DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells.

No abstract is available for this paper.

• Publication year

  2010

• Venue

  Cold Spring Harbor Protocols

• Publication date

  2010-02-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1101/pdb.prot5384PMID 20150147PMCID PMC3627383
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

  2009influential reference
• Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip).

  2009cited by this paper
• High-resolution mapping and characterization of open chromatin across the genome.

  2008influential reference
• Identification and Characterization of Cell Type–Specific and Ubiquitous Chromatin Regulatory Structures in the Human Genome

  2007influential reference
• Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

  2007cited by this paper
• Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays

  2006influential reference
• DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays

  2006influential reference
• Nuclease hypersensitive sites in chromatin.

  1988cited by this paper
• Chromatin fine structure of active and repressed genes

  1981cited by this paper
• DNase I hypersensitive sites in Drosophila chromatin occur at the 5' ends of regions of transcription.

  1981cited by this paper
• The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I

  1980cited by this paper
• The chromatin structure of specific genes: II. Disruption of chromatin structure during gene activity.

  1979cited by this paper

• ChromBERT: A foundation model for learning interpretable representations for context-specific transcriptional regulatory networks.

  2026cites this paper
• Synthetic promoter design in plants: integration of computational and experimental approaches.

  2026cites this paper
• AI-Enhanced CRISPR Diagnostics: From gRNA Design to Cas Protein Engineering and Signal Analytics

  2026cites this paper
• A pipeline for single-cell chromatin accessibility data analysis.

  2026cites this paper
• PEAKQC: Periodicity Evaluation in scATAC-seq data for quality assessment

  2025cites this paper
• Chromatin and transcriptional dynamics underlying the immune-modulatory effects of vitamin D3 in vivo

  2025cites this paper
• ATAC-seq for Characterizing Host and Pathogen Genome Accessibility During Virus Infection.

  2025cites this paper
• Transformers and genome language models

  2025cites this paper
• Systematic pegRNA design with PRIDICT2.0 and ePRIDICT for efficient prime editing.

  2025cites this paper
• Applications of high-throughput reporter assays to gene regulation studies.

  2025cites this paper
• Exploring Chromoanagenesis with DAFCA (Dam Assisted Fluorescent Tagging of Chromatin Accessibility): Integrating Chromatin Accessibility and Optical Genome Mapping for Enhanced Structural Variant Detection.

  2025cites this paper
• Programming human cell type-specific gene expression via an atlas of AI-designed enhancers

  2025cites this paper
• Aberrant Enhancer Regulation, Phase Separation, and Autoimmune Diseases

  2025cites this paper
• Benchmarking PWM and SVM-based Models for Transcription Factor Binding Site Prediction: A Comparative Analysis on Synthetic and Biological Data

  2025cites this paper
• Advances in Epigenomic Sequencing and Their Applications in Cancer Diagnostics

  2025cites this paper
• Inhibition of triglyceride metabolism‐associated enhancers alters lipid deposition during adipocyte differentiation

  2025cites this paper
• Integrating the ENCODE blocklist for machine learning quality control of ChIP-seq data with seqQscorer

  2025cites this paper
• Mapping Protein Occupancy on DNA with an Unnatural Cytosine Modification in Bio-orthogonal Contexts

  2025cites this paper
• Revealing long-range heterogeneous organization of nucleoproteins with 6mA footprinting by ipdTrimming

  2025cites this paper
• Benchmarking transcription factor binding site prediction models: a comparative analysis on synthetic and biological data

  2025cites this paper
• CREATE: cell-type-specific cis-regulatory element identification via discrete embedding

  2025cites this paper
• Early feature extraction drives model performance in high-resolution chromatin accessibility prediction: A systematic evaluation of deep learning architectures

  2025cites this paper
• PEAKQC: periodicity evaluation in single-cell ATAC-seq data for quality assessment

  2025cites this paper
• CUT&RUN as a Powerful Tool for Chromatin Profiling: a Focus on Neuropsychiatric Disorders.

