The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension

Cited by (805)

Items 601–700 of 805

  1. Constructing polymorphonuclear cells: chromatin folding shapes nuclear morphology
    Cornelis Murre, Indumathi Patta, Shreya V. Mishra, Ming Hu · 2024 · Trends in Immunology
  2. HiCrayon reveals distinct layers of multi-state 3D chromatin organization
    Ben Nolan, Hannah L. Harris, Achyuth Kalluchi, Timothy E. Reznicek, Christopher T. Cummings, M. Jordan Rowley · 2024 · NAR Genomics and Bioinformatics
  3. Convergent pairs of highly transcribed genes restrict chromatin looping in Dictyostelium discoideum
    Irina V. Zhegalova, Sergey V. Ulianov, Aleksandra A. Galitsyna, Ilya A Pletenev, Olga V. Tsoy, Artem V. Luzhin, Petr A. Vasiluev, Egor S. Bulavko, Dmitry N. Ivankov, Alexey A. Gavrilov et al. · 2025 · Nucleic Acids Research
  4. Control of directionality of chromatin folding for the inter- and intra-domain contacts at the Tfap2c–Bmp7 locus
    Taro Tsujimura, Osamu Takase, Masahiro Yoshikawa, Etsuko Sano, Matsuhiko Hayashi, Tsuyoshi Takato, Atsushi Toyoda, Hideyuki Okano, Keiichi Hishikawa · 2018 · Epigenetics & Chromatin
  5. Hot debate in hot springs: Report on the second international meeting on SMC proteins
    Tatsuya Hirano, Tomoko Nishiyama, Katsuhiko Shirahige · 2017 · Genes to Cells
  6. Nucleokinesis
    Orly Reiner, Eyal Karzbrun · 2020 · Elsevier eBooks
  7. Genetic variation as a long-distance modulator of RAD21 expression in humans
    William S. Schierding, Julia A. Horsfield, Justin Martin O'Sullivan · 2022 · Scientific Reports
  8. Rearrangement of T Cell genome architecture regulates GVHD
    Yaping Sun, Gabrielle A. Dotson, Lindsey A. Muir, Scott Ronquist, Katherine I. Oravecz-Wilson, Daniel Peltier, Keisuke Seike, Lu Li, Walter Meixner, Indika Rajapakse et al. · 2022 · iScience
  9. Loop competition and extrusion model predicts CTCF interaction specificity
    Xi Wang, M Beer · 2021 · RePEc: Research Papers in Economics
  10. High resolution genetic mapping of causal regulatory interactions in the human genome
    N. Kumasaka, A. Knights, D. Gaffney · 2017 · bioRxiv
  11. Cohesin interacts with a panoply of splicing factors required for cell cycle progression and genomic organization
    Jung-Sik Kim, Xiaoyuan He, Jie Liu, Zhijun Duan, Taeyeon Kim, Julia Gerard, Brian Kim, William S. Lane, William Stafford Noble, Bogdan Budnik et al. · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  12. Loop competition and extrusion model predicts CTCF interaction specificity
    Wang Xi, M Beer · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  13. Distinct roles for CDK-Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction
    Emilia Dimitrova, Angelika Feldmann, Robin H. van der Weide, Koen D. Flach, Anna Lastuvkova, Elzo de Wit, Robert J. Klose · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  14. Context-dependent 3D genome regulation by cohesin and related factors
    Ryuichiro Nakato, Toyonori Sakata, Jiankang Wang, Luís Augusto Eijy Nagai, Gina Miku Oba, Masashige Bando, Katsuhiko Shirahige · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  15. Hi-TrAC reveals fractal nesting of super-enhancers
    Yaqiang Cao, Shuai Liu, Kairong Cui, Qingsong Tang, Keji Zhao · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  16. Cohesin regulates promoter-proximal pausing of RNA Polymerase II by limiting recruitment of super elongation complex
