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
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- Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C dataWenyuan Li, Ke Gong, Qing-Jiao Li, F. Alber, X. Zhou · 2014 · Bioinform.
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- Causes and consequences of nuclear gene positioningSigal Shachar, Tom Misteli · 2017 · Journal of Cell Science
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- Nonlinear control of transcription through enhancer-promoter interactionsZuin, Jessica, Roth, Gregory, Zhan, Yinxiu, Cramard, Julie, Redolfi, Josef, Piskadlo, Ewa, Mach, Pia, Kryzhanovska, Mariya, Tihanyi, Gergely, Kohler, Hubertus et al. · 2021
- Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deerYuan Yin, Hui-Zhong Fan, Botong Zhou, Yi-Bo Hu, G. Fan, Jin-Huan Wang, Fan Zhou, Wen-Hui Nie, Chen-Zhou Zhang, Lin Liu et al. · 2021 · Nature Communications
- Software tools for visualizing Hi-C dataG. Yardımcı, William Stafford Noble · 2016 · Genome Biology
- HPV-CCDC106 integration alters local chromosome architecture and hijacks an enhancer by three-dimensional genome structure remodeling in cervical cancerCanhui Cao, Ping Hong, Xingyu Huang, Da Lin, Gang Cao, Liming Wang, Bei Feng, Ping Wu, Hui Shen, Qian Xu et al. · 2020 · Journal of genetics and genomics/Journal of Genetics and Genomics
- SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clusteringKellen G. Cresswell, John C. Stansfield, Mikhail G. Dozmorov · 2020 · BMC Bioinformatics
- Defining the relative and combined contribution of CTCF and CTCFL to genomic regulationMayilaadumveettil Nishana, Caryn J. Ha, Javier Rodriguez-Hernaez, Ali Ranjbaran, Erica Chio, Elphège Pierre Nora, Sana Badri, Andreas Kloetgen, Benoit G. Bruneau, Aristotelis Tsirigos et al. · 2020 · Genome biology
- Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcriptionYing Feng, Yao Wang, Xiangnan Wang, Xiaohui He, Yang Chen, Ardalan Naseri, Thoru Pederson, Jing Zheng, Shaojie Zhang, Xiao Xiao et al. · 2020 · Genome biology
- DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity.Q. Du, Grady C. Smith, Phuc-Loi Luu, James M. Ferguson, Nicola J. Armstrong, C. E. Caldon, Elyssa M. Campbell, S. Nair, E. Zotenko, Cathryn M. Gould et al. · 2021 · Cell Reports
- Interplay between CTCF boundaries and a super enhancer controls cohesin extrusion trajectories and gene expressionErica S.M. Vos, Christian Valdes‐Quezada, Yike Huang, Amin Allahyar, Marjon J.A.M. Verstegen, Anna-Karina Felder, Floor van der Vegt, Esther C. H. Uijttewaal, Peter H.L. Krijger, Wouter L. de Laat · 2021 · Molecular Cell
- Assessing the limits of restraint-based 3D modeling of genomes and genomic domainsMarie Trussart, François Serra, Davide Baù, Ivan Junier, Luis G. Serrano, Marc A. Martı́-Renom · 2015 · Nucleic Acids Research
- Analysis of the relationship between coexpression domains and chromatin 3D organizationMaría Eugenia Soler-Oliva, Jose Antonio Guerrero-Martinez, Valentina Bachetti, José C. Reyes · 2017 · PLoS Computational Biology
- Genome sequences reveal global dispersal routes and suggest convergent genetic adaptations in seahorse evolutionChunyan Li, Melisa Olave, Yali Hou, Geng Qin, Ralf Schneider, Zexia Gao, Xiaolong Tu, Xin Wang, Furong Qi, Alexander Nater et al. · 2021 · Nature Communications
- Determining chromatin architecture with Micro Capture-CJoseph C. Hamley, Hang-Peng Li, N. Denny, D. Downes, James O. J. Davies · 2023 · Nature Protocols
- An integrated view of the structure and function of the human 4D nucleomeJob Dekker, Betül Akgöl Oksuz, Yang Zhang, Ye Wang, Miriam K. Minsk, Shuzhen Kuang, Liyan Yang, Johan Harmen Gibcus, Nils Krietenstein, Oliver J. Rando et al. · 2025 · Nature
- Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome OrganizationYifeng Qi, Alejandro Reyes, Sarah E. Johnstone, Martin J. Aryee, B Bernstein, Bin Zhang · 2020 · Biophysical Journal
