 2019 - Springer
Background Long terminal repeat retrotransposons are the most abundant transposons in
plants. They play important roles in alternative splicing, recombination, gene regulation, and …

Tools and databases for solving problems in detection and identification of repetitive DNA sequences

E Šatović, M Tunjić Cvitanić, M Plohl - Periodicum biologorum, 2020 - hrcak.srce.hr
Sažetak Genome compartments known to carry out very important biological functions (eg.
centromeres and telomeres) are mostly constituted of repetitive sequences. At the same …