    Shoin Tei, Toyonori Sakata, Atsunori Yoshimura, Toyoaki Natsume, Masato T. Kanemaki, Masashige Bando, Katsuhiko Shirahige · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  17. A guide to studying 3D genome structure and dynamics in the kidney
    Brian J. Beliveau, Shreeram Akilesh · 2024 · Nature Reviews Nephrology
  18. A Bird’s-Eye View of the Wings Apart-Like Protein in Cell Biology and Implications for Disease and Therapeutics
    Pathiyil Sajini Sekhar, Amal Fahma, Suhail Subair, Athira Perunally Gopalakrishnan, Prathik Basthikoppa Shivamurthy, Shuvechha Chakraborty, Rajesh Raju · 2025 · OMICS A Journal of Integrative Biology
  19. Exuberant long noncoding RNA expression may sculpt Igh locus topology
    Ellen Drake, Sarah Naiyer, Xiaoyu Qu, Khalid Hussain Bhat, Hammad Farooq, Mark Maienschein‐Cline, Jie Liang, Amy L. Kenter · 2025 · Frontiers in Immunology
  20. Aberrant cohesin function in Saccharomyces cerevisiae activates Mcd1 degradation to promote cell lethality
    Gurvir Singh, Robert V. Skibbens · 2025 · PLoS Genetics
  21. CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igκ repertoire
    Emma L. Bush, Brigette Berke-Reynolds, Kaitlyn M. Hutchins, Xinrui Yu, Jorge A. Colón-Rosado, Fu‐Jung Chang, John Curran, Jiaxin Yang, Liangliang Sun, Jianrong Wang et al. · 2025 · Nature Communications
  22. Spatial Chromatin Organization Across the Cell Cycle: Insights from Auxin-Inducible Protein Depletion
    Artem R. Nurislamov, Anastasia Yunusova · 2025 · Cells
  23. Endless forms – how genome organization underlies evolution and development
    Alexandra N. Edwards, Elizabeth H. Finn · 2026 · Journal of Cell Science
  24. Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling
    Jiahu Tang, Cibo Feng, Haibin Su, Xiakun Chu · 2026 · Advanced Science
  25. Deficiency of Polη in Saccharomyces cerevisiae reveals the impact of transcription on damage-induced cohesion
    Pei‐Shang Wu, Jan Grosser, Donald P. Cameron, Laura Baranello, Lena Ström · 2021 · PLoS Genetics
  26. Functional diversity of chromosome cohesion proteins
    Yajuan Lu, Changyin Zhou, Bo Xiong · 2021 · Scientia Sinica Vitae
  27. MC4C: Locus-Specific Enhancer Hubs And Architectural Loop Collisions Uncovered From Single Allele DNA Topologies
    Amin Allahyar · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  28. How the Genome Folds, Divides, Lives, and Dies
    Whitney L. Johnson, Kathleen T. Xie, Mijung Kwon, Shiwei Liu, David S. Pellman · 2017 · Cold Spring Harbor Symposia on Quantitative Biology
  29. Single particle trajectory statistic to reconstruct chromatin organization and dynamics
    Ofir Shukron, Andrew Seeber, Assaf Amitai, David Holcman · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  30. The CTCF Anatomy of Topologically Associating Domains
    Luca Nanni, Cheng Wang, Freek Manders, Laszlo A. Groh, Paula Haro, Roel Oldenkamp, Stefano Ceri, Colin Logie · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  31. MyoD is a structure organizer of 3D genome architecture in muscle cells
    Qian Chen, Fengling Chen, Ruiting Wang, Minglei Shi, Antony K. Chen, Zhao Ma, Guohong Li, Min Wang, Hu Li, Xu Zhang et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  32. CONTEXT-INDEPENDENT FUNCTION OF A CHROMATIN BOUNDARY IN VIVO
    Andréa Willemin, Lucille Lopez‐Delisle, Christopher Chase Bolt, Marie-Laure Gadolini, Denis Duboule, Eddie Rodríguez-Carballo · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  33. Rad21 is the core subunit of the cohesin complex involved in directing genome organization
