Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations.
PMID:35817938
3D Genome Organization as an Epigenetic Determinant of Transcription Regulation in T Cells.
PMID:35812421
3DFAACTS-SNP: using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of type 1 diabetes (T1D) risk.
PMID:35773720
TCF-1 promotes chromatin interactions across topologically associating domains in T cell progenitors.
PMID:35726060
Nucleome programming is required for the foundation of totipotency in mammalian germline development.
PMID:35703121
3DGenBench: a web-server to benchmark computational models for 3D Genomics.
PMID:35639501
Reconstruct high-resolution 3D genome structures for diverse cell-types using FLAMINGO.
PMID:35551182
Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data.
PMID:35516811
An improved 4'-aminomethyltrioxsalen-based nucleic acid crosslinker for biotinylation of double-stranded DNA or RNA.
PMID:35515418
The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data.
PMID:35501320
Understanding Regulatory Mechanisms of Brain Function and Disease through 3D Genome Organization.
PMID:35456393
WashU Epigenome Browser update 2022.
PMID:35412637
Epigenetic patterns in a complete human genome.
PMID:35357915
HiCuT: An efficient and low input method to identify protein-directed chromatin interactions.
PMID:35320278
Androgen Receptor-Mediated Transcription in Prostate Cancer.
PMID:35269520
Deciphering the Retinal Epigenome during Development, Disease and Reprogramming: Advancements, Challenges and Perspectives.
PMID:35269428
HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization.
PMID:35196517
Somatic structural variant formation is guided by and influences genome architecture.
PMID:35177558
Uncovering the Quantitative Relationships Among Chromosome Fluctuations, Epigenetics, and Gene Expressions of Transdifferentiation on Waddington Landscape.
PMID:35104056
Dynamics and Pathways of Chromosome Structural Organizations during Cell Transdifferentiation.
PMID:35098228
A Liquid State Perspective on Dynamics of Chromatin Compartments.
PMID:35096966
Diurnal RNAPII-tethered chromatin interactions are associated with rhythmic gene expression in rice.
PMID:34991658
Integrative approaches in genome structure analysis.
PMID:34963059
Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective.
PMID:34957106
Epigenome rewiring in human pluripotent stem cells.
PMID:34955367
Leveraging cell-type-specific regulatory networks to interpret genetic variants in abdominal aortic aneurysm.
PMID:34930827
cLoops2: a full-stack comprehensive analytical tool for chromatin interactions.
PMID:34928392
Characterization of Mammalian In Vivo Enhancers Using Mouse Transgenesis and CRISPR Genome Editing.
PMID:34913122
Regulation of Gene Expression by Telomere Position Effect.
PMID:34884608
Functional organization of the maternal and paternal human 4D Nucleome.
PMID:34877507
Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications.
PMID:34862503
Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model.
PMID:34862501
Nuclear deformation guides chromatin reorganization in cardiac development and disease.
PMID:34857921
Delayed DNA replication in haploid human embryonic stem cells.
PMID:34810218
Powerful gene-based testing by integrating long-range chromatin interactions and knockoff genotypes.
PMID:34799441
Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors.
PMID:34789735
Fast alignment and preprocessing of chromatin profiles with Chromap.
PMID:34772935
The 3D Genome: From Structure to Function.
PMID:34769016
Deciphering the molecular mechanism of the cancer formation by chromosome structural dynamics.
PMID:34752443
Encounters in Three Dimensions: How Nuclear Topology Shapes Genome Integrity.
PMID:34745220
RNA promotes the formation of spatial compartments in the nucleus.
PMID:34739832
Differentially accessible, single copy sequences form contiguous domains along metaphase chromosomes that are conserved among multiple tissues.
PMID:34670606
Multiscale and integrative single-cell Hi-C analysis with Higashi.
PMID:34635838
Polycomb condensates can promote epigenetic marks but are not required for sustained chromatin compaction.
PMID:34620850
Investigation of the Basic Steps in the Chromosome Conformation Capture Procedure.
PMID:34616432
Gosling: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization.
PMID:34596551
Nuclear dynamics and stress responses in Alzheimer's disease.
PMID:34535174
Plant 3D Chromatin Organization: Important Insights from Chromosome Conformation Capture Analyses of the Last 10 Years.
PMID:34486654
Systematic evaluation of chromosome conformation capture assays.
