ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide.
paper
Cited
Public
- Authors
- Buenrostro, Jason D; Wu, Beijing; Chang, Howard Y; Greenleaf, William J
- Year
- 2015
- Journal
- Current protocols in molecular biology
- PMID
- 25559105
- DOI
- 10.1002/0471142727.mb2129s109
- PMCID
- PMC4374986
This unit describes Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq), a method for mapping chromatin accessibility genome-wide. This method probes DNA accessibility with hyperactive Tn5 transposase, which inserts sequencing adapters into accessible regions of chromatin. Sequencing reads can then be used to infer regions of increased accessibility, as well as to map regions of transcription-factor binding and nucleosome position. The method is a fast and sensitive alternative to DNase-seq for assaying chromatin accessibility genome-wide, or to MNase-seq for assaying nucleosome positions in accessible regions of the genome.
(A) Library preparation schematic. (B) Transposition results in fragmented DNA. Prior to amplification, adapters have to be completed with a 72Β°C extension step. During the subsequent PCR additional sequence is incorporated into the adapters, which include common sequencing ends and a sequencing barcode.
Fragment sizes for amplified ATAC-seq libraries, determined by (A) Gel electrophoresis and (B) Bioanalyzer. Bioanalyzer image contrast has been enhanced from its original image for clarity. (C) Insert sizes determined by high-throughput sequencing. Adapters are an additional 124 bps and are not included when measuring fragment size in this panel.
1β16 of 16
| Name | Type |
|---|---|
| Agilent 2100 Bioanalyzer | drug |
| ATAC-seq | drug |
| Bioanalyzer High Sensitivity DNA Analysis kit local | drug |
| cell number local | drug |
| clustering efficiency local | phenotype |
| DNA | drug |
| DNA fragments local | drug |
| fixatives local | drug |
| GC bias local | phenotype |
| gel local | drug |
| high quality libraries local | phenotype |
| human | cohort |
| human samples | cohort |
| Illumina high-throughput sequencing instruments local | drug |
| Illumina Sequencing Platforms local | drug |
| KAPA Library Quant Kit local | drug |
| large fragments local | phenotype |
| library complexity local | phenotype |
| lysis methods local | drug |
| Mitochondrial reads local | phenotype |
| NEB ladder local | drug |
| Nextera DNA Sample Preparation kit local | drug |
| Nextera workflow local | drug |
| nucleosomal banding pattern local | phenotype |
| Nucleosome mapping local | phenotype |
| over transposition local | phenotype |
| Paired-end sequencing local | drug |
| PCR method local | drug |
| qPCR | drug |
| Qubit | drug |
| reaction local | drug |
| short fragments local | phenotype |
| size bias local | phenotype |
| SYBR green | drug |
| Tn5 | drug |
| Tn5 transposase | drug |
| Typhoon TRIO Variable Mode Imager local | drug |
| under transposition local | phenotype |
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| EpiMapper: A new tool for analyzing high-throughput sequencing from CUT&Tag. | Dragland JS et al. | β | 2025 | β |
| EQTL analyses are a formidable tool to define the immunogenetic mechanisms underpinning Spondyloarthropathies. | Vecellio M et al. | β | 2025 | β |
| Evolution of a SHOOTMERISTEMLESS transcription factor binding site promotes fruit shape determination. | Hu ZC et al. | β | 2025 | β |
| Exuberant long noncoding RNA expression may sculpt Igh locus topology. | Drake EB et al. | β | 2025 | β |
| Fetal hepatocytes protect the HSPC genome via fetuin-A. | Guo XL et al. | β | 2025 | β |
| FOXM1 expression reverts aging chromatin profiles through repression of the senescence-associated pioneer factor AP-1. | Ferreira FJ et al. | β | 2025 | β |
| Functional genomics of human skeletal development and the patterning of height heritability. | Richard D et al. | β | 2025 | β |
| Fundamentals of DNA methylation in development. | Gillespie CA et al. | β | 2025 | β |
| Genetic and epigenetic regulation of Treg cell fitness by autism-related chromatin remodeler CHD8. | Yang JQ et al. | β | 2025 | β |
| Genetic coupling of enhancer activity and connectivity in gene expression control. | Ray-Jones H et al. | β | 2025 | β |
| Genetic variation in IL-4 activated tissue resident macrophages determines strain-specific synergistic responses to LPS epigenetically. | Zhao M et al. | β | 2025 | β |
| Genome-wide CRISPR screen in human T cells reveals regulators of FOXP3. | Chen KY et al. | β | 2025 | β |
| Genomic and cell-specific regulation of benzylisoquinoline alkaloid biosynthesis in opium poppy. | Hong UVT et al. | β | 2025 | β |
| Genomic regions occupied by both RARΞ± and VDR are involved in the convergence and cooperation of retinoid and vitamin D signaling pathways. | Mianesaz H et al. | β | 2025 | β |
| Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms. | Wenz BM et al. | β | 2025 | β |
| G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer cells. | Robinson J et al. | β | 2025 | β |
| Graph neural networks for single-cell omics data: a review of approaches and applications. | Li S et al. | β | 2025 | β |
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| High PRMT5 levels, maintained by KEAP1 inhibition, drive chemoresistance in high-grade serous ovarian cancer. | Ozturk H et al. | β | 2025 | β |
| HIVEP1 aggravates NASH by reprogramming polyamine metabolism in T<sub>H</sub>17 cells. | Ren Y et al. | β | 2025 | β |
| Hmgb2 improves astrocyte to neuron conversion by increasing the chromatin accessibility of genes associated with neuronal maturation in a proneuronal factor-dependent manner. | Maddhesiya P et al. | β | 2025 | β |
| Human brain vascular multi-omics elucidates disease-risk associations. | Reid MM et al. | β | 2025 | β |
| Human iPSCs-based modeling unveils SETBP1 as a driver of chromatin rewiring in GATA2 deficiency. | Pera J et al. | β | 2025 | β |
| Human monocyte inflammation in patients with Lp(a) or atherosclerotic cardiovascular disease is not accompanied by changes in chromatin accessibility in circulating classical monocytes. | Kempkes RWM et al. | β | 2025 | β |
| Human Ξ³Ξ΄ T Cell Function Is Impaired Upon Mevalonate Pathway Inhibition. | Suen TK et al. | β | 2025 | β |
| Hypoxia increases methylated histones to prevent histone clipping and heterochromatin redistribution during Raf-induced senescence. | Chang S et al. | β | 2025 | β |
| Hypoxic stress dysregulates functions of glioma-associated myeloid cells through epigenomic and transcriptional programs. | Dzwigonska M et al. | β | 2025 | β |
| IL-10 targets IRF transcription factors to suppress IFN and inflammatory response genes by epigenetic mechanisms. | Mishra B et al. | β | 2025 | β |
| IL-25-induced memory type 2 innate lymphoid cells enforce mucosal immunity. | Cortez VS et al. | β | 2025 | β |
| Inference of transcriptional regulation from STARR-seq data. | Safaeesirat A et al. | β | 2025 | β |
| Inflammation switches the chemoattractant requirements for naive lymphocyte entry into lymph nodes. | Chen KY et al. | β | 2025 | β |
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| Inhibition of triglyceride metabolism-associated enhancers alters lipid deposition during adipocyte differentiation. | Zeng S et al. | β | 2025 | β |
| iNOME-seq: in vivo simultaneous genome-wide mapping of chromatin accessibility, nucleosome positioning, DNA-binding protein sites, and DNA methylation in Arabidopsis. | Hussain N et al. | β | 2025 | β |
| Insect Resistance in <i>Quercus robur</i>: A Comparative Metabolomic and Transcriptomic Analysis of Normal and Curly Leaf Varieties. | Liao KY et al. | β | 2025 | β |
| Integrated analysis of ATAC-seq and RNA-seq reveals the chromatin accessibility and transcriptional landscape of immunoglobulin a nephropathy. | Gao ZX et al. | β | 2025 | β |
| Integrated functional genomic analysis identifies regulatory variants underlying a major QTL for disease resistance in European sea bass. | Mukiibi R et al. | β | 2025 | β |
| Integrated Genomic Analysis Reveals the Impact of Avermectin on Chromatin Structure and Gene Expression Regulation in <i>Bombyx mori</i>. | Guo Y et al. | β | 2025 | β |
| Integrated single-cell multiomic profiling of caudate nucleus suggests key mechanisms in alcohol use disorder. | Green NC et al. | β | 2025 | β |
| Integrated time-series analysis and high-content CRISPR screening delineate the dynamics of macrophage immune regulation. | Traxler P et al. | β | 2025 | β |
| Integrative ATAC-Seq and RNA-Seq Analysis Reveals Key Transcription Factors Mediating Low Salinity Adaptation in Penaeid Shrimp. | Zhang C et al. | β | 2025 | β |
| Integrative multi-omics data provide insights into the biosynthesis of furanocoumarins and mechanisms regulating their accumulation in Angelica dahurica. | Ji J et al. | β | 2025 | β |
| Integrative multi-omics identifies AP-1 transcription factor as a targetable mediator of acquired osimertinib resistance in non-small cell lung cancer. | Dayanc B et al. | β | 2025 | β |
| Integrative Transcriptomic and Epigenomic Profiling for Signature Identification in Coronary Artery Disease: A Pilot Study. | Zanfardino M et al. | β | 2025 | β |
| Interrogating the regulatory epigenome of cellular senescence. | Thanos DF et al. | β | 2025 | β |
| Introduction of epigenetic variation contribute to resistance against the human parasite Schistosoma mansoni. | Luviano-Aparicio N et al. | β | 2025 | β |
| IRX3 controls a SUMOylation-dependent differentiation switch in adipocyte precursor cells. | Bjune JI et al. | β | 2025 | β |
| <i>Trithorax</i> balances ISC fate decisions via Ptx1-mediated repression of EE specification | Fasoulaki V et al. | β | 2025 | β |
| KAT6A and KAT7 Histone Acetyltransferase Complexes Are Molecular Dependencies and Therapeutic Targets in NUP98-Rearranged Acute Myeloid Leukemia. | Michmerhuizen NL et al. | β | 2025 | β |
| KAT6B is required for histone 3 lysine 9 acetylation and SOX gene expression in the developing brain. | Bergamasco MI et al. | β | 2025 | β |
| KAT6B overexpression in mice causes aggression, anxiety, and epilepsy. | Bergamasco MI et al. | β | 2025 | β |
| KDM4C inhibition blocks tumor growth in basal breast cancer by promoting cathepsin L-mediated histone H3 cleavage. | Li Z et al. | β | 2025 | β |
| Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants. | Liu H et al. | β | 2025 | β |
| LATS1-modulated ZBTB20 perturbing cartilage matrix homeostasis contributes to early-stage osteoarthritis. | Hao X et al. | β | 2025 | β |
| Linkage: an interactive web application for linking of DNA regulatory peaks to genes. | Xu S et al. | β | 2025 | β |
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| Lipolysis-microlipophagy cascade regulated by adipose triglyceride lipase drives pathogenic adaptive type 2 immunity. | Yagyu H et al. | β | 2025 | β |
| Long non-coding RNAs direct the SWI/SNF complex to cell type-specific enhancers. | Oo JA et al. | β | 2025 | β |
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| <i>CancerTrace</i>: Multi-stage single-cell analysis of networked cancer evolution for driver and modulator gene identification. | Atitey K et al. | β | 2025 | β |
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| Mapping the transcriptional and epigenetic landscape of organotypic endothelial diversity in the developing and adult mouse. | Cantu Gutierrez ME et al. | β | 2025 | β |
| Microbiota translocation following intestinal barrier disruption promotes Mincle-mediated training of myeloid progenitors in the bone marrow. | Robles-Vera I et al. | β | 2025 | β |
| Microglia endotoxin tolerance is retained after enforced repopulation. | Medeiros-Furquim T et al. | β | 2025 | β |
| MicroRNA bioinformatics in precision oncology: an integrated pipeline from NGS to AI-based target discovery. | Dey M et al. | β | 2025 | β |
| Mitochondria-derived nuclear ATP surge protects against confinement-induced proliferation defects. | Ghose R et al. | β | 2025 | β |
| Mitotic chromosomes harbor cell type- and species-specific structural features within a universal loop array conformation. | Oomen ME et al. | β | 2025 | β |
| Modeling <i>SMAD2</i> Mutations in Induced Pluripotent Stem Cells Provides Insights Into Cardiovascular Disease Pathogenesis. | Ward T et al. | β | 2025 | β |
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| Molecular Characterization of Three Novel Large Deletions Causing Ξ±<sup>0</sup>-Thalassemia. | Ferrer-Benito S et al. | β | 2025 | β |
| Monod: model-based discovery and integration through fitting stochastic transcriptional dynamics to single-cell sequencing data. | Gorin G et al. | β | 2025 | β |
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| Multi-omics data-based modeling reveals tumorigenesis- and prognosis-associated genes with clinical potential in lung adenocarcinoma. | Lu Z et al. | β | 2025 | β |
| Multi-omics elucidation of KDM5C, KDM6A, and KMT2B roles in cancer epigenetic dysregulation and transcriptional reprogramming. | Li T et al. | β | 2025 | β |
| Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot. | Aramburu O et al. | β | 2025 | β |
| Muscle metabolic resilience and enhanced exercise adaptation by Esr1-induced remodeling of mitochondrial cristae-nucleoid architecture in males. | Zhou Z et al. | β | 2025 | β |
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| Natural Killer Cell-Mediated Cytotoxicity Shapes the Clonal Evolution of B-cell Leukemia. | Buri MC et al. | β | 2025 | β |
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| NLRP3-mediated glutaminolysis controls microglial phagocytosis to promote Alzheimer's disease progression. | McManus RM et al. | β | 2025 | β |
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| Platelets sequester extracellular DNA, capturing tumor-derived and free fetal DNA. | Murphy L et al. | β | 2025 | β |
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| Recent advances in omics and the integration of multi-omics in osteoarthritis research. | Liu Y et al. | β | 2025 | β |
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| Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysis. | Goliasse M et al. | β | 2025 | β |
| Uncovering the transcriptional regulatory network underlying selenium tolerance in maize seedlings. | Wang R et al. | β | 2025 | β |
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| WSTF nuclear autophagy regulates chronic but not acute inflammation. | Wang Y et al. | β | 2025 | β |
| Z-GENIE: a user-friendly R/Shiny resource for predicting Z-DNA forming regions in DNA. | Garza Reyna A et al. | β | 2025 | β |
| 12,13-diHOME Promotes Inflammatory Macrophages and Epigenetically Modifies Their Capacity to Respond to Microbes and Allergens. | Lin DL et al. | β | 2024 | β |
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| Agricultural insect pests as models for studying stress-induced evolutionary processes. | Gunn JC et al. | β | 2024 | β |
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| A review of Ribosome profiling and tools used in Ribo-seq data analysis. | Limbu MS et al. | β | 2024 | β |
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| Bhlhe40 Promotes CD4+ T Helper 1 Cell and Suppresses T Follicular Helper Cell Differentiation during Viral Infection. | Nguyen C et al. | β | 2024 | β |
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| CDX2 dose-dependently influences the gene regulatory network underlying human extraembryonic mesoderm development. | Bulger EA et al. | β | 2024 | β |
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| CFTR represses a PDX1 axis to govern pancreatic ductal cell fate. | Rotti PG et al. | β | 2024 | β |
| Changes in Phenotypic and Molecular Features of NaΓ―ve and Central Memory T Helper Cell Subsets following SARS-CoV-2 Vaccination. | Mosavie M et al. | β | 2024 | β |
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| Chromatin Accessibility and Gene Expression Vary Between a New and Evolved Autopolyploid of Arabidopsis arenosa. | Srikant T et al. | β | 2024 | β |
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| Chromatin accessibility mediated by CHROMATIN REMODELING 11 promotes chilling tolerance in rice. | Li J et al. | β | 2024 | β |
| Chromatin accessibility profiling reveals that human fibroblasts respond to mechanical stimulation in a cell-specific manner. | Logan NJ et al. | β | 2024 | β |
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| Complex regulatory networks influence pluripotent cell state transitions in human iPSCs. | Arthur TD et al. | β | 2024 | β |
| Comprehensive analysis of computational approaches in plant transcription factors binding regions discovery. | Jyoti et al. | β | 2024 | β |
| Connecting the dots: investigating the link between environmental, genetic, and epigenetic influences in metabolomic alterations in oral squamous cell carcinoma. | Gupta I et al. | β | 2024 | β |
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| CYP1B1 promotes PARPi-resistance via histone H1.4 interaction and increased chromatin accessibility in ovarian cancer. | Xue Y et al. | β | 2024 | β |
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| DeepOCR: A multi-species deep-learning framework for accurate identification of open chromatin regions in livestock. | Zhao L et al. | β | 2024 | β |
| Detecting Small Cell Transformation in Patients with Advanced EGFR Mutant Lung Adenocarcinoma through Epigenomic cfDNA Profiling. | El Zarif T et al. | β | 2024 | β |
| Differential chromatin accessibility and Gene Expression Associated with Backfat Deposition in pigs. | Zhang Z et al. | β | 2024 | β |
| Disease-associated astrocyte epigenetic memory promotes CNS pathology. | Lee HG et al. | β | 2024 | β |
| Disease related changes in ATAC-seq of iPSC-derived motor neuron lines from ALS patients and controls. | Tsitkov S et al. | β | 2024 | β |
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| DNA Methylation and Chromatin Accessibility Impact Subgenome Expression Dominance in the Common Carp (<i>Cyprinus carpio</i>). | Yu ST et al. | β | 2024 | β |
| Dominance reversals: the resolution of genetic conflict and maintenance of genetic variation. | Grieshop K et al. | β | 2024 | β |
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| Dynamic Chromatin Accessibility and Gene Expression Regulation During Maize Leaf Development. | Wang Y et al. | β | 2024 | β |
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| Dynamics of Chromatin Opening across Larval Development in the Urochordate Ascidian <i>Ciona savignyi</i>. | He M et al. | β | 2024 | β |
| Early life vaccination reprograms the metabolism and function of myeloid cells in neonates. | Chen Y et al. | β | 2024 | β |
| Emerging Approaches to Profile Accessible Chromatin from Formalin-Fixed Paraffin-Embedded Sections. | Sunitha Kumary VUN et al. | β | 2024 | β |
| Emerging toolkits for decoding the co-occurrence of modified histones and chromatin proteins. | Pepin AS et al. | β | 2024 | β |
| Emerging trends in the study of spiralian larvae. | Liang Y et al. | β | 2024 | β |
| Emx2 underlies the development and evolution of marsupial gliding membranes. | Moreno JA et al. | β | 2024 | β |
| Eomes-dependent mitochondrial regulation promotes survival of pathogenic CD4+ T cells during inflammation. | Joulia E et al. | β | 2024 | β |
| EP300/CREBBP acetyltransferase inhibition limits steroid receptor and FOXA1 signaling in prostate cancer cells. | Huttunen J et al. | β | 2024 | β |
| Epigenetic control of cell signalling in cancer stem cells. | Joshi G et al. | β | 2024 | β |
| Epigenetic memory of radiotherapy in dermal fibroblasts impairs wound repair capacity in cancer survivors. | Bian X et al. | β | 2024 | β |
| Epigenetic modulation of myeloid cell functions in HIV and SARS-CoV-2 infection. | Krause C et al. | β | 2024 | β |
| Epigenetic Regulation of Ameloblast Differentiation by HMGN Proteins. | He B et al. | β | 2024 | β |
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| Epigenetics of Hypertensive Nephropathy. | Zhang Y et al. | β | 2024 | β |
| Epigenome-wide impact of MAT2A sustains the androgen-indifferent state and confers synthetic vulnerability in ERG fusion-positive prostate cancer. | Cacciatore A et al. | β | 2024 | β |
| Epstein-Barr virus induces germinal center light zone chromatin architecture and promotes survival through enhancer looping at the <i>BCL2A1</i> locus. | Dai J et al. | β | 2024 | β |
| Establishing an optimized ATAC-seq protocol for the maize. | Hsieh JA et al. | β | 2024 | β |
| Establishment and Maintenance of Heat-Stress Memory in Plants. | Zheng S et al. | β | 2024 | β |
| Evidence of innate training in bovine Ξ³Ξ΄ T cells following subcutaneous BCG administration. | Samuel BER et al. | β | 2024 | β |
| Evolution and genetics of accessory gland transcriptome divergence between Drosophila melanogaster and D. simulans. | Majane AC et al. | β | 2024 | β |
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| Fibroblasts as an in vitro model of circadian genetic and genomic studies. | Francia M et al. | β | 2024 | β |
| Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish. | Venu V et al. | β | 2024 | β |
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| Genome evolution and divergence in cis-regulatory architecture is associated with condition-responsive development in horned dung beetles. | Davidson PL et al. | β | 2024 | β |
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| HIRA protects telomeres against R-loop-induced instability in ALT cancer cells. | Lynskey ML et al. | β | 2024 | β |
| Histone lysine demethylase 4 family proteins maintain the transcriptional program and adrenergic cellular state of MYCN-amplified neuroblastoma. | Abu-Zaid A et al. | β | 2024 | β |
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| HNF4A guides the MLL4 complex to establish and maintain H3K4me1 at gene regulatory elements. | Thakur A et al. | β | 2024 | β |
| How Transcription Factor Clusters Shape the Transcriptional Landscape. | Munshi R | β | 2024 | β |
| Identification, Design, and Application of Noncoding Cis-Regulatory Elements. | Xu L et al. | β | 2024 | β |
| Ileal Crohn's Disease Exhibits Reduced Activity of Phospholipase C-Ξ²3-Dependent Wnt/Ξ²-Catenin Signaling Pathway. | Ando T et al. | β | 2024 | β |
| Impact of c-JUN deficiency on thalamus development in mice and human neural models. | Shi J et al. | β | 2024 | β |
| Inhibition of CAF-1 histone chaperone complex triggers cytosolic DNA and dsRNA sensing pathways and induces intrinsic immunity of hepatocellular carcinoma. | Chan FF et al. | β | 2024 | β |
| Innovative Insights into Single-Cell Technologies and Multi-Omics Integration in Livestock and Poultry. | Lu Y et al. | β | 2024 | β |
| Integrated enhancer regulatory network by enhancer-promoter looping in gastric cancer. | Zhu T et al. | β | 2024 | β |
| Integrated multi-omics analysis identifies features that predict human pluripotent stem cell-derived progenitor differentiation to cardiomyocytes. | Simmons AD et al. | β | 2024 | β |
| Integrating evolutionary genomics of forest trees to inform future tree breeding amidΒ rapid climate change. | Feng J et al. | β | 2024 | β |
| Integrating Multi-Omics Data to Identify Key Functional Variants Affecting Feed Efficiency in Large White Boars. | Xiang Y et al. | β | 2024 | β |
| Integration of epigenomic and transcriptomic profiling uncovers EZH2 target genes linked to cysteine metabolism in hepatocellular carcinoma. | Lee J et al. | β | 2024 | β |
| Integrative analysis of chromatin accessibility and transcriptome landscapes in the induction of peritoneal fibrosis by high glucose. | Song Q et al. | β | 2024 | β |
| Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Dorsi Muscle of Gannan Yak and Jeryak. | Zhao Z et al. | β | 2024 | β |
| Integrative multi-omics increase resolution of the sea urchin posterior gut gene regulatory network at single-cell level. | Voronov D et al. | β | 2024 | β |
| Interconnected lineage trajectories link conventional and natural killer (NK)-like exhausted CD8<sup>+</sup> T cells beneficial in type 1 diabetes. | Witkop EM et al. | β | 2024 | β |
| Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition. | Tremblay BJM et al. | β | 2024 | β |
| Intestinal damage is required for the pro-inflammatory differentiation of commensal CBir1-specific T cells. | Sorini C et al. | β | 2024 | β |
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| KLF13 promotes SLE pathogenesis by modifying chromatin accessibility of key proinflammatory cytokine genes. | Wang A et al. | β | 2024 | β |
| Leveraging Tissue-Specific Enhancer-Target Gene Regulatory Networks Identifies Enhancer Somatic Mutations That Functionally Impact Lung Cancer. | Hariprakash JM et al. | β | 2024 | β |
| Lineage-specific intolerance to oncogenic drivers restricts histological transformation. | Gardner EE et al. | β | 2024 | β |
| Liver kinase B1 (LKB1) regulates the epigenetic landscape of mouse pancreatic beta cells. | Haberman N et al. | β | 2024 | β |
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| Mef2d potentiates type-2 immune responses and allergic lung inflammation. | Szeto ACH et al. | β | 2024 | β |
| Microfluidic Biochips for Single-Cell Isolation and Single-Cell Analysis of Multiomics and Exosomes. | Wang C et al. | β | 2024 | β |
| MINI-AC: inference of plant gene regulatory networks using bulk or single-cell accessible chromatin profiles. | Manosalva PΓ©rez N et al. | β | 2024 | β |
| miR-193b-365 microcluster downstream of <i>Fezf2</i> coordinates neuron-subtype identity and dendritic morphology in cortical projection neurons. | Iyer A et al. | β | 2024 | β |
| MMGAT: a graph attention network framework for ATAC-seq motifs finding. | Wu X et al. | β | 2024 | β |
| MOCHA's advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human cohorts. | Rachid Zaim S et al. | β | 2024 | β |
| Molecular basis of urostyle development in frogs: genes and gene regulation underlying an evolutionary novelty. | Senevirathne G et al. | β | 2024 | β |
| Molecular Signatures of CB-6644 Inhibition of the RUVBL1/2 Complex in Multiple Myeloma. | Yi W et al. | β | 2024 | β |
| MUC1-C regulates NEAT1 lncRNA expression and paraspeckle formation in cancer progression. | Bhattacharya A et al. | β | 2024 | β |
| Multimodal Analytical Tools to Enhance Mechanistic Understanding of Aortic Valve Calcification. | Perez KA et al. | β | 2024 | β |
| MYBL2 Drives Prostate Cancer Plasticity: Inhibiting Its Transcriptional Target CDK2 for RB1-Deficient Neuroendocrine Prostate Cancer. | German B et al. | β | 2024 | β |
| MYC Family Amplification Dictates Sensitivity to BET Bromodomain Protein Inhibitor Mivebresib (ABBV075) in Small-Cell Lung Cancer. | Plotnik JP et al. | β | 2024 | β |
| Neuronal MAPT expression is mediated by long-range interactions with cis-regulatory elements. | Rogers BB et al. | β | 2024 | β |
| Neutrophils Recruited by NKX2-1 Suppression via Activation of CXCLs/CXCR2 Axis Promote Lung Adenocarcinoma Progression. | La'ah AS et al. | β | 2024 | β |
| Next-generation forward genetic screens: uniting high-throughput perturbations with single-cell analysis. | Morris JA et al. | β | 2024 | β |
| NFΞΊB dynamics-dependent epigenetic changes modulate inflammatory gene expression and induce cellular senescence. | Tabata S et al. | β | 2024 | β |
| Non-CG DNA hypomethylation promotes photosynthesis and nitrogen fixation in soybean. | Xun H et al. | β | 2024 | β |
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| OCRClassifier: integrating statistical control chart into machine learning framework for better detecting open chromatin regions. | Lai X et al. | β | 2024 | β |
| ONECUT2 acts as a lineage plasticity driver in adenocarcinoma as well as neuroendocrine variants of prostate cancer. | Qian C et al. | β | 2024 | β |
| Opportunities and Challenges in Advancing Plant Research with Single-cell Omics. | Rhaman MS et al. | β | 2024 | β |
| Osteoarthritis as an Enhanceropathy: Gene Regulation in Complex Musculoskeletal Disease. | Roberts JB et al. | β | 2024 | β |
| PeNAC67-PeKAN2-PeSCL23 and B-class MADS-box transcription factors synergistically regulate the specialization process from petal to lip in Phalaenopsis equestris. | Xu Q et al. | β | 2024 | β |
| Performance evaluation of a CRISPR Cas9-based selective exponential amplification assay for the detection of KRAS mutations in plasma of patients with advanced pancreatic cancer. | Shen Y et al. | β | 2024 | β |
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| Pre-hypertrophic chondrogenic enhancer landscape of limb and axial skeleton development. | Darbellay F et al. | β | 2024 | β |
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| Proteasome Inhibition Reprograms Chromatin Landscape in Breast Cancer. | Kinyamu HK et al. | β | 2024 | β |
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| Protocol to isolate nuclei from Chlamydomonas reinhardtii for ATAC sequencing. | Santhanagopalan I et al. | β | 2024 | β |
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| TEAD2 Promotes Hepatocellular Carcinoma Development and Sorafenib Resistance via TAK1 Transcriptional Activation. | Zhang Y et al. | β | 2024 | β |
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| Advanced Omics Techniques for Understanding Cochlear Genome, Epigenome, and Transcriptome in Health and Disease. | Tisi A et al. | β | 2023 | β |
| Advancements in Focal Amplification Detection in Tumor/Liquid Biopsies and Emerging Clinical Applications. | Arshadi A et al. | β | 2023 | β |
| Aged intestinal stem cells propagate cell-intrinsic sources of inflammaging in mice. | Funk MC et al. | β | 2023 | β |
| A gene regulatory network for neural induction. | Trevers KE et al. | β | 2023 | β |
| Aging-associated HELIOS deficiency in naive CD4<sup>+</sup> T cells alters chromatin remodeling and promotes effector cell responses. | Zhang H et al. | β | 2023 | β |
| A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest. | Kessler S et al. | β | 2023 | β |
| A-MYB and BRDT-dependent RNA Polymerase II pause release orchestrates transcriptional regulation in mammalian meiosis. | Alexander AK et al. | β | 2023 | β |
| Analysis of Chromatin Accessibility and DNA Methylation to Reveal the Functions of Epigenetic Modifications in <i>Cyprinus carpio</i> Gonads. | Hou M et al. | β | 2023 | β |
| Analysis of Chromatin Accessibility, Histone Modifications, and Transcriptional States in Specific Cell Types Using Flow Cytometry. | Berendzen KW et al. | β | 2023 | β |
| Analyzes In Silico Indicate the lncRNAs MIR31HG and LINC00939 as Possible Epigenetic Inhibitors of the Osteogenic Differentiation in PDLCs. | Ferreira RS et al. | β | 2023 | β |
| Analyzing genomic and epigenetic profiles in single cells by hybrid transposase (scGET-seq). | Cittaro D et al. | β | 2023 | β |
| An atrial fibrillation-associated regulatory region modulates cardiac <i>Tbx5</i> levels and arrhythmia susceptibility. | Bosada FM et al. | β | 2023 | β |
| An injury-responsive <i>mmp14b</i> enhancer is required for heart regeneration. | Zlatanova I et al. | β | 2023 | β |
| An Integrative ATAC-Seq and RNA-Seq Analysis of the Endometrial Tissues of Meishan and Duroc Pigs. | Zhang H et al. | β | 2023 | β |
| A non-coding variant linked to metabolic obesity with normal weight affects actin remodelling in subcutaneous adipocytes. | Glunk V et al. | β | 2023 | β |
| An organoid-based CRISPR-Cas9 screen for regulators of intestinal epithelial maturation and cell fate. | Hansen SL et al. | β | 2023 | β |
| A NPAS4-NuA4 complex couples synaptic activity to DNA repair. | Pollina EA et al. | β | 2023 | β |
| Antagonism among DUX family members evolved from an ancestral toxic single homeodomain protein. | Bosnakovski D et al. | β | 2023 | β |
| Antagonistic action of GPS2 and KDM1A at enhancers governs alternative macrophage activation by interleukin 4. | Huang Z et al. | β | 2023 | β |
| AP-1 is a regulatory transcription factor of inflammaging in the murine kidney and liver. | Yu X et al. | β | 2023 | β |
| Application of single-cell multi-omics approaches in horticulture research. | Zhang J et al. | β | 2023 | β |
| Application of single cell multiomics points to changes in chromatin accessibility near calcitonin receptor like receptor and a possible role for adrenomedullin in the post-shock lung. | Armstead BE et al. | β | 2023 | β |
| Aryl hydrocarbon receptor is a tumor promoter in <i>MYCN</i>-amplified neuroblastoma cells through suppression of differentiation. | Chaudhry KA et al. | β | 2023 | β |
| A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer. | Antal CE et al. | β | 2023 | β |
| ATAC-seq protocol for the profiling of chromatin accessibility of in situ fixed quiescent and activated muscle stem cells. | Dong A et al. | β | 2023 | β |
| ATAC-seq reveals the roles of chromatin accessibility in the chondrocytes of Kashin-Beck disease compared with primary osteoarthritis. | Wang S et al. | β | 2023 | β |
| A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements. | Idriss S et al. | β | 2023 | β |
| A tissue injury sensing and repair pathway distinct from host pathogen defense. | Liu S et al. | β | 2023 | β |
| A transcriptional and regulatory map of mouse somite maturation. | Ibarra-Soria X et al. | β | 2023 | β |
| A wheat integrative regulatory network from large-scale complementary functional datasets enables trait-associated gene discovery for crop improvement. | Chen Y et al. | β | 2023 | β |
| BATF is Required for Treg Homeostasis and Stability to Prevent Autoimmune Pathology. | Khatun A et al. | β | 2023 | β |
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| Bcl11b sustains multipotency and restricts effector programs of intestinal-resident memory CD8<sup>+</sup> T cells. | Helm EY et al. | β | 2023 | β |
| Binary Colloidal Crystals Promote Cardiac Differentiation of Human Pluripotent Stem Cells via Nuclear Accumulation of SETDB1. | Lin Y et al. | β | 2023 | β |
| Bioinformatics for wet-lab scientists: practical application in sequencing analysis. | Laub V et al. | β | 2023 | β |
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| Characterization of De Novo Promoter Variants in Autism Spectrum Disorder with Massively Parallel Reporter Assays. | Koesterich J et al. | β | 2023 | β |
| Characterizing the biology of primary brain tumors and their microenvironment via single-cell profiling methods. | Gonzalez Castro LN et al. | β | 2023 | β |
| Chemical modulation of <i>Schistosoma mansoni</i> lysine specific demethylase 1 (SmLSD1) induces wide-scale biological and epigenomic changes. | Padalino G et al. | β | 2023 | β |
| Cholinergic control of Th17 cell pathogenicity in experimental autoimmune encephalomyelitis. | Nechanitzky R et al. | β | 2023 | β |
| Chromatin accessibility differences between alpha, beta, and delta cells identifies common and cell type-specific enhancers. | Mawla AM et al. | β | 2023 | β |
| Chromatin and gene expression changes during female <i>Drosophila</i> germline stem cell development illuminate the biology of highly potent stem cells. | Pang LY et al. | β | 2023 | β |
| Chromosome conformation capture approaches to investigate 3D genome architecture in Ankylosing Spondylitis. | Davidson C et al. | β | 2023 | β |
| Cisplatin exposure alters tRNA-derived small RNAs but does not affect epimutations in C. elegans. | Fallet M et al. | β | 2023 | β |
| c-Jun as a one-way valve at the naive to primed interface. | Li D et al. | β | 2023 | β |
| c-JUN is a barrier in hESC to cardiomyocyte transition. | Zhong H et al. | β | 2023 | β |
| Collateral lethality between HDAC1 and HDAC2 exploits cancer-specific NuRD complex vulnerabilities. | Zhang Y et al. | β | 2023 | β |
| Combination Therapies to Improve the Efficacy of Immunotherapy in Triple-negative Breast Cancer. | AleΔkoviΔ M et al. | β | 2023 | β |
| Comprehensive epigenomic profiling reveals the extent of disease-specific chromatin states and informs target discovery in ankylosing spondylitis. | Brown AC et al. | β | 2023 | β |
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| CRISPR screens identify gene targets at breast cancer risk loci. | Tuano NK et al. | β | 2023 | β |
| Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays. | Nifker G et al. | β | 2023 | β |
| Deciphering the chromatin spatial organization landscapes during BMMSC differentiation. | Teng Z et al. | β | 2023 | β |
| DeepSATA: A Deep Learning-Based Sequence Analyzer Incorporating the Transcription Factor Binding Affinity to Dissect the Effects of Non-Coding Genetic Variants. | Ma W et al. | β | 2023 | β |
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| Differential Expression Enrichment Tool (DEET): an interactive atlas of human differential gene expression. | Sokolowski DJ et al. | β | 2023 | β |
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| Direct cardiac reprogramming: A new technology for cardiac repair. | Brlecic PE et al. | β | 2023 | β |
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| Discordance between chromatin accessibility and transcriptional activity during the human primed-to-naΓ―ve pluripotency transition process. | Tu Z et al. | β | 2023 | β |
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| Dissecting the role of SWI/SNF component ARID1B in steady-state hematopoiesis. | Madan V et al. | β | 2023 | β |
| Distinct and opposite effects of leukemogenic <i>Idh</i> and <i>Tet2</i> mutations in hematopoietic stem and progenitor cells. | Fortin J et al. | β | 2023 | β |
| Distinct subsets of multi-lymphoid progenitors support ontogeny-related changes in human lymphopoiesis. | Keita S et al. | β | 2023 | β |
| DNA-initiated epigenetic cascades driven by C9orf72 hexanucleotide repeat. | Liu Y et al. | β | 2023 | β |
| Donafenib and GSK-J4 Synergistically Induce Ferroptosis in Liver Cancer by Upregulating HMOX1 Expression. | Zheng C et al. | β | 2023 | β |
| Dose rate dependent reduction in chromatin accessibility at transcriptional start sites long time after exposure to gamma radiation. | Dahl H et al. | β | 2023 | β |
| Dynamic chromatin accessibility licenses STAT5- and STAT6-dependent innate-like function of T<sub>H</sub>9 cells to promote allergic inflammation. | Son A et al. | β | 2023 | β |
| Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. | Zhao L et al. | β | 2023 | β |
| Dynamic Phosphorylation of G9a Regulates its Repressive Activity on Chromatin Accessibility and Mitotic Progression. | Geng Q et al. | β | 2023 | β |
| Dynamics of chromatin accessibility and genome wide control of desiccation tolerance in the resurrection plant Haberlea rhodopensis. | Mladenov P et al. | β | 2023 | β |
| Dynamics of Chromatin Accessibility During Hematopoietic Stem Cell Differentiation Into Progressively Lineage-Committed Progeny. | Martin EW et al. | β | 2023 | β |
| E2F regulation of the <i>Phosphoglycerate kinase</i> gene is functionally important in <i>Drosophila</i> development. | Zappia MP et al. | β | 2023 | β |
| Editorial: Impact of genome instability on human health. | Ray S et al. | β | 2023 | β |
| Effects and regulatory pathway of proopinmelanocortin on feeding habit domestication in mandarin fish. | Lu HL et al. | β | 2023 | β |
| Emergence and fate of stem cell-like <i>Tcf7</i><sup>+</sup> CD8<sup>+</sup> T cells during a primary immune response to viral infection. | Silva JG et al. | β | 2023 | β |
| Endocrine Therapy Synergizes with SMAC Mimetics to Potentiate Antigen Presentation and Tumor Regression in Hormone Receptor-Positive Breast Cancer. | Hermida-Prado F et al. | β | 2023 | β |
| Endogenous renal adiponectin drives gluconeogenesis through enhancing pyruvate and fatty acid utilization. | Onodera T et al. | β | 2023 | β |
| Epigenetic control of cellular crosstalk defines gastrointestinal organ fate and function. | Smith RJ et al. | β | 2023 | β |
| Epigenetic dysregulation from chromosomal transit in micronuclei. | Agustinus AS et al. | β | 2023 | β |
| Epigenetics in cardiovascular health and disease. | Chew NWS et al. | β | 2023 | β |
| Epigenomic charting and functional annotation of risk loci in renal cell carcinoma. | Nassar AH et al. | β | 2023 | β |
| ETV6 represses inflammatory response genes and regulates HSPC function during stress hematopoiesis in mice. | Bloom M et al. | β | 2023 | β |
| Expansion of ventral foregut is linked to changes in the enhancer landscape for organ-specific differentiation. | Wong YF et al. | β | 2023 | β |
| Explainable multi-task learning for multi-modality biological data analysis. | Tang X et al. | β | 2023 | β |
| Exploring plant cis-regulatory elements at single-cell resolution: overcoming biological and computational challenges to advance plant research. | Mendieta JP et al. | β | 2023 | β |
| Exploring the genetic basis of coronary artery disease using functional genomics. | LΓ³pez RodrΓguez M et al. | β | 2023 | β |
| Exploring the impact of dexamethasone on gene regulation in myeloma cells. | Bessonneau-Gaborit V et al. | β | 2023 | β |
| Factors and Methods for the Detection of Gene Expression Regulation. | Wang M et al. | β | 2023 | β |
| Fam20c regulates the calpain proteolysis system through phosphorylating Calpasatatin to maintain cell homeostasis. | Liu X et al. | β | 2023 | β |
| Fishing for Developmental Regulatory Regions: Zebrafish Tissue-Specific ATAC-seq. | Dhillon-Richardson RM et al. | β | 2023 | β |
| Fluctuations in chromatin state at regulatory loci occur spontaneously under relaxed selection and are associated with epigenetically inherited variation in C. elegans gene expression. | Wilson R et al. | β | 2023 | β |