    Yujie Sun, Yuao Sun, Xin Xu, Wenxue Zhao, Yu Zhang, Keyang Chen, Yongzheng Li, Xiaotian Wang, Mengling Zhang, Boxin Xue et al. · 2021 · Research Square
  34. Hi-TrAC reveals fine-scale chromatin structures organized by transcription factors
    Shuai Liu, Yaqiang Cao, Kairong Cui, Qingsong Tang, Keji Zhao · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  35. Decreasing Wapl dosage partially corrects transcriptome phenotypes in Nipbl -/+ embryonic mouse brain
    Connor M. Kean, Christopher J. Tracy, Apratim Mitra, Matthew T. Van Winkle, Claudia M. Gebert, Jacob A. Noeker, Anne L. Calof, Arthur D. Lander, Judith A. Kassis, Karl E. Pfeifer · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  36. Different NIPBL requirements of cohesin-STAG1 and cohesin-STAG2
    Dácil Alonso Gil, Ana Cuadrado, Daniel Giménez-Llorente, Miriam Rodríguez-Corsino, Ana Losada · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  37. BRWD1 orchestrates chromatin topology by converting static to dynamic cohesin complexes
    Malay Mandal, Mark Maienschein‐Cline, Yeguang Hu, Azam Mohsin, Margaret Veselits, Nathaniel E. Wright, Michael K. Okoreeh, Young me Yoon, Jacob Veselits, Katia Georgopoulos et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  38. STAG2 mutations regulate 3D genome organization, chromatin loops, and Polycomb signaling in glioblastoma multiforme
    Todd A. Waldman, Jun-Sik Kim, Wanying Xu, Tianyi Yang, Alvin Ya, Luke J. Tallon, Lisa Sadzewicz, Brent T. Harris, Jann Nagina Sarkaria, Fulai Jin · 2023 · Research Square
  39. Unique territorial and compartmental organization of chromosomes in the holocentric silkmoth
    J. Gil, E. Navarrete, L. F. Rosin, N. Chowdhury, S. Abraham, G. Cornilleau, Elissa P. Lei, J. Mozziconacci, L. Mirny, H. Muller et al. · 2024 · Research Square
  40. PDS5s control the Arabidopsis 3D genome by suppressing the formation of TAD-like domains
    Anna-Maria Göbel, Sida Zhou, Zhidan Wang, Sofia Tzourtzou, Axel Himmelbach, Shiwei Zheng, Mónica Pradillo, Chang Liu, Hua Liang Jiang · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  41. Context-dependent epigenome rewiring during neuronal differentiation
    Vera Manelli, Jeisimhan Diwakar, Sude Beşkardeş, Dácil Alonso Gil, Ignasi Forné, Faye Chong, Axel Imhof, Boyan Bonev · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  42. Replisomes restrict SMC-mediated DNA-loop extrusion in vivo
    Liao, Qin, Brandão, Hugo B., Ren, Zhongqing, Wang, Xindan · 2025
  43. Dynamic changes in chromosome and nuclear architecture during maturation of normal and ALS C9orf72 motor neurons
    Özgün Uyan, Snehal Sambare, Marlies E. Oomen, Nicholas Wightman, Allana Schooley, Joseph R. Klim, Houda Belaghzal, Özkan Aydemir, Betül Akgöl Oksuz, Zeynep Sena AGIM USLU et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  44. A dual role for CTCF in development
    Noemí Alonso Saiz, Moreno Martinovic, Miguel Rubio, Pinak Samal, Stefan Giselbrecht, Luca Braccioli, Elzo de Wit · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  45. Cohesin extrudes chromatin loop unidirectionally through two modes of mechanisms in human cells
    Ping Wang, Lingyun Meng, Linghan Jiang, Yang Li, Jiaxiang Huang, Tiancheng YU, Haoxi Chai, Minji Kim, Xia Wang, Yijun Ruan · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  46. Roles of the Brca2 and Wapl complexes with Pds5 in sister chromatid cohesion, cohesin localization, and gene expression