PMID:34480151
Visualizing and Annotating Hi-C Data.
PMID:34415532
The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research.
PMID:34357286
Revealing protein-protein interactions at the transcriptome scale by sequencing.
PMID:34348091
Peax: Interactive Visual Pattern Search in Sequential Data Using Unsupervised Deep Representation Learning.
PMID:34334852
Gaining insight into metabolic diseases from human genetic discoveries.
PMID:34315631
Expanding studies of chromosome structure and function in the era of T2T genomics.
PMID:34302168
Suv4-20h2 protects against influenza virus infection by suppression of chromatin loop formation.
PMID:34169237
Live imaging of chromatin distribution reveals novel principles of nuclear architecture and chromatin compartmentalization.
PMID:34078602
The Role of Epigenomic Regulatory Pathways in the Gut-Brain Axis and Visceral Hyperalgesia.
PMID:34057682
Age-related telomere attrition causes aberrant gene expression in sub-telomeric regions.
PMID:34018656
Regulation and functional roles of chemokines in liver diseases.
PMID:33976393
Advances in higher-order chromatin architecture: the move towards 4D genome.
PMID:33972012
Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin.
PMID:33963348
Engineering three-dimensional genome folding.
PMID:33958782
The Need for a Human Pangenome Reference Sequence.
PMID:33929893
Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance.
PMID:33848455
GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data.
PMID:33830196
The NIH Somatic Cell Genome Editing program.
PMID:33828315
4DNvestigator: time series genomic data analysis toolbox.
PMID:33794739
Molecular and computational approaches to map regulatory elements in 3D chromatin structure.
PMID:33741028
Epigenetic and metabolic regulation of epidermal homeostasis.
PMID:33600038
Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics.
PMID:33574602
Plant 3D genomics: the exploration and application of chromatin organization.
PMID:33560539
Engineering 3D genome organization.
PMID:33558716
Pancreatic progenitor epigenome maps prioritize type 2 diabetes risk genes with roles in development.
PMID:33544077
Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data.
PMID:33509077
Integrated spatial genomics reveals global architecture of single nuclei.
PMID:33505024
Remodeling the chromatin landscape in T lymphocytes by a division of labor among transcription factors.
PMID:33452686
Resources and challenges for integrative analysis of nuclear architecture data.
PMID:33450522
SPIN reveals genome-wide landscape of nuclear compartmentalization.
PMID:33446254
Enhancer redundancy in development and disease.
PMID:33442000
Recent Progress in Small Spirocyclic, Xanthene-Based Fluorescent Probes.
PMID:33339370
A New Era for Space Life Science: International Standards for Space Omics Processing.
PMID:33336201
FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data.
PMID:33334380
In silico APC/C substrate discovery reveals cell cycle-dependent degradation of UHRF1 and other chromatin regulators.
PMID:33306668
4D nucleome modeling.
PMID:33253996
Computer vision for pattern detection in chromosome contact maps.
PMID:33199682
Inferring chromosome radial organization from Hi-C data.
PMID:33167851
Driven progressive evolution of genome sequence complexity in Cyanobacteria.
PMID:33149190
HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data.
PMID:33136153
TriTag: an integrative tool to correlate chromatin dynamics and gene expression in living cells.
PMID:33104788
Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble.
PMID:33020654
Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation.
PMID:32998764
Inner Workings: Researchers peek into chromosomes' 3D structure in unprecedented detail.
PMID:32968013
Post-GWAS knowledge gap: the how, where, and when.
PMID:32964108
Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data.
PMID:32946435
Cell cycle dynamics of lamina-associated DNA.
PMID:32893442
3DeFDR: statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data.
PMID:32859248
ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization.
PMID:32832596
Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin.
PMID:32822575
Sizing Up Extracellular DNA: Instant Chromatin Discharge From Cells When Placed in Serum-Free Conditions.
PMID:32793591
Transcription factors: building hubs in the 3D space.
PMID:32783593
Expanded ENCODE delivers invaluable genomic encyclopedia.
PMID:32728235
Using RNA Tags for Multicolor Live Imaging of Chromatin Loci and Transcription in Drosophila Embryos.
PMID:32710421
3D genome organization contributes to genome instability at fragile sites.
PMID:32680994
A supervised learning framework for chromatin loop detection in genome-wide contact maps.
