ArticleNucleic acids research2022
cLoops2: a full-stack comprehensive analytical tool for chromatin interactions.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 39 citations in OpenAlex.
- Replication-independent eviction of the histone variant H2B.8 reveals chromatin reprogramming during seed imbibition.Nature communications · 2026Article
- Accurate and efficient HiChIP interaction detection by modeling restriction enzyme cut site density as biological signal.Briefings in bioinformatics · 2026Article
- Chromatin reorganization drives overexpression of a Btaf1 variant underpinning hematopoietic aging.Nature communications · 2026Article
- Correction to "Spatial Reorganization of Chromatin Architecture Shapes the Expression Phenotype of Therapy-Induced Senescent Cells".Aging cell · 2026Article
- Robin: an advanced tool for comparative loop caller result analysis leveraging large language models.NAR genomics and bioinformatics · 2026Article
- Elucidation of chromatin loops among regulatory regions using Hi-TrAC.Frontiers in epigenetics and epigenomics · 2026Article
- NPM1 mislocalization mediated by RNA Pol I inhibition alters chromatin landscape.bioRxiv : the preprint server for biology · 2025Article
- Loopsim: enrichment analysis of chromosome conformation capture with fast empirical distribution simulation.NAR genomics and bioinformatics · 2025Article
- Changes in 3D Chromatin Organization Drive Topologically Determined Gene Expression in the Poststroke Mouse Cortex.Stroke · 2025Article
- BLIMP1 negatively regulates IL-2 signaling in T cells.Science advances · 2025Article
- A novel deep learning framework with dynamic tokenization for identifying chromatin interactions along with motif importance investigation.Briefings in bioinformatics · 2025Article
- Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes.Communications biology · 2025Article
- Article
- Essential roles of CTCF binding sites at TAD boundaries in modulating chromatin interactions and transcriptional regulation at theFrontiers in immunology · 2025Article
- The cells are all-right: Regulation of the Lefty genes by separate enhancers in mouse embryonic stem cells.PLoS genetics · 2024Article
- Three-dimensional chromatin reorganization regulates B cell development during ageing.Nature cell biology · 2024Article
- Regulation of T helper cell differentiation by the interplay between histone modification and chromatin interaction.Immunity · 2024Article
- MMCT-Loop: a mix model-based pipeline for calling targeted 3D chromatin loops.Nucleic acids research · 2024Article
- Comparative study on chromatin loop callers using Hi-C data reveals their effectiveness.BMC bioinformatics · 2024Article
- Stromal Pbrm1 mediates chromatin remodeling necessary for embryo implantation in the mouse uterus.The Journal of clinical investigation · 2024Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Investigating chromatin interactions between regulatory regions such as enhancer and promoter elements is vital for understanding the regulation of gene expression. Compared to Hi-C and its variants, the emerging 3D mapping technologies focusing on enriched signals, such as TrAC-looping, reduce the sequencing cost and provide higher interaction resolution for cis-regulatory elements. A robust pipeline is needed for the comprehensive interpretation of these data, especially for loop-centric analysis. Therefore, we have developed a new versatile tool named cLoops2 for the full-stack analysis of these 3D chromatin interaction data. cLoops2 consists of core modules for peak-calling, loop-calling, differentially enriched loops calling and loops annotation. It also contains multiple modules for interaction resolution estimation, data similarity estimation, features quantification, feature aggregation analysis, and visualization. cLoops2 with documentation and example data are open source and freely available at GitHub: https://github.com/KejiZhaoLab/cLoops2.
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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.