Multiscale 3D Genome Rewiring during Mouse Neural Development

Bonev, Boyan, Mendelson Cohen, Netta, Szabo, Quentin, Fritsch, Lauriane, Papadopoulos, Giorgio L., Lubling, Yaniv, Xu, Xiaole, Lv, Xiaodan +3 more·2017·Cell

Cited by (1,000)

Items 501–600 of 1,000

  1. LncRNA:DNA triplex-forming sites are positioned at specific areas of genome organization and are predictors for Topologically Associated Domains
    Benjamin Soibam, Ayzhamal Zhamangaraeva · 2021 · BMC Genomics
  2. Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos
    Alison C. McGarvey, Wolfgang Kopp, Dubravka Vučićević, Kenny Mattonet, Rieke Kempfer, Antje Hirsekorn, Ilija Bilić, Marine Gil, Alexandra Trinks, Anne Margarete Merks et al. · 2022 · Cell Genomics
  3. Unraveling three-dimensional chromatin structural dynamics during spermatogonial differentiation
    Yi Zheng, Lingkai Zhang, Long Guo Jin, Pengfei Zhang, Fuyuan Li, Ming Zhou Guo, Qiang Gao, Yao Ying Zeng, Mingzhou Li, Wenxian Zeng · 2022 · Journal of Biological Chemistry
  4. Regulation of 3D Organization and Its Role in Cancer Biology
    Anghui Peng, Wang Peng, Ruiqi Wang, Hao Zhao, Xinyang Yu, Yihao Sun · 2022 · Frontiers in Cell and Developmental Biology
  5. Network models of chromatin structure
    Véra Pancaldi · 2023 · Current Opinion in Genetics & Development
  6. Co-option of endogenous retroviruses through genetic escape from TRIM28 repression
    Rocio Enriquez-Gasca, Poppy A. Gould, Hale Tunbak, Lucía Conde, Javier Herrero, Alexandra Chittka, Christine R. Beck, Robert James Gifford, Helen M. Rowe · 2023 · Cell Reports
  7. Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis
    Francesca Mastropasqua, Marika Oksanen, Cristina Soldini, Shemim Alatar, Abishek Arora, Roberto Ballarino, Maya Molinari, Federico Agostini, Axel Poulet, Michelle Evelyn Watts et al. · 2023 · Biology Open
  8. Loss of cohesin regulator PDS5A reveals repressive role of Polycomb loops
    Daniel Bsteh, H. F. Moussa, Georg Michlits, R. Yelagandula, Jing-Kui Wang, U. Elling, O. Bell · 2021 · bioRxiv
  9. 4D nucleome equation predicts gene expression controlled by long-range enhancer-promoter interaction
    Zi-Hao Wang, Song-Hao Luo, Zhen-Quan Zhang, Tian-Shou Zhou, Jiajun Zhang · 2023 · PLoS Comput. Biol.
