Iterative correction of Hi-C data reveals hallmarks of chromosome organization

Imakaev, Maxim, Fudenberg, Geoffrey, McCord, Rachel Patton, Naumova, Natalia, Goloborodko, Anton, Lajoie, Bryan R, Dekker, Job, Mirny, Leonid A·2012·Nature Methods
DOI 10.1038/nmeth.2148

Cited by (1,000)

Items 901–1,000 of 1,000

  1. Chromosome Conformation Capture Followed by Genome-Wide Sequencing (Hi-C) in Drosophila Embryos
    Francesco Cardamone, Yinxiu Zhan, Nicola Iovino, Fides Lea Zenk · 2023 · Methods in molecular biology
  2. An upgraded method of high-throughput chromosome conformation capture (Hi-C 3.0) in cotton (Gossypium spp.)
    Jin Han, Siyuan Wang, Hongyu Wu, Ting Zhao, Xueying Guan, Lei Fang · 2023 · Frontiers in Plant Science
  3. A continuum of zinc finger transcription factor retention on native chromatin underlies dynamic genome organization
    Siling Hu, Yangying Liu, Qifan Zhang, Juan Bai, Chenhuan Xu · 2024 · Molecular Systems Biology
  4. Development and evolution of Drosophila chromatin landscape in a 3D genome context
    Mujahid Ali, Lubna Younas, Jing Liu, Huangyi He, Xinpei Zhang, Qi Zhou · 2024 · Nature Communications
  5. Enhancer jungles establish robust tissue-specific regulatory control in the human genome
    Shan Li, Ivan Ovcharenko · 2019 · Genomics
  6. Freeze substitution Hi-C, a convenient and cost-effective method for capturing the natural 3D chromatin conformation from frozen samples
    Wu Zheng, Zhaoen Yang, Xiaoyang Ge, Yijia Feng, Ye Wang, Chengwei Liu, Yanan Luan, Kun Cai, Serhii Vakal, Feng You et al. · 2020 · Journal of genetics and genomics/Journal of Genetics and Genomics
  7. Reference panel-guided super-resolution inference of Hi-C data
    Yanlin Zhang, Mathieu Blanchette · 2023 · Bioinformatics
  8. Nucleosome spacing controls chromatin spatial structure and accessibility
    Tilo Zülske, Aymen Attou, Laurens Groß, David Hörl, Hartmann Harz, Gero Wedemann · 2024 · Biophysical Journal
  9. Reference genome provide insights into sex determination of silver aworana (Osteoglossum bicirrhosum)
    Yi Liu, Chao Bian, Ka-Yan Ma, Ye-Xin Yang, Yuan-Yuan Wang, Chao Liu, Guochang Ouyang, Meng Xu, Jin-Hui Sun, C. Shao et al. · 2025 · BMC Biology
  10. A mechanistic basis for genetic assimilation in natural fly populations
    Gonzalo Sabarís, Bernd Schuettengruber, Giorgio Lucio Papadopoulos, Marta Coronado‐Zamora, Maximilian H. Fitz-James, Josefa González, Giacomo Cavalli · 2025 · Proceedings of the National Academy of Sciences
  11. Measuring the three-dimensional structural properties of topologically associating domains
    Tong Liu, Zheng Wang · 2018 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
  12. Distinguishing cell phenotype using cell epigenotype
    Thomas P. Wytock, Adilson E. Motter · 2020 · Science Advances
  13. The corrected gene proximity map for analyzing the 3D genome organization using Hi-C data
    Cheng Ye, Alberto Paccanaro, Mark Gerstein, Koon‐Kiu Yan · 2020 · BMC Bioinformatics
  14. IGAP-integrative genome analysis pipeline reveals new gene regulatory model associated with nonspecific TF-DNA binding affinity
    Alireza Sahaf Naeini, Amna Farooq, Magnar Bjørås, Junbai Wang · 2020 · Computational and Structural Biotechnology Journal
  15. Integrated Analysis of Hi-C and RNA-Seq Reveals the Molecular Mechanism of Autopolyploid Growth Advantages in Pak Choi (Brassica rapa ssp. chinensis)
    Huiyuan Wu, Xiaoming Song, Shanwu Lyu, Yiming Ren, Tongkun Liu, Xilin Hou, Ying Li, Changwei Zhang · 2022 · Frontiers in Plant Science
