ReviewBriefings in bioinformatics2017
Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation.
Review in Briefings in bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers.
What it found
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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
80 citing papers in PubMed.
- Identification of cis-regulatory elements provides insights into tissue-specific gene regulation in the sheep genome.Nature communications · 2026Article
- A rapid test for protein-DNA interactions.Nucleic acids research · 2026Article
- ChIP happens: from biochemical origins to the modern omics toolbox for understanding steroid hormone receptors.The Biochemical journal · 2026Review
- SNAP: Streamlined Nextflow Analysis Pipeline for Immunoprecipitation-Based Epigenomic Profiling of Circulating Chromatin.bioRxiv : the preprint server for biology · 2025Article
- Epigenetics in forest trees- key driver to phenotypic plasticity and adaptation under stress.Functional & integrative genomics · 2025Review
- Bulk-level maps of pioneer factor binding dynamics during the Drosophila maternal-to-zygotic transition.Development (Cambridge, England) · 2025Article
- Preliminary investigation of the epigenetic regulation of KMT2D via H3K4me1/H3K27ac in oral squamous cell carcinoma.Cellular and molecular life sciences : CMLS · 2025Article
- Leveraging the MethMotif Toolkit to Characterize Context-Specific Features and Roles of Methylation Sensitive Transcription Factors.Current protocols · 2025Article
- Asymmetry of Motif Conservation Within Their Homotypic Pairs Distinguishes DNA-Binding Domains of Target Transcription Factors in ChIP-Seq Data.International journal of molecular sciences · 2025Article
- Annotation of cis-regulatory-associated histone modifications in the genomes of two Thoroughbred stallions.Frontiers in genetics · 2025Article
- Guidelines to Analyze ChIP-Seq Data: Journey Through QC and Analysis Considerations.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Crossing epigenetic frontiers: the intersection of novel histone modifications and diseases.Signal transduction and targeted therapy · 2024Review
- Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data.Genomics, proteomics & bioinformatics · 2024Review
- Genomic background sequences systematically outperform synthetic ones in de novo motif discovery for ChIP-seq data.NAR genomics and bioinformatics · 2024Article
- PTFSpot: deep co-learning on transcription factors and their binding regions attains impeccable universality in plants.Briefings in bioinformatics · 2024Article
- Churros: a Docker-based pipeline for large-scale epigenomic analysis.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Peak-agnostic high-resolution cis-regulatory circuitry mapping using single cell multiome data.Nucleic acids research · 2024Article
- Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks.International journal of molecular sciences · 2024Article
- Transcriptomic era of cancers in females: new epigenetic perspectives and therapeutic prospects.Frontiers in oncology · 2024Review
- Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors.Nature communications · 2023Article
20 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
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis can detect protein/DNA-binding and histone-modification sites across an entire genome. Recent advances in sequencing technologies and analyses enable us to compare hundreds of samples simultaneously; such large-scale analysis has potential to reveal the high-dimensional interrelationship level for regulatory elements and annotate novel functional genomic regions de novo. Because many experimental considerations are relevant to the choice of a method in a ChIP-seq analysis, the overall design and quality management of the experiment are of critical importance. This review offers guiding principles of computation and sample preparation for ChIP-seq analyses, highlighting the validity and limitations of the state-of-the-art procedures at each step. We also discuss the latest challenges of single-cell analysis that will encourage a new era in this field.
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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.