    Ziva Misulovin, Michelle Pherson, Maria Gause, Kathie A. Mihindukulasuriya, Dale Dorsett · 2017 · Greater South Information System
  47. Twenty-First Century Glucocorticoid Receptor Molecular Biology
    Cheng Wang, Roel Oldenkamp, Ronald Oellers, Colin Logie · 2018 · InTech eBooks
  48. Organizing Principles for the Spatial Folding of Chromosomes
    Nataša Josipović, Argyris Papantonis · 2019 · Elsevier eBooks
  49. The intriguing dynamics of chromatin folding and assembly
    Zhihua Yang, W. Miao, Mohammad R. K. Mofrad · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  50. Extrusion without a motor: a new take on the loop extrusion model of genome organization
    Chris A. Brackley, Johnson, J., Davide Michieletto, A. N. Morozov, Mario Nicodemi, Peter R. Cook, Davide Marenduzzo · 2020 · arXiv (Cornell University)
  51. Nipped-B-like Protein Sensitizes Esophageal Squamous Cell Carcinoma Cells to Cisplatin via Upregulation of PUMA
    Shengjie Zhang, Yun Fei Zhou, Qinchuan Wang, Kristine Donahue, Jianguo Feng, Yinli Yao, Aiping Chen, Xia Li, Lian‐Lian Hong · 2020 · Technology in Cancer Research & Treatment
  52. Mechanistic Modelling of Chromatin Folding to Understand Function
    Chris A. Brackley, Davide Marenduzzo, Nick Gilbert · 2020 · arXiv (Cornell University)
  53. The assisting role of Polη in transcription facilitates formation of damage-induced cohesion
    Pei‐Shang Wu, Donald P. Cameron, Jan Grosser, Laura Baranello, Lena Ström · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  54. Biop-C: A Method for Chromatin Interactome Analysis of Solid Cancer Needle Biopsy Samples
    Sambhavi Animesh, Ruchi Choudhary, Xin Yi Ng, Joshua K. Tay, Wan-Qin Chong, Boon Cher Goh, Melissa J. Fullwood · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  55. Effects of forced cohesin eviction and retention on X-inactivation and autosomes
    Andrea J. Kriz, David Colognori, Hongjae Sunwoo, Behnam Nabet, Jeannie T. Lee · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  56. 4D chromosome reconstruction elucidates the spatial reorganization of the mammalian X-chromosome
    Anna Lappala, Chen‐Yu Wang, Andrea J. Kriz, Hunter Michalk, Kevin Tan, Jeannie T. Lee, Karissa Y. Sanbonmatsu · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  57. Eukaryotic Genome in Three Dimensions
    Sergey V. Razin, Alexey A. Gavrilov, Sergey V. Ulianov · 2020 · Springer eBooks
  58. Meiosis-Specific Cohesin Complexes Display Distinct and Essential Roles in Mitotic ESC Chromosomes
    Eui-Hwan Choi, Young Eun Koh, Seobin Yoon, Yoonsoo Hahn, Keun Pil Kim · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  59. Characterization of DNA extrusion scenarios underlying aggregate Hi-C patterns by a new computational framework
    Xizhe Zhang, G. Gogoshin, S. Branciamore · 2021 · bioRxiv
  60. DNA damage signaling regulates cohesin stabilization and promotes meiotic chromosome axis morphogenesis
    Zhouliang Yu, Abby F. Dernburg · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  61. The loader complex Scc2/4 forms co-condensates with DNA as loading sites for cohesin
    Sarah Zernia, Dieter Kamp, Johannes Stigler · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  62. Rearrangement of T Cell Genome Architecture Regulates GVHD
    Yaping Sun, Gabrielle A. Dotson, Lindsey A. Muir, Scott Ronquist, Katherine I. Oravecz-Wilson, Daniel Peltier, Keisuke Seike, Lu Li, Walter Meixner, Indika Rajapakse et al. · 2021 · SSRN Electronic Journal