  16. PfSET2 Is Involved in Genome Organization of Var Gene Family in Plasmodium falciparum
    Xuan Duc Cao, Yuhao Wen, Ying Li, Xuying Ma, Qingqing Jing, Lubin Jiang, Gang Wei · 2023 · Microbiology Spectrum
  17. Conserved noncoding sequences correlate with distant gene contacts in Arabidopsis and Brassica
    Lei Zhang, Jian Wu, Jianli Liang, Runmao Lin, Chao Sun, Qirui Dai, Lupeng Zhang, Huiling Guo, Ranze Zhao, Xiaowu Wang · 2023 · Journal of Integrative Plant Biology
  18. Sequence-based multiscale modeling for high-throughput chromosome conformation capture (Hi-C) data analysis
    Kelin Xia · 2018 · PLoS ONE
  19. Comprehensive in virio structure probing analysis of the influenza A virus identifies a functional RNA structure involved in replication and segment interactions
    Naoki Takizawa, Koichi Higashi, Risa Karakida Kawaguchi, Yasuhiro Gotoh, Yutaka Suzuki, Tetsuya Hayashi, Ken Kurokawa · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  20. Metabolic resilience is encoded in genome plasticity
    Leandro Z. Agudelo, Rémy Tuyéras, Claudia Llinares, Álvaro Morcuende, Yongjin Park, Na Sun, Suvi Linna-Kuosmanen, Naeimeh Atabaki‐Pasdar, Li‐Lun Ho, Kyriaki Galani et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  21. In vivo temporal resolution of acute promyelocytic leukemia progression reveals a role of Klf4 in suppressing early leukemic transformation
    Glòria Mas Martín, Fabio Santoro, Enrique Blanco, Gianni Paolo Gamarra Figueroa, François Le Dily, Gianmaria Frigè, Enrique Vidal, Francesca Mugianesi, Cecilia Ballaré, Arantxa Gutiérrez et al. · 2022 · Genes & Development
  22. Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen
    David Eduardo Torres, H. Martin Kramer, Vittorio Tracanna, Gabriel L. Fiorin, David E. Cook, Michael F. Seidl, Bart P. H. J. Thomma · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  23. Humanized nucleosomes reshape replication initiation and rDNA/nucleolar integrity in yeast
    Luciana Lazar‐Stefanita, Max A. B. Haase, Jef D. Boeke · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  24. HIRA-dependent provision of histone H3.3 in active chromatin ensures genome compartmentalisation
    T. Karagyozova, A. Gatto, A. Forest, J. Quivy, M. Marti-Renom, L. Mirny, G. Almouzni · 2024 · bioRxiv
  25. Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells
    Nicholas M. Adams, Aleksandra A. Galitsyna, Ioanna Tiniakou, Eduardo Esteva, Colleen M. Lau, Jojo Reyes, Nezar A. Abdennur, Alexey Shkolikov, George S. Yap, Alireza Khodadadi‐Jamayran et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  26. Cohesin guides homology search during DNA repair via loops and sister chromatid linkages
    Federico Teloni, Zsuzsanna Takács, Michael Mitter, Christoph C. H. Langer, Inès Prlesi, Thomas L. Steinacker, Vincent P. Reuter, Dmitry Evgenevich Mylarshchikov, Daniel W. Gerlich · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  27. Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
    Marlies E. Oomen, A. Nicole Fox, Inma González, Amandine Molliex, Thaleia Papadopoulou, Pablo Navarro, Job Dekker · 2025 · Genome Research
  28. Regulation of pericentromeric DNA loop size via Scc2-cohesin interaction
    Sao Anh Nguyen, Toyonori Sakata, Katsuhiko Shirahige, Takashi Sutani · 2025 · iScience
  29. Genetically regulated eRNA expression predicts chromatin contact frequency and reveals genetic mechanisms at GWAS loci
    Michael J. Betti, Phillip Lin, Melinda C. Aldrich, Eric R. Gamazon · 2025 · Nature Communications