  2025cites this paper
• R-loops shape chromatin architecture to promote balanced lineage allocation during differentiation

  2025cites this paper
• Regulatory Elements for Gene Therapy of Epilepsy

  2025cites this paper
• A tree-based kernel for densities and its applications in clustering DNase-seq profiles

  2025cites this paper
• Mapping Protein-ssDNA Interactions at Single Nucleotide Resolution by Dual Nucleases-Assisted Next-Generation Sequencing.

  2025cites this paper
• Applications of single-cell technologies in drug discovery for tumor treatment

  2024cites this paper
• Single-cell omics: experimental workflow, data analyses and applications

  2024cites this paper
• Chromatin Immunoprecipitation Using Imbibed Seeds of Arabidopsis thaliana.

  2024cites this paper
• Integrating evolutionary genomics of forest trees to inform future tree breeding amid rapid climate change

  2024cites this paper
• Cellular zinc status alters chromatin accessibility and binding of p53 to DNA

  2024cites this paper
• Establishing an optimized ATAC-seq protocol for the maize

  2024cites this paper
• The Role of Changes in Structure and Dynamics of Chromatin due to COVID-19

  2024cites this paper
• From sequence to consequence: Deciphering the complex cis-regulatory landscape

  2024cites this paper
• Differences in transcription initiation directionality underlie distinctions between plants and animals in chromatin modification patterns at genes and cis-regulatory elements

  2024cites this paper
• A new method for detecting differential peaks from ATAC-seq data

  2024cites this paper
• Unravelling the genetic basis of Schizophrenia.

  2024cites this paper
• Reduction of ETV1 is Identified as a Prominent Feature of Age-Related Cataract

  2024cites this paper
• Integrative ATAC-seq and RNA-seq analysis of myogenic differentiation of ovine skeletal muscle satellite cell.

  2024cites this paper
• Deep learning approaches for non-coding genetic variant effect prediction: current progress and future prospects

  2024cites this paper
• Epigenetic regulation of cardiovascular diseases induced by behavioral and environmental risk factors: Mechanistic, diagnostic, and therapeutic insights

  2024cites this paper
• Data enhancement in the age of spatial biology.

  2024cites this paper
• Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data

  2024cites this paper
• iDHS-RGME: Identification of DNase I hypersensitive sites by integrating information on nucleotide composition and physicochemical properties.

  2024cites this paper
• Revealing long-range heterogeneous organization of nucleoproteins with N6-methyladenine footprinting

  2024cites this paper
• Perspective on recent developments and challenges in regulatory and systems genomics

  2024cites this paper
• CRISPRoffT: comprehensive database of CRISPR/Cas off-targets

  2024cites this paper
• EpiGePT: a pretrained transformer-based language model for context-specific human epigenomics

  2024cites this paper
• Translation of genome-wide association study: from genomic signals to biological insights

  2024cites this paper
• Detecting gene expression in Caenorhabditis elegans

  2024cites this paper
• Profiling of chromatin accessibility and regulatory elements toward understanding the mechanisms underlying growth regulation in the Pacific oyster (Crassostrea gigas)

  2024cites this paper
• PPRTGI: A Personalized PageRank Graph Neural Network for TF-Target Gene Interaction Detection

  2024cites this paper
• XL-DNase-Seq: Footprinting Analysis of Dynamic Transcription Factors.

  2024cites this paper
• quaqc: efficient and quick ATAC-seq quality control and filtering

  2024cites this paper
• OneSC: a computational platform for recapitulating cell state transitions

  2024cites this paper
• Acute depletion of BRG1 reveals its primary function as an activator of transcription

  2024cites this paper
• DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA

  2024cites this paper
• Identification, Design, and Application of Noncoding Cis-Regulatory Elements

  2024cites this paper
• The link between the ANPEP gene and type 2 diabetes mellitus may be mediated by the disruption of glutathione metabolism and redox homeostasis.

