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Powerful gene-based testing by integrating long-range chromatin interactions and knockoff genotypes

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Extensive long-range polycomb interactions and weak compartmentalization are hallmarks of human neuronal 3D genome

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3D chromatin hubs as regulatory units of identity and survival in human acute leukemia

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HiC1Dmetrics: framework to extract various one-dimensional features from chromosome structure data

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Clonal evolution of the 3D chromatin landscape in patients with relapsed pediatric B-cell acute lymphoblastic leukemia

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A double-negative thymocyte-specific enhancer augments Notch1 signaling to direct early T cell progenitor expansion, lineage restriction and β-selection

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Molecular and computational approaches to map regulatory elements in 3D chromatin structure

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The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data

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Dynamic alternations of three-dimensional chromatin architecture contribute to phenotypic characteristics of breast muscle in chicken

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Machine Learning and Deep Learning in Genetics and Genomics

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Chromatin conformation of human oral epithelium can identify orofacial cleft missing functional variants

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Chromosome-level genome assembly of the Muscovy duck provides insight into fatty liver susceptibility

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Genetics of varicose veins reveals polygenic architecture and genetic overlap with arterial and venous disease

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Comparative study on chromatin loop callers using Hi-C data reveals their effectiveness

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Structural Variations Associated with Adaptation and Coat Color in Qinghai-Tibetan Plateau Cattle

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Systematic prioritization of functional variants and effector genes underlying colorectal cancer risk

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Mutations of PDS5 genes enhance TAD-like domain formation in Arabidopsis thaliana

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Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C

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A comprehensive review of bioinformatics tools for chromatin loop calling

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MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments

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GILoop: Robust chromatin loop calling across multiple sequencing depths on Hi-C data

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Modeling and analysis of Hi-C data by HiSIF identifies characteristic promoter-distal loops

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Computational characterization of domain‐segregated 3D chromatin structure and segmented DNA methylation status in carcinogenesis

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Evolution of plant cell-type-specific cis -regulatory elementsPreprint

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Hi-C, a chromatin 3D structure technique advancing the functional genomics of immune cells

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Mustache: Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space RepresentationPreprint

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Hi-C profiling in tissues reveals 3D chromatin-regulated breast tumor heterogeneity informing a looping-mediated therapeutic avenue

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RNA Biogenesis Instructs Functional Inter-Chromosomal Genome Architecture

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Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure

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Single cell variant to enhancer to gene map for coronary artery diseasePreprint

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A deep-time landscape of plant cis-regulatory sequence evolution

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ZipHiC: a novel Bayesian framework to identify enriched interactions and experimental biases in Hi-C data

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Insights into the convergent evolution of fructan biosynthesis in angiosperms from the highly characteristic chicory genome

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Multiple strategies, including 6mA methylation, affecting plant alternative splicing in allopolyploid peanut

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3D genomic organization in cancers

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3D genomic features across >50 diverse cell types reveal insights into the genomic architecture of childhood obesity

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Genetic transcriptional regulation profiling of cartilage reveals pathogenesis of osteoarthritis

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BaRDIC: robust peak calling for RNA–DNA interaction data

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Mapping the 3D genome architecture

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Mapping nucleosome and chromatin architectures: A survey of computational methods

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3D genome organization and its study in livestock breeding

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Recipes and ingredients for deep learning models of 3D genome folding

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Comparison of Capture Hi-C Analytical Pipelines

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Dynamic chromatin architectures provide insights into the genetics of cattle myogenesis

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Assessing and assuring interoperability of a genomics file format

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FIREcaller: Detecting Frequently Interacting Regions from Hi-C DataPreprint

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SnapHiC: a computational pipeline to map chromatin contacts from single cell Hi-C dataPreprint

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Deciphering the generation of heterogeneity in esophageal squamous cell carcinoma metastasis via single-cell multiomics analysis

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Profiling of 3D Genome Organization in Nasopharyngeal Cancer Needle Biopsy Patient Samples by a Modified Hi-C Approach

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MaxHiC: robust estimation of chromatin interaction frequency in Hi-C and capture Hi-C experimentsPreprint

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Tensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolution

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Dynamic chromatin architecture identifies new autoimmune-associated enhancers for IL2 and novel genes regulating CD4+ T cell activation

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Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysis

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Statistical confidence estimation for Hi-C data reveals regulatory chromatin contactsPreprint

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Identification of significant chromatin contacts from HiChIP data by FitHiChIP

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Fine mapping chromatin contacts in capture Hi-C data

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SOFTWARE Open Access ChromContact: A web tool for analyzing

(2016)