  30. The genomic architecture of introgression during Rhododendron speciation
    Han‐Tao Qin, Alex D. Twyford, Wei Hao Zheng, RICHARD IAN MILNE, Li‐Jun Yan, Zhi‐Qiong Mo, Ming‐Shu Zhu, Hans‐Wilhelm Nützmann, De-Zhu Li, Hongtao Li et al. · 2025 · New Phytologist
  31. Boosting the detection of enhancer-promoter loops via normalization methods for chromatin interaction data
    Xiaotao Wang, Detong Shi, Feiyang Xue, Yunxia Liu, Hongbo Yang, Ling-Han Jiang · 2026 · Nature Communications
  32. Chromatin-mediated anticipatory control of type I interferon production in plasmacytoid dendritic cells
    Nicholas M. Adams, Aleksandra A. Galitsyna, Ioanna Tiniakou, Eduardo Esteva, Ai C. Ra, Simon Ullrich, Stephen T. Yeung, Yanjun Tan, Joseph N. Pucella, Igor Dolgalev et al. · 2026 · Immunity
  33. Identifying topologically associating domains using differential kernels
    Luka Maisuradze, Megan C. King, Ivan Vladimirovich Surovtsev, S. G. J. Mochrie, Mark D. Shattuck, Corey S. O’Hern · 2024 · PLoS Computational Biology
  34. Distinct structural and functional heterochromatin partitioning of lamin B1 and lamin B2 revealed using genome-wide nicking enzyme epitope targeted DNA sequencing
    Sagnik Sen, Pierre‐Olivier Estève, Raman Karthikeyan, Julie Beaulieu, Hang Gyeong Chin, George R. Feehery, Udayakumar S. Vishnu, S.-y. Xu, James C. Samuelson, Sriharsa Pradhan · 2024 · Nucleic Acids Research
  35. The synergy between compartmentalization and motorization in chromatin architecture
    Ronaldo Junio de Oliveira, Antonio Bento de Oliveira Junior, Vinícius G. Contessoto, José N. Onuchic · 2025 · The Journal of Chemical Physics
  36. Single-stranded DNA binding proteins are essential components of the architectural LDB1 protein complex
    Xiaokang Wang, Nicholas G. Aboreden, Ying Cai, Jessica C. Lam, Kate A. Henderson, Jiaqi Xiang, Belinda M. Giardine, Ross C. Hardison, Cheryl A. Keller, Lalitha Nagarajan et al. · 2025 · Molecular Cell
  37. Flexibility and rigidity index for chromosome packing, flexibility and dynamics analysis
    Jiajie Peng, Jinjin Yang, D. Vijay Anand, Xuequn Shang, Kelin Xia · 2021 · Frontiers of Computer Science
  38. Improved genome assembly of Chinese sucker (Myxocyprinus asiaticus) provides insights into the identification and characterization of pharyngeal teeth related maker genes in Cyprinoidei
    Xin Liu, Honghui Zeng, Cheng Hai Wang, Bo Jing, Xiaoni Gan, Chengchi Fang, Shunping He · 2022 · Water Biology and Security
  39. A constitutive heterochromatic region shapes genome organization and impacts gene expression in Neurospora crassa
    Andrew T. Reckard, Abhishek Pandeya, Jacob M. Voris, Carlos G. Gonzalez Cruz, Oluwatosin Oluwadare, Andrew D. Klocko · 2024 · BMC Genomics
  40. Capturing genomic relationships that matter
    Cameron S. Osborne, Borbála Mifsud · 2017 · Chromosome Research
  41. Computational Analysis of Hi-C Data
    Mattia Forcato, Silvio Bicciato · 2020 · Methods in molecular biology
  42. 3D reconstruction of genomic regions from sparse interaction data
    Julen Mendieta-Esteban, Marco Di Stefano, David Castillo, Irene Farabella, Marc A. Martı́-Renom · 2021 · NAR Genomics and Bioinformatics
  43. Methods to Assess the Reproducibility and Similarity of Hi-C Data
    Tao Yang, Xi He, Lin An, Qunhua Li · 2021 · Methods in molecular biology
  44. Chromatin accessibility shapes meiotic recombination in mouse primordial germ cells through assisting double-strand breaks and loop formation
