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1. Full Text Comparison of normalization methods for Hi-C data
by Lyu, Hongqiang and Liu, Erhu and Wu, Zhifang
BioTechniques, ISSN 0736-6205, 10/2019
Hi-C has been predominately used to study the genome-wide interactions of genomes. In Hi-C experiments, it is believed that biases originating from different... 
comprehensive comparison | Hi-C data | normalization methods
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2. Full Text The three-dimensional landscape of the genome in human brain tissue unveils regulatory mechanisms leading to schizophrenia risk
by Mah, Won and Won, Hyejung
Schizophrenia Research, ISSN 0920-9964, 2019
Recent advances in our understanding of the genetic architecture of schizophrenia have shed light on the schizophrenia etiology. While common variation is one... 
Schizophrenia | Chromosome conformation | GWAS | Hi-C
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3. Full Text Long-range chromatin interactions in the kidney
by Guan, Yuting and Liu, Hongbo and Susztak, Katalin
Journal of the American Society of Nephrology, ISSN 1046-6673, 03/2019, Volume 30, Issue 3, pp. 367 - 369
UROLOGY & NEPHROLOGY | kidney | DAB2 | GWAS | Hi-C
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4. Full Text Comparison of computational methods for 3D genome analysis at single-cell Hi-C level
by Li, Xiao and An, Ziyang and Zhang, Zhihua
Methods (San Diego, Calif.), ISSN 1046-2023, 08/2019
Hi-C is a high-throughput chromosome conformation capture technology that is becoming routine in the literature. Although the price of sequencing has been... 
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5. Full Text BAT Hi-C maps global chromatin interactions in an efficient and economical way
by Huang, Jie and Jiang, Yongpeng and Zheng, Haonan and Ji, Xiong
Methods (San Diego, Calif.), ISSN 1046-2023, 08/2019
Chromosome Conformation Capture (3C)-based technologies, such as Hi-C, have represented a significant breakthrough in investigating the structure and function... 
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6. Full Text A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation
by Minajigi, Anand and Froberg, John E and Wei, Chunyao and Sunwoo, Hongjae and Kesner, Barry and Colognori, David and Lessing, Derek and Payer, Bernhard and Boukhali, Myriam and Haas, Wilhelm and Lee, Jeannie T
Science, ISSN 0036-8075, 07/2015, Volume 349, Issue 6245, pp. 1DUIMMY - aab2276
The inactive X chromosome (Xi) serves as a model to understand gene silencing on a global scale. Here, we perform "identification of direct RNA interacting... 
PATERNAL X-CHROMOSOME | HI-C REVEALS | DIFFERENTIAL EXPRESSION | DOSAGE COMPENSATION | MULTIDISCIPLINARY SCIENCES | GENE-EXPRESSION | INACTIVE-X | CTCF | REGULATORY ELEMENTS | BINDING | GENOME | Proteins | Epigenetics | Ribonucleic acid--RNA | Chromosomes | Cohesion | Ribonucleic acids | Genes | Shutdowns | Mammals | Three dimensional models
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7. Full Text HiCUP: pipeline for mapping and processing Hi-C data [version 1; peer review: 2 approved, 1 approved with reservations]
by Wingett, Steven W and Ewels, Philip and Furlan-Magaril, Mayra and Nagano, Takashi and Schoenfelder, Stefan and Fraser, Peter and Andrews, Simon
F1000Research, ISSN 2046-1402, 2015, Volume 4, p. 1310
HiCUP is a pipeline for processing sequence data generated by Hi-C and Capture Hi-C (CHi-C) experiments, which are techniques used to investigate... 
Bioinformatics | Genomics
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8. Full Text Genome wide mapping of long range contacts unveils DNA Double Strand Breaks clustering at damaged active genes
by Aymard, François and Aguirrebengoa, Marion and Guillou, Emmanuelle and Javierre, Biola M and Bugler, Beatrix and Arnould, Coline and Rocher, Vincent and Iacovoni, Jason S and Biernacka, Anna and Skrzypczak, Magdalena and Ginalski, Krzysztof and Rowicka, Maga and Fraser, Peter and Legube, Gaëlle
Nature structural & molecular biology, ISSN 1545-9993, 4/2017, Volume 24, Issue 4, pp. 353 - 361
The ability of DNA Double Strand Breaks (DSBs) to cluster in mammalian cells has been subjected to intense debate over the past few years. Here we used a high... 
DSB repair | Capture Hi-C | clustering | translocation | transcription
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9. Full Text WashU Epigenome Browser update 2019
by Li, DF and Hsu, S and Purushotham, D and Sears, RL and Wang, T
NUCLEIC ACIDS RESEARCH, ISSN 0305-1048, 07/2019, Volume 47, Issue W1, pp. W158 - W165
The WashU Epigenome Browser (https: //epigenomegateway.wustl.edu/) provides visualization, integration and analysis tools for epigenomic datasets. Since 2010,... 
