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De Novo Annotation of Transposable Elements: Tackling the Fat Genome Issue

https://doi.org/10.1109/jproc.2016.2590833

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Roadmap for Annotating Transposable Elements in Eukaryote Genomes

inferredcites →https://doi.org/10.1007/s00239-003-0007-2openalex-snapshot

Detection of New Transposable Element Families in Drosophila melanogaster and Anopheles gambiae Genomes

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Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets

inferredcites →https://doi.org/10.1016/s0097-8485(96)80013-1openalex-snapshot

Censor—a program for identification and elimination of repetitive elements from DNA sequences

inferredcites →https://doi.org/10.1038/hdy.2009.165openalex-snapshot

Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs

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Evolution of genes and genomes on the Drosophila phylogeny

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Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

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The Ectocarpus genome and the independent evolution of multicellularity in brown algae

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Pan genome of the phytoplankton Emiliania underpins its global distribution

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The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

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Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

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Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

inferredcites →https://doi.org/10.1038/ng.2669openalex-snapshot

The Capsella rubella genome and the genomic consequences of rapid mating system evolution

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The wheat powdery mildew genome shows the unique evolution of an obligate biotroph

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The genome of the stress-tolerant wild tomato species Solanum pennellii

inferredcites →https://doi.org/10.1038/nplants.2014.23openalex-snapshot

Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation

inferredcites →https://doi.org/10.1038/nrg2165openalex-snapshot

A unified classification system for eukaryotic transposable elements

inferredcites →https://doi.org/10.1073/pnas.1019315108openalex-snapshot

Obligate biotrophy features unraveled by the genomic analysis of rust fungi

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On global sequence alignment

inferredcites →https://doi.org/10.1093/bioinformatics/bti1003openalex-snapshot

PILER: identification and classification of genomic repeats

inferredcites →https://doi.org/10.1093/bioinformatics/bti1018openalex-snapshot

De novo identification of repeat families in large genomes

inferredcites →https://doi.org/10.1093/nar/27.2.573openalex-snapshot

Tandem repeats finder: a program to analyze DNA sequences

inferredcites →https://doi.org/10.1093/nar/gkg617openalex-snapshot

mreps: efficient and flexible detection of tandem repeats in DNA

inferredcites →https://doi.org/10.1101/gr.88502openalex-snapshot

Automated De Novo Identification of Repeat Sequence Families in Sequenced Genomes

inferredcites →https://doi.org/10.1105/tpc.110.074187openalex-snapshot

Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces

inferredcites →https://doi.org/10.1126/science.1138878openalex-snapshot

Genome Sequence of Aedes aegypti , a Major Arbovirus Vector

inferredcites →https://doi.org/10.1126/science.1143708openalex-snapshot

The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization

inferredcites →https://doi.org/10.1126/science.1178534openalex-snapshot

The B73 Maize Genome: Complexity, Diversity, and Dynamics

inferredcites →https://doi.org/10.1126/science.1194573openalex-snapshot

Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism

inferredcites →https://doi.org/10.1126/science.1249721openalex-snapshot

Structural and functional partitioning of bread wheat chromosome 3B

inferredcites →https://doi.org/10.1186/1471-2105-9-18openalex-snapshot

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

inferredcites →https://doi.org/10.1186/preaccept-3807289381373584openalex-snapshot

Organization and evolution of transposable elements along the bread wheat chromosome 3B

inferredcites →https://doi.org/10.1371/journal.pbio.1000313openalex-snapshot

Genome Sequence of the Pea Aphid Acyrthosiphon pisum

inferredcites →https://doi.org/10.1371/journal.pcbi.0010022openalex-snapshot

Combined Evidence Annotation of Transposable Elements in Genome Sequences

inferredcites →https://doi.org/10.1371/journal.pgen.1000732openalex-snapshot

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome

inferredcites →https://doi.org/10.1371/journal.pgen.1002230openalex-snapshot

Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

inferredcites →https://doi.org/10.1371/journal.pone.0016526openalex-snapshot

Considering Transposable Element Diversification in De Novo Annotation Approaches

inferredcites →https://doi.org/10.1371/journal.pone.0091929openalex-snapshot

PASTEC: An Automatic Transposable Element Classification Tool

inferredcites →https://doi.org/10.1534/genetics.113.159996openalex-snapshot

Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Hybrid assembly of Penicillium rubens genomes unveils high conservation of genome structural organisation and the presence of Numts in nuclear DNA

inferred← citeshttps://doi.org/10.1016/bs.adgen.2017.09.011openalex-snapshot

Phylogenetics and Phylogenomics of Rust Fungi

inferred← citeshttps://doi.org/10.1016/j.cois.2026.101610openalex-snapshot

Computational tools and lessons learned from annotating transposable elements in insect genomes

inferred← citeshttps://doi.org/10.1016/j.fgb.2019.06.002openalex-snapshot

Whole-genome sequencing reveals recent and frequent genetic recombination between clonal lineages of Cryphonectria parasitica in western Europe