    Guoqing Liu, Yu Sun, Lumeng Jia, Ruifeng Li, Yongchun Zuo · 2022 · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
  45. Quantifying the large-scale chromosome structural dynamics during the mitosis-to-G1 phase transition of cell cycle
    Xiakun Chu, Jin Wang · 2023 · Open Biology
  46. A systematic analyses of different bioinformatics pipelines for genomic data and its impact on deep learning models for chromatin loop prediction
    Anup Kumar Halder, Abhishek Agarwal, Karolina Jodkowska, Dariusz Plewczyński · 2024 · Briefings in Functional Genomics
  47. iced: fast and memory efficient normalization of contact maps
    Nelle Varoquaux, Nicolas Servant · 2019 · The Journal of Open Source Software
  48. ParticleChromo3D: a Particle Swarm Optimization algorithm for chromosome 3D structure prediction from Hi-C data
    David Vadnais, Michael Middleton, Oluwatosin Oluwadare · 2022 · BioData Mining
  49. Utilizing networks for differential analysis of chromatin interactions
    Lu Liu, Jianhua Ruan · 2017 · Journal of Bioinformatics and Computational Biology
  50. Computer methods of analysis of chromosome contacts in the cell nucleus based on sequencing technology data
    Yuriy Lvovich Orlov, O. Thierry, Anton G. Bogomolov, A. V. Tsukanov, E.V. Kulakova, Галиева Эльвира Расимовна, Брагин Анатолий Олегович, Guoliang Li · 2017 · Biomeditsinskaya Khimiya
  51. Characterization of chromosome organization in the differentiation of acute myeloid leukemia cells by all-trans retinoic acid
    Yanping Hu, Hongchao Zhao, Yixun Zhao, Jiawen Zheng, Yongjun Guo, Jie Ma · 2020 · Life Sciences
  52. Mixed secondary chromatin structure revealed by modeling radiation-induced DNA fragment length distribution
    Wenzong Ma, Chenyang Gu, Lin Ma, Caoqi Fan, Chao Zhang, Yujie Sun, Cheng Li, Gen Yang · 2020 · Science China Life Sciences
  53. Randomized Ligation Control for Chromosome Conformation Capture
    Jon-Matthew Belton, Job Dekker · 2015 · Cold Spring Harbor Protocols
  54. Histone H3 Lysine 4 methyltransferases MLL3 and MLL4 Modulate Long-range Chromatin Interactions at Enhancers
    Jian Yan, Shi-An A. Chen, Andrea Local, Tristin Liu, Yunjiang Qiu, Ah Young Lee, Inkyung Jung, Sebastian Preißl, Chloe M. Rivera, Chaochen Wang et al. · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  55. Chromatin-lamin B1 interaction promotes genomic compartmentalization and constrains chromatin dynamics
    Lei Chang, Mengfan Li, Shipeng Shao, Boxin Xue, Yingping Hou, Yiwen Zhang, Ruifeng Li, Cheng Li, Yujie Sun · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  56. Identifying regulatory and spatial genomic architectural elements using cell type independent machine and deep learning models
    Laura D. Martens, Oisín Faust, Liviu Pirvan, Dóra Bihary, Shamith Samarajiwa · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  57. Cis -regulatory Element Hijacking by Structural Variants Overshadows Higher-Order Topological Changes in Prostate Cancer
    James R. Hawley, Stanley Zhou, Christopher Arlidge, Giacomo Grillo, Ken Kron, Rupert Hugh-White, Theodorus van der Kwast, Michael E. Fraser, Paul C. Boutros, Robert Glen Bristow et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  58. NSD2 E1099K drives relapse in pediatric acute lymphoblastic leukemia by disrupting 3D chromatin organization