PMID:32647330
Functional genomics links genetic origins to pathophysiology in neurodegenerative and neuropsychiatric disease.
PMID:32634676
Epigenetic biomarkers and preterm birth.
PMID:32551139
Epigenetic Regulation of Kaposi's Sarcoma-Associated Herpesvirus Latency.
PMID:32508765
Centromere studies in the era of 'telomere-to-telomere' genomics.
PMID:32504677
The corrected gene proximity map for analyzing the 3D genome organization using Hi-C data.
PMID:32471347
Advances in technologies for 3D genomics research.
PMID:32394244
Controlling gene activation by enhancers through a drug-inducible topological insulator.
PMID:32369019
The PRR14 heterochromatin tether encodes modular domains that mediate and regulate nuclear lamina targeting.
PMID:32317397
Architectural proteins for the formation and maintenance of the 3D genome.
PMID:32249389
An in-silico human cell model reveals the influence of spatial organization on RNA splicing.
PMID:32210422
3D ATAC-PALM: super-resolution imaging of the accessible genome.
PMID:32203384
Loop-closure kinetics reveal a stable, right-handed DNA intermediate in Cre recombination.
PMID:32182357
Genome Dashboards: Framework and Examples.
PMID:32171420
Genomic Repeats Categorize Genes with Distinct Functions for Orchestrated Regulation.
PMID:32160538
Three-dimensional genome: developmental technologies and applications in precision medicine.
PMID:32152365
Exonuclease combinations reduce noises in 3D genomics technologies.
PMID:32128590
Integrating transposable elements in the 3D genome.
PMID:32042316
Distribution and storage of inflammatory memory in barrier tissues.
PMID:32015472
Histone H3 Lysine 56 Acetylation Is Required for Formation of Normal Levels of Meiotic DNA Breaks in S. cerevisiae.
PMID:31998719
Evaluation of 3D Chromatin Interactions Using Hi-C.
PMID:31960372
Genome organization in proximity to the BAP1 locus appears to play a pivotal role in a variety of cancers.
PMID:31957195
The Promises and Challenges of Toxico-Epigenomics: Environmental Chemicals and Their Impacts on the Epigenome.
PMID:31950866
normGAM: an R package to remove systematic biases in genome architecture mapping data.
PMID:31888469
Methods for mapping 3D chromosome architecture.
PMID:31848476
Protect-seq: genome-wide profiling of nuclease inaccessible domains reveals physical properties of chromatin.
PMID:31819993
Epigenetics and the dynamics of chromatin during adenovirus infections.
PMID:31769503
Tasks, Techniques, and Tools for Genomic Data Visualization.
PMID:31768085
Autonomous Pathway: FLOWERING LOCUS C Repression through an Antisense-Mediated Chromatin-Silencing Mechanism.
PMID:31740502
Analysis of the structural variability of topologically associated domains as revealed by Hi-C.
PMID:31687663
Evidence for and against Liquid-Liquid Phase Separation in the Nucleus.
PMID:31683819
Mapping RNA-chromatin interactions by sequencing with iMARGI.
PMID:31619811
Joint inference and alignment of genome structures enables characterization of compartment-independent reorganization across cell types.
PMID:31594535
H3K9me2 orchestrates inheritance of spatial positioning of peripheral heterochromatin through mitosis.
PMID:31573510
Druggable Transcriptional Networks in the Human Neurogenic Epigenome.
PMID:31530573
Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data.
PMID:31470090
Pattern-Driven Navigation in 2D Multiscale Visualizations with Scalable Insets.
PMID:31442989
Chromosomics: Bridging the Gap between Genomes and Chromosomes.
PMID:31434289
Transient crosslinking kinetics optimize gene cluster interactions.
PMID:31433796
Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation.
PMID:31409785
Visual Pattern-Driven Exploration of Big Data.
PMID:31396383
Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy.
PMID:31395619
Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes.
PMID:31299961
Biological characterization of expression quantitative trait loci (eQTLs) showing tissue-specific opposite directional effects.
PMID:31296926
Blood disease-causing and -suppressing transcriptional enhancers: general principles and GATA2 mechanisms.
PMID:31289032
Three-dimensional chromosome architecture and drug addiction.
PMID:31276935
Super-Resolution Microscopy of Chromatin.
PMID:31261775
Mapping chromatin modifications at the single cell level.
