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■ Abbreviation / Long Form : TAD / topologically associating domain

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Total Number of Papers: 94
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Abbreviation:   TAD  (>> Co-occurring Abbreviation)
Long Form:   topologically associating domain
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No. Year Title Co-occurring Abbreviation
2021 A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals. ---
2021 A Reassessment of Copy Number Variations in Congenital Heart Defects: Picturing the Whole Genome. CHD, CNV-US, CNVs, lncRNAs
2021 Comparative Genome Analyses Highlight Transposon-Mediated Genome Expansion and the Evolutionary Architecture of 3D Genomic Folding in Cotton. TE
2021 CTCF-binding element regulates ESC differentiation via orchestrating long-range chromatin interaction between enhancers and HoxA. EEIC, ESC, HoxA, RA
2021 DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell. ---
2021 Epithelial Cells in 2D and 3D Cultures Exhibit Large Differences in Higher-order Genomic Interactions. ---
2021 Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival. DepMap, SV
2021 HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. ---
2021 Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression. AK58, TEs
10  2021 M1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity. M1BP
11  2021 Multiple CTCF sites cooperate with each other to maintain a TAD for enhancer-promoter interaction in the β-globin locus. CTCF
12  2021 NoRCE: non-coding RNA sets cis enrichment tool. ncRNAs
13  2021 Novel MYT1 variants expose the complexity of oculo-auriculo-vertebral spectrum genetic mechanisms. CNVs, OAVS, SNVs
14  2021 Position effects of 22q13 rearrangements on candidate genes in Phelan-McDermid syndrome. PMS
15  2021 The essential but enigmatic regulatory role of HERVH in pluripotency. HERVH, lncRNAs
16  2021 The hierarchical folding dynamics of topologically associating domains are closely related to transcriptional abnormalities in cancers. TH score
17  2021 The human β-globin enhancer LCR HS2 plays a role in forming a TAD by activating chromatin structure at neighboring CTCF sites. HS2, LCR
18  2021 WNT2 activation through proximal germline deletion predisposes to small intestinal neuroendocrine tumors and intestinal adenocarcinomas. ---
19  2020 Alteration of CTCF-associated chromatin neighborhood inhibits TAL1-driven oncogenic transcription program and leukemogenesis. ---
20  2020 Characterizing chromatin folding coordinate and landscape with deep learning. VAE
21  2020 Chromatin Architectures Are Associated with Response to Dark Treatment in the Oil Crop Sesamum indicum, Based on a High-Quality Genome Assembly. DEGs, GO
22  2020 Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains. KLK, LREA
23  2020 Enhancer-gene rewiring in the pathogenesis of Quebec platelet disorder. QPD
24  2020 HPV-CCDC106 integration alters local chromosome architecture and hijacks an enhancer by three-dimensional genome structure remodeling in cervical cancer. Hi-C, HPV
25  2020 Impact of 3D genome organization, guided by cohesin and CTCF looping, on sex-biased chromatin interactions and gene expression in mouse liver. ---
26  2020 Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells. CRE
27  2020 Structural Variants Create New Topological-Associated Domains and Ectopic Retinal Enhancer-Gene Contact in Dominant Retinitis Pigmentosa. adRP, iPSCs, PPCs, ROs, RP17, SVs
28  2020 TADBD: a sensitive and fast method for detection of typologically associated domain boundaries. TADBD
29  2020 TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription. ---
30  2020 The matrix revolutions: towards the decoding of the plant chromatin three-dimensional reality. ---
31  2020 The regulatory landscape of the Dlx gene system in branchial arches: Shared characteristics among Dlx bigene clusters and evolution. ---
32  2020 Visualizing the Role of Boundary Elements in Enhancer-Promoter Communication. ---
33  2019 A computational method to predict topologically associating domain boundaries combining histone Marks and sequence information. CTCF
34  2019 A principled strategy for mapping enhancers to genes. ---
35  2019 Broken by the Cut: A Journey into the Role of Topoisomerase II in DNA Fragility. CTCF
36  2019 Cell-Selective Regulation of CFTR Gene Expression: Relevance to Gene Editing Therapeutics. CF, CFTR, CREs, CTCF
37  2019 Characterization of Button Loci that Promote Homologous Chromosome Pairing and Cell-Type-Specific Interchromosomal Gene Regulation. ---
38  2019 Deciphering essential cistromes using genome-wide CRISPR screens. ---
39  2019 Enhancer accessibility and CTCF occupancy underlie asymmetric TAD architecture and cell type specific genome topology. ESC
40  2019 FACT mediates cohesin function on chromatin. ---
41  2019 Hierarchical Reconstruction of High-Resolution 3D Models of Large Chromosomes. KB
42  2019 HOTTIP lncRNA Promotes Hematopoietic Stem Cell Self-Renewal Leading to AML-like Disease in Mice. AML, HSC, lncRNAs
43  2019 Identification of candidate genes affecting chronic subclinical mastitis in Norwegian Red cattle: combining genome-wide association study, topologically associated domains and pathway enrichment analysis. ACOT2, CCNB1, FOS, LSCS, NR, SCC, SCM