| Fluid shear stress-modulated chromatin accessibility reveals the mechano-dependency of endothelial SMAD1/5-mediated gene transcription. | Jatzlau J et al. | β | 2023 | β |
| Forkhead box protein D2 suppresses colorectal cancer by reprogramming enhancer interactions. | Kim HM et al. | β | 2023 | β |
| FoxM1 coordinates cell division, protein synthesis, and mitochondrial activity in a subset of Ξ² cells during acute metabolic stress. | Kobiita A et al. | β | 2023 | β |
| Functional annotation of the animal genomes: An integrated annotation resource for the horse. | Peng S et al. | β | 2023 | β |
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| Genetic risk of osteoarthritis operates during human skeletogenesis. | Rice SJ et al. | β | 2023 | β |
| Genome-wide chromatin accessibility and gene expression profiling during flatfish metamorphosis. | Guerrero-PeΓ±a L et al. | β | 2023 | β |
| Genome-wide identification of accessible chromatin regions by ATAC-seq upon induction of the transcription factor bZIP11 in Arabidopsis. | Hellens AM et al. | β | 2023 | β |
| Genome-wide profiling of transcription factor activity in primary liver cancer using single-cell ATAC sequencing. | Craig AJ et al. | β | 2023 | β |
| Genomic glucocorticoid action in embryonic mouse neural stem cells. | Berry KJ et al. | β | 2023 | β |
| Genomic profiling of HIV-1 integration in microglia cells links viral integration to the topologically associated domains. | Rheinberger M et al. | β | 2023 | β |
| Genotyping MUltiplexed-Sequencing of CRISPR-Localized Editing (GMUSCLE): An Experimental and Computational Approach for Analyzing CRISPR-Edited Cells. | Zhang P et al. | β | 2023 | β |
| Graded BMP signaling within intestinal crypt architecture directs self-organization of the Wnt-secreting stem cell niche. | Kraiczy J et al. | β | 2023 | β |
| GRHL2 and AP2a coordinate early surface ectoderm lineage commitment during development. | Collier AE et al. | β | 2023 | β |
| Harnessing matrix stiffness to engineer a bone marrow niche for hematopoietic stem cell rejuvenation. | Zhang X et al. | β | 2023 | β |
| Hepatocyte SREBP signaling mediates clock communication within the liver. | Guan D et al. | β | 2023 | β |
| Heritable transcriptional defects from aberrations of nuclear architecture. | Papathanasiou S et al. | β | 2023 | β |
| High-dimensional immune cell profiling of cerebrospinal fluid from patients with metastatic breast cancer and leptomeningeal disease. | Im KW et al. | β | 2023 | β |
| High-fat diet in early life triggers both reversible and persistent epigenetic changes in the medaka fish (Oryzias latipes). | Inoue Y et al. | β | 2023 | β |
| Hippocampus-based behavioral, structural, and molecular dynamics across the estrous cycle. | Rocks D et al. | β | 2023 | β |
| HIV-1 active and latent infections induce disparate chromatin reorganization and transcriptional regulation of mRNAs and lncRNAs in SupT1 cells. | LΓͺ-Bury G et al. | β | 2023 | β |
| Hormone-induced enhancer assembly requires an optimal level of hormone receptor multivalent interactions. | Chen L et al. | β | 2023 | β |
| How enhancers regulate wavelike gene expression patterns. | Mau C et al. | β | 2023 | β |
| Hybrid Epigenomes Reveal Extensive Local Genetic Changes to Chromatin Accessibility Contribute to Divergence in Embryonic Gene Expression Between Species. | Devens HR et al. | β | 2023 | β |
| Hypoxia-mediated regulation of DDX5 through decreased chromatin accessibility and post-translational targeting restricts R-loop accumulation. | Leszczynska KB et al. | β | 2023 | β |
| Identification of angiogenesis-related genes signature for predicting survival and its regulatory network in glioblastoma. | Wan Z et al. | β | 2023 | β |
| Identification of the enhancer RNAs related to tumorgenesis of pituitary neuroendocrine tumors. | Wang L et al. | β | 2023 | β |
| IDH2 and TET2 mutations synergize to modulate T Follicular Helper cell functional interaction with the AITL microenvironment. | Leca J et al. | β | 2023 | β |
| Improved quality metrics for association and reproducibility in chromatin accessibility data using mutual information. | Roth C et al. | β | 2023 | β |
| Increased chromatin accessibility promotes the evolution of a transcriptional silencer in <i>Drosophila</i>. | Ling L et al. | β | 2023 | β |
| Inference of putative cell-type-specific imprinted regulatory elements and genes during human neuronal differentiation. | Liang D et al. | β | 2023 | β |
| Inhibiting stromal Class I HDACs curbs pancreatic cancer progression. | Liang G et al. | β | 2023 | β |
| Integrated analysis of ATAC-seq and RNA-seq reveals the transcriptional regulation network in SLE. | Wu J et al. | β | 2023 | β |
| Integrated analysis of ATAC-seq and RNA-seq unveils the role of ferroptosis in PM2.5-induced asthma exacerbation. | Zhang Y et al. | β | 2023 | β |
| Integration of chromatin accessibility and gene expression reveals new regulators of cold hardening to enhance freezing tolerance in Prunus mume. | Li P et al. | β | 2023 | β |
| Integrative analyses highlight functional regulatory variants associated with neuropsychiatric diseases. | Guo MG et al. | β | 2023 | β |
| Integrative approaches based on genomic techniques in the functional studies on enhancers. | Wang Q et al. | β | 2023 | β |
| Integrative epigenome profiling of 47XXY provides insights into whole genomic DNA hypermethylation and active chromatin accessibility. | Miao N et al. | β | 2023 | β |
| Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils. | Herrera-Uribe J et al. | β | 2023 | β |
| Interactions between BRD4S, LOXL2, and MED1 drive cell cycle transcription in triple-negative breast cancer. | Pascual-Reguant L et al. | β | 2023 | β |
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| Kinetic networks identify TWIST2 as a key regulatory node in adipogenesis. | Dutta AB et al. | β | 2023 | β |
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| Lamin A upregulation reorganizes the genome during rod photoreceptor degeneration. | Herrera I et al. | β | 2023 | β |
| Large-Scale Chromosomal Changes Lead to Genome-Level Expression Alterations, Environmental Adaptation, and Speciation in the Gayal (Bos frontalis). | Li Y et al. | β | 2023 | β |
| Lessons on fruiting body morphogenesis from genomes and transcriptomes of <i>Agaricomycetes</i>. | Nagy LG et al. | β | 2023 | β |
| Limited expression of Nrf2 in neurons across the central nervous system. | Levings DC et al. | β | 2023 | β |
| Lineage-specific differences and regulatory networks governing human chondrocyte development. | Richard D et al. | β | 2023 | β |
| LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways. | Kshirsagar A et al. | β | 2023 | β |
| Loss of cohesin regulator PDS5A reveals repressive role of Polycomb loops. | Bsteh D et al. | β | 2023 | β |
| Loss of phosphatase CTDNEP1 potentiates aggressive medulloblastoma by triggering MYC amplification and genomic instability. | Luo Z et al. | β | 2023 | β |
| Loss of the crumbs cell polarity complex disrupts epigenetic transcriptional control and cell cycle progression in the developing retina. | Owen N et al. | β | 2023 | β |
| Low HER2 expression in normal breast epithelium enables dedifferentiation and malignant transformation via chromatin opening. | Hayat A et al. | β | 2023 | β |
| Low level of ARID1A contributes to adaptive immune resistance and sensitizes triple-negative breast cancer to immune checkpoint inhibitors. | Chen XY et al. | β | 2023 | β |
| Low-nutrient diet in <i>Drosophila</i> larvae stage causes enhancement in dopamine modulation in adult brain due epigenetic imprinting. | ZΓΊΓ±iga-HernΓ‘ndez JM et al. | β | 2023 | β |
| LPS induces SGPP2 to participate metabolic reprogramming in endothelial cells. | Yi X et al. | β | 2023 | β |
| MacroH2A restricts inflammatory gene expression in melanoma cancer-associated fibroblasts by coordinating chromatin looping. | Filipescu D et al. | β | 2023 | β |
| Mammalian SWI/SNF chromatin remodeling complexes promote tyrosine kinase inhibitor resistance in EGFR-mutant lung cancer. | de Miguel FJ et al. | β | 2023 | β |
| Mapping the epigenomic landscape of human monocytes following innate immune activation reveals context-specific mechanisms driving endotoxin tolerance. | Amarasinghe HE et al. | β | 2023 | β |
