Functional implications of genome topology
Cavalli, Giacomo, Misteli, Tom·2013·Nature Structural & Molecular Biology
Cited by (416)
Items 301–400 of 416
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- Insights into genome architecture deduced from the properties of short Lac repressor-mediated DNA loopsPamela J. Perez, Wilma K. Olson · 2016 · Biophysical Reviews
- Rich chromatin structure prediction from Hi-C dataLaraib Malik, Rob Patro · 2015 · bioRxiv
- Multiscale Identification of Topological Domains in ChromatinD. Filippova, Rob Patro, G. Duggal, C. Kingsford · 2013 · Workshop on Algorithms in Bioinformatics
- Sequence-based multiscale modeling for high-throughput chromosome conformation capture (Hi-C) data analysisKelin Xia · 2018 · PLoS ONE
- Metabolic resilience is encoded in genome plasticityLeandro Z. Agudelo, Rémy Tuyéras, Claudia Llinares, Álvaro Morcuende, Yongjin Park, Na Sun, Suvi Linna-Kuosmanen, Naeimeh Atabaki‐Pasdar, Li‐Lun Ho, Kyriaki Galani et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
- Systems Biology Approaches for Understanding Genome ArchitectureSven A. Sewitz, Karen Lipkow · 2016 · Methods in molecular biology
- Quantifying the large-scale chromosome structural dynamics during the mitosis-to-G1 phase transition of cell cycleXiakun Chu, Jin Wang · 2023 · Open Biology
- A novel chromatin insulator regulates the chicken folate receptor gene from the influence of nearby constitutive heterochromatin and the β-globin locusEdgar González-Buendía, Martín Escamilla-Del-Arenal, Rosario Pérez‐Molina, Juan J. Tena, Georgina Guerrero, Fernando Suaste-Olmos, Erandi Ayala-Ortega, José Luis Gómez-Skármeta, Félix Recillas Targa · 2015 · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
- 5D superresolution imaging for a live cell nucleusLi‐An Chu, Shu‐Wei Chang, Wei‐Chun Tang, Yu‐Ting Tseng, Peilin Chen, Bi‐Chang Chen · 2020 · Current Opinion in Genetics & Development
- Bringing the Signal into the NucleusIJsbrand M. Kramer · 2015 · