Chromatin accessibility: a window into the genome.

paper Cited Public

Authors: Tsompana, Maria; Buck, Michael J
Year: 2014
Journal: Epigenetics & chromatin
PMID: 25473421
DOI: 10.1186/1756-8935-7-33
PMCID: PMC4253006

#	Section	Preview
40	Review — Chromatin accessibility high-throughput sequence data analysis — Detection of enriched regions — ATAC-seq data	ATAC-sec peak calling (Step 13) can be performed also by using ZINBA [103]. Alternatively, our group…
41	Review — Chromatin accessibility high-throughput sequence data analysis — Stage 3 analysis	This stage of analysis involves estimation of various parameters of the epigenomic landscape,…
42	Review — Chromatin accessibility high-throughput sequence data analysis — Stage 3 analysis — MNase-seq data	Nucleosome or translational positioning indicates the position of a population of nucleosomes in…
43	Review — Chromatin accessibility high-throughput sequence data analysis — Stage 3 analysis — MNase-seq data	genomic configurations [56]. A number of methods have been applied to measure nucleosome positioning…
44	Review — Chromatin accessibility high-throughput sequence data analysis — Stage 3 analysis — DNase-seq data	Stable binding of TFs in the vicinity of DHSs protects DNA from nuclease cleavage and generates…
45	Review — Chromatin accessibility high-throughput sequence data analysis — Stage 3 analysis — DNase-seq data	The recently reported modified approach DNase I-released fragment-length analysis of…
46	Review — Chromatin accessibility high-throughput sequence data analysis — Stage 3 analysis — ATAC-seq data	Analysis of ATAC-seq paired-end data can reveal indispensable information on nucleosome packing and…
47	Review — Chromatin accessibility high-throughput sequence data analysis — Stage 4 analysis	Data annotation and integration represents the final and most informative stage of analysis and…
48	Review — Chromatin accessibility high-throughput sequence data analysis — Stage 4 analysis	One can also inspect enriched regions of interest for discovery of putative TF binding events using…
49	Review — Chromatin accessibility high-throughput sequence data analysis — Stage 4 analysis	For DNase-seq and ATAC-seq experiments TF footprints can be analyzed with CENTIPEDE [151]. CENTIPEDE…
50	Conclusions	Each of the chromatin accessibility assays discussed here has inherent limitations in identifying…
51	Conclusions	Functional annotation of accessible regions is factor-dependent and relies highly on the…
52	Conclusions	comprehensive TF motif databases generated using in vivo/in vitro assays or computationally based de…
53	Conclusions	Currently, most researchers compare their chromatin accessibility data to other published datasets.…
54	Authors’ information	MJB is an associate professor at the Department of Biochemistry at the State University of New York…

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In this knowledge base

Title	Year	PMID
Integrated single-cell multiomic profiling of caudate nucleus suggests key mechanisms in alcohol use disorder.	2025	41083468

External

Title	Authors	Journal	Year	Link
An experimentally-informed polymer model reveals high resolution organization of genomic loci.	Mittal R et al.	—	2026	→
ATAC-Seq and RNA-Seq Integration Reveals Chromatin Accessibility and Transcriptional Dynamics During Fruit Color Development in Mulberry.	Zeng Y et al.	—	2026	→
Chromatin accessibility landscapes define stromal cell identities across tissues.	Nooranikhojasteh A et al.	—	2026	→
Deacetylase-independent HDAC1 condensation defines temozolomide response in glioblastoma.	Zhang Q et al.	—	2026	→
Euchromatin and Heterochromatin: Implications for DNA Accessibility and Transcription.	Minami K et al.	—	2026	→
Exploratory analysis of epigenetic dynamics and small extracellular vesicles in Penaeus vannamei hemocytes under inactivated Vibrio parahaemolyticus priming.	Lin YR et al.	—	2026	→
Practical NicE-seq workflow for chromatin accessibility analysis in plants.	Bader ZE et al.	—	2026	→
Single cell multiomic analysis of the impact of Delta-9-tetrahydrocannabinol on HIV infected CD4 T cells.	Ashokkumar M et al.	—	2026	→
BIT: Bayesian Identification of Transcriptional regulators from epigenomics-based query region sets.	Lu Z et al.	—	2025	→
cis- and trans-elements for the transcriptional regulation of sugar responsive genes: from current knowledge to future applications.	Cruz-López MI et al.	—	2025	→
Comprehensive guide for epigenetics and transcriptomics data quality control.	Comendul A et al.	—	2025	→
Convergent Evolution and the Epigenome.	Alvarado SG et al.	—	2025	→
Coordinated regulation by lncRNAs results in tight lncRNA-target couplings.	Chiu HS et al.	—	2025	→
Cross-cellular analysis of chromatin accessibility markers H3K4me3 and DNase in the context of detecting cell-identity genes: An "all-or-nothing" approach.	Low BH et al.	—	2025	→
Crosstalk between metabolism and epigenetics during macrophage polarization.	Zhang K et al.	—	2025	→
Decoding the epigenetic and transcriptional basis of direct cardiac reprogramming.	Peng WG et al.	—	2025	→
Defining transcription factor nucleosome binding with Pioneer-seq.	Tsompana M et al.	—	2025	→
Differential regulation during development, aging, and disease implies heart cell specific functions of the Mediator Complex.	Kolonay DW et al.	—	2025	→
DNA intercalating drugs: Mechanisms of action in cancer treatment.	Oyeyode M et al.	—	2025	→
Dynamic chromatin accessibility landscape changes in cardiac fibrosis.	Liu ZY et al.	—	2025	→
EpiMapper: A new tool for analyzing high-throughput sequencing from CUT&Tag.	Dragland JS et al.	—	2025	→
Genomes of the Caribbean reef-building corals Colpophyllia natans, Dendrogyra cylindrus, and Siderastrea siderea.	Locatelli NS et al.	—	2025	→
HBV-driven host chromatin accessibility changes affect liver metabolic pathways, iron homeostasis and promote a preneoplastic phenotype.	Alfano V et al.	—	2025	→
IMATAC imputes single-cell ATAC-seq data by deep hierarchical network with denoising autoencoder.	Li Y et al.	—	2025	→
Inferring differential protein binding from time-series chromatin accessibility data.	Mitra S et al.	—	2025	→
INSTINCT: Multi-sample integration of spatial chromatin accessibility sequencing data via stochastic domain translation.	Liu Y et al.	—	2025	→
Integrated single-cell multiomic profiling of caudate nucleus suggests key mechanisms in alcohol use disorder.	Green NC et al.	—	2025	→
Integrative Analysis of ATAC-Seq and RNA-Seq Identifies Key Genes Affecting Muscle Development in Ningxiang Pigs.	Tan W et al.	—	2025	→
Integrative Multi-Omics Approaches for Identifying and Characterizing Biological Elements in Crop Traits: Current Progress and Future Prospects.	Fan BL et al.	—	2025	→
ISDH-seq: a robust methodology for profiling and characterization of open chromatin.	Li Z et al.	—	2025	→
NuclampFISH enables cell sorting based on nuclear RNA expression for chromatin analysis.	Liu Y et al.	—	2025	→
Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites.	Wilson PD et al.	—	2025	→
Probing the effect of PEG-DNA interactions and buffer viscosity on tethered DNA in shear flow.	Zohra FT et al.	—	2025	→
Protocol for transcriptomic and epigenomic analysis of JAK inhibitor sensitivity in IFN-γ-primed human macrophages using ATAC-seq and RNA-seq.	Kwon G et al.	—	2025	→
The Converging Roles of Nucleases and Helicases in Genome Maintenance and the Aging Process.	Margariti A et al.	—	2025	→
The Link Between TGF-β Signaling and Chromatin Dynamics Takes an Unexpected Path.	Mallo M	—	2025	→
The role of DNA content in shaping chromatin architecture and gene expression.	Barragán-Rosillo AC et al.	—	2025	→
Time-course transcriptome and chromatin accessibility analyses reveal the dynamic transcriptional regulation shaping spikelet hull size.	Chen S et al.	—	2025	→
Transcriptional interferences ensure one olfactory receptor per ant neuron.	Sieriebriennikov B et al.	—	2025	→
Transient alterations in nucleosome distribution and sensitivity to nuclease define the THP-1 monocyte-to-macrophage transition.	Benoit JM et al.	—	2025	→
A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity.	Li Z et al.	—	2024	→
Assessing next-generation sequencing-based computational methods for predicting transcriptional regulators with query gene sets.	Lu Z et al.	—	2024	→
Century-old chromatin architecture revealed in formalin-fixed vertebrates.	Hahn EE et al.	—	2024	→
Chromatin accessibility mediated transcriptome changes contribute to flavor substance alterations and jasmonic acid hyperaccumulation during oolong tea withering process.	Kong W et al.	—	2024	→
Chromatin accessibility profiling reveals that human fibroblasts respond to mechanical stimulation in a cell-specific manner.	Logan NJ et al.	—	2024	→
Chromatin remodeling in tissue stem cell fate determination.	Li X et al.	—	2024	→
Decoding the epigenetics and chromatin loop dynamics of androgen receptor-mediated transcription.	Altıntaş UB et al.	—	2024	→
Differences in transcription initiation directionality underlie distinctions between plants and animals in chromatin modification patterns at genes and cis-regulatory elements.	Silver BD et al.	—	2024	→
Differential chromatin accessibility and Gene Expression Associated with Backfat Deposition in pigs.	Zhang Z et al.	—	2024	→
Dissecting the Immune System through Gene Regulation.	Yoshida H	—	2024	→
Dynamic Chromatin Accessibility and Gene Expression Regulation During Maize Leaf Development.	Wang Y et al.	—	2024	→
Emerging Approaches to Profile Accessible Chromatin from Formalin-Fixed Paraffin-Embedded Sections.	Sunitha Kumary VUN et al.	—	2024	→
Endothelial cells adopt a pro-reparative immune responsive signature during cardiac injury.	Long H et al.	—	2024	→
Eomes-dependent mitochondrial regulation promotes survival of pathogenic CD4+ T cells during inflammation.	Joulia E et al.	—	2024	→
Epigenetic Effects of Resveratrol on Oncogenic Signaling in Breast Cancer.	Kurzava Kendall L et al.	—	2024	→
Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton.	Hu G et al.	—	2024	→
Experimental evidence for cancer resistance in a bat species.	Hua R et al.	—	2024	→
Genome-wide mapping of DNase I hypersensitive sites revealed differential chromatin accessibility and regulatory DNA elements under drought stress in rice cultivars.	Rajkumar MS et al.	—	2024	→
How chromatin senses plant hormones.	Shao Z et al.	—	2024	→
Increased DNA damage in full-grown oocytes is correlated with diminished autophagy activation.	Sun F et al.	—	2024	→
Integrated ATAC-seq and RNA-seq data analysis identifies transcription factors related to rice stripe virus infection in Oryza sativa.	Li M et al.	—	2024	→
NFIC mediates m6A mRNA methylation to orchestrate transcriptional and post-transcriptional regulation to represses malignant phenotype of non-small cell lung cancer cells.	Shi K et al.	—	2024	→
OliTag-seq enhances in cellulo detection of CRISPR-Cas9 off-targets.	Yang ZX et al.	—	2024	→
scACT: Accurate Cross-modality Translation via Cycle-consistent Training from Unpaired Single-cell Data.	Xu S et al.	—	2024	→
Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes.	Irwin NAT et al.	—	2024	→
Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue.	Farzad N et al.	—	2024	→
The importance of DNA sequence for nucleosome positioning in transcriptional regulation.	Sahrhage M et al.	—	2024	→
The importance of functional genomics studies in precision rheumatology.	Piedade AP et al.	—	2024	→
The ncBAF Complex Regulates Transcription in AML Through H3K27ac Sensing by BRD9.	Klein DC et al.	—	2024	→
Transcriptional landscape and dynamics involved in sugar and acid accumulation during apple fruit development.	Li B et al.	—	2024	→
Transcriptomic Approaches to Cardiomyocyte-Biomaterial Interactions: A Review.	Wen Y et al.	—	2024	→
Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements.	Wirthlin ME et al.	—	2024	→
WRN loss accelerates abnormal adipocyte metabolism in Werner syndrome.	Tian Y et al.	—	2024	→
Aneuploidy effects on human gene expression across three cell types.	Liu S et al.	—	2023	→
Application of ATAC-seq in tumor-specific T cell exhaustion.	Chen C et al.	—	2023	→
BIND&MODIFY: a long-range method for single-molecule mapping of chromatin modifications in eukaryotes.	Weng Z et al.	—	2023	→
C/EBPα Confers Dependence to Fatty Acid Anabolic Pathways and Vulnerability to Lipid Oxidative Stress-Induced Ferroptosis in FLT3-Mutant Leukemia.	Sabatier M et al.	—	2023	→
Cellcano: supervised cell type identification for single cell ATAC-seq data.	Ma W et al.	—	2023	→
Characterization and Optimization of Multiomic Single-Cell Epigenomic Profiling.	Sandoval L et al.	—	2023	→
Characterization of the angiotensin-converting enzyme 2 (ACE2), the main receptor for the SARS-CoV-2 virus.	Jami G et al.	—	2023	→
Chromatin accessibility memory of donor cells disrupts bovine somatic cell nuclear transfer blastocysts development.	Huang Y et al.	—	2023	→
cisDynet: An integrated platform for modeling gene-regulatory dynamics and networks.	Zhu T et al.	—	2023	→
Comparative valuation of the chlorpyrifos, acetamiprid, and lambda-cyhalothrin toxicity and their hematological and histopathological consequences in pigeons.	Noreen S et al.	—	2023	→
C<sub>4</sub> gene induction during de-etiolation evolved through changes in cis to allow integration with ancestral C<sub>3</sub> gene regulatory networks.	Singh P et al.	—	2023	→
Dose rate dependent reduction in chromatin accessibility at transcriptional start sites long time after exposure to gamma radiation.	Dahl H et al.	—	2023	→
Dynamic chromatin architectures provide insights into the genetics of cattle myogenesis.	Cheng J et al.	—	2023	→
Epigenetic Landscape Is Largely Shaped by Diversiform Transposons in <i>Aegilops tauschii</i>.	Kong C et al.	—	2023	→
Factors and Methods for the Detection of Gene Expression Regulation.	Wang M et al.	—	2023	→
Genome-Wide Identification of Open Chromatin in Plants Using MH-Seq.	Zhang A et al.	—	2023	→
High-capacity sample multiplexing for single cell chromatin accessibility profiling.	Booth GT et al.	—	2023	→