    Sonali Narang, Nikki Ann Evensen, Jason Saliba, Joanna Pierro, Mignon L. Loh, Patrick Andrew Brown, Heather L. Mulder, Ying Shao, John B. Easton, Xiaotu Ma et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  59. 3D genomic features across >50 diverse cell types reveal insights into the genomic architecture of childhood obesity
    Bao Khanh Trang, Matthew C. Pahl, James A. Pippin, Chun Su, Sheridan H. Littleton, Prabhat Kumar Sharma, Nikhil Nitin Kulkarni, Louis R. Ghanem, Natalie A. Terry, Joan M. O’Brien et al. · 2024 · eLife
  60. Genome organization by SATB1 binding to base-unpairing regions (BURs) provides a scaffold for SATB1-regulated gene expression
    Yoshinori Kohwi, Xianrong Wong, Mari Grange, Tom Sexton, Hunter W. Richards, Yohko Kitagawa, Shimon Sakaguchi, Ya‐Chen Liang, Cheng‐Ming Chuong, Vladimir A. Botchkarev et al. · 2025 · eLife
  61. RobusTAD: reference panel based annotation of nested topologically associating domains
    Yanlin Zhang, Rola Dali, Mathieu Blanchette · 2025 · Genome biology
  62. Integrated analysis of differential intra-chromosomal community interactions: A study of breast cancer
    Zhihao Yao, Kun Fang, Gege Liu, Magnar Bjørås, Victor X. Jin, Junbai Wang · 2025 · Artificial Intelligence in Medicine
  63. Histone Acetylation Differentially Modulates CTCF-CTCF Loops and Intra-TAD Interactions
    Rebecca G. Smith, Yu Fu, Kathleen L Schiela, Madison Dautle, Ryan A. Williams, Hannah M. Wilson, Chloe Azadegan, Johnathan R. Whetstine, Job Dekker, Yu Liu · 2026 · Nature Communications
  64. 3D chromatin-based variant-to-gene maps across 57 human cell types reveal the cellular and genetic architecture of autoimmune disease susceptibility
    Bao Khanh Trang, Prabhat Kumar Sharma, Laura E. Cook, Zachary Mount, Rajan M. Thomas, Nikhil Nitin Kulkarni, Emylette Cruz Cabrera, Suzanna Rachimi, Matthew C. Pahl, James A. Pippin et al. · 2025 · Genome biology
  65. Dynamic reorganization of three-dimensional genome architecture during Populus diversification
    Tingting Shi, Tao Long, Jiali Wu, Xinying Zeng, Yiman Zhu, Changfu Jia, Xinyi Zhou, Jiajun Feng, Zeng Wang, Xuming Dan et al. · 2026 · Nature Ecology & Evolution
  66. Evaluation of the gene fusion landscape in early onset sporadic rectal cancer reveals association with chromatin architecture and genome stability
    Asmita Gupta, Sumedha Avadhanula, Murali Dharan Bashyam · 2024 · Oncogene
  67. Probing long-range interactions by extracting free energies from genome-wide chromosome conformation capture data
    Saeed Saberi, Pau Farré, Olivier Cuvier, Eldon G. Emberly · 2015 · BMC Bioinformatics
  68. Integration of Multiple Resolution Data in 3D Chromatin Reconstruction Using ChromStruct
    Claudia Caudai, Monica Zoppè, Anna Tonazzini, Ivan Merelli A, Emanuele Salerno · 2021 · Biology
  69. HiConfidence: a novel approach uncovering the biological signal in Hi-C data affected by technical biases
    Victoria A Kobets, Sergey V. Ulianov, Aleksandra A. Galitsyna, Semen A. Doronin, Elena A. Mikhaleva, Mikhail Sergeevich Gelfand, Yuri Y. Shevelyov, Sergey V. Razin, Ekaterina E. Khrameeva · 2023 · Briefings in Bioinformatics
  70. Delta.EPI: a probabilistic voting-based enhancer–promoter interaction prediction platform
    Yuyang Zhang, Haoyu Wang, Jing Liu, Junlin Li, Qing Zhang, Bixia Tang, Zhihua Zhang · 2023 · Journal of genetics and genomics/Journal of Genetics and Genomics
  71. CscoreTool-M infers 3D sub-compartment probabilities within cell population
    Xiaobin Zheng, Joseph R. Tran, Yixian Zheng · 2023 · Bioinformatics
  72. Imaging analysis of six human histone H1 variants reveals universal enrichment of H1.2, H1.3, and H1.5 at the nuclear periphery and nucleolar H1X presence
