ReviewNature reviews. Genetics2012
ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions.
Review in Nature reviews. Genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 394 papers, 3 of them syntheses that pooled it.
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
394 citing papers in PubMed, 3 syntheses or guidelines pooled it, 862 citations in OpenAlex.
- A systematic review of single-cell RNA sequencing applications and insights in Oryza sativa response to environmental stresses.Molecular biology reports · 2025Pooled it
- ChIP-Hub provides an integrative platform for exploring plant regulome.Nature communications · 2022Pooled it
- Improved linking of motifs to their TFs using domain information.Bioinformatics (Oxford, England) · 2020Pooled it
- Inferring Gene Regulatory Networks in Stem Cells: Methods and Applications.Methods in molecular biology (Clifton, N.J.) · 2027Review
- Decoding chromosome organization using proximity labeling and long-read sequencing.Journal of genetics and genomics = Yi chuan xue bao · 2026Article
- CUT&ID for simultaneous profiling of protein-DNA and protein-protein interactions.Nucleic acids research · 2026Article
- Quantitative analysis of DNA-GATA1 binding alterations linked to hematopoietic disorders.The FEBS journal · 2026Article
- Targeting SIRT6 epigenetically restrains neutrophil hyperplasia and enhances chemotherapeutic efficacy.Acta pharmaceutica Sinica. B · 2026Article
- ChEA-KG and ChEA-KG-TS: a network-based transcription factor enrichment analysis tool with an accompanying time-series workflow.Nucleic acids research · 2026Article
- Light-based footprinting of a eukaryotic genome.Science advances · 2026Article
- Functional Genomics Studies of Psychiatric Disorders in Individuals of Latin American Populations: A Scoping Review.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2026Article
- Probing transcription factor subsets in gene regulatory networks.Algorithms for molecular biology : AMB · 2026Article
- Molecular Genetics and Epigenetics Regulatory Role of miRNAs on Adipogenesis and Intramuscular Fat Development in Beef Cattle: In the Context of Meat Quality.Molecular biotechnology · 2026Review
- mChIP-seq for Multiplex and Multifactorial Epigenomic Profiling Uncovers Cancer-specific Histone Features in Cellular and Circulating Nucleosomes.bioRxiv : the preprint server for biology · 2026Article
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- Post-replicative chromatin accessibility predicts cell fate change.Stem cell reports · 2026Article
- Mixing features of transcription factors and genes enable accurate prediction of gene regulation relationships for unknown transcription factors.NAR genomics and bioinformatics · 2026Article
- The ChIP-FRiP pipeline quantifies co-binding and reveals how antibody background contributes to cohesin ChIP-seq patterns.bioRxiv : the preprint server for biology · 2026Article
- A rapid test for protein-DNA interactions.Nucleic acids research · 2026Article
334 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
1 author at 1 institution in 1 country.
Funding
Abstract
Chromatin immunoprecipitation experiments followed by sequencing (ChIP-seq) detect protein-DNA binding events and chemical modifications of histone proteins. Challenges in the standard ChIP-seq protocol have motivated recent enhancements in this approach, such as reducing the number of cells that are required and increasing the resolution. Complementary experimental approaches - for example, DNaseI hypersensitive site mapping and analysis of chromatin interactions that are mediated by particular proteins - provide additional information about DNA-binding proteins and their function. These data are now being used to identify variability in the functions of DNA-binding proteins across genomes and individuals. In this Review, I describe the latest advances in methods to detect and functionally characterize DNA-bound proteins.
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.