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
Cited by (999)
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- Current trend of annotating single nucleotide variation in humans – A case study on SNVrapMulin Jun Li, Junwen Wang · 2014 · Methods
- A modified protocol of Capture-C allows affordable and flexible high-resolution promoter interactome analysisArkadiy K. Golov, Dmitrii A. Abashkin, Nikolay V. Kondratyev, Sergey V. Razin, Alexey A. Gavrilov, Вера Евгеньевна Голимбет · 2020 · Scientific Reports
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- Exploring the mechanisms of genome-wide long-range interactions: interpreting chromosome organizationJingjing Wang, Xianwen Meng, Hongjun Chen, Chunhui Yuan, Xue Li, Yincong Zhou, Ming Chen · 2016 · Briefings in Functional Genomics
- Modelling genome-wide topological associating domains in mouse embryonic stem cellsYinxiu Zhan, Luca Giorgetti, Guido Tiana · 2017 · Chromosome Research
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- Super-enhancer interactomes from single cells link clustering and transcriptionDerek J. Le, Antonina Hafner, Sadhana Gaddam, Ke Wang, Alistair Nicol Boettiger · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
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- Computational methods for analyzing genome-wide chromosome conformation capture data.C. Nicoletti, M. Forcato, S. Bicciato · 2018 · Current Opinion in Biotechnology
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- Distance-based assessment of the localization of functional annotations in 3D genome reconstructionsDaniel Capurso, Mark Robert Segal · 2014 · BMC Genomics
- Tracking the evolution of 3D gene organization demonstrates its connection to phenotypic divergenceAlon Diament, Tamir Tuller · 2017 · Nucleic Acids Research
- A Polymer Physics View on Universal and Sequence-Specific Aspects of Chromosome FoldingDaniel Jost, Angelo Rosa, Cédric Vaillant, Ralf Everaers · 2017 · Elsevier eBooks
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- De novo formation of cis-regulatory contacts in the absence of NIPBL-driven chromatin loop extrusionNicholas G. Aboreden, Han Zhao, Jin Yang, Fengnian Shan, Fuhai Liu, Anders S. Hansen, Haoyue Zhang, Gerd A. Blobel · 2026 · Nature Genetics
- PDS5 proteins control genome architecture by limiting the lifetime of cohesin-NIPBL complexes.G. Wutz, I. Davidson, E. Banigan, Roman R. Stocsits, Ryotaro Kawasumi, Wen Tang, Kota Nagasaka, Lorenzo Costantino, Ralf-Peter Jansen, Kouji Hirota et al. · 2026 · Molecules and Cells
- Chromosome-scale assembly of the Sparassis latifolia genome obtained using long-read and Hi-C sequencingChi Yang, Lu Ma, Donglai Xiao, Xiaoyu Liu, Xiaoling Jiang, Zhenghe Ying, Yanquan Lin · 2021 · G3 Genes Genomes Genetics
- Integrative analysis of the 3D genome structure reveals that CTCF maintains the properties of mouse female germline stem cellsGeng G. Tian, Xinyan Zhao, Changliang Hou, Wenhai Xie, Xiaoyong Li, Yinjuan Wang, Lijuan Wang, Hua Li, Xiaodong Zhao, Jing Li et al. · 2022 · Cellular and Molecular Life Sciences
- Remodeling of the 3D chromatin architecture in the marine microalga Nannochloropsis oceanica during lipid accumulationTongtong Yan, Kexin Wang, Kexin Feng, Xiangchen Gao, Yinghong Jin, Hongping Wu, Wenfei Zhang, Li Wei · 2023 · Biotechnology for Biofuels and Bioproducts
- Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genesOlga Mielczarek, Carolyn H. Rogers, Yinxiu Zhan, Louise S. Matheson, Michael J. T. Stubbington, Stefan Schoenfelder, Daniel J. Bolland, Biola M. Javierre, Steven Wingett, Csilla Várnai et al. · 2023 · Cell Reports
- hictk: blazing fast toolkit to work with .hic and .cool filesRoberto Rossini, Jonas Paulsen · 2024 · Bioinformatics
- Stratifying TAD boundaries pinpoints focal genomic regions of regulation, damage, and repairBijia Chen, Chao Ren, Zhangyi Ouyang, Jingxuan Xu, Kang Xu, Yaru Li, Hejiang Guo, Xuemei Bai, Mengge Tian, Xiang Xu et al. · 2024 · Briefings in Bioinformatics
- Evolutionary patterns and functional effects of 3D chromatin structures in butterflies with extensive genome rearrangementsBotong Zhou, Ping Hu, Guichun Liu, Zhou Chang, Zhiwei Dong, Zihe Li, Yuan Yin, Zunzhe Tian, Ge Han, Wen Wang et al. · 2024 · Nature Communications