- FIND: difFerential chromatin INteractions Detection using a spatial Poisson processM. N. Djekidel, Yang Chen, Michael Q. Zhang · 2018 · Genome Research
- HiFive: a tool suite for easy and efficient HiC and 5C data analysisMichael E.G. Sauria, Jennifer E. Phillips‐Cremins, Victor G. Corces, James Taylor · 2015 · Genome biology
- HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIPMerve Sahin, Wilfred Wong, Ying-Qian A. Zhan, Kinsey Van Deynze, R. Koche, C. Leslie · 2021 · Nature Communications
- CTCF–CTCF loops and intra-TAD interactions show differential dependence on cohesin ring integrityYu Liu, Job Dekker · 2022 · Nature Cell Biology
- Shape Transitions and Chiral Symmetry Breaking in the Energy Landscape of the Mitotic ChromosomeBin Zhang, Peter Guy Wolynes · 2016 · Physical Review Letters
- A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactionsJonas Paulsen, Einar Andreas Rødland, Lars Holden, Marit Holden, Eivind J. Hovig · 2014 · Nucleic Acids Research
- HiCdat: a fast and easy-to-use Hi-C data analysis toolMarc W. Schmid, S. Grob, U. Grossniklaus · 2015 · BMC Bioinformatics
- The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryosJelena Erceg, Jumana AlHaj Abed, Anton A. Goloborodko, Bryan R. Lajoie, Geoffrey Fudenberg, Nezar A. Abdennur, Maxim Imakaev, Ruth B. McCole, Son C. Nguyen, Wren Saylor et al. · 2019 · Nature Communications
- A model of active transcription hubs that unifies the roles of active promoters and enhancersZhu, Iris, Song, Wei, Ovcharenko, Ivan, Landsman, David · 2021 · Nucleic Acids Research
- Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubsMarco Di Stefano, Ralph Stadhouders, Irene Farabella, David Castillo, François Serra, Thomas Graf, Marc A. Martı́-Renom · 2020 · Nature Communications
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- MOGEN: a tool for reconstructing 3D models of genomes from chromosomal conformation capturing dataTuan Trieu, Jianlin Jack Cheng · 2015 · Bioinformatics
- A maximum likelihood algorithm for reconstructing 3D structures of human chromosomes from chromosomal contact dataOluwatosin Oluwadare, Yuxiang Zhang, Jianlin Jack Cheng · 2018 · BMC Genomics
- MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutionsKoon-Kiu Yan, Shaoke Lou, M. Gerstein · 2016 · bioRxiv
- Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?M. Kadota, Osamu Nishimura, Hisashi Miura, Kaori Tanaka, Ichiro Hiratani, S. Kuraku · 2019 · bioRxiv
- Reorganized 3D Genome Structures Support Transcriptional Regulation in Mouse SpermatogenesisZheng-Yu Luo, Xiaorong Wang, Hong Jiang, Ruo-Yu Wang, Jian Chen, Yusheng Chen, Qianlan Xu, Jun Cao, Xiaowen Gong, Ji Wu et al. · 2020 · iScience
- Involvement of condensin in cellular senescence through gene regulation and compartmental reorganizationIwasaki, Osamu, Tanizawa, Hideki, Kim, Kyoung-Dong, Kossenkov, Andrew, Nacarelli, Timothy, Tashiro, Sanki, Majumdar, Sonali, Showe, Louise C., Zhang, Rugang, Noma, Ken-ichi · 2019 · Nature Communications
- Computational 3D genome modeling using Chrom3DJonas Paulsen, Tharvesh M. Liyakat Ali, Philippe Collas · 2018 · Nature Protocols
- Chromosome compartments on the inactive X guide TAD formation independently of transcription during X-reactivationMoritz Bauer, Enrique Vidal, Eduard Valera Zorita, Nil Üresin, Stefan F. Pinter, Guillaume J. P. Filion, Bernhard Payer · 2021 · Nature Communications
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- Multiscale Dynamic Structuring of Bacterial Chromosomes.Virginia S. Lioy, I. Junier, F. Boccard · 2021 · Annual Review of Microbiology
- The three-dimensional structure of Epstein-Barr virus genome varies by latency type and is regulated by PARP1 enzymatic activitySarah M. Morgan, Hideki Tanizawa, Lisa Beatrice Caruso, Michael Hulse, Andrew V. Kossenkov, Jozef Madžo, Kelsey Keith, Yinfei Tan, Sarah Boyle, Paul M. Lieberman et al. · 2022 · Nature Communications
