TIP_finder: An HPC Software to Detect Transposable Element Insertion Polymorphisms in Large Genomic Datasets

SciPy 1.0: fundamental algorithms for scientific computing in Python

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Resequencing 93 accessions of coffee unveils independent and parallel selection during Coffea species divergence

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Expressional activation and functional roles of human endogenous retroviruses in cancers

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Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification

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TIR-Learner, a New Ensemble Method for TIR Transposable Element Annotation, Provides Evidence for Abundant New Transposable Elements in the Maize Genome

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Roles of Transposable Elements in the Different Layers of Gene Expression Regulation

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A benchmark of transposon insertion detection tools using real data

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

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Use of a draft genome of coffee (Coffea arabica ) to identify SNPs associated with caffeine content

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Earth BioGenome Project: Sequencing life for the future of life

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10KP: A phylodiverse genome sequencing plan

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Retrotranspositional landscape of Asian rice revealed by 3000 genomes

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Expression of human endogenous retrovirus-K is strongly associated with the basal-like breast cancer phenotype

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Benchmarking computational tools for polymorphic transposable element detection

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LTR retrotransposons, handy hitchhikers of plant regulation and stress response

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Detecting dispersed duplications in high-throughput sequencing data using a database-free approach

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MetaSV: an accurate and integrative structural-variant caller for next generation sequencing

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ITIS, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data

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Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution

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Terminal-Repeat Retrotransposons with GAG Domain in Plant Genomes: A New Testimony on the Complex World of Transposable Elements

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Human endogenous retrovirus HERV-K(HML-2) activity in prostate cancer is dominated by a few loci

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Transposable element detection from whole genome sequence data

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iTIS-PseTNC: A sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition

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Population Genomics of Transposable Elements inDrosophila

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An introduction to the vast world of transposable elements – what about the diatoms?

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Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing

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Structural and functional partitioning of bread wheat chromosome 3B

(2014) F. Choulet et al.   SCIENCE

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

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Retroviruses facilitate the rapid evolution of the mammalian placenta

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Human endogenous retroviruses and cancer prevention: evidence and prospects

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Transcriptional Profiling of Human Endogenous Retrovirus Group HERV-K(HML-2) Loci in Melanoma

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The impact of transposable elements in environmental adaptation

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Quantitative assessment of single-cell RNA-sequencing methods

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A transposable element is domesticated for service in the plant immune system

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Active human retrotransposons: variation and disease

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Fast gapped-read alignment with Bowtie 2

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How important are transposons for plant evolution?

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LINE-1 Elements in Structural Variation and Disease

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A “mille-feuille” of silencing: Epigenetic control of transposable elements

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Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals

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Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses

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Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

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BEDTools: a flexible suite of utilities for comparing genomic features

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The Sequence Read Archive

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MPI for Python: Performance improvements and MPI-2 extensions

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