Innate Immune Memory in Macrophages.	Maheshwari A	—	2023	→
Integration of ATAC-Seq and RNA-Seq reveals FOSL2 drives human liver progenitor-like cell aging by regulating inflammatory factors.	Ding M et al.	—	2023	→
Integration of RNA-seq and ATAC-seq analyzes the effect of low dose neutron-γ radiation on gene expression of lymphocytes from oilfield logging workers.	Li W et al.	—	2023	→
Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells.	Senapati P et al.	—	2023	→
Predicting chromosomal compartments directly from the nucleotide sequence with DNA-DDA.	Lainscsek X et al.	—	2023	→
Prediction accuracy of regulatory elements from sequence varies by functional sequencing technique.	Nowling RJ et al.	—	2023	→
Prevention, Diagnosis and Eradication of Mycoplasma Contamination in Cell Culture.	Huang X et al.	—	2023	→
Profiling Chromatin Accessibility Responses in Goat Bronchial Epithelial Cells Infected with <i>Pasteurella multocida</i>.	Chen Q et al.	—	2023	→
Prospects and perspectives: inferring physiological and regulatory targets for CAM from molecular and modelling approaches.	Chomthong M et al.	—	2023	→
RefTM: reference-guided topic modeling of single-cell chromatin accessibility data.	Zhang Z et al.	—	2023	→
Regulation of chromatin accessibility and gene expression in the developing hippocampal primordium by LIM-HD transcription factor LHX2.	Suresh V et al.	—	2023	→
The Current Therapeutic Role of Chromatin Remodeling for the Prognosis and Treatment of Heart Failure.	Kraus L et al.	—	2023	→
Transcriptional responses of cancer cells to heat shock-inducing stimuli involve amplification of robust HSF1 binding.	Dastidar SG et al.	—	2023	→
Universal NicE-Seq: A Simple and Quick Method for Accessible Chromatin Detection in Fixed Cells.	Chin HG et al.	—	2023	→
When Dad's Stress Gets under Kid's Skin-Impacts of Stress on Germline Cargo and Embryonic Development.	Kretschmer M et al.	—	2023	→
Accessible Region Conformation Capture (ARC-C) gives high-resolution insights into genome architecture and regulation.	Huang N et al.	—	2022	→
A chromatin accessibility landscape during early adipogenesis of human adipose-derived stem cells.	Li S et al.	—	2022	→
A Multigraph-Based Representation of Hi-C Data.	Makai D et al.	—	2022	→
A network of transcription factors governs the dynamics of NODAL/Activin transcriptional responses.	Coda DM et al.	—	2022	→
CharID: a two-step model for universal prediction of interactions between chromatin accessible regions.	Shen Y et al.	—	2022	→
Chromatin Dynamics in Digestive System Cancer: Commander and Regulator.	Li Z et al.	—	2022	→
Computational modeling of chromatin accessibility identified important epigenomic regulators.	Zhao Y et al.	—	2022	→
Confined migration induces heterochromatin formation and alters chromatin accessibility.	Hsia CR et al.	—	2022	→
Epigenetic regulation of white adipose tissue plasticity and energy metabolism by nucleosome binding HMGN proteins.	Nanduri R et al.	—	2022	→
Epigenetics of wheat-rust interaction: an update.	Shilpa et al.	—	2022	→
Epigenomic dynamics of early Xenopus Embryos.	Zhou JJ et al.	—	2022	→
Establishment and Maintenance of Open Ribosomal RNA Gene Chromatin States in Eukaryotes.	Schächner C et al.	—	2022	→
Etv2 regulates enhancer chromatin status to initiate Shh expression in the limb bud.	Koyano-Nakagawa N et al.	—	2022	→
Fragile sites, chromosomal lesions, tandem repeats, and disease.	Mirceta M et al.	—	2022	→
Mapping open chromatin by ATAC-seq in bread wheat.	Wang X et al.	—	2022	→
MEPP: more transparent motif enrichment by profiling positional correlations.	Delos Santos NP et al.	—	2022	→
Proximal and Distal Regions of Pathogenic Th17 Related Chromatin Loci Are Sequentially Accessible During Pathogenicity of Th17.	Hu L et al.	—	2022	→
Regulatory variants in a novel distal enhancer regulate the expression of CYP3A4 and CYP3A5.	Collins JM et al.	—	2022	→
SAFA facilitates chromatin opening of immune genes through interacting with anti-viral host RNAs.	Cao L et al.	—	2022	→
SMOC: a smart model for open chromatin region prediction in rice genomes.	Guo W et al.	—	2022	→
Tethered MNase Structure Probing as Versatile Technique for Analyzing RNPs Using Tagging Cassettes for Homologous Recombination in Saccharomyces cerevisiae.	Teubl F et al.	—	2022	→
The HCV Envelope Glycoprotein Down-Modulates NF-κB Signalling and Associates With Stimulation of the Host Endoplasmic Reticulum Stress Pathway.	McKay LGA et al.	—	2022	→
The landscape of accessible chromatin in quiescent cardiac fibroblasts and cardiac fibroblasts activated after myocardial infarction.	Li C et al.	—	2022	→
Thermodynamics-based modeling reveals regulatory effects of indirect transcription factor-DNA binding.	Bhogale S et al.	—	2022	→