  10. Cohesin prevents cross-domain gene coactivation
    Peng Dong, Shu Zhang, Valentina Gandin, Liangqi Xie, Lihua Wang, Andrew L. Lemire, Wenhong Li, Hideo Otsuna, Takashi Kawase, Arthur D. Lander et al. · 2024 · Nature Genetics
  11. EVR: reconstruction of bacterial chromosome 3D structure models using error-vector resultant algorithm
    K. Hua, Bin-Guang Ma · 2018 · BMC Genomics
  12. Characterizing Genetic Regulatory Elements in Ovine Tissues
    Kimberly M Davenport, Alisha T. Massa, Suraj Bhattarai, Stephanie McKay, Michelle R. Mousel, Maria K. Herndon, Stephen N. White, Noelle E. Cockett, Timothy P. L. Smith, Brenda M. Murdoch · 2021 · Frontiers in Genetics
  13. Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin
    Ezequiel Miron, Roel Oldenkamp, Jill M. Brown, David M. S. Pinto, C. Shan Xu, Ana R. Faria, Haitham Ahmed Shaban, James D. P. Rhodes, Cassandravictoria Innocent, Sara de Ornellas et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  14. The impact of the embryonic DNA methylation program on CTCF-mediated genome regulation
    Ana Monteagudo-Sánchez, Julien Richard Albert, Margherita Scarpa, D. Noordermeer, Maxim V. C. Greenberg · 2024 · Nucleic Acids Research
  15. Terminal neuron localization to the upper cortical plate is controlled by the transcription factor NEUROD2
    Gizem Guzelsoy, Cansu Akkaya, Dila Atak, Cory D. Dunn, Alkan Kabakçıoğlu, Nurhan Özlü, Gulayse Ince-Dunn · 2019 · Scientific Reports
  16. Cell cycle dynamics and developmental dynamics of the 3D genome: toward linking the two timescales
    Hisashi Miura, Ichiro Hiratani · 2022 · Current Opinion in Genetics & Development
  17. SnapHiC2: A computationally efficient loop caller for single cell Hi-C data
    Xiaoqi Li, Lindsay Lee, Armen Abnousi, Miao Yu, Weifang Liu, Le Huang, Yun Li, Ming Hu · 2022 · Computational and Structural Biotechnology Journal
  18. The RNA cap methyltransferases RNMT and CMTR1 co-ordinate gene expression during neural differentiation
    Shang Liang, Rajaei Almohammed, Victoria H. Cowling · 2023 · Biochemical Society Transactions
  19. Conserved H3K27me3‐associated chromatin looping mediates physical interactions of gene clusters in plants
    Linhua Sun, Yuxin Cao, Zhu Li, Yi Liu, Xiaochang Yin, Xing Wang Deng, Hang He, Weiqiang Qian · 2023 · Journal of Integrative Plant Biology
  20. Clusters of lineage-specific genes are anchored by ZNF274 in repressive perinucleolar compartments
    Martina Begnis, Julien Duc, Sandra Eloise Offner, Delphine Grün, Shaoline Sheppard, Olga Rosspopoff, Didier Trono · 2024 · Science Advances
  21. An Introduction to Epigenetic Mechanisms
    Elizabeth J. Radford · 2018 · Progress in molecular biology and translational science
  22. A distal enhancer maintaining Hoxa1 expression orchestrates retinoic acid-induced early ESCs differentiation
    Guang-Song Su, Dianhao Guo, Jun Chen, Man Liu, Jian Zheng, Wenbin Wang, Xueyuan Zhao, Qingqing Yin, Lei Zhang, Zhong-Fang Zhao et al. · 2019 · Nucleic Acids Research
  23. PRC1 sustains the integrity of neural fate in the absence of PRC2 function
    Ayana Sawai, Sarah Pfennig, Milica Bulajić, Alexander Miller, Alireza Khodadadi‐Jamayran, Esteban O. Mazzoni, Jeremy S. Dasen · 2022 · eLife
  24. From Nucleus to Organs: Insights of Aryl Hydrocarbon Receptor Molecular Mechanisms
    Claudia M. Rejano-Gordillo, Beatriz Marín-Díaz, Ana Ordiales-Talavero, Jaime M. Merino, Francisco Javier González-Rico, Pedro M. Fernández‐Salguero · 2022 · International Journal of Molecular Sciences
  25. Live-Cell Imaging Reveals Enhancer-dependent Sox2 Transcription in the Absence of Enhancer Proximity
    Jeffrey M. Alexander, Juan Guan, Bo Huang, Stavros Lomvardas, Orion David Weiner · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  26. Cooperative insulation of regulatory domains by CTCF-dependent physical insulation and promoter competition
    Thais Ealo, Víctor Sánchez-Gaya, Patricia Respuela, María Muñoz‐San Martín, Elva Martín-Batista, Endika Haro, Álvaro Rada-Iglesias · 2024 · Nature Communications
  27. Transcription bursting and epigenetic plasticity: an updated view
    William F. Beckman, Miguel Ángel Lermo Jiménez, Pernette J. Verschure · 2021 · Epigenetics Communications
  28. Identification of chromatin loops from Hi-C interaction matrices by CTCF–CTCF topology classification
    Silvia Galan, François Serra, Marc A. Martı́-Renom · 2022 · NAR Genomics and Bioinformatics