    Mónica Salinas‐Pena, Elena Rebollo, Albert Jordan · 2023 · eLife
  73. MMCT-Loop: a mix model-based pipeline for calling targeted 3D chromatin loops
    Li Tang, Jiaqi Liao, M. Hill, Jiaxin Hu, Yi-Chao Zhao, P. Ellinor, Min Li · 2024 · Nucleic Acids Research
  74. 3D genomic alterations during development of skeletal muscle in chicken
    Zhongxian Xu, Tao Wang, Wei Zhu, Maosen Yang, Dong Leng, Ziyu Li, Jiaman Zhang, Pengliang Liu, Zhoulin Wu, Mengnan He et al. · 2024 · Journal of Integrative Agriculture
  75. Combined Study of Gene Expression and Chromosome Three-Dimensional Structure in Escherichia coli During Growth Process
    Hao Zhang, Changjun Shao, Jian Wang, Yanan Chu, Jingfa Xiao, Kang Yu, Zhewen Zhang · 2024 · Current Microbiology
  76. The effect of trisomic chromosomes on spatial genome organization and global transcription in embryonic stem cells
    Mengfan Li, Junsheng Yang, Rong Xiao, Yunjie Liu, Jiaqi Hu, Tingting Li, Pengze Wu, Zhang Mei-li, Yue Huang, Yujie Sun et al. · 2024 · Cell Proliferation
  77. Deciphering the dynamical chromosome structural reorganizations in human neural development
    Xiakun Chu, Cibo Feng, Jin Wang · 2024 · Physical Review Research
  78. Footprint-C reveals transcription factor modes in local clusters and long-range chromatin interactions
    Xiaokun Liu, Hanhan Wei, Qifan Zhang, Na Zhang, Qingqing Wu, Chenhuan Xu · 2024 · Nature Communications
  79. Spatiotemporal 3D chromatin organization across multiple brain regions during human fetal development
    Yaoyu Sun, Min Li, Chao Ning, Lei Gao, Zhenbo Liu, Suijuan Zhong, Junjie Lv, Yuwen Ke, Xinxin Wang, Qiang Ma et al. · 2025 · Cell Discovery
  80. GDNorm: An Improved Poisson Regression Model for Reducing Biases in Hi-C Data
    Ei-Wen Yang, Tao Jiang · 2014 · Lecture notes in computer science
  81. LSCC SNP variant regulates SOX2 modulation of VDAC3
    Jacqueline Chyr, Dongmin Guo, Xiaobo Zhou · 2018 · Oncotarget
  82. Cumulative contact frequency of a chromatin region is an intrinsic property linked to its function
    Margarita D. Samborskaia, Aleksandra A. Galitsyna, Ilya A Pletenev, Anna B. Trofimova, Andrey A. Mironov, Mikhail Sergeevich Gelfand, Ekaterina E. Khrameeva · 2020 · PeerJ
  83. Analysis, Modeling, and Visualization of Chromosome Conformation Capture Experiments
    Marco Di Stefano, David Castillo, François Serra, Irene Farabella, Mike N. Goodstadt, Marc A. Martı́-Renom · 2020 · Methods in molecular biology
  84. Symmetric Iterative Proportional Fitting
    Sven Kurras · 2015 · International Conference on Artificial Intelligence and Statistics
  85. Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C
    Antonia Hauth, Rafael Galupa, Nicolas Servant, Laura Villacorta, Kai Hauschulz, Joke Gerarda van Bemmel, Agnese Loda, Édith Heard · 2022 · Journal of Visualized Experiments
  86. Benchmark of software tools for prokaryotic chromosomal interaction domain identification
    Mikhail D. Magnitov, Veronika Kuznetsova, Sergey V. Ulianov, Sergey V. Razin, Alexander Tyakht · 2020 · Bioinformatics
  87. Capture Hi-C: Characterization of chromatin contacts
    Ryan R. Davis, Mel Campbell, Yoshihiro Izumiya, Clifford G. Tepper · 2020 · Elsevier eBooks
  88. GAMtools: an automated pipeline for analysis of Genome Architecture Mapping data
    Robert A. Beagrie, Markus Schueler · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  89. Effective normalization for copy number variation in Hi-C data