CONSORTIUM | ELEMENTS | HI-C | ENSEMBL | BIOCHEMISTRY & MOLECULAR BIOLOGY | Web Server Issue
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10. Full Text TADs as the caller calls them
by Wit, Elzo de
Journal of Molecular Biology, ISSN 0022-2836, 10/2019
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11. Full Text Cohesin Loss Eliminates All Loop Domains
by Rao, Suhas S.P and Huang, Xingfan and Huang, Su-Chen and Glenn St Hilaire, Brian and Engreitz, Jesse M and Perez, Elizabeth M and Kieffer-Kwon, Kyong-Rim and Sanborn, Adrian L and Johnstone, Sarah E and Bascom, Gavin D and Bochkov, Ivan D and Shamim, Muhammad S and Shin, Jaeweon and Turner, Douglass and Ye, Ziyi and Omer, Arina D and Robinson, James T and Schlick, Tamar and Bernstein, Bradley E and Casellas, Rafael and Lander, Eric S and Aiden, Erez Lieberman
Cell, ISSN 0092-8674, 10/2017, Volume 171, Issue 2, pp. 305 - 320.e24
The human genome folds to create thousands of intervals, called “contact domains,” that exhibit enhanced contact frequency within themselves. “Loop domains”... 
chromatin loops | superenhancers | gene regulation | Hi-C | nuclear compartments | 4D Nucleome | cohesion | CTCF | genome architecture | loop extrusion | PHASE-SEPARATION | SYSTEM | READ ALIGNMENT | CHROMATIN | BIOCHEMISTRY & MOLECULAR BIOLOGY | TRANSCRIPTION | GENE-EXPRESSION | ARCHITECTURE | MODEL | GENOME | CELL BIOLOGY | Chromosomal Proteins, Non-Histone - metabolism | Humans | Cell Cycle Proteins - metabolism | Nucleosomes - metabolism | Nuclear Proteins - metabolism | Phosphoproteins - metabolism | Cell Nucleus - genetics | Enhancer Elements, Genetic | CCCTC-Binding Factor | Cell Line, Tumor | Chromosomes - metabolism | Histone Code | Genome, Human | Repressor Proteins - metabolism | Chromosomes | Analysis | Genomics | Medical colleges | Chromatin
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12. Full Text Unfolding the Genome: The Case Study of P. falciparum
by Varoquaux, Nelle
International Journal of Biostatistics, ISSN 1557-4679, 06/2018
The development of new ways to probe samples for the three-dimensional (3D) structure of DNA paves the way for in depth and systematic analyses of the genome... 
3D structure | inference | Hi-C | P. falciparum
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13. Full Text Chromatin Domains: The Unit of Chromosome Organization
by Dixon, Jesse R and Gorkin, David U and Ren, Bing
Molecular Cell, ISSN 1097-2765, 06/2016, Volume 62, Issue 5, pp. 668 - 680
How eukaryotic chromosomes fold inside the nucleus is an age-old question that remains unanswered today. Early biochemical and microscopic studies revealed the... 
SINGLE-CELL | HI-C REVEALS | 3D GENOME | BIOCHEMISTRY & MOLECULAR BIOLOGY | GENE-EXPRESSION | STABLE UNITS | CTCF | TOPOLOGICAL DOMAINS | REPLICON CLUSTERS | REGULATORY LANDSCAPE | PRINCIPLES | CELL BIOLOGY | Chromatin - metabolism | Interphase | Humans | Gene Expression Regulation | Chromatin Assembly and Disassembly | Structure-Activity Relationship | Animals | Cell Nucleus - metabolism | Chromosomes - genetics | Chromosomes - metabolism | Protein Conformation | Chromosomes - chemistry | Genome | Genomics - methods | Nucleic Acid Conformation | Chromatin - genetics | Chromatin - chemistry | Medical colleges | Chromatin | Analysis | Genomics | Genetic research | Chromosomes | Cells
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14. Full Text Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells
by Kind, Jop and Pagie, Ludo and de Vries, Sandra S and Nahidiazar, Leila and Dey, Siddharth S and Bienko, Magda and Zhan, Ye and Lajoie, Bryan and de Graaf, Carolyn A and Amendola, Mario and Fudenberg, Geoffrey and Imakaev, Maxim and Mirny, Leonid A and Jalink, Kees and Dekker, Job and van Oudenaarden, Alexander and van Steensel, Bas
Cell, ISSN 0092-8674, 09/2015, Volume 163, Issue 1, pp. 134 - 147
Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large lamina-associated domains (LADs). We report a method to map NL... 