  29. The importance of considering regulatory domains in genome-wide analyses – the nearest gene is often wrong!
    Ellora Hui Zhen Chua, Samen Yasar, Nathan Harmston · 2022 · Biology Open
  30. 3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells
    Karolina Jodkowska, Véra Pancaldi, Maria Rigau, Ricardo Almeida, José Miguel Fernández-Justel, Osvaldo Graña‐Castro, Sara Rodríguez‐Acebes, Miriam Rubio-Camarillo, Enrique Carrillo de Santa Pau, David G. Pisano et al. · 2022 · Nucleic Acids Research
  31. Remembering through the genome: the role of chromatin states in brain functions and diseases
    Rodrigo G. Arzate‐Mejía, Isabelle M. Mansuy · 2023 · Translational Psychiatry
  32. RNA polymerase II pausing regulates chromatin organization in erythrocytes
    Andrés Pénagos-Puig, Sherlyn Claudio-Galeana, Aura Stephenson-Gussinye, Karina Jácome-López, Amaury Aguilar-Lomas, Xingqi Chen, R. Pérez-Molina, M. Furlan-Magaril · 2023 · Nature Structural & Molecular Biology
  33. A common genomic code for chromatin architecture and recombination landscape
    Kamel Jabbari, Johannes Wirtz, Martina Rauscher, Thomas Wiehe · 2019 · PLoS ONE
  34. TOPORS, a tumor suppressor protein, contributes to the maintenance of higher-order chromatin architecture.
    Lu-Zhang Ji, Xiangru Huo, Yuwen Zhang, Zixiang Yan, Qian-Feng Wang, Bo Wen · 2020 · Biochimica et Biophysica Acta. Gene Regulatory Mechanisms
  35. Microrheology for Hi-C Data Reveals the Spectrum of the Dynamic 3D Genome Organization
    Soya Shinkai, Takeshi Sugawara, Hisashi Miura, Ichiro Hiratani, Shuichi Onami · 2020 · Biophysical Journal
  36. ARID4B is critical for mouse embryonic stem cell differentiation towards mesoderm and endoderm, linking epigenetics to pluripotency exit
    Nihal Terzi Çizmecioğlu, Jialiang Huang, Ezgi Gül Keskin, Xiaofeng Wang, İdil Esen, Fei Chen, Stuart H. Orkin · 2020 · Journal of Biological Chemistry
  37. Integrative studies of 3D genome organization and chromatin structure
    Marco Di Stefano, Giacomo Cavalli · 2022 · Current Opinion in Structural Biology
  38. Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding
    Paldi, Flora, Szalay, Michael-Florian, Dufau, Solène, Di Stefano, Marco, Reboul, Hadrien, Jost, Daniel, Bantignies, Frédéric, Cavalli, Giacomo · 2026 · Nature Genetics
  39. Discrete cis-acting element regulates developmentally timed gene-lamina relocation and neural progenitor competence in vivo
    Tanguy Lucas, Terry L Hafer, Harrison G. Zhang, Natalia Molotkova, Minoree Kohwi · 2021 · Developmental Cell
  40. Embryonic heat conditioning in chicks induces transgenerational heat/immunological resilience via methylation on regulatory elements
    Tali Rosenberg, Asaf Marco, Tatiana Kisliouk, Amit Haron, Dmitry Shinder, S. Druyan, Noam Meiri · 2022 · The FASEB Journal
  41. Modulation of the high-order chromatin structure by Polycomb complexes
    Yiran Guo, Gang Greg Wang · 2022 · Frontiers in Cell and Developmental Biology
  42. Loops and the activity of loop extrusion factors constrain chromatin dynamics
    Mary Lou P. Bailey, Ivan Vladimirovich Surovtsev, Jessica F. Williams, Hao Yan, Tianyu Yuan, Kevin Li, Katherine Duseau, S. G. J. Mochrie, Megan C. King · 2023 · Molecular Biology of the Cell
