Long-Range Chromatin Interactions

Dekker, Job, Misteli, Tom·2015·Cold Spring Harbor Perspectives in Biology

Cited by (255)

Items 201–255 of 255

  1. Hi-C Resolution Enhancement with Genome Sequence Data
    Dmitrii V. Kriukov, Mark Zaretckii, Igor Kozlovskii, Mikhail Zybin, Nikita Koritskiy, Mariia Bazarevich, Ekaterina E. Khrameeva · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  2. Polymer dynamics relates chromosome mixing to temporal changes in biological contact maps
    Gaurav Bajpai, Samuel A. Safran · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  3. Yeast ATM and ATR use different mechanisms to spread histone H2A phosphorylation around a DNA double-strand break
    Kevin Li, Gabriel Bronk, Jané Kondev, James E. Haber · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  4. Spatial proximity and gene function: a new dimension in prokaryotic gene association network analysis with 3D-GeneNet
    Yuan Gao, Bin Ma, Qianshuai Xu, Yuna Peng, Huimin Gong, Aohan Guan, Kexin Hua, Paul Richard Langford, Hui Jin, Rui Luo · 2024 · Briefings in Bioinformatics
  5. StripePy: fast and robust characterization of architectural stripes
    Andrea Raffo, Roberto Rossini, Jonas Paulsen · 2025 · Bioinformatics
  6. Mapping of chromatin architecture and enhancer-promoter interactions in the cochlea
    Tuba Ege, Celia R. Bloom, Mi Ζhou, Huizhan Liu, Litao Tao · 2025 · Frontiers in Molecular Biosciences
  7. High-throughput capture of actively transcribed region-interacting sequences reveals an intricate promoter-centered regulatory network
    Xinxin Li, Jinsheng Xu, Xiaohao Yan, Jiayong Zhong, Chunhui Hou, Chuan‐Le Xiao, Longjian Niu, Wei Chi · 2025 · Molecular Cell
  8. Image-based epigenetic profiling with deep learning and high-speed super-resolution microscopy
    Yicheng Wang, Nur Syatila Ab Ghani, Munmee Dutta, Shungo Adachi, Kaoru Katoh, Masakazu Namihira, Toutai Mitsuyama, Yutaka Saito · 2026 · Epigenetics & Chromatin
  9. Cell Division: Single-Cell Physiology Reveals Secrets of Chromosome Condensation
    Kerry Bloom · 2018 · Current Biology
  10. Inner and Outer DNA Loops in Cell Nuclei: Evidence from Pulsed-Field Comet Assay
    Marianna Chopei, V. Olefirenko, K. S. Afanasieva, Andrei Sivolob · 2022 · Cytology and Genetics
  11. The PENGUIN approach to reconstruct protein interactions at enhancer-promoter regions and its application to prostate cancer
    Alexandros Armaos, François Serra, Iker Núñez‐Carpintero, Ji-Heui Seo, Sylvan C. Baca, Stefano Gustincich, Alfonso Valencia, Matthew L. Freedman, Davide Cirillo, Claudia Giambartolomei et al. · 2023 · Nature Communications
  12. Multiscale 3D genome organization underlies duck fatty liver with no adipose inflammation or serious injury
    Mengfei Ning, Linfei Song, Xinyu Niu, Yiming Wang, Wenjie Liu, Jiaxiang Hu, Han Cai, Weitao Song, Long Liu, Huifang Li et al. · 2024 · International Journal of Biological Macromolecules
