ArticleGenome biology2019
ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Chromosome-level genome assembly of the small-sized Taihang donkey (Equus asinus).Scientific data · 2026Article
- De novo genome assembly of Yanbian cattle using PacBio HiFi and Hi-C combined with RNA-seq data.Scientific data · 2025Article
- Read Mapping for Hi-C Analysis.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Using paired-end read orientations to assess technical biases in capture Hi-C.NAR genomics and bioinformatics · 2024Article
- CD-Loop: a chromatin loop detection method based on the diffusion model.Frontiers in genetics · 2024Article
- Transcription induces context-dependent remodeling of chromatin architecture during differentiation.PLoS biology · 2023Article
- A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest.Nature communications · 2023Article
- The histone variant macroH2A1.1 regulates RNA polymerase II-paused genes within defined chromatin interaction landscapes.Journal of cell science · 2022Article
- 3D genome organization links non-coding disease-associated variants to genes.Frontiers in cell and developmental biology · 2022Review
- Comparison of Capture Hi-C Analytical Pipelines.Frontiers in genetics · 2022Article
- Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools.Nature protocols · 2021Article
- Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C.Epigenetics & chromatin · 2021Review
- Myod1 and GR coordinate myofiber-specific transcriptional enhancers.Nucleic acids research · 2021Article
- Identifying high-confidence capture Hi-C interactions using CHiCANE.Nature protocols · 2021Article
- 3D reconstruction of genomic regions from sparse interaction data.NAR genomics and bioinformatics · 2021Article
- Assessment of 3D Interactions Between Promoters and Distal Regulatory Elements with Promoter Capture Hi-C (PCHi-C).Methods in molecular biology (Clifton, N.J.) · 2021Article
- A supervised learning framework for chromatin loop detection in genome-wide contact maps.Nature communications · 2020Article
- Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks.Nucleic acids research · 2020Article
- Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction.Computational and structural biotechnology journal · 2020Review
- ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C.Genome biology · 2019Article
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5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Capture Hi-C (CHi-C) is a new technique for assessing genome organization based on chromosome conformation capture coupled to oligonucleotide capture of regions of interest, such as gene promoters. Chromatin loop detection is challenging because existing Hi-C/4C-like tools, which make different assumptions about the technical biases presented, are often unsuitable. We describe a new approach, ChiCMaxima, which uses local maxima combined with limited filtering to detect DNA looping interactions, integrating information from biological replicates. ChiCMaxima shows more stringency and robustness compared to previously developed tools. The tool includes a GUI browser for flexible visualization of CHi-C profiles alongside epigenomic tracks.
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