  43. Genome-wide analysis of histone modifications that underlie the dynamic changes in gene expression during decidualization in human endometrial stromal cells
    Isao Tamura, Amon Shiroshita, Taishi Fujimura, Yumiko Doi‐Tanaka, Yuichiro Shirafuta, Ryo Maekawa, Toshiaki Taketani, Shun Sato, Norihiro Sugino · 2023 · Molecular Human Reproduction
  44. Emerging insights into enhancer biology and function
    Mirjam Arnold, Kristy R. Stengel · 2023 · Transcription
  45. A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2
    Marta Losa, Iros Barozzi, Marco Osterwalder, Viviana E. Hermosilla, Angela Morabito, Brandon Chacón, Peyman Zarrineh, Aušra Girdžiušaitė, Jean Denis Benazet, Jianjian Zhu et al. · 2023 · Nature Communications
  46. Machine and Deep Learning Methods for Predicting 3D Genome Organization
    Brydon P. G. Wall, My Nguyen, Joshua Chuck Harrell, Mikhail G. Dozmorov · 2024 · Methods in molecular biology
  47. Extensive long-range polycomb interactions and weak compartmentalization are hallmarks of human neuronal 3D genome
    Ilya A Pletenev, Mariia Bazarevich, Diana Zagirova, Anna D. Kononkova, Alexander V. Cherkasov, Olga Efimova, Eugenia A. Tiukacheva, Kirill V. Morozov, Kirill A. Ulianov, Dmitriy Komkov et al. · 2024 · Nucleic Acids Research
  48. Transcriptional machinery as an architect of genome structure
    Nadezda A. Fursova, Daniel R. Larson · 2024 · Current Opinion in Structural Biology
  49. Boost-HiC: computational enhancement of long-range contacts in chromosomal contact maps
    Léopold Carron, Jean Baptiste Morlot, V. Matthys, Annick Lesne, Julien Mozziconacci · 2018 · Bioinformatics
  50. Exploring Mammalian Genome within Phase-Separated Nuclear Bodies: Experimental Methods and Implications for Gene Expression
    Annick Lesne, Marie-Odile Baudement, Cosette Rebouissou, Thierry Forné · 2019 · Genes
  51. Alu retrotransposons modulate Nanog expression through dynamic changes in regional chromatin conformation via aryl hydrocarbon receptor
    Francisco Javier González-Rico, Cristina Vicente‐García, Almudena Fernández, Diego Muñoz‐Santos, Lluı́s Montoliu, Antonio Morales‐Hernández, Jaime M. Merino, Ángel Román, Pedro M. Fernández‐Salguero · 2020 · Epigenetics & Chromatin
  52. HiC1Dmetrics: framework to extract various one-dimensional features from chromosome structure data
    Jiankang Wang, Ryuichiro Nakato · 2021 · Briefings in Bioinformatics
  53. Systems genetics identifies a macrophage cholesterol network associated with physiological wound healing
    Marta Bagnati, Aida Moreno‐Moral, Jeong‐Hun Ko, Jérôme Nicod, Nathan Harmston, Martha Imprialou, Laurence Gamé, Jesús Gil, Enrico G. Petretto, Jacques V. Behmoaras · 2019 · JCI Insight
  54. Highly rigid H3.1/H3.2–H3K9me3 domains set a barrier for cell fate reprogramming in trophoblast stem cells
    Masashi Hada, Hisashi Miura, Akie Tanigawa, Shogo Matoba, Kimiko Inoue, Narumi Ogonuki, Michiko Hirose, Naomi Watanabe, Ryuichiro Nakato, Katsunori Fujiki et al. · 2022 · Genes & Development
  55. Cohesin is required for long-range enhancer action
    Kane, Lauren, Williamson, Iain, Flyamer, Ilya M., Kumar, Yatendra, Hill, Robert E., Lettice, Laura A., Bickmore, Wendy A. · 2021
  56. Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci
    Eva D’haene, Víctor López-Soriano, Pedro Manuel Martínez‐García, Soraya Kalayanamontri, Alfredo Dueñas Rey, Ana Sousa‐Ortega, Silvia Naranjo, Stijn Van de Sompele, Lies Vantomme, Quinten Mahieu et al. · 2024 · Genome biology
  57. Promoter capture Hi-C identifies promoter-related loops and fountain structures in Arabidopsis
    Ding-Yue Wang, Suxin Xiao, Jia Shu, Lingxiao Luo, Min-Qi Yang, M. Calonje, Hang He, Bao-Xing Song, Yue Zhou · 2024 · Genome Biology
  58. Transcription and epigenetic factor dynamics in neuronal activity-dependent gene regulation
    Noriyuki Sugo, Yuri Atsumi, Nobuhiko Yamamoto · 2025 · Trends in Genetics
  59. Sex-specific role of the 5-HT2A receptor in psilocybin-induced extinction of opioid reward
    Alaina M. Jaster, Thomas M Hadlock, Belle Buzzi, Jessica L. Maltman, Gabriella M. Silva, Somdatta Saha, Eda Köşeli, Abby M Pondelick, Nikita Thakur, Xin Zhang et al. · 2025 · Nature Communications
  60. Chromatin structure changes during various processes from a DNA sequence view
    Hui Quan, Ying Yang, Sirui Liu, Hao Tian, Yue Xue, Yi Qin Gao · 2019 · Current Opinion in Structural Biology
  61. Global Genome Conformational Programming during Neuronal Development Is Associated with CTCF and Nuclear FGFR1—The Genome Archipelago Model
    Brandon Decker, Michał Liput, Hussam Abdellatif, Donald Albert Yergeau, Yongho Bae, Josep Miquel Jornet, Ewa K. Stachowiak, Michal K. Stachowiak · 2020 · International Journal of Molecular Sciences
  62. Enhancer-Promoter Communication: It’s Not Just About Contact
    Annabelle Wurmser, Srinjan Basu · 2022 · Frontiers in Molecular Biosciences
  63. Developmental genome-wide occupancy analysis of bZIP transcription factor NRL uncovers the role of c-Jun in early differentiation of rod photoreceptors in the mammalian retina
    Xulong Liang, Matthew J. Brooks, Anand Swaroop · 2022 · Human Molecular Genetics
  64. Balanced SET levels favor the correct enhancer repertoire during cell fate acquisition
    Mattia Zaghi, Federica Banfi, Luca Massimino, Monica Volpin, Edoardo Niccolò Bellini, Simone Brusco, Ivan Merelli A, Cristiana Barone, Michela Bruni, Linda Bossini et al. · 2023 · Nature Communications
  65. Three‐dimensional genome structure and function
    Hao Liu, Hsiangyu Tsai, Maoquan Yang, Guozhi Li, Qian Bian, Gang Ding, Dandan Wu, Jiewen Dai · 2023 · MedComm
  66. Proximity-dependent recruitment of Polycomb repressive complexes by the lncRNA Airn
    Aki K. Braceros, Megan D. Schertzer, Arina D. Omer, Jackson B. Trotman, Eric S. Davis, Jill M. Dowen, Douglas H. Phanstiel, Erez Lieberman Aiden, J. Mauro Calabrese · 2023 · Cell Reports
  67. Transcription induces context-dependent remodeling of chromatin architecture during differentiation
    Sanjay Chahar, Yousra Ben Zouari, Hossein Salari, Anne Marie Molitor, Dominique Kobi, Manon Maroquenne, Cathie Erb, Audrey Mossler, Nezih Karasu, Daniel Jost et al. · 2023 · PLoS Biology
  68. Pre-hypertrophic chondrogenic enhancer landscape of limb and axial skeleton development
    Fabrice Darbellay, Anna Ramisch, Lucille Lopez‐Delisle, Michael Kosicki, Antonella Rauseo, Zahra Jouini, Axel Visel, Guillaume Andrey · 2024 · Nature Communications
  69. 40 years of the homeobox: mechanisms of Hox spatial-temporal collinearity in vertebrates
    Rodrigue Peraldi, Marie Kmita · 2024 · Development