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Whole Genome Assembly and Full-Length Transcriptome Sequencing of the Uncaria rhynchophylla Provides Insights into Genetic Control of Bioactive Alkaloid Biosynthesis

inferred← citeshttps://doi.org/10.1038/s41588-019-0480-1openalex-snapshot

A reference genome for pea provides insight into legume genome evolution

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The genome of the simultaneously hermaphroditic snail Lymnaea stagnalis reveals an evolutionary expansion of FMRFamide-like receptors

inferred← citeshttps://doi.org/10.1093/gbe/evaf131openalex-snapshot

Chromosomal Inversions Mediated by Tandem Insertions of Transposable Elements

inferred← citeshttps://doi.org/10.1093/gbe/evag137openalex-snapshot

Biological Implications of a Detailed Repeat Annotation in Octopus vulgaris

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Comprehensive Annotation of Olfactory and Gustatory Receptor Genes and Transposable Elements Revealed Their Evolutionary Dynamics in Aphids

inferred← citeshttps://doi.org/10.1101/2022.06.13.495685openalex-snapshot

The soybean rust pathogen Phakopsora pachyrhizi displays transposable element proliferation that correlates with broad host-range adaptation on legumes

inferred← citeshttps://doi.org/10.1101/2024.06.17.598857openalex-snapshot

panREPET: a reference-free pipeline for detecting shared Transposable Elements from pan-genomes to retrace their dynamics in a species

inferred← citeshttps://doi.org/10.1101/2025.07.22.665893openalex-snapshot

Building pangenomes for domesticated and wild tree species: genomic complexity and strategies

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Contrasting genomic routes to domestication in Occidental and Oriental pears

inferred← citeshttps://doi.org/10.1101/547877openalex-snapshot

Traces of transposable elements in genome dark matter co-opted by flowering gene regulation networks

inferred← citeshttps://doi.org/10.1101/gr.278821.123openalex-snapshot

MCHelper automatically curates transposable element libraries across eukaryotic species

inferred← citeshttps://doi.org/10.1109/jproc.2017.2680218openalex-snapshot

Corrections to “De Novo Annotation of Transposable Elements: Tackling the Fat Genome Issue” [Jamilloux et al., Proc. IEEE, vol. 105, no. 3, pp. 474–481, Mar. 2017, DOI: 10.1109/JPROC.2016.2590833]

inferred← citeshttps://doi.org/10.1109/jproc.2018.2884160openalex-snapshot

2016-2018 Index|Proceedings of the IEEE Vol. 104-106

inferred← citeshttps://doi.org/10.1186/s12870-018-1603-zopenalex-snapshot

The transcriptome of zinc deficient maize roots and its relationship to DNA methylation loss

inferred← citeshttps://doi.org/10.1186/s13059-026-03984-5openalex-snapshot

A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a species

inferred← citeshttps://doi.org/10.1186/s13100-026-00405-zopenalex-snapshot

TE_Bench: a foundational benchmarking workflow for transposable element annotation pipelines

inferred← citeshttps://doi.org/10.12688/f1000research.74524.1openalex-snapshot

An Atlas of Plant Transposable Elements

inferred← citeshttps://doi.org/10.1371/journal.pone.0257996openalex-snapshot

A Genomic Survey of Mayetiola destructor Mobilome Provides New Insights into the Evolutionary History of Transposable Elements in the Cecidomyiid Midges

inferred← citeshttps://doi.org/10.24072/pcjournal.68openalex-snapshot

Traces of transposable elements in genome dark matter co-opted by flowering gene regulation networks

inferred← citeshttps://doi.org/10.3389/fpls.2018.00497openalex-snapshot

Massive Loss of DNA Methylation in Nitrogen-, but Not in Phosphorus-Deficient Zea mays Roots Is Poorly Correlated With Gene Expression Differences

inferred← citeshttps://doi.org/10.3390/biology11010024openalex-snapshot

Transposable Elements in the Genome of the Lichen-Forming Fungus Umbilicaria pustulata and Their Distribution in Different Climate Zones along Elevation

inferred← citeshttps://doi.org/10.3390/genes8100290openalex-snapshot

Chromosome Evolution in Connection with Repetitive Sequences and Epigenetics in Plants

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Structural and Functional Annotation of Transposable Elements Revealed a Potential Regulation of Genes Involved in Rubber Biosynthesis by TE-Derived siRNA Interference in Hevea brasiliensis

inferred← citeshttps://doi.org/10.3390/insects13050396openalex-snapshot

Genome-Wide Screening of Transposable Elements in the Whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae), Revealed Insertions with Potential Insecticide Resistance Implications

inferred← citeshttps://doi.org/10.64898/2026.07.23.736688openalex-snapshot

Chromosome-scale assembly of the Cupressus sempervirens genome unravels new insights into the evolutionary history of conifers

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