AIMC Topic: DNA Transposable Elements
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Genome-wide annotation and comparative analysis of miniature inverted-repeat transposable elements (MITEs) in six pear species.
Planta
Jun 16, 2025
Through multi-faceted comparative analysis of MITEs across six pear genomes, we revealed their distribution patterns, functional impacts and their significant role as genomic origins for miRNAs, with copy number being the most critical factor for MIT...
Landscape of essential growth and fluconazole-resistance genes in the human fungal pathogen Cryptococcus neoformans.
PLoS biology
May 22, 2025
Fungi can cause devastating invasive infections, typically in immunocompromised patients. Treatment is complicated both by the evolutionary similarity between humans and fungi and by the frequent emergence of drug resistance. Studies in fungal pathog...
Effective genome editing with an enhanced ISDra2 TnpB system and deep learning-predicted ωRNAs.
Nature methods
Sep 23, 2024
Transposon (IS200/IS605)-encoded TnpB proteins are predecessors of class 2 type V CRISPR effectors and have emerged as one of the most compact genome editors identified thus far. Here, we optimized the design of Deinococcus radiodurans (ISDra2) TnpB ...
Identification of Functional piRNAs Using a Convolutional Neural Network.
IEEE/ACM transactions on computational biology and bioinformatics
Jun 3, 2022
Piwi-interacting RNAs (piRNAs) are a distinct sub-class of small non-coding RNAs that are mainly responsible for germline stem cell maintenance, gene stability, and maintaining genome integrity by repression of transposable elements. piRNAs are also ...
ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements.
Scientific data
Jan 20, 2022
Bacterial integrative and conjugative elements (ICEs) are highly modular mobile genetic elements critical to the horizontal transfer of antibiotic resistance and virulence factor genes. To better understand and analyze the ongoing increase of ICEs, w...
Unsupervised Learning Approach for Comparing Multiple Transposon Insertion Sequencing Studies.
mSphere
Feb 20, 2019
Transposon insertion sequencing (TIS) is a widely used technique for conducting genome-scale forward genetic screens in bacteria. However, few methods enable comparison of TIS data across multiple replicates of a screen or across independent screens,...
Gene Essentiality Analyzed by Transposon Mutagenesis and Machine Learning in a Stable Haploid Isolate of .
mBio
Oct 30, 2018
Knowing the full set of essential genes for a given organism provides important information about ways to promote, and to limit, its growth and survival. For many non-model organisms, the lack of a stable haploid state and low transformation efficien...
PlaNC-TE: a comprehensive knowledgebase of non-coding RNAs and transposable elements in plants.
Database : the journal of biological databases and curation
Jan 1, 2018
Transposable elements (TEs) play an essential role in the genetic variability of eukaryotic species. In plants, they may comprise up to 90% of the total genome. Non-coding RNAs (ncRNAs) are known to control gene expression and regulation. Although th...
Computational identification of piRNA targets on mouse mRNAs.
Bioinformatics (Oxford, England)
Dec 16, 2015
MOTIVATION: PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that are highly abundant in the germline. One important role of piRNAs is to defend genome integrity by guiding PIWI proteins to silence transposable elements (TEs), whic...
Prediction of prokaryotic transposases from protein features with machine learning approaches.
Microbial genomics
Jul 1, 2021
Identification of prokaryotic transposases (Tnps) not only gives insight into the spread of antibiotic resistance and virulence but the process of DNA movement. This study aimed to develop a classifier for predicting Tnps in bacteria and archaea usin...
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