  70. Functional characterization of theZEB2regulatory landscape
    Reut Bar-Yaacov, Reut Eshel, Einan Farhi, Fania Shemuluvich, Tommy Kaplan, Ramon Y. Birnbaum · 2018 · Human Molecular Genetics
  71. Landscape of Enhancer-Enhancer Cooperative Regulation during Human Cardiac Commitment
    Hong Chen, Jun Ying Xiao, Tingting Shao, Li Wang, Jing Bai, Xia Li, Na Ding, Yinwei Qu, Yi Tian, Xiang Chen et al. · 2019 · Molecular Therapy — Nucleic Acids
  72. 3DeFDR: statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data
    Lindsey R. Fernandez, Thomas G. Gilgenast, Jennifer E. Phillips‐Cremins · 2020 · Genome biology
  73. Chromatin Network Analyses: Towards Structure-Function Relationships in Epigenomics
    Véra Pancaldi · 2021 · Frontiers in Bioinformatics
  74. 3DGenBench: a web-server to benchmark computational models for 3D Genomics
    Polina S. Belokopytova, Emil Viesná, Mateusz Chiliński, Yifeng Qi, Hossein Salari, Marco Di Stefano, Andrea Esposito, Mattia Conte, Andrea M. Chiariello, Vladimir B. Teif et al. · 2022 · Nucleic Acids Research
  75. Dynamical modeling of the H3K27 epigenetic landscape in mouse embryonic stem cells
    Kapil Newar, Amith Z. Abdulla, Hossein Salari, Éric Fanchon, Daniel Jost · 2022 · PLoS Computational Biology
  76. An Igh distal enhancer modulates antigen receptor diversity by determining locus conformation
    Khalid Hussain Bhat, Saurabh Priyadarshi, Sarah Naiyer, Xiaoyu Qu, Hammad Farooq, Eden Kleiman, Jeffery Xu, Xue Lei, José Fernando Cantillo, Robert Wuerffel et al. · 2023 · Nature Communications
  77. Systematic Evaluation of Statistical Methods for Identifying Looping Interactions in 5C Data
    Thomas G. Gilgenast, Jennifer E. Phillips‐Cremins · 2019 · Cell Systems
  78. Induced Pluripotent Stem Cells to Study Mechanisms of Laminopathies: Focus on Epigenetics
    Silvia Crasto, Elisa Di Pasquale · 2018 · Frontiers in Cell and Developmental Biology
  79. Single-cell molecular connectomics of intracortically-projecting neurons
    Esther Klingler, Julien Prados, Justus M. Kebschull, Alexandre G. Dayer, Anthony M. Zador, Denis Jabaudon · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  80. Dosage sensitivity of the loop extrusion rate confers tunability to genome folding while creating vulnerability to genetic disruption
    Shah, Rini, Tortora, Maxime M. C., Louafi, Nessim, Rahmaninejad, Hadi, Hansen, Karissa L., Anderson, Erika C., Wen, David, Giorgetti, Luca, Fudenberg, Geoffrey, Nora, Elphège P. · 2025
  81. Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics
    Honggui Wu, Maoxu Wang, Yinghui Zheng, Xiaoliang Sunney Xie · 2025 · Cell Discovery
  82. MeCP2 and non-CG DNA methylation stabilize the expression of long genes that distinguish closely related neuron types
    J. Russell Moore, Mati T. Nemera, Rinaldo D. D’Souza, Nicole Hamagami, Adam W. Clemens, Diana C. Beard, Alaina Urman, Yasmin Razia, Victoria Rodriguez Mendoza, Travis E. Law et al. · 2025 · Nature Neuroscience
  83. β-actin mediated H3K27ac changes demonstrate the link between compartment switching and enhancer-dependent transcriptional regulation
    Syed Raza Mahmood, Nadine Hosny El Said, Kristin C. Gunsalus, Piergiorgio Percipalle · 2023 · Genome biology