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- Pan-3D genome analysis reveals structural and functional differentiation of soybean genomesLingbin Ni, Yu-Cheng Liu, Xin Ma, Teng-Fei Liu, Xiaoyue Yang, Zhao Wang, Qian-Jin Liang, Shu-Lin Liu, Min Zhang, Zheng Wang et al. · 2023 · Genome Biology
- 3D genome structure modeling by Lorentzian objective functionTuan Trieu, Jianlin Jack Cheng · 2016 · Nucleic Acids Research
- Non-coding genetic variation in cancerTawny N. Cuykendall, Mark A. Rubin, Ekta Khurana · 2017 · Current Opinion in Systems Biology
- Endothelial cell differentiation is encompassed by changes in long range interactions between inactive chromatin regionsHenri Niskanen, Irina Tuszyńska, Rafał Zaborowski, Merja Heinäniemi, Seppo Ylä‐Herttuala, Bartek Wilczyński, Minna Unelma Kaikkonen · 2017 · Nucleic Acids Research
- Nucleotide sequence and DNaseI sensitivity are predictive of 3D chromatin architectureJacob Matthew Schreiber, Maxwell W. Libbrecht, Jeffrey A. Bilmes, William Stafford Noble · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
- Chromatin architecture reorganization during neuronal cell differentiation in Drosophila genomeKeerthi T. Chathoth, Nicolae Radu Zabet · 2019 · Genome Research
- A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomesJing Liu, Zongji Wang, Jing Li, Luohao Xu, Jiaqi Liu, Shao-Hong Feng, Chunxue Guo, Shengchang Chen, Zhan-Jun Ren, Jinpeng Rao et al. · 2021 · Genome Research
- ZNF143 is a regulator of chromatin loopWen, Zi, Huang, Zhi-Tao, Zhang, Ran, Peng, Cheng · 2018 · Cell Biology and Toxicology
- Comparative 3D genome architecture in vertebratesDiyan Li, Mengnan He, Qianzi Tang, Shilin Tian, Jiaman Zhang, Yán Li, Danyang Wang, Long Guo Jin, Chunyou Ning, Wei Zhu et al. · 2022 · BMC Biology
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- X Chromosome Domain Architecture Regulates Caenorhabditis elegans Lifespan but Not Dosage CompensationErika C. Anderson, Phillip Andrew Frankino, Ryo Higuchi‐Sanabria, Qiming Yang, Qian Bian, Katie Podshivalova, Aram Shin, Cynthia J. Kenyon, Andrew G. Dillin, Barbara J Meyer · 2019 · Developmental Cell
- Detecting chromatin interactions between and along sister chromatids with SisterCMarlies E. Oomen, Adam K. Hedger, Jonathan K. Watts, Job Dekker · 2020 · Nature Methods
- Mitotic chromosomes are self-entangled and disentangle through a topoisomerase-II-dependent two-stage exit from mitosisErica M. Hildebrand, Kirill Polovnikov, Bastiaan Dekker, Yu Liu, Denis L. J. Lafontaine, A. Nicole Fox, Ying Li, Sergey V. Venev, Leonid A. Mirny, Job Dekker · 2024 · Molecular Cell
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- Dynamic properties of independent chromatin domains measured by correlation spectroscopy in living cellsMalte Wachsmuth, Tobias Knoch, Karsten Rippe · 2016 · Epigenetics & Chromatin
- Constricted migration is associated with stable 3D genome structure differences in cancer cellRosela Golloshi, Christopher Playter, Trevor F. Freeman, Priyojit Das, T. Raines, Joshua H. Garretson, D. Thurston, R. McCord · 2019 · bioRxiv
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- Transcription-induced domains form the elementary constraining building blocks of bacterial chromosomesAmaury Bignaud, Charlotte A. Cockram, Céline Borde, Justine Groseille, E. Allemand, Agnès Thierry, M. Marbouty, J. Mozziconacci, O. Espéli, R. Koszul · 2024 · Nature Structural & Molecular Biology
- The 3D Organization of the Yeast Genome Correlates with Co-Expression and Reflects Functional Relations between GenesDirar Homouz, Andrzej S. Kudlicki · 2013 · PLoS ONE
- instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolderLyam Baudry, Martial Marbouty, Hervé Marie-Nelly, Alexandre Cormier, Nadège Guiglielmoni, Komlan Avia, Yann Loe-Mie, Olivier Godfroy, Lieven Sterck, Jeremy Mark Cock et al. · 2020 · Genome biology