ArticleBMC bioinformatics2020
2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
27 citing papers in PubMed, 56 citations in OpenAlex.
- A Ferroptosis-Related LncRNA Signature Associated with Prognosis, Tumor Immune Environment, and Genome Instability in Hepatocellular Carcinoma.Computational and mathematical methods in medicine · 2022Trial
- ExIR enables prioritizing driver and biomarker genes from omics data in a reference free manner.iScience · 2026Article
- Current state and future prospects of Horizontal Gene Transfer detection.NAR genomics and bioinformatics · 2025Review
- Identification of Key Biomarkers and Immune Microenvironment Features in Ulcerative Colitis: An Integrated Analysis Using WGCNA and Multiple Machine Learning Algorithms.Journal of inflammation research · 2025Article
- Comprehensive pan-cancer analysis reveals CGB5 is a potential promising predictive and immunotherapeutic biomarker.Frontiers in medicine · 2025Article
- An integrated machine learning framework for developing and validating diagnostic models and drug predictions based on ulcerative colitis genes.Frontiers in medicine · 2025Article
- Comprehensive Bioinformatics Analysis for the Identification of Hub Genes and Critical Signaling Pathways Differentiating Latent and Active Tuberculosis.Combinatorial chemistry & high throughput screening · 2025Article
- Multimodal deep learning for predicting protein ubiquitination sites.Bioinformatics advances · 2025Article
- Computational strategies in tumor phylogenetics: evaluating multimodal integration and methodological trade-offs across study designs.Bioinformatics advances · 2025Review
- Rore: robust and efficient antioxidant protein classification via a novel dimensionality reduction strategy based on learning of fewer features.Genomics & informatics · 2024Article
- Article
- Enhancing genomic disorder prediction through Feynman Concordance and Interpolated Nearest Centroid techniques.Scientific reports · 2024Article
- Scm6A: A Fast and Low-cost Method for Quantifying m6A Modifications at the Single-cell Level.Genomics, proteomics & bioinformatics · 2024Article
- FEOpti-ACVP: identification of novel anti-coronavirus peptide sequences based on feature engineering and optimization.Briefings in bioinformatics · 2024Article
- Using the Random Forest for Identifying Key Physicochemical Properties of Amino Acids to Discriminate Anticancer and Non-Anticancer Peptides.International journal of molecular sciences · 2023Article
- Genomic Signature in Evolutionary Biology: A Review.Biology · 2023Review
- iEnhancer-DCSV: Predicting enhancers and their strength based on DenseNet and improved convolutional block attention module.Frontiers in genetics · 2023Article
- Identification of dynamic gene expression profiles during sequential vaccination with ChAdOx1/BNT162b2 using machine learning methods.Frontiers in microbiology · 2023Article
- Mitochondria dysfunction in airway epithelial cells is associated with type 2-low asthma.Frontiers in genetics · 2023Article
- Identification of genes related to immune enhancement caused by heterologous ChAdOx1-BNT162b2 vaccines in lymphocytes at single-cell resolution with machine learning methods.Frontiers in immunology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundGenomic islands are associated with microbial adaptations, carrying genomic signatures different from the host. Some methods perform an overall test to identify genomic islands based on their local features. However, regions of different scales will display different genomic features.
resultsWe proposed here a novel method "2SigFinder ", the first combined use of small-scale and large-scale statistical testing for genomic island detection. The proposed method was tested by genomic island boundary detection and identification of genomic islands or functional features of real biological data. We also compared the proposed method with the comparative genomics and composition-based approaches. The results indicate that the proposed 2SigFinder is more efficient in identifying genomic islands.
conclusionsFrom real biological data, 2SigFinder identified genomic islands from a single genome and reported robust results across different experiments, without annotated information of genomes or prior knowledge from other datasets. 2SigHunter identified 25 Pathogenicity, 1 tRNA, 2 Virulence and 2 Repeats from 27 Pathogenicity, 1 tRNA, 2 Virulence and 2 Repeats, and detected 101 Phage and 28 HEG out of 130 Phage and 36 HEGs in S. enterica Typhi CT18, which shows that it is more efficient in detecting functional features associated with GIs.
Indexed as
Identifiers
What OpenQuestion holds
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.