ReviewComputational and structural biotechnology journal2019
Computational Biology Solutions to Identify Enhancers-target Gene Pairs.
Review in Computational and structural biotechnology journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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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.
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Who cites it
28 citing papers in PubMed.
- Article
- Predicting enhancer-gene links from single-cell multi-omics data by integrating prior Hi-C information.Nucleic acids research · 2026Article
- Profiling the transcriptional regulatory network reveals putative shared regulatory elements within homoeologs in polyploid Brassica napus.Genome biology · 2026Article
- Prediction of target genes and functional types of cis-regulatory modules in the human genome reveals their distinct properties.BMC biology · 2025Article
- SEgene identifies links between super enhancers and gene expression across cell types.NPJ systems biology and applications · 2025Article
- Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages.BMC genomics · 2025Article
- Active enhancers: recent research advances and insights into disease.Biology direct · 2024Review
- Decoding polygenic diseases: advances in noncoding variant prioritization and validation.Trends in cell biology · 2024Review
- Omics-based construction of regulatory variants can be applied to help decipher pig liver-related traits.Communications biology · 2024Article
- Summary of ChIP-Seq Methods and Description of an Optimized ChIP-Seq Protocol.Methods in molecular biology (Clifton, N.J.) · 2024Article
- CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms.Genome biology · 2023Article
- Predicting patient-specific enhancer-promoter interactions.Cell reports methods · 2023Article
- Impact of supraphysiologic MDM2 expression on chromatin networks and therapeutic responses in sarcoma.Cell genomics · 2023Article
- Esearch3D: propagating gene expression in chromatin networks to illuminate active enhancers.Nucleic acids research · 2023Article
- Statistical Analysis in ChIP-seq-Related Applications.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Enhancer/gene relationships: Need for more reliable genome-wide reference sets.Frontiers in bioinformatics · 2023Review
- Functional genomic assays to annotate enhancer-promoter interactions genome wide.Human molecular genetics · 2022Review
- Genome-wide analysis of cis-regulatory changes underlying metabolic adaptation of cavefish.Nature genetics · 2022Article
- Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data.Genome biology · 2022Article
- The importance of considering regulatory domains in genome-wide analyses - the nearest gene is often wrong!Biology open · 2022Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Enhancers are non-coding regulatory elements that are distant from their target gene. Their characterization still remains elusive especially due to challenges in achieving a comprehensive pairing of enhancers and target genes. A number of computational biology solutions have been proposed to address this problem leveraging the increasing availability of functional genomics data and the improved mechanistic understanding of enhancer action. In this review we focus on computational methods for genome-wide definition of enhancer-target gene pairs. We outline the different classes of methods, as well as their main advantages and limitations. The types of information integrated by each method, along with details on their applicability are presented and discussed. We especially highlight the technical challenges that are still unresolved and hamper the effective achievement of a satisfactory and comprehensive solution. We expect this field will keep evolving in the coming years due to the ever-growing availability of data and increasing insights into enhancers crucial role in regulating genome functionality.
Identifiers
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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.