ArticleNAR genomics and bioinformatics2022
ICEscreen: a tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.
Article in NAR genomics and bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 28 citations in OpenAlex.
- Emerging trends in invasiveEuro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2026Article
- Perturbations shift the composition of bacterial DNA carried by virus-like particles in the murine gut microbiome.bioRxiv : the preprint server for biology · 2026Article
- Evidence of transfer of antimicrobial resistance genes from the porcine pathogenOne health (Amsterdam, Netherlands) · 2026Article
- Dominance of the ST20Microorganisms · 2026Article
- Macrolide resistance determinants and their associations in streptococci from selected livestock and wildlife species from Catalonia, Northeast Spain.Microbiology spectrum · 2026Article
- The dynamic Alp landscape ofFrontiers in cellular and infection microbiology · 2026Article
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- Pan-immune system, mobilome and resistome inMicrobial genomics · 2025Article
- Giant extrachromosomal element "Inocle" potentially expands the adaptive capacity of the human oral microbiome.Nature communications · 2025Article
- Global dissemination of npmA mediated pan-aminoglycoside resistance via a mobile genetic element in Gram-positive bacteria.Nature communications · 2025Article
- Comprehensive profiling of integrative conjugative elements (ICEs) in Mollicutes: distinct catalysts of gene flow and genome shaping.NAR genomics and bioinformatics · 2025Article
- Massive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gut.Scientific reports · 2025Article
- Carbapenem-ResistantAntibiotics (Basel, Switzerland) · 2025Review
- Geographic diversity of theFrontiers in veterinary science · 2025Article
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- Genomic analysis of conjugative and chromosomally integrated mobile genetic elements in oral streptococci.Applied and environmental microbiology · 2024Article
- Virulence genes, resistome and mobilome ofMicrobial genomics · 2024Article
- ICEberg 3.0: functional categorization and analysis of the integrative and conjugative elements in bacteria.Nucleic acids research · 2024Article
- Detection and Quantification of Conjugative Transfer of Mobile Genetic Elements Carrying Antibiotic Resistance Genes.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Novel insights into phage biology of the pathogenFrontiers in microbiology · 2024Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mobile Genetic Elements (MGEs) are integrated in bacterial genomes and key elements that drive prokaryote genome evolution. Among them are Integrative and Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) which are important for bacterial fitness since they frequently carry genes participating in important bacterial adaptation phenotypes such as antibiotic resistance, virulence or specialized metabolic pathways. Although ICEs and IMEs are widespread, they are as yet almost never annotated in public bacterial genomes. To address the need of dedicated strategies for the annotation of these elements, we developed ICEscreen, a tool that introduces two new features to detect ICEs and IMEs in Firmicute genomes. First, ICEscreen uses an efficient strategy to detect Signature Proteins of ICEs and IMEs based on a database dedicated to Firmicutes and composed of manually curated proteins and Hidden Markov Models (HMM) profiles. Second, ICEscreen includes a new original algorithm that detects composite structures of ICEs and IMEs that are frequent in genomes of Firmicutes but are currently not resolved by any other tool. We benchmarked ICEscreen on experimentally supported elements and on a public dataset of 246 manually annotated elements including the genomes of 40 Firmicutes and demonstrate its efficiency to detect ICEs and IMEs.
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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.