  84. Spatial chromatin accessibility sequencing resolves high-order spatial interactions of epigenomic markers
    Yeming Xie, Fengying Ruan, Yaning Li, Meng Luo, Chen Zhang, Zhichao Chen, Zhe Xie, Zhe Weng, Weitian Chen, Wenfang Chen et al. · 2023 · eLife
  85. Chromatin remodeling analysis reveals the RdDM pathway responds to low‐phosphorus stress in maize
    Bowen Luo, Ziqi Zhang, Binyang Li, Haiying Zhang, Junchi Ma, Jing Li, Han Zheng, Chong Zhang, Shuhao Zhang, Ting Yu et al. · 2023 · The Plant Journal
  86. Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation
    Rotem Ben‐Tov Perry, Michael Tsoory, Michael Tolmasov, Igor Ulitsky · 2023 · Cell Reports
  87. Accessible gene borders establish a core structural unit for chromatin architecture in Arabidopsis
    Hongwoo Lee, Pil Joon Seo · 2023 · Nucleic Acids Research
  88. The scales, mechanisms, and dynamics of the genome architecture
    Ludvig Lizana, Yuri B. Schwartz · 2024 · Science Advances
  89. Evolution of 3D Chromatin Folding
    Lucía Álvarez-González, Aurora Ruiz‐Herrera · 2024 · Annual Review of Animal Biosciences
  90. Nucleosome wrapping states encode principles of 3D genome organization
    Zengqi Wen, Ruixin Fang, Ruxin Zhang, Xinqian Yu, Fanli Zhou, Haizhen Long · 2025 · Nature Communications
  91. A combination of transcription factors mediates inducible interchromosomal contacts
    Seungsoo Kim, Maitreya J. Dunham, Jay Shendure · 2019 · eLife
  92. Interplay between regulatory elements and chromatin topology in cellular lineage determination.
    Vallari Shukla, A. Cetnarowska, Mette Hyldahl, S. Mandrup · 2022 · Trends in Genetics
  93. LYL1 facilitates AETFC assembly and gene activation by recruiting CARM1 in t(8;21) AML
    Qian Chen, Murat Alper Cevher, Qi Jiang, Saisai Wang, Xiao‐Jian Sun, Robert G. Roeder, Mo Chen · 2022 · Proceedings of the National Academy of Sciences
  94. Statistics of chromatin organization during cell differentiation revealed by heterogeneous cross-linked polymers
    Ofir Shukron, Vincent Piras, Daan Noordermeer, David Holcman · 2019 · Nature Communications
  95. Genome anchoring to nuclear landmarks drives functional compartmentalization of the nuclear space
    Antoine Canat, Adeline Veillet, Amandine Bonnet, Pierre Therizols · 2020 · Briefings in Functional Genomics
  96. Biased visibility in Hi-C 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 · 2020 · BMC Genomics
  97. An atlas of endogenous DNA double-strand breaks arising during human neural cell fate determination
    Roberto Ballarino, Britta A. M. Bouwman, Federico Agostini, Luuk Harbers, Constantin Diekmann, Erik Wernersson, Magda Bienko, Nicola Crosetto · 2022 · Scientific Data
  98. Epigenetic and metabolic regulation of developmental timing in neocortex evolution
    Matilde Aquilino, Nora Ditzer, Takashi Namba, Mareike Albert · 2025 · Trends in Neurosciences
  99. Genomic exploration of the targets of FOXL2 and ESR2 unveils their implication in cell migration, invasion, and adhesion
    Laetitia Herman, Bérangère Legois, Anne‐Laure Todeschini, Reiner A. Veitia · 2021 · The FASEB Journal
  100. Machine Learning and Deep Learning in Genetics and Genomics
    Di Wu, D. S. Karhade, M. Pillai, Min-Zhi Jiang, Le Huang, Gang Li, Hunyong Cho, J. Roach, Yun Li, K. Divaris · 2021 · Machine Learning in Dentistry