  63. Faculty Opinions recommendation of Loop extrusion as a mechanism for formation of DNA damage repair foci.
    Sophie E. Polo · 2021 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  64. Bioinformatics analysis of multi-omics data elucidates the primary function of Oct4 in gene regulation and pluripotency maintenance
    Le Xiong · 2022 · eDiss (Georg-August-Universität Göttingen)
  65. Chromatin reorganization, signaling responses and non-coding RNA regulators in homeostasis and senescence
    Nataša Josipović · 2022 · eDiss (Georg-August-Universität Göttingen)
  66. Rearrangement of T Cell Genome Architecture Regulates GVHD
    Yaping Sun, Gabrielle A. Dotson, Lindsey A. Muir, Scott Ronquist, Katherine I. Oravecz-Wilson, Daniel Peltier, Keisuke Seike, Lu Li, Walter Meixner, Indika Rajapakse et al. · 2022 · SSRN Electronic Journal
  67. Faculty Opinions recommendation of Organizational principles of 3D genome architecture.
    Mary Grace Goll · 2020 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  68. Faculty Opinions recommendation of Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development.
    Amy L. Kenter · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  69. Faculty Opinions recommendation of Human cohesin compacts DNA by loop extrusion.
    Wei Xie · 2020 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  70. Faculty Opinions recommendation of Genome organization drives chromosome fragility.
    Sherif F. El‐Khamisy · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  71. Faculty Opinions recommendation of Transcription elongation can affect genome 3D structure.
    Daniel Reines · 2020 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  72. Faculty Opinions recommendation of Human cohesin compacts DNA by loop extrusion.
    Giacomo Cavalli, Ivana Jerković · 2020 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  73. Faculty Opinions recommendation of Genome organization drives chromosome fragility.
    Scott H. Kaufmann · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  74. Faculty Opinions recommendation of Cohesin loss eliminates all loop domains.
    William James Greenleaf, Viviana I. Risca · 2017 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  75. Faculty Opinions recommendation of Principles of Chromosome Architecture Revealed by Hi-C.
    Roderic Guigó · 2018 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  76. Random folding drives the emergence of topologically associating domains in chromatin three-dimensional structure
    Luming Meng, Qiong Luo · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  77. A de novo Transcription-Dependent TAD Boundary Underpins Critical Multiway Interactions During Antibody Class Switch Recombination
    Julia Costea, Ursula E. Schoeberl, Daniel Malzl, Maximilian von der Linde, Johanna Fitz, Marina Makharova, Anton A. Goloborodko, Rushad Pavri · 2022 · SSRN Electronic Journal
  78. Genomic tools and models for investigating the role of germline diversity in mouse antibody repertoire development.
    Justin T. Kos · 2022
  79. Structural basis for preservation of a subset of Topologically Associating Domains in Interphase Chromosomes upon cohesin depletion
    Davin Jeong, Guang Shi, Xin Li, Dave Thirumalai · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  80. Exploring the roles of RNAPII in genome organization
    Shu Zhang · 2022 · eDiss (Georg-August-Universität Göttingen)
  81. Women’s contribution in understanding how topoisomerases, supercoiling, and transcription control genome organization
    Laura Martin, Maria Victoria Neguembor, Maria Pia Cosma · 2023 · Frontiers in Molecular Biosciences
  82. Contribution of the IGCR1 regulatory element and the 3’Igh CBEs to Regulation of Igh V(D)J Recombination
    Zhuoyi Liang, Li-Juan Zhao, Adam Yongxin Ye, Sherry G. Lin, Yiwen Zhang, Chun-Guang Guo, Hai-Qiang Dai, Zhao-Qing Ba, F. Alt · 2023 · bioRxiv