  2024cites this paper
• Polymorphisms of ANPEP Gene Are Associated with Microvascular Complications of Type 2 Diabetes

  2024cites this paper
• Comprehensive analysis of computational approaches in plant transcription factors binding regions discovery

  2024cites this paper
• Hybrid Epigenomes Reveal Extensive Local Genetic Changes to Chromatin Accessibility Contribute to Divergence in Embryonic Gene Expression Between Species

  2023cites this paper
• Аpplication of massive parallel reporter analysis in biotechnology and medicine

  2023cites this paper
• Developing OCHROdb, a comprehensive quality checked database of open chromatin regions from sequencing data

  2023cites this paper
• EpiGePT : a Pretrained Transformer model for epigenomics 1

  2023cites this paper
• LangMoDHS: A deep learning language model for predicting DNase I hypersensitive sites in mouse genome.

  2023cites this paper
• ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs

  2023cites this paper
• Spatial chromatin accessibility sequencing resolves high-order spatial interactions of epigenomic markers

  2023cites this paper
• Cellular zinc status alters chromatin accessibility and binding of transcription factor p53 to genomic sites

  2023cites this paper
• A method of nuclei extraction and library construction for chromatin transposase accessibility sequencing in gramineous plants

  2023cites this paper
• cisDynet: An integrated platform for modeling gene‐regulatory dynamics and networks

  2023cites this paper
• Integrative approaches based on genomic techniques in the functional studies on enhancers

  2023cites this paper
• Differences in transcription initiation directionality underlie distinctions between plants and animals in chromatin modification patterns at genes and cis-regulatory elements

  2023cites this paper
• Profiling Chromatin Accessibility in Humans Using Adenine Methylation and Long-Read Sequencing

  2023cites this paper
• Single-cell sequencing technology applied to epigenetics for the study of tumor heterogeneity

  2023cites this paper
• Computational tools for inferring transcription factor activity

  2023cites this paper
• Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals

  2023cites this paper
• Interpretable models of gene expression in single-cell immunology

  2023cites this paper
• Advances in transposable elements: from mechanisms to applications in mammalian genomics

  2023cites this paper
• A computational approach to demonstrate the control of gene expression via chromosomal access in colorectal cancer

  2023cites this paper
• EpiGePT: a Pretrained Transformer model for epigenomics

  2023cites this paper
• DeepSATA: A Deep Learning-Based Sequence Analyzer Incorporating the Transcription Factor Binding Affinity to Dissect the Effects of Non-Coding Genetic Variants

  2023cites this paper
• Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays

  2023cites this paper
• Prediction accuracy of regulatory elements from sequence varies by functional sequencing technique

  2023cites this paper
• The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity

  2023cites this paper
• Optimized protocol for assay for transposase-accessible chromatin by sequencing (ATAC-seq) from Drosophila melanogaster brain tissue

  2023cites this paper
• Data navigation on the ENCODE portal

  2023cites this paper
• Advanced Omics Techniques for Understanding Cochlear Genome, Epigenome, and Transcriptome in Health and Disease

  2023cites this paper
• Uncovering Co-regulatory Modules and Gene Regulatory Networks in the Heart through Machine Learning-based Analysis of Large-scale Epigenomic Data

  2023cites this paper
• Discordance between chromatin accessibility and transcriptional activity during the human primed-to-naïve pluripotency transition process

  2023cites this paper
• Novel enhancers conferring compensatory transcriptional regulation of Nkx2-5 in heart development.

  2023cites this paper
• Visualization of the landscape of the read alignment shape of ATAC‐seq data using Hellinger distance metric

  2023cites this paper
• iDHS-DPPE: a method based on dual-path parallel ensemble decision for DNase I hypersensitive sites prediction

  2023cites this paper
• Spatial chromatin accessibility sequencing resolves high-order spatial interactions of 1 epigenomic markers 2

  2023cites this paper
• Cis-Regulatory Elements in Mammals

  2023cites this paper
• Deep Learning on Chromatin Accessibility.

  2023cites this paper
• Computational and Structural

  2023cites this paper
• Are extraordinary nucleosome structures more ordinary than we thought?

  2023cites this paper