44  2019 Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication. ERCEs, RT
45  2019 Identifying clusters of cis-regulatory elements underpinning TAD structures and lineage-specific regulatory networks. COREs, CREAM, CREs, HCTs
46  2019 Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma. GC, SVs, WGS
47  2019 Joint analyses of multi-tissue Hi-C and eQTL data demonstrate close spatial proximity between eQTLs and their target genes. eQTLs, FIREs, Hi-C
48  2019 Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs. BOFS, hNCCs
49  2019 Non-coding RNAs and chromatin domains. ncRNAs
50  2019 NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains. ---
51  2019 Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia. ALL
52  2019 Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation. ---
53  2019 Sex-specific SNP-SNP interaction analyses within topologically associated domains reveals ANGPT1 as a novel tumor suppressor gene for lung cancer. ---
54  2019 Single Chromosome Aneuploidy Induces Genome-Wide Perturbation of Nuclear Organization and Gene Expression. ---
55  2019 Specific Contributions of Cohesin-SA1 and Cohesin-SA2 to TADs and Polycomb Domains in Embryonic Stem Cells. PRC1
56  2019 Stabilization of chromatin topology safeguards genome integrity. DSBs
57  2019 The Eleanor ncRNAs activate the topological domain of the ESR1 locus to balance against apoptosis. LTED, ncRNAs
58  2019 Transcriptional Enhancers in the FOXP2 Locus Underwent Accelerated Evolution in the Human Lineage. FOXP2
59  2019 [Advances in mammalian three-dimensional genome by using Hi-C technology approach]. CT
60  2019 [Bioinformatics analysis of Alu components at the level of genome 3D structure]. ---
61  2018 4Cin: A computational pipeline for 3D genome modeling and virtual Hi-C analyses from 4C data. vHi-C
62  2018 An extended regulatory landscape drives Tbx18 activity in a variety of prostate-associated cell lineages. UGS
63  2018 Argonaute2 and LaminB modulate gene expression by controlling chromatin topology. Ago2, LADs, RNAi
64  2018 Computational 3D genome modeling using Chrom3D. LADs
65  2018 Decoding topologically associating domains with ultra-low resolution Hi-C data by graph structural entropy. deDoc, Hi-C
66  2018 Enhancers in the Peril lincRNA locus regulate distant but not local genes. Hi-C, lincRNA, MPRA
67  2018 Generation of Genome-wide Chromatin Conformation Capture Libraries from Tightly Staged Early Drosophila Embryos. ---
68  2018 Lamin B1 mapping reveals the existence of dynamic and functional euchromatin lamin B1 domains. eLADs, EMT, LADs, NL
69  2018 LSCC SNP variant regulates SOX2 modulation of VDAC3. eQTLs, LSCC
70  2018 MCM2 promotes symmetric inheritance of modified histones during DNA replication. PTMs
71  2018 Producing genome structure populations with the dynamic and automated PGS software. ---
72  2018 Regulatory variants of FOXG1 in the context of its topological domain organisation. FIREs, LRPE, SRO
73  2017 3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations. CNVs, MM, WGS
74  2017 Alterations in Three-Dimensional Organization of the Cancer Genome and Epigenome. LREA, LRES
75  2017 Architectural alterations of the fission yeast genome during the cell cycle. ---
76  2017 Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription. ---
77  2017 cis-Acting Complex-Trait-Associated lincRNA Expression Correlates with Modulation of Chromosomal Architecture. lincRNAs, TR-lincRNAs
78  2017 ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data. ChIP
79  2017 Cooperation between a hierarchical set of recruitment sites targets the X chromosome for dosage compensation. DCC
80  2017 Copy number variants analysis in a cohort of isolated and syndromic developmental delay/intellectual disability reveals novel genomic disorders, position effects and candidate disease genes. array-CGH, CNVs
81  2017 Genetic association of FTO/IRX region with obesity and overweight in the Polish population. BMI, GWAS, LD
82  2017 Regulatory dynamics of 11p13 suggest a role for EHF in modifying CF lung disease severity. APIP, CF, CFTR, CTCF, EHF, ELF5, GWAS
83  2017 Single-molecule compaction of megabase-long chromatin molecules by multivalent cations. DLS, FM, HO
84  2017 Transcription-induced supercoiling as the driving force of chromatin loop extrusion during formation of TADs in interphase chromosomes. ---
85  2016 Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming. iPSCs
86  2016 Differentenhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture. dCP, hkCP
87  2016 RUNX1 contributes to higher-order chromatin organization and gene regulation in breast cancer cells. ---
88  2016 Shh and ZRS enhancer colocalisation is specific to the zone of polarising activity. FISH
89  2016 SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells. ECM
90  2015 High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila. HAS, MSL
91  2015 Predicting chromatin organization using histone marks. ---
92  2015 Structural heterogeneity and functional diversity of topologically associating domains in mammalian genomes. AP
93  2015 The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains. NMC
94  2014 Mapping the Shh long-range regulatory domain. ---