| Marine Invertebrates One Cell at A Time: Insights from Single-Cell Analysis. | Bump P et al. | β | 2023 | β |
| Maternal antibiotic exposure enhances ILC2 activation in neonates via downregulation of IFN1 signaling. | Xu H et al. | β | 2023 | β |
| MATR3-antisense LINE1 RNA meshwork scaffolds higher-order chromatin organization. | Zhang Y et al. | β | 2023 | β |
| Mechanisms underlying the effect of voluntary running on adult hippocampal neurogenesis. | Gao Y et al. | β | 2023 | β |
| Methods, bioinformatics tools and databases in ecDNA research: An overview. | Zhao X et al. | β | 2023 | β |
| MINE is a method for detecting spatial density of regulatory chromatin interactions based on a multi-modal network. | Gong H et al. | β | 2023 | β |
| Molecular landscape and emerging therapeutic strategies in breast cancer brain metastasis. | Xiong S et al. | β | 2023 | β |
| MUC1-C intersects chronic inflammation with epigenetic reprogramming by regulating the set1a compass complex in cancer progression. | Bhattacharya A et al. | β | 2023 | β |
| Multidimensional scaling methods can reconstruct genomic DNA loops using Hi-C data properties. | Ishibashi R | β | 2023 | β |
| Multi-omic atlas of the parahippocampal gyrus in Alzheimer's disease. | Coleman C et al. | β | 2023 | β |
| Multiomics of Bohring-Opitz syndrome truncating ASXL1 mutations identify canonical and noncanonical Wnt signaling dysregulation. | Lin I et al. | β | 2023 | β |
| MultiVI: deep generative model for the integration of multimodal data. | Ashuach T et al. | β | 2023 | β |
| Myelomonocytic cells in giant cell arteritis activate trained immunity programs sustaining inflammation and cytokine production. | Cantoni E et al. | β | 2023 | β |
| Nanoparticle-mediated targeting of the fusion gene RUNX1/ETO in t(8;21)-positive acute myeloid leukaemia. | Issa H et al. | β | 2023 | β |
| Neural cell diversity in the light of single-cell transcriptomics. | FernΓ‘ndez-Moya SM et al. | β | 2023 | β |
| Neuroprotective protein ADNP-dependent histone remodeling complex promotes T helper 2 immune cell differentiation. | Ferreira ACF et al. | β | 2023 | β |
| Nickle-cobalt alloy nanocrystals inhibit activation of inflammasomes. | Lin J et al. | β | 2023 | β |
| Nr2f1a maintains atrial <i>nkx2.5</i> expression to repress pacemaker identity within venous atrial cardiomyocytes of zebrafish. | Martin KE et al. | β | 2023 | β |
| Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation. | Torre D et al. | β | 2023 | β |
| OBERON3 and SUPPRESSOR OF MAX2 1-LIKE proteins form a regulatory module driving phloem development. | Wallner ES et al. | β | 2023 | β |
| OCRFinder: a noise-tolerance machine learning method for accurately estimating open chromatin regions. | Ren J et al. | β | 2023 | β |
| Olig1/2-Expressing Intermediate Lineage Progenitors Are Predisposed to PTEN/p53-Loss-Induced Gliomagenesis and Harbor Specific Therapeutic Vulnerabilities. | Verma R et al. | β | 2023 | β |
| Omics data integration in computational biology viewed through the prism of machine learning paradigms. | FouchΓ© A et al. | β | 2023 | β |
| Optimization of ATAC-seq in wheat seedling roots using INTACT-isolated nuclei. | Debernardi JM et al. | β | 2023 | β |
| Organoid modeling of human fetal lung alveolar development reveals mechanisms of cell fate patterning and neonatal respiratory disease. | Lim K et al. | β | 2023 | β |
| Paired ATAC- and RNA-seq offer insight into the impact of HIV on alveolar macrophages: a pilot study. | Staitieh BS et al. | β | 2023 | β |
| Parallel recovery of chromatin accessibility and gene expression dynamics from frozen human regulatory T cells. | Wong YY et al. | β | 2023 | β |
| Past history of obesity triggers persistent epigenetic changes in innate immunity and exacerbates neuroinflammation. | Hata M et al. | β | 2023 | β |
| Pharmacological disruption of mSWI/SNF complex activity restricts SARS-CoV-2 infection. | Wei J et al. | β | 2023 | β |
| Photoselective sequencing: microscopically guided genomic measurements with subcellular resolution. | Mangiameli SM et al. | β | 2023 | β |
| PLA2G2E-mediated lipid metabolism triggers brain-autonomous neural repair after ischemic stroke. | Nakamura A et al. | β | 2023 | β |
| Prediction accuracy of regulatory elements from sequence varies by functional sequencing technique. | Nowling RJ et al. | β | 2023 | β |
| Premature aging of skeletal stem/progenitor cells rather than osteoblasts causes bone loss with decreased mechanosensation. | Yang R et al. | β | 2023 | β |
| Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages. | Bai J et al. | β | 2023 | β |
| Profiling the immune epigenome across global cattle breeds. | Powell J et al. | β | 2023 | β |
| Protocol for bulk and single-nuclei chromatin accessibility quantification in mouse liver tissue. | Korenfeld N et al. | β | 2023 | β |
| Protocol for Bulk-ATAC sequencing in head and neck squamous cell carcinoma. | Chen N et al. | β | 2023 | β |
| Pyruvate dehydrogenase fuels a critical citrate pool that is essential for Th17 cell effector functions. | Soriano-Baguet L et al. | β | 2023 | β |
| Quantification of absolute transcription factor binding affinities in the native chromatin context using BANC-seq. | Neikes HK et al. | β | 2023 | β |
| RAS and PP2A activities converge on epigenetic gene regulation. | Aakula A et al. | β | 2023 | β |
| Readout of histone methylation by Trim24 locally restricts chromatin opening by p53. | Isbel L et al. | β | 2023 | β |
| Recent Thymic Emigrants Require RBPJ-Dependent Notch Signaling to Transition into Functionally Mature Naive T Cells. | Teichman S et al. | β | 2023 | β |
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| Retinoid X receptor promotes hematopoietic stem cell fitness and quiescence and preserves hematopoietic homeostasis. | MenΓ©ndez-GutiΓ©rrez MP et al. | β | 2023 | β |
| Revisiting chromatin packaging in mouse sperm. | Yin Q et al. | β | 2023 | β |
| Rho enhancers play unexpectedly minor roles in Rhodopsin transcription and rod cell integrity. | Sun C et al. | β | 2023 | β |
| Ribosome biogenesis disruption mediated chromatin structure changes revealed by SRAtac, a customizable end to end analysis pipeline for ATAC-seq. | Freeman TF et al. | β | 2023 | β |
| RNA polymerase II pausing regulates chromatin organization in erythrocytes. | Penagos-Puig A et al. | β | 2023 | β |
| ROCCO: a robust method for detection of open chromatin via convex optimization. | Hamilton NH et al. | β | 2023 | β |
| Runx factors launch T cell and innate lymphoid programs via direct and gene network-based mechanisms. | Shin B et al. | β | 2023 | β |
| SALL1 enforces microglia-specific DNA binding and function of SMADs to establish microglia identity. | Fixsen BR et al. | β | 2023 | β |
| Sample Preparation and Integrative Data Analysis of a Droplet-based Single-Cell ATAC-sequencing Using Murine Thymic Epithelial Cells. | Ishikawa T et al. | β | 2023 | β |
| SAP30 promotes breast tumor progression by bridging the transcriptional corepressor SIN3 complex and MLL1. | Bao L et al. | β | 2023 | β |
| scATAC-seq preprocessing and imputation evaluation system for visualization, clustering and digital footprinting. | Akhtyamov P et al. | β | 2023 | β |
| Selection on the promoter regions plays an important role in complex traits during duck domestication. | Yin ZT et al. | β | 2023 | β |
| Semi-Autonomic AI LF-NMR Sensor for Industrial Prediction of Edible Oil Oxidation Status. | Osheter T et al. | β | 2023 | β |
| SENIES: DNA Shape Enhanced Two-Layer Deep Learning Predictor for the Identification of Enhancers and Their Strength. | Li Y et al. | β | 2023 | β |
| Separation of transcriptional repressor and activator functions in Drosophila HDAC3. | Tang M et al. | β | 2023 | β |
| Seq2science: an end-to-end workflow for functional genomics analysis. | van der Sande M et al. | β | 2023 | β |
| Sex-associated early-life viral innate immune response is transcriptionally associated with chromatin remodeling of type-I IFN-inducible genes. | Malinczak CA et al. | β | 2023 | β |
| Single-cell analysis reveals transcriptomic and epigenomic impacts on the maternal-fetal interface following SARS-CoV-2 infection. | Gao L et al. | β | 2023 | β |