  13. PETScan: score-based genome-wide association analysis of RNA-Seq and ATAC-Seq data
    Yajing B. Hao, Tal Kafri, Fei Zou · 2026 · Bioinformatics
  14. Chromosome Territorial Organization Drives Efficient Protein Complex Formation: A Hypothesis.
    Manindra Bera, Ramalingam Venkat Kalyana Sundaram · 2019 · Europe PMC (PubMed Central)
  15. 3D-FISH Analysis of the Spatial Genome Organization in Skin Cells in Situ
    Andrei N. Mardaryev, Michael Y. Fessing · 2020 · Methods in molecular biology
  16. Microbiota in the context of epigenetics of the immune system
    Katarzyna Placek · 2020 · Elsevier eBooks
  17. Systematic discovery of directional regulatory motifs associated with human insulator sites
    Naoki Osato, Michiaki Hamada · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  18. Genomic Atlas 2.0 Emerging Strategies and Technologies in Advanced Genetic Mapping
    Mohammad Odah · 2024 · Preprints.org
  19. Promoter interactions direct chromatin folding in embryonic stem cells
    Swastika Sanyal, Lucia Molnárová, Juraj Gregáň · 2017 · Nature Structural & Molecular Biology
  20. Three-dimensional Folding of Eukaryotic Genomes
    Tsung-Han S. Hsieh · 2017 · eScholarship@UMassChan
  21. Epigenome comparisons reveal linkage between gene expression and postnatal remodeling of chromatin domain topology
    Bruce H. Howard, Tazuko H. Hirai, Valya R. RUSSANOVA · 2018 · PLoS ONE
  22. Ubiquitylation and SUMOylation: An Orchestrated Regulation During DNA Damage Repair
    Sara Espinoza-Corona, María Luisa Bazán‐Tejeda, Ulises Omar García‐Lepe, Rosa María Bermúdez‐Cruz · 2018 · InTech eBooks
  23. Analysis of Chromatin Interactions of BEAF-associated Promoters Using 4C
    Shraddha Shrestha · 2018
  24. Cellular structure and molecular cell biology
    Luciana Amaral Haddad · 2019 · Elsevier eBooks
  25. Characterizing the Genome-wide Associations of Somatic Mutations and Chromatin Accessibility in Cancer
    Oliver Ocsenas · 2020 · TSpace (University of Toronto)
  26. Analysis of Genome Architecture Mapping Data with a Machine Learning and Polymer-Physics-Based Tool
    Luca Fiorillo, Mattia Conte, Andrea Esposito, Francesco Musella, Francesco Flora, Andrea M. Chiariello, Simona Bianco · 2021 · Lecture notes in computer science
  27. Genome Organization and Dynamics Specialty Grand Challenge
    Brian Freeman · 2021 · Frontiers in Molecular Biosciences
  28. Long non-coding RNA functional annotation : machine learning approaches
    Yu Zhang · 2021
  29. Faculty Opinions recommendation of Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer.
    Michael Cole, Evelien Schaafsma · 2020 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  30. Faculty Opinions recommendation of Epigenetic plasticity and the hallmarks of cancer.
    Robert A. Copeland · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  31. Model-based distance embedding with applications to chromosomal conformation biology
    Yuping Zhang, Disheng Mao, Zhengqing Ouyang · 2022 · The Annals of Applied Statistics
  32. Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration
    Nana Matoba, Ivana Yoseli Quiroga, Douglas H. Phanstiel, Hyejung Won · 2020 · Journal of Visualized Experiments
  33. Combined promoter-capture Hi-C and Hi-C analysis reveals a fine-tuned regulation of 3D chromatin architecture in colorectal cancer
    Ajay Kumar Saw, Ayush Madhok, Anupam Bhattacharya, Soumyadeep Nandi, Sanjeev Galande · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  34. The molecular principles of chromosomal translocations
    Patrick Streb · 2023
  35. Epigenetic regulation: Histone modifying enzymes as targets for novel therapeutics
    Nicholas Dietrich, Trevor Archer · 2023 · Elsevier eBooks
  36. Discovering causal genes and comorbidities for asthma
    Roan E. Zaied, Justin Martin O'Sullivan, Sreemol Gokuladhas, Caroline G. Walker · 2023 · Research Square