Tracing the Origin of Cell-Free DNA Molecules through Tissue-Specific Epigenetic Signatures.	Oberhofer A et al.	—	2022	→
Transcriptomic and chromatin accessibility dynamics of porcine alveolar macrophages in exposure to fumonisin B1.	Jin J et al.	—	2022	→
Translator: A <i>Trans</i>fer <i>L</i>earning Approach to Facilitate Single-Cell <i>AT</i>AC-Seq Data Analysis fr<i>o</i>m <i>R</i>eference Dataset.	Xu S et al.	—	2022	→
Whole-genome methods to define DNA and histone accessibility and long-range interactions in chromatin.	Marr LT et al.	—	2022	→
Biophysics is reshaping our perception of the epigenome: from DNA-level to high-throughput studies.	Kanapeckaitė A et al.	—	2021	→
CD4+ T cells from children with active juvenile idiopathic arthritis show altered chromatin features associated with transcriptional abnormalities.	Tarbell E et al.	—	2021	→
CharPlant: A De Novo Open Chromatin Region Prediction Tool for Plant Genomes.	Shen Y et al.	—	2021	→
Chromatin accessibility and regulatory vocabulary across indicine cattle tissues.	Alexandre PA et al.	—	2021	→
Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors.	Ding P et al.	—	2021	→
Chromatin accessibility profiling provides insights into larval cuticle color and adult longevity in butterflies.	Wan WT et al.	—	2021	→
Chromatin Dynamics and Gene Expression Response to Heat Exposure in Field-Conditioned versus Laboratory-Cultured <i>Nematostella vectensis</i>.	Weizman E et al.	—	2021	→
Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay.	Tachiwana H et al.	—	2021	→
cinaR: A comprehensive R package for the differential analyses and functional interpretation of ATAC-seq data	Karakaslar EO et al.	—	2021	—
Circular dichroism spectroscopy of DNA duplexes at near-biological concentrations.	Vanloon J et al.	—	2021	→
Comparative Enhancer Map of Cattle Muscle Genome Annotated by ATAC-Seq.	Cao X et al.	—	2021	→
Differential analysis of chromatin accessibility and gene expression profiles identifies cis-regulatory elements in rat adipose and muscle.	Nair VD et al.	—	2021	→
Epigenetic regulation during human cortical development: Seq-ing answers from the brain to the organoid.	Lewis EMA et al.	—	2021	→
Epigenetic regulation of ACE2, the receptor of the SARS-CoV-2 virus<sup>1</sup>.	Beacon TH et al.	—	2021	→
Evidence of widespread, independent sequence signature for transcription factor cobinding.	Zhou M et al.	—	2021	→
Filtering the Junk: Assigning Function to the Mosquito Non-Coding Genome.	Farley EJ et al.	—	2021	→
Insights into epigenetic patterns in mammalian early embryos.	Xu R et al.	—	2021	→
Integrated transcription factor profiling with transcriptome analysis identifies L1PA2 transposons as global regulatory modulators in a breast cancer model.	Jiang JC et al.	—	2021	→
Local states of chromatin compaction at transcription start sites control transcription levels.	Ishihara S et al.	—	2021	→
Molecular and computational approaches to map regulatory elements in 3D chromatin structure.	Lee BH et al.	—	2021	→
Multi-omic analysis suggests tumor suppressor genes evolved specific promoter features to optimize cancer resistance.	Huang D et al.	—	2021	→
Pan-cancer chromatin analysis of the human vtRNA genes uncovers their association with cancer biology.	Fort RS et al.	—	2021	→
Panobinostat Effectively Increases Histone Acetylation and Alters Chromatin Accessibility Landscape in Canine Embryonic Fibroblasts but Does Not Enhance Cellular Reprogramming.	Moshref M et al.	—	2021	→
PeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element map.	Nowling RJ et al.	—	2021	→
Profiling chromatin accessibility in pediatric acute lymphoblastic leukemia identifies subtype-specific chromatin landscapes and gene regulatory networks.	Diedrich JD et al.	—	2021	→
RA3 is a reference-guided approach for epigenetic characterization of single cells.	Chen S et al.	—	2021	→
Regulatory association of long noncoding RNAs and chromatin accessibility facilitates erythroid differentiation.	Ren Y et al.	—	2021	→
SAILER: scalable and accurate invariant representation learning for single-cell ATAC-seq processing and integration.	Cao Y et al.	—	2021	→
Sites of active gene regulation in the prenatal frontal cortex and their role in neuropsychiatric disorders.	Kouakou MR et al.	—	2021	→
The landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs.	Yue J et al.	—	2021	→
The native cistrome and sequence motif families of the maize ear.	Savadel SD et al.	—	2021	→
Are Parallel Proliferation Pathways Redundant?	Nussinov R et al.	—	2020	→
ATACgraph: Profiling Genome-Wide Chromatin Accessibility From ATAC-seq.	Lu RJ et al.	—	2020	→
ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation.	Reske JJ et al.	—	2020	→
CATA: a comprehensive chromatin accessibility database for cancer.	Zhou J et al.	—	2020	→
Chromatin accessibility dynamics of Chlamydia-infected epithelial cells.	Hayward RJ et al.	—	2020	→
Chromatin Remodeling and Immediate Early Gene Activation by SLFN11 in Response to Replication Stress.	Murai J et al.	—	2020	→
DNA Rchitect: an R based visualizer for network analysis of chromatin interaction data.	Ramirez RN et al.	—	2020	→
Enhancer-Driven Gene Expression (EDGE) enables the generation of cell type specific tools for the analysis of neural circuits.	Blankvoort S et al.	—	2020	→
Eosinophil diversity in asthma.	Van Hulst G et al.	—	2020	→
From reads to insight: a hitchhiker's guide to ATAC-seq data analysis.	Yan F et al.	—	2020	→
Genome-wide identification of accessible chromatin regions in bumblebee by ATAC-seq.	Zhao X et al.	—	2020	→
Genomic methods in profiling DNA accessibility and factor localization.	Klein DC et al.	—	2020	→
Genomic resources for dissecting the role of non-protein coding variation in gene-environment interactions.	Levings D et al.	—	2020	→
HiCoP, a simple and robust method for detecting interactions of regulatory regions.	Zhang Y et al.	—	2020	→
Human L1 Transposition Dynamics Unraveled with Functional Data Analysis.	Chen D et al.	—	2020	→
LOXL2-mediated H3K4 oxidation reduces chromatin accessibility in triple-negative breast cancer cells.	Cebrià-Costa JP et al.	—	2020	→
MEDEA: analysis of transcription factor binding motifs in accessible chromatin.	Mariani L et al.	—	2020	→
Nucleosome Positioning around Transcription Start Site Correlates with Gene Expression Only for Active Chromatin State in Drosophila Interphase Chromosomes.	Levitsky VG et al.	—	2020	→
Predicting transcription factor binding in single cells through deep learning.	Fu L et al.	—	2020	→
Quantification of the effect of site-specific histone acetylation on chromatin transcription rate.	Wakamori M et al.	—	2020	→
Revisiting the organization of Polycomb-repressed domains: 3D chromatin models from Hi-C compared with super-resolution imaging.	Liu L et al.	—	2020	→
Single-cell multiomics: technologies and data analysis methods.	Lee J et al.	—	2020	→
SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery.	Hu-Lieskovan S et al.	—	2020	→
Specification of the First Mammalian Cell Lineages In Vivo and In Vitro.	White MD et al.	—	2020	→
Universal NicE-seq for high-resolution accessible chromatin profiling for formaldehyde-fixed and FFPE tissues.	Chin HG et al.	—	2020	→
Agent-Based Modelling to Delineate Spatiotemporal Control Mechanisms of the Stem Cell Niche.	Mines R et al.	—	2019	→
A practical guide for DNase-seq data analysis: from data management to common applications.	Liu Y et al.	—	2019	→
B4GALT1 Is a New Candidate to Maintain the Stemness of Lung Cancer Stem Cells.	De Vitis C et al.	—	2019	→
Biochemical analysis of nucleosome targeting by Tn5 transposase.	Sato S et al.	—	2019	→
Chromatin condensation fluctuations rather than steady-state predict chromatin accessibility.	Audugé N et al.	—	2019	→
Chromatin dynamics enable transcriptional rhythms in the cnidarian Nematostella vectensis.	Weizman EN et al.	—	2019	→
Classifying cells with Scasat, a single-cell ATAC-seq analysis tool.	Baker SM et al.	—	2019	→
Computational Biology Solutions to Identify Enhancers-target Gene Pairs.	Hariprakash JM et al.	—	2019	→
CRISPR/Cas9 guided genome and epigenome engineering and its therapeutic applications in immune mediated diseases.	Singh DD et al.	—	2019	→
Defining TP53 pioneering capabilities with competitive nucleosome binding assays.	Yu X et al.	—	2019	→
Determination of Chromatin Accessibility in <i>Drosophila</i> MidgutEnterocytes by <i>in situ</i> 5mC Labeling.	Bitman-Lotan E et al.	—	2019	→
Differential viral accessibility (DIVA) identifies alterations in chromatin architecture through large-scale mapping of lentiviral integration sites.	Timms RT et al.	—	2019	→
Epigenetic regulation of renal development.	El-Dahr SS et al.	—	2019	→
FOXA2 Is Required for Enhancer Priming during Pancreatic Differentiation.	Lee K et al.	—	2019	→
Genome-wide identification of enhancer elements in the placenta.	Abdulghani M et al.	—	2019	→
Genomic insights into chromatin reprogramming to totipotency in embryos.	Ladstätter S et al.	—	2019	→
HMMRATAC: a Hidden Markov ModeleR for ATAC-seq.	Tarbell ED et al.	—	2019	→
Human transposons are an abundant supply of transcription factor binding sites and promoter activities in breast cancer cell lines.	Jiang JC et al.	—	2019	→
Integrated Epigenetic Mapping of Human and Mouse Salivary Gene Regulation.	Michael DG et al.	—	2019	→