CHROMATIN | HI-C | BIOCHEMISTRY & MOLECULAR BIOLOGY | SEQUENCE | COMPARTMENTALIZATION | ARCHITECTURE | DYNAMICS | CHROMOSOMES | CONFORMATION | DOMAIN ORGANIZATION | PRINCIPLES | CELL BIOLOGY | Chromatin - metabolism | Genome-Wide Association Study | Nuclear Lamina - metabolism | Interphase | Single-Cell Analysis - methods | Humans | Cell Line, Tumor | Chromosomes - metabolism | In Situ Hybridization, Fluorescence | Chromosomes - chemistry | Chromatin - chemistry | Genetic research | Chromosomes | Analysis | Genomics | Cells | Chromatin | Genes | Genomes
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15. Full Text Transferable model for chromosome architecture
by Michele Di Pierro and Bin Zhang and Erez Lieberman Aiden and Peter G. Wolynes and José N. Onuchic
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 10/2016, Volume 113, Issue 43, pp. 12168 - 12173
In vivo, the human genome folds into a characteristic ensemble of 3D structures. The mechanism driving the folding process remains unknown. We report a... 
Molecular dynamics | Genome architecture | Human genome | Hi-C | Maximum entropy | CHROMATIN | MULTIDISCIPLINARY SCIENCES | maximum entropy | molecular dynamics | genome architecture | PRINCIPLES | DROSOPHILA | ORGANIZATION | ELEMENTS | CONFORMATION CAPTURE | human genome | DYNAMICS | DOMAINS | Structure | Chromosomes | Models | Biological Sciences | Physical Sciences
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16. Full Text The 3D Genome as Moderator of Chromosomal Communication
by Dekker, Job and Mirny, Leonid
Cell, ISSN 0092-8674, 03/2016, Volume 164, Issue 6, pp. 1110 - 1121
Proper expression of genes requires communication with their regulatory elements that can be located elsewhere along the chromosome. The physics of chromatin... 
enhancer | cohesin | condensin | gene regulation | Hi-C | domains | promoter | polymers | CTCF | biophysics | gene expression | simulations | X-INACTIVATION | ASSOCIATING DOMAINS | REGULATORY DOMAINS | INTERPHASE CHROMOSOMES | DROSOPHILA GENOME | DOSAGE COMPENSATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | GENE-EXPRESSION | CHROMATIN INTERACTIONS | SPATIAL-ORGANIZATION | TOPOLOGICAL DOMAINS | CELL BIOLOGY | DNA-Binding Proteins - metabolism | Multiprotein Complexes - metabolism | Animals | Mitosis | CCCTC-Binding Factor | Humans | Repressor Proteins | Adenosine Triphosphatases - metabolism | Chromosomes - metabolism | Female | Genome | X Chromosome Inactivation | Genetic research | Chromatin | Chromosomes | Genomics | Biomedical engineering | Genes | Genomes | Gene expression
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17. Full Text Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters
by Javierre, Biola M and Burren, Oliver S and Wilder, Steven P and Kreuzhuber, Roman and Hill, Steven M and Sewitz, Sven and Cairns, Jonathan and Wingett, Steven W and Várnai, Csilla and Thiecke, Michiel J and Burden, Frances and Farrow, Samantha and Cutler, Antony J and Rehnström, Karola and Downes, Kate and Grassi, Luigi and Kostadima, Myrto and Freire-Pritchett, Paula and Wang, Fan and Martens, Joost H and Kim, Bowon and Sharifi, Nilofar and Janssen-Megens, Eva M and Yaspo, Marie-Laure and Linser, Matthias and Kovacsovics, Alexander and Clarke, Laura and Richardson, David and Datta, Avik and Flicek, Paul and Stunnenberg, Hendrik G and Todd, John A and Zerbino, Daniel R and Stegle, Oliver and Ouwehand, Willem H and Frontini, Mattia and Wallace, Chris and Spivakov, Mikhail and Fraser, Peter and BLUEPRINT Consortium
Cell, ISSN 0092-8674, 11/2016, Volume 167, Issue 5, pp. 1369 - 1384.e19
Long-range interactions between regulatory elements and gene promoters play key roles in transcriptional regulation. The vast majority of interactions are... 
promoter capture Hi-C | non-coding genetic variation | disease gene prioritization | gene regulation | chromosome conformation | RHEUMATOID-ARTHRITIS | RISK LOCI | R/BIOCONDUCTOR PACKAGE | INTEGRATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | TRANSCRIPTION | R PACKAGE | WIDE ASSOCIATION | INTERACTIONS REVEALS | EXPRESSION ANALYSES | RANGE | CELL BIOLOGY | Promoter Regions, Genetic | Chromatin | Genetic Predisposition to Disease | Genome-Wide Association Study | Epigenomics | Disease - genetics | Cell Separation | Humans | Cell Lineage | Blood Cells - cytology | Enhancer Elements, Genetic | Hematopoiesis | Polymorphism, Single Nucleotide | Quantitative Trait Loci | Genes | Genomics | Genetic aspects | Medical research | Medical genetics | Medicine, Experimental | Resource
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