- Super RNA Pol II domains enhance minor ZGA through 3D interaction to ensure the integrity of major transcriptional waves in late-ZGA mammalsJingcheng Zhang, Hengkuan Li, Linmi Li, Jie Wu, Linjie Song, Xin Liu, Zhangyuan Pan, Chuan Zhou, Wenying Li, Zixiao Liu et al. · 2025 · Cell Genomics
- A novel method for discovering local spatial clusters of genomic regions with functional relationships from DNA contact mapsXihao Sherlock Hu, Christina Huan Shi, Kevin Yuk-Lap Yip · 2016 · Bioinformatics
- BPscore: An Effective Metric for Meaningful Comparisons of Structural Chromosome SegmentationsRafał Zaborowski, Bartek Wilczyński · 2019 · Journal of Computational Biology
- Gene Regulatory Elements Extraction in Breast Cancer by Hi-C Data Using a Meta-Heuristic MethodMohammadjavad Hosseinpoor, Hamïd Parvïn, Samad Nejatian, V. Rezaie · 2019 · Russian Journal of Genetics
- ZipHiC: a novel Bayesian framework to identify enriched interactions and experimental biases in Hi-C dataItunu Godwin Osuntoki, Andrew Harrison, Hongsheng Dai, Yanchun Bao, Nicolae Radu Zabet · 2022 · Bioinformatics
- Detecting TAD-like domains from RNA-associated interactionsYuwei Zhang, Lingxi Chen, Shuai Cheng Li · 2022 · Nucleic Acids Research
- Genomic and transcriptomic-based analysis of agronomic traits in sugar beet (Beta vulgaris L.) pure line IMA1Xiaodong Li, Wenjin He, Jingping Fang, Yahui Liang, Huizhong Zhang, Duo Chen, Xingrong Wu, Ziqiang Zhang, Liang Wang, Pingan Han et al. · 2022 · Frontiers in Plant Science
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- How computer science can help in understanding the 3D genome architectureYoli Shavit, Ivan Merelli, Luciano Milanesi, Píetro Lió · 2015 · Briefings in Bioinformatics
- Dynamic chromatin accessibility modeled by Markov process of randomly-moving molecules in the 3D genomeYinan Wang, Caoqi Fan, Yuxuan Zheng, Cheng Li · 2017 · Nucleic Acids Research
- A maximum-entropy model for predicting chromatin contactsPau Farré, Eldon G. Emberly · 2018 · PLoS Computational Biology
- GrapHi-C: graph-based visualization of Hi-C datasetsKimberly MacKay, ANTHONY J. KUSALIK, Christopher H. Eskiw · 2018 · BMC Research Notes
- covNorm: An R package for coverage based normalization of Hi-C and capture Hi-C dataKyukwang Kim, Inkyung Jung · 2021 · Computational and Structural Biotechnology Journal
- Improving 3D Genome Reconstructions Using Orthologous and Functional ConstraintsAlon Diament, Tamir Tuller · 2015 · PLoS Computational Biology
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- Neuronal and glial 3D chromatin architecture illustrates cellular etiology of brain disordersBenxia Hu, Hyejung Won, Won Mah, Royce Park, Bibi S. Kassim, Keeley Spiess, Alexey Kozlenkov, Cheynna Crowley, Sirisha Pochareddy, Yun Li et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- Viral proteins activate PARIS-mediated tRNA degradation and viral tRNAs rescue infectionNathaniel Burman, Svetlana Belukhina, Florence Depardieu, Royce A. Wilkinson, Mikhail A. Skutel, Andrew Santiago‐Frangos, Ava B. Graham, Alexei Livenskyi, Anna Chechenina, Natalia Evgenevna Morozova et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Genome structure mapping with high-resolution 3D genomics and deep learningClarice KY Hong, Fan Feng, Varshini Ramanathan, Jie Liu, Anders S. Hansen · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- 4D nucleome Analysis Toolbox: analysis of Hi-C data with abnormal karyotype and time series capabilitiesLaura Seaman, Indika Rajapakse · 2017 · Bioinformatics
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- Genome-wide chromosome architecture prediction reveals biophysical principles underlying gene structureM. Chiang, C. Brackley, C. Naughton, Ryu-Suke Nozawa, Cleis Battaglia, D. Marenduzzo, N. Gilbert · 2024 · Cell Genomics
- Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2Paulina N. Smaruj, Fahad Kamulegeya, David R. Kelley, Geoffrey Fudenberg · 2025 · PLoS Computational Biology
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- Multidisciplinary perspectives on bacterial genome organization and dynamicsRemus Thei Dame, Olivier Espéli, David C. Grainger, Paul A. Wiggins · 2012 · Molecular Microbiology
- Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C)Matthew Z. DeMaere, Aaron E. Darling · 2016 · PeerJ
- GiniQC: a measure for quantifying noise in single-cell Hi-C dataConnor A. Horton, B. Alver, Peter J. Park · 2020 · Bioinformatics