Intercalation of small molecules into DNA in chromatin is primarily controlled by superhelical constraint.	Bosire R et al.	—	2019	→
MeCP2 inhibits cell functionality through FoxO3a and autophagy in endothelial progenitor cells.	Zha S et al.	—	2019	→
Modulating chromatin accessibility by transactivation and targeting proximal dsgRNAs enhances Cas9 editing efficiency in vivo.	Liu G et al.	—	2019	→
Multi-study inference of regulatory networks for more accurate models of gene regulation.	Castro DM et al.	—	2019	→
Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression.	Sasse SK et al.	—	2019	→
Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of Proteins.	Kanada R et al.	—	2019	→
Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways.	Zhao Y et al.	—	2019	→
SCALE method for single-cell ATAC-seq analysis via latent feature extraction.	Xiong L et al.	—	2019	→
Specific chromatin changes mark lateral organ founder cells in the Arabidopsis inflorescence meristem.	Frerichs A et al.	—	2019	→
The role of chromatin dynamics under global warming response in the symbiotic coral model Aiptasia.	Weizman E et al.	—	2019	→
Advances of DNase-seq for mapping active gene regulatory elements across the genome in animals.	Chen A et al.	—	2018	→
Analysis of rat cardiac myocytes and fibroblasts identifies combinatorial enhancer organization and transcription factor families.	Golan-Lagziel T et al.	—	2018	→
An optimized FAIRE procedure for low cell numbers in yeast.	Segorbe D et al.	—	2018	→
ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.	Ou J et al.	—	2018	→
CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo.	Aughey GN et al.	—	2018	→
Chromatin accessibility is associated with CRISPR-Cas9 efficiency in the zebrafish (Danio rerio).	Uusi-Mäkelä MIE et al.	—	2018	→
Computational Methods for Assessing Chromatin Hierarchy.	Chang P et al.	—	2018	→
Developmental Chromatin Restriction of Pro-Growth Gene Networks Acts as an Epigenetic Barrier to Axon Regeneration in Cortical Neurons.	Venkatesh I et al.	—	2018	→
Epigenetic Applications in Adverse Outcome Pathways and Environmental Risk Evaluation.	Angrish MM et al.	—	2018	→
Epigenome in Early Mammalian Development: Inheritance, Reprogramming and Establishment.	Xu Q et al.	—	2018	→
Human Papillomavirus Replication Regulation by Acetylation of a Conserved Lysine in the E2 Protein.	Thomas Y et al.	—	2018	→
Identification of cis-regulatory elements by chromatin structure.	Lu Z et al.	—	2018	→
Integrating ChIP-seq with other functional genomics data.	Jiang S et al.	—	2018	→
Interferon regulatory factor 1 and a variant of heterogeneous nuclear ribonucleoprotein L coordinately silence the gene for adhesion protein CEACAM1.	Dery KJ et al.	—	2018	→
Investigating Nucleosome Accessibility for MNase, Fe<sup>II</sup> Peplomycin, and Duocarmycin B<sub>2</sub> by Using Capillary Electrophoresis.	Zou T et al.	—	2018	→
MeCP2-mediated epigenetic regulation in senescent endothelial progenitor cells.	Wang C et al.	—	2018	→
Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution.	Roscito JG et al.	—	2018	→
Proliferation of Regulatory DNA Elements Derived from Transposable Elements in the Maize Genome.	Zhao H et al.	—	2018	→
Quantitative imaging of chromatin decompaction in living cells.	Dultz E et al.	—	2018	→
Regulatory chromatin landscape in <i>Arabidopsis thaliana</i> roots uncovered by coupling INTACT and ATAC-seq.	Tannenbaum M et al.	—	2018	→
Single-Cell (Multi)omics Technologies.	Chappell L et al.	—	2018	→
Single Copy Transgene Integration in a Transcriptionally Active Site for Recombinant Protein Synthesis.	O'Brien SA et al.	—	2018	→
Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns.	Javasky E et al.	—	2018	→
The Identification and Interpretation of <i>cis</i>-Regulatory Noncoding Mutations in Cancer.	Patel MB et al.	—	2018	→
Translating GWAS in rheumatic disease: approaches to establishing mechanism and function for genetic associations with ankylosing spondylitis.	Osgood JA et al.	—	2018	→
Cell identity bookmarking through heterogeneous chromatin landscape maintenance during the cell cycle.	Luo H et al.	—	2017	→
Chromatin accessibility dynamics reveal novel functional enhancers in <i>C. elegans</i>.	Daugherty AC et al.	—	2017	→
Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings.	Sauerwald N et al.	—	2017	→
Computational inference of gene regulatory networks: Approaches, limitations and opportunities.	Banf M et al.	—	2017	→
Contribution of Neuroepigenetics to Huntington's Disease.	Francelle L et al.	—	2017	→
dCATCH-Seq: improved sequencing of large continuous genomic targets with double-hybridization.	Zhang Y et al.	—	2017	→
Dynamic chromatin accessibility modeled by Markov process of randomly-moving molecules in the 3D genome.	Wang Y et al.	—	2017	→
