ArticleNucleic acids research2017
ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 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
72 citing papers in PubMed.
- Developmental expression of the skeletal muscle determination gene,bioRxiv : the preprint server for biology · 2026Article
- Accurate prediction of cohesin and RNA Polymerase II-associated chromatin interactions using convolutional neural networks.Nucleic acids research · 2026Article
- 3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice.Genome biology · 2026Article
- CNNKSCEC: a deep learning-based framework for chromatin loop prediction with multi-source feature integration.Frontiers in genetics · 2026Article
- Gaining insights into Alzheimer's disease by predicting chromatin spatial organization.Bioinformatics advances · 2025Article
- Drought-responsive dynamics of H3K9ac-marked 3D chromatin interactions are integrated by OsbZIP23-associated super-enhancer-like promoter regions in rice.Genome biology · 2024Article
- Decoding the genomic landscape of chromatin-associated biomolecular condensates.Nature communications · 2024Article
- CTCF mutation at R567 causes developmental disorders via 3D genome rearrangement and abnormal neurodevelopment.Nature communications · 2024Article
- A continuum of zinc finger transcription factor retention on native chromatin underlies dynamic genome organization.Molecular systems biology · 2024Article
- Statistical modeling and significance estimation of multi-way chromatin contacts with HyperloopFinder.Briefings in bioinformatics · 2024Article
- TEAD2 initiates ground-state pluripotency by mediating chromatin looping.The EMBO journal · 2024Article
- MMCT-Loop: a mix model-based pipeline for calling targeted 3D chromatin loops.Nucleic acids research · 2024Article
- BL-Hi-C reveals the 3D genome structure ofHorticulture research · 2024Article
- ChIPr: accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features.Genome biology · 2024Article
- Domains Rearranged Methylase 2 maintains DNA methylation at large DNA hypomethylated shores and long-range chromatin interactions in rice.Plant biotechnology journal · 2023Article
- Integrated 3D genome, epigenome and transcriptome analyses reveal transcriptional coordination of circadian rhythm in rice.Nucleic acids research · 2023Article
- Inferring CTCF-binding patterns and anchored loops across human tissues and cell types.Patterns (New York, N.Y.) · 2023Article
- 3D organization of regulatory elements for transcriptional regulation in Arabidopsis.Genome biology · 2023Article
- Multiomic analysis of cohesin reveals that ZBTB transcription factors contribute to chromatin interactions.Nucleic acids research · 2023Article
- Anchoring super-enhancer-driven oncogenic lncRNAs for anti-tumor therapy in hepatocellular carcinoma.Molecular therapy : the journal of the American Society of Gene Therapy · 2023Article
12 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
ChIA-PET2 is a versatile and flexible pipeline for analyzing different types of ChIA-PET data from raw sequencing reads to chromatin loops. ChIA-PET2 integrates all steps required for ChIA-PET data analysis, including linker trimming, read alignment, duplicate removal, peak calling and chromatin loop calling. It supports different kinds of ChIA-PET data generated from different ChIA-PET protocols and also provides quality controls for different steps of ChIA-PET analysis. In addition, ChIA-PET2 can use phased genotype data to call allele-specific chromatin interactions. We applied ChIA-PET2 to different ChIA-PET datasets, demonstrating its significantly improved performance as well as its ability to easily process ChIA-PET raw data. ChIA-PET2 is available at https://github.com/GuipengLi/ChIA-PET2.
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.