- TADfit is a multivariate linear regression model for profiling hierarchical chromatin domains on replicate Hi-C dataErhu Liu, Hongqiang Lyu, Qinke Peng, Yuan Liu, Tian Wang, Jiuqiang Han · 2022 · Communications Biology
- ChromStruct 4: A Python Code to Estimate the Chromatin Structure from Hi-C DataClaudia Caudai, Emanuele Salerno, Monica Zoppè, Ivan Merelli A, Anna Tonazzini · 2018 · IEEE Transactions on Computational Biology and Bioinformatics
- Detection of Point Mutations and Chromosomal Translocations Based on Massive Parallel Sequencing of Enriched 3C LibrariesEvgeniy Mozheiko, Veniamin Fishman · 2019 · Russian Journal of Genetics
- Persistent spectral simplicial complex-based machine learning for chromosomal structural analysis in cellular differentiationWeikang Gong, JunJie Wee, Min-Chun Wu, Xiaohan Sun, Chunhua Li, Kelin Xia · 2022 · Briefings in Bioinformatics
- Karyotype engineering reveals spatio-temporal control of replication firing and gene contactsLuciana Lazar‐Stefanita, Jingchuan Luo, Rémi Montagne, Agnès Thierry, Xiaoji Sun, Guillaume Mercy, Julien Mozziconacci, Romain Koszul, Jef D. Boeke · 2022 · Cell Genomics
- Three‐dimensional analysis reveals altered chromatin interaction by enhancer inhibitors harbors TCF7L2‐regulated cancer gene signatureDiana L. Gerrard, Yao Wang, Malaina Gaddis, Yufan Zhou, Junbai Wang, Heather N. Witt, Shili Lin, Peggy Farnham, Victor X. Jin, Seth E. Frietze · 2018 · Journal of Cellular Biochemistry
- Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture dataDario Meluzzi, Gaurav Arya · 2019 · Methods
- GOTHiC, a simple probabilistic model to resolve complex biases and to identify real interactions in Hi-C dataBorbála Mifsud, Iñigo Martincorena, Élodie Darbo, Robert Sugar, Stefan Schoenfelder, Peter Fraser, Nicholas M. Luscombe · 2015 · bioRxiv (Cold Spring Harbor Laboratory)
- RobusTAD: A Tool for Robust Annotation of Topologically Associating Domain BoundariesRola Dali, Guillaume Bourque, Mathieu Blanchette · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
- Orc4 spatiotemporally stabilizes centromeric chromatinLakshmi Sreekumar, Kiran Kumari, Krishnendu Guin, Asif Bakshi, Neha Varshney, Bhagya C. Thimmappa, Leelavati Narlikar, Ranjith Padinhateeri, Rahul Siddharthan, Kaustuv Sanyal · 2021 · Genome Research
- Transient histone deacetylase inhibition induces cellular memory of gene expression and three-dimensional genome foldingFlora Paldi, Michael F Szalay, Marco Di Stefano, Daniel Jost, Hadrien Reboul, Giacomo Cavalli · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Biochemical properties of chromatin domains define genome compartmentalizationFederica Lucini, Cristiano Petrini, Elisa Salviato, Koustav Pal, Valentina Rosti, Francesca Gorini, Philina Santarelli, Roberto Quadri, Giovanni Lembo, Giulia Graziano et al. · 2024 · Nucleic Acids Research
- Disorganized chromatin hierarchy and stem cell aging in a male patient of atypical laminopathy-based progeria mandibuloacral dysplasia type AWei Zhu Jin, Shaoshuai Jiang, Xinyi Liu, Yi He, Tuo Li, Jingchun Ma, Zhihong Chen, Xiaomei Lu, Xinguang Liu, Weinian Shou et al. · 2024 · Nature Communications
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- Deciphering histone mark-specific fine-scale chromatin organization at high resolution with Micro-C-ChIPMariia Metelova, Maria Louisa Vigh, Nils Krietenstein · 2025 · Nature Communications
- Euchromatin forms condensed domains with short active regions on the surfaceJoseph M. Paggi, Lü Long, Bin Zhang · 2026 · Nature Genetics
- Organization and replicon interactions within the highly segmented genome of Borrelia burgdorferiZhongqing Ren, Constantin N. Takacs, Hugo B. Brandão, Christine Jacobs, Xindan Wang · 2023 · PLoS Genetics
- A deep learning method for replicate-based analysis of chromosome conformation contacts using Siamese neural networksEdiem Al-Jibury, James W. D. King, Ya Guo, Boris Lenhard, Amanda G. Fisher, Matthias Merkenschlager, Daniel Rueckert · 2023 · Nature Communications
- Three-dimensional genome architecture coordinates key regulators of lineage specification in mammary epithelial cellsM. Milevskiy, H. Coughlan, Serena R. Kane, Timothy M. Johanson, Somayeh Kordafshari, Wing-Fuk Chan, Minhsuang Tsai, Elliot E. Surgenor, Stephen Wilcox, R. Allan et al. · 2023 · Cell Genomics