ArticleNucleic acids research2024
ICEberg 3.0: functional categorization and analysis of the integrative and conjugative elements in bacteria.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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Who cites it
67 citing papers in PubMed.
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- Antimicrobial Resistance and Genomic Characteristics of ESBL-ProducingAntibiotics (Basel, Switzerland) · 2026Article
- Horizontal transfer of chromosomal DNA mediated by an integrative and conjugative element generates frequent localized recombination inJournal of bacteriology · 2026Article
- Interspecies Exchange of Mobile Genetic Elements During a Plant Disease Outbreak.Genome biology and evolution · 2026Article
- Emerging trends in invasiveEuro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2026Article
- Convergence of Plasmid-Mediated tmexCD-toprJ With Critical Resistance Genes Fuels Spread of Multidrug Resistant Bacteria.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Characterization of a novel gene, Lsa(F), conferring resistance to pleuromutilins, lincosamides and streptogramin A in Streptococcus parasuis.Veterinary research · 2026Article
- In Silico Genomic Analysis of Antibiotic Resistance Genes Carried by Mobile Genetic Elements inInternational journal of molecular sciences · 2026Article
- Pangenome analysis ofAntimicrobial agents and chemotherapy · 2026Article
- Comparative genomics and methylome profiling ofMicrobial genomics · 2026Article
- Genomic analysis identifies candidate SOS-associated and EPS/envelope-remodeling islands in a drinking-water Stenotrophomonas maltophilia complex isolate.Scientific reports · 2026Article
- Initial identification of genomic islands in Taylorella equigenitalis and Taylorella asinigenitalis and their distribution in isolates from around the world.BMC microbiology · 2026Article
- Multi-metal contamination shapes abundance, co-occurrence, and mobility potential of resistance and virulence genes in mining-impacted soils.Infectious medicine · 2026Article
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- Decoding extremophiles: insights from bioinformatics, machine learning, and data-driven approaches.Briefings in bioinformatics · 2026Review
- Identification of the Integration/Excision Module and Regulatory Elements Involved in the Mobility of IME8, an Integrative and Mobilizable Element From Mosquitocidal Lysinibacillus sphaericus.Microbial biotechnology · 2026Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- State-dependent promoter switching mediates integrase gene transcription in the integrative and conjugative element ICEKp1 of Klebsiella pneumoniae.Nucleic acids research · 2026Article
7 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
Abstract
ICEberg 3.0 (https://tool2-mml.sjtu.edu.cn/ICEberg3/) is an upgraded database that provides comprehensive insights into bacterial integrative and conjugative elements (ICEs). In comparison to the previous version, three key enhancements were introduced: First, through text mining and manual curation, it now encompasses details of 2065 ICEs, 607 IMEs and 275 CIMEs, including 430 with experimental support. Secondly, ICEberg 3.0 systematically categorizes cargo gene functions of ICEs into six groups based on literature curation and predictive analysis, providing a profound understanding of ICEs'diverse biological traits. The cargo gene prediction pipeline is integrated into the online tool ICEfinder 2.0. Finally, ICEberg 3.0 aids the analysis and exploration of ICEs from the human microbiome. Extracted and manually curated from 2405 distinct human microbiome samples, the database comprises 1386 putative ICEs, offering insights into the complex dynamics of Bacteria-ICE-Cargo networks within the human microbiome. With the recent updates, ICEberg 3.0 enhances its capability to unravel the intricacies of ICE biology, particularly in the characterization and understanding of cargo gene functions and ICE interactions within the microbiome. This enhancement may facilitate the investigation of the dynamic landscape of ICE biology and its implications for microbial communities.
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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.