ArticleNature methods2016
Analysis of computational footprinting methods for DNase sequencing experiments.
Article in Nature methods, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers.
What it found
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Who cites it
94 citing papers in PubMed.
- Robust footprinting with sample-specific Tn5 bias correction for bulk and single cell ATAC-seq.Nature communications · 2026Article
- COCA-seq: genome-wide mapping of O-GlcNAc-associated open chromatin.Acta biochimica et biophysica Sinica · 2025Article
- Dissecting regulatory non-coding GWAS loci reveals fibroblast causal genes with pathophysiological relevance to heart failure.Nature communications · 2025Article
- Simulating CD8 T cell exhaustion: A comprehensive approach.iScience · 2025Article
- The chromatin accessibility landscape during early maize seed development.The Plant journal : for cell and molecular biology · 2025Article
- Unveiling Tissue-Specific RNA Landscapes in Mouse Organs During Fasting and Feeding Using Nanopore Direct RNA Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants.bioRxiv : the preprint server for biology · 2025Article
- Integrative multiomics reveals common endotypes across PSEN1, PSEN2, and APP mutations in familial Alzheimer's disease.Alzheimer's research & therapy · 2025Article
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- Cellular zinc status alters chromatin accessibility and binding of p53 to DNA.Life science alliance · 2024Article
- An autoimmune transcriptional circuit drives FOXP3Science translational medicine · 2024Article
- The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation.G3 (Bethesda, Md.) · 2024Article
- XL-DNase-Seq: Footprinting Analysis of Dynamic Transcription Factors.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Epigenomic mapping reveals distinct B cell acute lymphoblastic leukemia chromatin architectures and regulators.Cell genomics · 2023Article
- Cellular zinc status alters chromatin accessibility and binding of transcription factor p53 to genomic sites.bioRxiv : the preprint server for biology · 2023Article
- Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics.Nature methods · 2023Article
- Transcriptional activation of Jun and Fos members of the AP-1 complex is a conserved signature of immune aging that contributes to inflammaging.Aging cell · 2023Article
- PlantCADB: A Comprehensive Plant Chromatin Accessibility Database.Genomics, proteomics & bioinformatics · 2023Article
- RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data.BMC bioinformatics · 2023Article
- Epigenetic and transcriptional regulations prime cell fate before division during human pluripotent stem cell differentiation.Nature communications · 2023Article
34 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNase-seq allows nucleotide-level identification of transcription factor binding sites on the basis of a computational search of footprint-like DNase I cleavage patterns on the DNA. Frequently in high-throughput methods, experimental artifacts such as DNase I cleavage bias affect the computational analysis of DNase-seq experiments. Here we performed a comprehensive and systematic study on the performance of computational footprinting methods. We evaluated ten footprinting methods in a panel of DNase-seq experiments for their ability to recover cell-specific transcription factor binding sites. We show that three methods--HINT, DNase2TF and PIQ--consistently outperformed the other evaluated methods and that correcting the DNase-seq signal for experimental artifacts significantly improved the accuracy of computational footprints. We also propose a score that can be used to detect footprints arising from transcription factors with potentially short residence times.
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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.