Enhanced chromatin accessibility of the dosage compensated Drosophila male X-chromosome requires the CLAMP zinc finger protein.	Urban J et al.	—	2017	→
Epigenetic Landscape during Coronavirus Infection.	Schäfer A et al.	—	2017	→
High fat diet-induced changes of mouse hepatic transcription and enhancer activity can be reversed by subsequent weight loss.	Siersbæk M et al.	—	2017	→
I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples.	Ahmed Z et al.	—	2017	→
Metazoan Nuclear Pores Provide a Scaffold for Poised Genes and Mediate Induced Enhancer-Promoter Contacts.	Pascual-Garcia P et al.	—	2017	→
NicE-seq: high resolution open chromatin profiling.	Ponnaluri VKC et al.	—	2017	→
Nucleosome Positioning Assay.	Zhao Z et al.	—	2017	→
Polymorphisms in sex steroid receptors: From gene sequence to behavior.	Maney DL	—	2017	→
Prediction of Chromatin Accessibility in Gene-Regulatory Regions from Transcriptomics Data.	Jung S et al.	—	2017	→
Regulatory and evolutionary signatures of sex-biased genes on both the X chromosome and the autosomes.	Shen JJ et al.	—	2017	→
Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints.	Schwessinger R et al.	—	2017	→
STAG-CNS: An Order-Aware Conserved Noncoding Sequences Discovery Tool for Arbitrary Numbers of Species.	Lai X et al.	—	2017	→
Towards genome-wide prediction and characterization of enhancers in plants.	Marand AP et al.	—	2017	→
Understanding nucleosome dynamics and their links to gene expression and DNA replication.	Lai WKM et al.	—	2017	→
Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens.	Deschamps S et al.	—	2016	→
ChIP bias as a function of cross-linking time.	Baranello L et al.	—	2016	→
Enhanced Identification of Transcriptional Enhancers Provides Mechanistic Insights into Diseases.	Murakawa Y et al.	—	2016	→
Epigenetic Changes During Food-Specific Immunotherapy.	Bunning BJ et al.	—	2016	→
Genetics of congenital heart disease: the contribution of the noncoding regulatory genome.	Postma AV et al.	—	2016	→
Genetics of movement disorders in the next-generation sequencing era.	Olgiati S et al.	—	2016	→
Genome-Scale Analysis of Cell-Specific Regulatory Codes Using Nuclear Enzymes.	Baek S et al.	—	2016	→
Genome-wide epigenomic profiling for biomarker discovery.	Dirks RA et al.	—	2016	→
High-throughput small molecule screen identifies inhibitors of aberrant chromatin accessibility.	Pattenden SG et al.	—	2016	→
Insights into the Ecology and Evolution of Polyploid Plants through Network Analysis.	Gallagher JP et al.	—	2016	→
Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes.	Ackermann AM et al.	—	2016	→
Molecular Actions of Glucocorticoids in Cartilage and Bone During Health, Disease, and Steroid Therapy.	Hartmann K et al.	—	2016	→
Occupancy of RNA Polymerase II Phosphorylated on Serine 5 (RNAP S5P) and RNAP S2P on Varicella-Zoster Virus Genes 9, 51, and 66 Is Independent of Transcript Abundance and Polymerase Location within the Gene.	Henderson HH et al.	—	2016	→
Open chromatin reveals the functional maize genome.	Rodgers-Melnick E et al.	—	2016	→
Pax6 associates with H3K4-specific histone methyltransferases Mll1, Mll2, and Set1a and regulates H3K4 methylation at promoters and enhancers.	Sun J et al.	—	2016	→
Persistent Chromatin Modifications Induced by High Fat Diet.	Leung A et al.	—	2016	→
Protein Palmitoylation Regulates Neural Stem Cell Differentiation by Modulation of EID1 Activity.	Chen X et al.	—	2016	→
Self-renewal of tumor cells: epigenetic determinants of the cancer stem cell phenotype.	Ravasio R et al.	—	2016	→
The Functionality and Evolution of Eukaryotic Transcriptional Enhancers.	Buffry AD et al.	—	2016	→
An increased expression of PI-PLCβ1 is associated with myeloid differentiation and a longer response to azacitidine in myelodysplastic syndromes.	Cocco L et al.	—	2015	→
Chemical tagging and customizing of cellular chromatin states using ultrafast trans-splicing inteins.	David Y et al.	—	2015	→
Chromatin features, RNA polymerase II and the comparative expression of lens genes encoding crystallins, transcription factors, and autophagy mediators.	Sun J et al.	—	2015	→
Do changes in the BDNF promoter methylation indicate the risk of alcohol relapse?	Heberlein A et al.	—	2015	→
Histone profiles in cancer.	Riedel SS et al.	—	2015	→
Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana.	Cumbie JS et al.	—	2015	→
On Accounting for Sequence-Specific Bias in Genome-Wide Chromatin Accessibility Experiments: Recent Advances and Contradictions.	Madrigal P	—	2015	→
Regulation of catalase expression in healthy and cancerous cells.	Glorieux C et al.	—	2015	→
Three-dimensional regulation of transcription.	Cao J et al.	—	2015	→