    Nicolas Servant, Nelle Varoquaux, Édith Heard, Jean‐Philippe Vert, Emmanuel Barillot · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  90. Long-range chromatin interactions on the inactive X and at Hox clusters are regulated by the non-canonical SMC protein Smchd1
    Natasha Jansz, Andrew Keniry, Marie Trussart, Heidi Bildsoe, Tamara J Beck, Ian D. Tonks, Arne W. Mould, Peter F. Hickey, Kelsey A. Breslin, Megan Iminitoff et al. · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  91. Modeling of DNA methylation in cis reveals principles of chromatin folding in vivo in the absence of crosslinking and ligation
    Josef Redolfi, Yinxiu Zhan, Christian Valdes, Mariya Kryzhanovska, Isabel Misteli Guerreiro, Vytautas Iešmantavičius, Guido Tiana, Tim Pollex, Jop Kind, Sébastien A. Smallwood et al. · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  92. Biased visibility in HiC datasets marks dynamically regulated condensed and decondensed chromatin states genome-wide
    Keerthivasan Raanin Chandradoss, Prashanth Kumar Guthikonda, Srinivas Kethavath, Monika Dass, Harpreet Singh, Rakhee Nayak, Sreenivasulu Kurukuti, Kuljeet Singh Sandhu · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  93. Coolpup.py – a versatile tool to perform pile-up analysis of Hi-C data
    Ilya M. Flyamer, Robert Scott Illingworth, Wendy A. Bickmore · 2019 · Figshare
  94. Dynamic simulations of transcriptional control during cell reprogramming reveal spatial chromatin caging
    Marco Di Stefano, Ralph Stadhouders, Irene Farabella, David Castillo, François Serra, Thomas Graf, Marc A. Martı́-Renom · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  95. Robust Hi-C chromatin loop maps in human neurogenesis and brain tissues at high-resolution
    Leina Lu, Xiaoxiao Liu, Wei‐Kai Huang, Paola Giusti‐Rodríguez, Jian Cui, Shanshan Zhang, Wanying Xu, Zhexing Wen, Shufeng Ma, Jonathan D. Rosen et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  96. A CRISPR Screen Identifies Myc-associated Zinc Finger Protein (MAZ) as an Insulator Functioning at CTCF boundaries in Hox Clusters
    Havva Ortabozkoyun, Pin‐Yao Huang, Hyunwoo Cho, Varun K. Narendra, Gary LeRoy, Jane A. Skok, Aristotelis Tsirigos, Esteban O. Mazzoni, Danny Reinberg · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  97. The role of insulators and transcription in 3D chromatin organisation of flies
    Keerthi T. Chathoth, Liudmila A Mikheeva, Gilles Crevel, Jareth C. Wolfe, Ioni Hunter, Saskia Beckett-Doyle, Sue Cotterill, Hongsheng Dai, Andrew Harrison, Nicolae Radu Zabet · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  98. Genome organization by SATB1 binding to base-unpairing regions (BURs) provides a scaffold for SATB1-regulated gene expression
    Yoshinori Kohwi, Xianrong Wong, Mari Grange, Tom Sexton, Hunter W. Richards, Yohko Kitagawa, Shimon Sakaguchi, Ya‐Chen Liang, Cheng‐Ming Chuong, Vladimir A. Botchkarev et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  99. Mitotic chromosomes harbor cell type and species-specific structural features within a universal looping architecture
    Marlies E. Oomen, A. Nicole Fox, Inma González, Amandine Molliex, Thaleia Papadopoulou, Pablo Navarro, Job Dekker · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  100. Reprogramming genetic circuits using space
    Lorea Alejaldre, Jesús Miró-Bueno, Ángeles Hueso‐Gil, Lewis Grozinger, Hüseyin Taş, Sina Geißler, Ángel Goñi‐Moreno · 2024 · bioRxiv (Cold Spring Harbor Laboratory)