  37. Hi-C sequencing unravels dynamic three-dimensional chromatin interactions in muntjac lineage: insights from chromosome fusions in Fea’s muntjac genome
    Maryam Jehangir, Syed Farhan Ahmad, Worapong Singchat, Thitipong Panthum, Thanyapat Thong, Pakpoom Aramsirirujiwet, Artem Lisachov, Narongrit Muangmai, Kyudong Han, Akihiko Koga et al. · 2023 · Chromosome Research
  38. An in silico procedure for generating protein-mediated chromatin interaction data and comparison of significant interaction calling methods
    Shuyuan Lou, Shi-Li Lin · 2024 · PLoS ONE
  39. Chromatin compaction
    Randall H. Morse · 2024 · Elsevier eBooks
  40. Análise do papel dos genes HOX na regulação de vias gênicas compartilhadas entre o desenvolvimento placentário e tumoral
    Danielle Barbosa Brotto · 2019 · Digital Library of Theses and Dissertations (Universidade de São Paulo)
  41. Step-by-Step Protocol to Generate Hi-C Contact Maps Using the rfy_hic2 Pipeline
    Hideki Tanizawa, Claire Chung, Shun-Ichiro Fuse, Tomomi Hayashi, Peter Weisel, Ken-ichi Noma · 2024 · Methods in molecular biology
  42. Outlining a Dialectical Hypothesis on the C-Value Paradox in the Light of Quantum Chemistry
    José M. Gómez · 2025 · SSRN Electronic Journal
  43. Sequence-independent 6mA methyltransferases for epigenetic profiling and editing
    Jiachen Zhang, Yumiao Zhang, Jinghan Diao, Yifan Liu, Shan Gao · 2025 · Trends in Genetics
  44. Effects of topological domain disruption on transcriptional regulation are chromatin context dependent
    Ángel Josué Cerecedo-Castillo, Diana Itzé Mojica-Santamaría, Hober Nelson Núñez-Martínez, Carlos Alberto Peralta‐Álvarez, Gustavo Tapia-Urzúa, Georgina Guerrero, Rodrigo G. Arzate‐Mejía, Félix Recillas Targa · 2026 · Epigenetics & Chromatin
  45. Etude de la topoisomérase VI et de l'interacteur TFIIFalpha dans les voies de signalisation rétrograde de l'oxygène singulet et antérograde impliquant les protéines PPR chez Arabidopsis thaliana
    Laura Dimnet · 2018
  46. Maintien de l'hétérochromatine en réponse aux dommages à l'ADN dans des cellules de mammifères
    Anna Fortuny · 2019 · theses.fr (ABES)
  47. Mécanismes transcriptionnels et épigénétiques dans la régulation de l'expression du locus IgH murin au cours du développement des lymphocytes B
    Chloé Oudinet · 2020
  48. Etude bioinformatique intégrative : déterminants et dynamique des interactions chromosomiques à longue distance
    Alexandre Heurteau · 2019
  49. Étude multi-omics des mutations des isocitrates déshydrogénases dans les leucémies aiguës myéloïdes
    Alexis Hucteau · 2023 · theses.fr (ABES)
  50. A unified photosensitizer platform for in situ DNA-, RNA-, and protein-directed proximity labeling
    Elijah Biletch, Conor P. Herlihy, Lidan Li, Mary Krebs, Conor J Kelly, Nicolas J. Longhi, Olivia Weissenfels, Hanna G. Goldberg, Kyle Brandt, Jonathan B. Grimm et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  51. 3D-FISH Analysis of the Spatial Genome Organization in Mammalian Tissue In Situ
    Andrei N. Mardaryev, Michael Y. Fessing · 2026 · Methods in molecular biology
  52. A cellular (bio) photon field in mitochondrial-chromatin cross-talk: a hypothesis
    Roeland Van Wijk, Eduard P.A. Van Wijk · 2026 · Frontiers in Photobiology
  53. Navigating the cancer cell nucleus: lamins at the interface of epigenetic regulation and tumorigenesis
    Subhadip Kundu · 2026 · Molecular Biology Reports
  54. ZBTB Transcription Factors Refine Cohesin Recruitment at Gene Promoters beyond CTCF
    Sumeyye Bakim, Elif GÜLBAHÇE MUTLU, Nahide Hakanoglu, Evin Uyar · 2026 · Cytology and Genetics
  55. Distinguishing insulators from enhancers by their ability to block long-range contacts using HiCAggR
    Naomi Schickele, Olivier Fosseprez, Robel Tesfaye, Charlène Perrois, Nicolas Chanard, Anne-Laure Finoux, Eldon G. Emberly, Pascal GP Martin, Stéphane Schaak, Olivier Cuvier · 2026 · Research Square