  83. Dependency of 3D chromatin folding on RNA polymerase II at different cell cycle stages
    Nadine Übelmesser · 2023 · eDiss (Georg-August-Universität Göttingen)
  84. Structural basis for preservation of a subset of Topologically Associating Domains in Interphase Chromosomes upon cohesin depletion
    Davin Jeong, Guang Shi, Xin Li, Dave Thirumalai · 2023 · eLife
  85. A practical guide for essential analyses of Hi-C data
    Yu Liu, Erica M. Hildebrand · 2024 · Elsevier eBooks
  86. Structural basis for preservation of a subset of Topologically Associating Domains in Interphase Chromosomes upon cohesin depletion
    Davin Jeong, Guang Shi, Xin Li, Dave Thirumalai · 2024 · eLife
  87. Additional file 1 of Multiple epigenetic factors co-localize with HMGN proteins in A-compartment chromatin
    Bing He, Iris Zhu, Yuri V. Postnikov, Takashi Furusawa, Lisa M. Miller Jenkins, Ravikanth Nanduri, Michael Bustin, David Landsman · 2022 · Figshare
  88. Additional file 5 of Multiple epigenetic factors co-localize with HMGN proteins in A-compartment chromatin
    Bing He, Iris Zhu, Yuri V. Postnikov, Takashi Furusawa, Lisa M. Miller Jenkins, Ravikanth Nanduri, Michael Bustin, David Landsman · 2022 · Figshare
  89. Additional file 3 of Multiple epigenetic factors co-localize with HMGN proteins in A-compartment chromatin
    Bing He, Iris Zhu, Yuri V. Postnikov, Takashi Furusawa, Lisa M. Miller Jenkins, Ravikanth Nanduri, Michael Bustin, David Landsman · 2022 · Figshare
  90. Additional file 4 of Multiple epigenetic factors co-localize with HMGN proteins in A-compartment chromatin
    Bing He, Iris Zhu, Yuri V. Postnikov, Takashi Furusawa, Lisa M. Miller Jenkins, Ravikanth Nanduri, Michael Bustin, David Landsman · 2022 · Figshare
  91. Additional file 2 of Contribution of variant subunits and associated factors to genome-wide distribution and dynamics of cohesin
    Ana Cuadrado, Daniel Giménez-Llorente, Magali De Koninck, Miguel Ruiz‐Torres, Aleksandar Kojic, Miriam Rodríguez-Corsino, Ana Losada · 2022 · Figshare
  92. Insights in Genetics of Common and Rare Diseases: 2022
    2024 · Frontiers research topics
  93. Exploring Contact Distance Distributions with Google Colaboratory
    Ryuichiro Nakato · 2024 · Methods in molecular biology
  94. Cohesin-dependent loop extrusion: molecular mechanics and role in cell physiology
    Arkadiy K. Golov, Alexey A. Gavrilov · 2024 · Biochemistry (Moscow)
  95. Hi-Compass resolves cell-type chromatin interactions by single-cell and spatial ATAC-seq data across biological scales
    Yuanchen Sun, Wenjie Jiang, Kang-Wen Cai, Na-Na Wei, Fu-Ting Lai, Rui-Xiang Gao, Ze-Yu Kuang, Jia-Lu Zhou, An Liu, Han-Wen Zhu et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  96. PARP1 Regulates 3D Structure and Function of Super-Enhancers and Hormone-Control Regions in Breast Cancer Cells
    Houda Baccara, François Le Dily, Davide Carnevali, Jofre Font-Mateu, Cristina Moreta-Moraleda, Alex Franco Galvez, José Carbonell-Caballero, Martin Teichmann, Miguel Beato, Roni H. G. Wright et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  97. The emerging sequence grammar of 3D genome organisation
    Liezel Tamon, James Ashford, Matthew Nicholls, Marella F. T. R. De Bruijn, Aleksandr B. Sahakyan · 2025 · Human Genetics
  98. Deciphering chromatin domain, domain community and chromunity for 3D genome maps with Mactop
    Ran Duan, Dachang Dang, Shichen Fan, Shaowen Yao, Shihua Zhang · 2025 · Communications Biology
  99. MIA-Jet: Multi-scale Identification Algorithm of Chromatin Jets
    Sion Kim, Minji Kim · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  100. Mechanistic Genome Folding at Scale through the Differentiable Loop Extrusion Model
    Tina Subic, Ali Tuğrul Balcı, Kristina Perevoshchikova, Diego Borges-Rivera, Jieni Hu, Geoffrey Fudenberg, Jacqueline Dresch, Maria D. Chikina · 2025 · bioRxiv (Cold Spring Harbor Laboratory)