| Single-cell and spatial multi-omics in the plant sciences: Technical advances, applications, and perspectives. | Yu X et al. | β | 2023 | β |
| Single-cell epigenome analysis identifies molecular events controlling direct conversion of human fibroblasts to pancreatic ductal-like cells. | Fei L et al. | β | 2023 | β |
| Single-cell genomics meets human genetics. | Cuomo ASE et al. | β | 2023 | β |
| Single-cell RNA sequencing in orthopedic research. | Wang T et al. | β | 2023 | β |
| Single-cell RNA sequencing in skeletal muscle developmental biology. | Cai C et al. | β | 2023 | β |
| Spatiotemporal resolution of germinal center Tfh cell differentiation and divergence from central memory CD4<sup>+</sup> T cell fate. | Zhu F et al. | β | 2023 | β |
| Spinal cord repair is modulated by the neurogenic factor Hb-egf under direction of a regeneration-associated enhancer. | Cigliola V et al. | β | 2023 | β |
| Spurious intragenic transcription is a feature of mammalian cellular senescence and tissue aging. | Sen P et al. | β | 2023 | β |
| Superenhancers as master gene regulators and novel therapeutic targets in brain tumors. | Zhuang HH et al. | β | 2023 | β |
| Super-enhancers include classical enhancers and facilitators to fully activate gene expression. | Blayney JW et al. | β | 2023 | β |
| Temporal analyses reveal a pivotal role for sense and antisense enhancer RNAs in coordinate immunoglobulin lambda locus activation. | Gao Z et al. | β | 2023 | β |
| TGFB1 induces fetal reprogramming and enhances intestinal regeneration. | Chen L et al. | β | 2023 | β |
| TGF-Ξ² broadly modifies rather than specifically suppresses reactivated memory CD8 T cells in a dose-dependent manner. | Taber A et al. | β | 2023 | β |
| The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data. | Hecker D et al. | β | 2023 | β |
| The aryl hydrocarbon receptor regulates lipid mediator production in alveolar macrophages. | Maier AM et al. | β | 2023 | β |
| The Chd4 Helicase Regulates Chromatin Accessibility and Gene Expression Critical for Ξ²-Cell Function InΒ Vivo. | Davidson RK et al. | β | 2023 | β |
| The dawn of spatial omics. | Bressan D et al. | β | 2023 | β |
| The end of the beginning: application of single-cell sequencing to chronic lymphocytic leukemia. | Nagler A et al. | β | 2023 | β |
| The endothelial-enriched lncRNA LINC00607 mediates angiogenic function. | Boos F et al. | β | 2023 | β |
| The enhancer landscape predetermines the skeletal regeneration capacity of stromal cells. | Hochmann S et al. | β | 2023 | β |
| The ETS transcription factor ETV6 constrains the transcriptional activity of EWS-FLI to promote Ewing sarcoma. | Lu DY et al. | β | 2023 | β |
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| The Force is Strong with This Epigenome: Chromatin Structure and Mechanobiology. | Hsia CR et al. | β | 2023 | β |
| The Landscape of Accessible Chromatin and Developmental Transcriptome Maps Reveal a Genetic Mechanism of Skeletal Muscle Development in Pigs. | Feng L et al. | β | 2023 | β |
| The long non-coding RNA MALAT1 regulates intestine host-microbe interactions and polyposis. | Long T et al. | β | 2023 | β |
| The master growth regulator DELLA binding to histone H2A is essential for DELLA-mediated global transcription regulation. | Huang X et al. | β | 2023 | β |
| The sex-specific factor SOA controls dosage compensation in Anopheles mosquitoes. | Kalita AI et al. | β | 2023 | β |
| The SWI/SNF chromatin-remodeling subunit DPF2 facilitates NRF2-dependent antiinflammatory and antioxidant gene expression. | Mas G et al. | β | 2023 | β |
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| Transcriptional regulation analysis reveals the complexity of metamorphosis in the Pacific oyster (<i>Crassostrea gigas</i>). | Xu F et al. | β | 2023 | β |
| Transcription factors and splice factors - interconnected regulators of stem cell differentiation. | Mehlferber MM et al. | β | 2023 | β |
| Transcription factors organize into functional groups on the linear genome and in 3D chromatin. | Vadnala RN et al. | β | 2023 | β |
| Translating non-coding genetic associations into a better understanding of immune-mediated disease. | Stankey CT et al. | β | 2023 | β |
| Transposable elements as tissue-specific enhancers in cancers of endodermal lineage. | Karttunen K et al. | β | 2023 | β |
| T-RHEX-RNAseq - a tagmentation-based, rRNA blocked, random hexamer primed RNAseq method for generating stranded RNAseq libraries directly from very low numbers of lysed cells. | Gustafsson C et al. | β | 2023 | β |
| TSLP shapes the pathogenic responses of memory CD4<sup>+</sup> T cells in eosinophilic esophagitis. | Rochman Y et al. | β | 2023 | β |
| Twist1-YY1-p300 complex promotes the malignant progression of HCC through activation of miR-9 by forming phase-separated condensates at super-enhancers and relieved by metformin. | Meng J et al. | β | 2023 | β |
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| ZBTB18 restricts chromatin accessibility and prevents transcriptional adaptations that drive metastasis. | Wang R et al. | β | 2023 | β |
| ΞNp63Ξ± facilitates proliferation and migration, and modulates the chromatin landscape in intrahepatic cholangiocarcinoma cells. | Peng A et al. | β | 2023 | β |
| A chromatin accessibility landscape during early adipogenesis of human adipose-derived stem cells. | Li S et al. | β | 2022 | β |
| Activation of OSM-STAT3 Epigenetically Regulates Tumor-Promoting Transcriptional Programs in Cervical Cancer. | Noh J et al. | β | 2022 | β |
| A pleiotropic hypoxia-sensitive <i>EPAS1</i> enhancer is disrupted by adaptive alleles in Tibetans. | Gray OA et al. | β | 2022 | β |
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| Chromatin accessibility: methods, mechanisms, and biological insights. | Mansisidor AR et al. | β | 2022 | β |
| Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants. | Aragam KG et al. | β | 2022 | β |
| EKLF/Klf1 regulates erythroid transcription by its pioneering activity and selective control of RNA Pol II pause-release. | Mukherjee K et al. | β | 2022 | β |
| Epigenetic priming of immune/inflammatory pathways activation and abnormal activity of cell cycle pathway in a perinatal model of white matter injury. | Schang AL et al. | β | 2022 | β |
| ERK1/2 signalling dynamics promote neural differentiation by regulating chromatin accessibility andΒ the polycomb repressive complex. | Semprich CI et al. | β | 2022 | β |
| Evaluating deep learning for predicting epigenomic profiles. | Toneyan S et al. | β | 2022 | β |
| Integrated chromatin accessibility and DNA methylation analysis to reveal the critical epigenetic modification and regulatory mechanism in gonadal differentiation of the sequentially hermaphroditic fish, Monopterus albus. | Hu Q et al. | β | 2022 | β |
| METTL4-mediated nuclear N6-deoxyadenosine methylation promotes metastasis through activating multiple metastasis-inducing targets. | Hsu KW et al. | β | 2022 | β |
| Postnatal expansion of mesenteric lymph node stromal cells towards reticular and CD34<sup>+</sup> stromal cell subsets. | Pezoldt J et al. | β | 2022 | β |
| Single-cell omics: A new direction for functional genetic research in human diseases and animal models. | Kong S et al. | β | 2022 | β |
| The autism risk factor CHD8 is a chromatin activator in human neurons and functionally dependent on the ERK-MAPK pathway effector ELK1. | Haddad Derafshi B et al. | β | 2022 | β |
| The early function of cortisol in liver during <i>Aeromonas hydrophila</i> infection: Dynamics of the transcriptome and accessible chromatin landscapes. | Jiang H et al. | β | 2022 | β |
| Transcriptional memory of dFOXO activation in youth curtails later-life mortality through chromatin remodeling and Xbp1. | MartΓnez Corrales G et al. | β | 2022 | β |
| Transcriptomic profiling implicates PAF1 in both active and repressive immune regulatory networks. | Kenaston MW et al. | β | 2022 | β |
| Usp22 is an intracellular regulator of systemic emergency hematopoiesis. | Dietlein N et al. | β | 2022 | β |
| Ξ²-hydroxybutyrate inhibits ferroptosis-mediated pancreatic damage in acute liver failure through the increase of H3K9bhb. | Zheng Y et al. | β | 2022 | β |
| ΞNp63/p73 drive metastatic colonization by controlling a regenerative epithelial stem cell program in quasi-mesenchymal cancer stem cells. | Lambert AW et al. | β | 2022 | β |