PMID:31249006
Sperm RNA code programmes the metabolic health of offspring.
PMID:31235802
Atlas of Subcellular RNA Localization Revealed by APEX-Seq.
PMID:31230715
WashU Epigenome Browser update 2019.
PMID:31165883
Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes.
PMID:31078526
Tibanna: software for scalable execution of portable pipelines on the cloud.
PMID:31077294
Nucleosome dynamics of human iPSC during neural differentiation.
PMID:31036712
High resolution discovery of chromatin interactions.
PMID:30953075
The Driving Force: Nuclear Mechanotransduction in Cellular Function, Fate, and Disease.
PMID:30916994
Systematic Evaluation of Statistical Methods for Identifying Looping Interactions in 5C Data.
PMID:30904376
Defining the Genetic, Genomic, Cellular, and Diagnostic Architectures of Psychiatric Disorders.
PMID:30901538
DNA Replication Timing Enters the Single-Cell Era.
PMID:30884743
Rhodamine-Hoechst positional isomers for highly efficient staining of heterochromatin.
PMID:30881625
Cohesin-Mediated Genome Architecture Does Not Define DNA Replication Timing Domains.
PMID:30836708
Determination of local chromatin interactions using a combined CRISPR and peroxidase APEX2 system.
PMID:30805613
Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization.
PMID:30799036
HDAC inhibitors rescue multiple disease-causing CFTR variants.
PMID:30753450
Lineage-specific reorganization of nuclear peripheral heterochromatin and H3K9me2 domains.
PMID:30723106
A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome.
PMID:30586383
Hi-C analysis: from data generation to integration.
PMID:30570701
GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data.
PMID:30553884
Nucleosome structure and dynamics are coming of age.
PMID:30532059
Chain organization of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci.
PMID:30507936
The senescent cell epigenome.
PMID:30391936
CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging.
PMID:30377374
From association to mechanism in complex disease genetics: the role of the 3D genome.
PMID:30268153
RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome.
PMID:30240742
Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations.
PMID:30239812
Control of directionality of chromatin folding for the inter- and intra-domain contacts at the Tfap2c-Bmp7 locus.
PMID:30213272
RNA, Action through Interactions.
PMID:30177410
HiGlass: web-based visual exploration and analysis of genome interaction maps.
PMID:30143029
Computational methods for analyzing and modeling genome structure and organization.
PMID:30022617
The anatomy of a nucleus: As revealed by chromosome painting.
PMID:30001330
Understanding the 3D genome: Emerging impacts on human disease.
PMID:29990539
Unsupervised embedding of single-cell Hi-C data.
PMID:29950005
Advances in the computational and molecular understanding of the prostate cancer cell nucleus.
PMID:29923622
CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci.
PMID:29912475
Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization.
PMID:29901812
Distinct epigenomic patterns are associated with haploinsufficiency and predict risk genes of developmental disorders.
PMID:29849042
The Cellosaurus, a Cell-Line Knowledge Resource.
PMID:29805321
GWAS4D: multidimensional analysis of context-specific regulatory variant for human complex diseases and traits.
PMID:29771388
Gene regulation in the 3D genome.
PMID:29767704
Functional Assays to Screen and Dissect Genomic Hits: Doubling Down on the National Investment in Genomic Research.
PMID:29654098
Chromatin Higher-Order Folding: A Perspective with Linker DNA Angles.
PMID:29628212
Opportunities and Challenges in Building a Spatiotemporal Multi-scale Model of the Human Pancreatic β Cell.
PMID:29570991
Streamlined histone-based fluorescence lifetime imaging microscopy (FLIM) for studying chromatin organisation.
PMID:29535103
Chromatin Regulation of Neuronal Maturation and Plasticity.
PMID:29530320
FIND: difFerential chromatin INteractions Detection using a spatial Poisson process.
PMID:29440282
Calculation of 3D genome structures for comparison of chromosome conformation capture experiments with microscopy: An evaluation of single-cell Hi-C protocols.
PMID:29431585
Separate roles for chromatin and lamins in nuclear mechanics.
PMID:29227210
Corrigendum: The 4D nucleome project.
PMID:29168505
The Encyclopedia of DNA elements (ENCODE): data portal update.
PMID:29126249
The biology and polymer physics underlying large-scale chromosome organization.
PMID:29105235