ReviewInternational journal of molecular sciences2019
Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning.
Review in International journal of molecular sciences, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
39 citing papers in PubMed, 112 citations in OpenAlex.
- "Quadrupling" the protein family space with global metagenomics.Nucleic acids research · 2026Article
- KNOX II Transcription Factor HOS59 Regulates Gypsy Transposable Elements to Modulate Panicle Development in Rice.Plant, cell & environment · 2026Article
- Evolutionary history and climate-driven dynamics of transposable elements has shaped genome evolution in the Coffea genus.Scientific reports · 2026Article
- EDTA-GUI: a plant-optimized graphical implementation of the EDTA pipeline enabling lineage-level classification and analysis.BMC genomics · 2026Article
- Diverging repeatomes in holoparasitic Hydnoraceae uncover a playground of genome evolution.The New phytologist · 2025Article
- GAG Protein ofPlants (Basel, Switzerland) · 2025Article
- Time-course transcriptome analysis reveals gene co-expression networks and transposable element responses to cold stress in cotton.BMC genomics · 2025Article
- Repeatome landscapes and cytogenetics of hortensias provide a framework to trace Hydrangea evolution and domestication.Annals of botany · 2025Article
- Chromosome distribution of four LTR retrotransposons and 18 S rDNA in coffea eugenioides.Scientific reports · 2025Article
- Evolution of Plant Genome Size and Composition.Genomics, proteomics & bioinformatics · 2024Review
- PTGS is dispensable for the initiation of epigenetic silencing of an active transposon in Arabidopsis.EMBO reports · 2024Article
- Association mapping and candidate gene identification for yield traits in European hazelnut (Plant direct · 2024Article
- Genome wide association studies on seven yield-related traits of 183 rice varieties in Bangladesh.Plant direct · 2024Article
- Transposable elements in Rosaceae: insights into genome evolution, expression dynamics, and syntenic gene regulation.Horticulture research · 2024Article
- From tradition to innovation: conventional and deep learning frameworks in genome annotation.Briefings in bioinformatics · 2024Review
- The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum.G3 (Bethesda, Md.) · 2023Article
- Conserved structured domains in plant non-coding RNA enod40, their evolution and recruitment of sequences from transposable elements.NAR genomics and bioinformatics · 2023Article
- Large-scale long terminal repeat insertions produced a significant set of novel transcripts in cotton.Science China. Life sciences · 2023Article
- Insights into the genomic evolution and the alkali tolerance mechanisms ofMicrobial genomics · 2023Article
- Inpactor2: a software based on deep learning to identify and classify LTR-retrotransposons in plant genomes.Briefings in bioinformatics · 2023Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
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 identification and classification of TEs remain a challenge in sequenced genomes. Although TEs were initially regarded as "junk DNA", it has been demonstrated that they play key roles in chromosome structures, gene expression, and regulation, as well as adaptation and evolution. A highly reliable annotation of these elements is, therefore, crucial to better understand genome functions and their evolution. To date, much bioinformatics software has been developed to address TE detection and classification processes, but many problematic aspects remain, such as the reliability, precision, and speed of the analyses. Machine learning and deep learning are algorithms that can make automatic predictions and decisions in a wide variety of scientific applications. They have been tested in bioinformatics and, more specifically for TEs, classification with encouraging results. In this review, we will discuss important aspects of TEs, such as their structure, importance in the evolution and architecture of the host, and their current classifications and nomenclatures. We will also address current methods and their limitations in identifying and classifying TEs.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.