ArticleNature communications2019
Identification of significant chromatin contacts from HiChIP data by FitHiChIP.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 174 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
174 citing papers in PubMed.
- p-LoopF is associated with chromatin looping in large introns of Ginkgo biloba.Cell research · 2026Article
- hnRNPK condensates facilitate enhancer-promoter looping and RNA polymerase II recruitment.Nature genetics · 2026Article
- Integrative multi-omics profiling and machine learning reveal enhancer RNA signatures for early detection and prognostic stratification in breast cancer.NAR cancer · 2026Article
- dcHiChIP: a comprehensive Nextflow-based pipeline for multiscale analysis of chromatin architecture from HiChIP data.Bioinformatics (Oxford, England) · 2026Article
- Chiron3D: an interpretable deep learning framework for understanding the DNA code of chromatin looping.Bioinformatics (Oxford, England) · 2026Article
- Article
- Leukemia risk factor ARID5B coordinates HDAC-mediated transcriptional repression.Nucleic acids research · 2026Article
- ATF4 and CHOP coordinate endoplasmic reticulum stress-responsive gene programs through enhancer activation and chromatin looping.Nucleic acids research · 2026Article
- Trans-regulation of heterochromatin underlies genetic variation in 3D genome contacts in mouse embryonic stem cells.Genome biology · 2026Article
- Initial leukemic epigenomic state determines hypomethylating agent response.Nature communications · 2026Article
- A high-penetrance intergenic variant at 9p21 confers melanoma susceptibility.Research square · 2026Article
- TCF3::HLF orchestrates an enhancer-promoter network with activation of MEF2C to promote immature HSC gene expression in leukemia.Science advances · 2026Article
- Accurate and efficient HiChIP interaction detection by modeling restriction enzyme cut site density as biological signal.Briefings in bioinformatics · 2026Article
- KLF5 controls subtype-independent highly interactive enhancers in pancreatic cancer to regulate cell survival.Science advances · 2026Article
- Differential chromatin looping regulated by two GA-binding transcription factors creates an X-specific chromatin environment for dosage compensation.bioRxiv : the preprint server for biology · 2026Article
- Impaired cohesin loading disrupts pancreatic differentiation by Polycomb-driven chromatin rewiring and loop collapse.Communications biology · 2026Article
- EpiExpr: Predicting gene expression using epigenetic data and chromatin interactions.bioRxiv : the preprint server for biology · 2026Article
- Robin: an advanced tool for comparative loop caller result analysis leveraging large language models.NAR genomics and bioinformatics · 2026Article
- Repeat-rich RNA guides repetitive genomic elements into biomolecular condensates for heterochromatin organization and muscle integrity.Nucleic acids research · 2026Article
- A scalable computational framework for predicting gene expression from candidateGenome research · 2026Article
114 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
HiChIP/PLAC-seq is increasingly becoming popular for profiling 3D chromatin contacts among regulatory elements and for annotating functions of genetic variants. Here we describe FitHiChIP, a computational method for loop calling from HiChIP/PLAC-seq data, which jointly models the non-uniform coverage and genomic distance scaling of contact counts to compute statistical significance estimates. We also develop a technique to filter putative bystander loops that can be explained by stronger adjacent loops. Compared to existing methods, FitHiChIP performs better in recovering contacts reported by Hi-C, promoter capture Hi-C and ChIA-PET experiments and in capturing previously validated promoter-enhancer interactions. FitHiChIP loop calls are reproducible among replicates and are consistent across different experimental settings. Our work also provides a framework for differential HiChIP analysis with an option to utilize ChIP-seq data for further characterizing differential loops. Even though designed for HiChIP, FitHiChIP is also applicable to other conformation capture assays.
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.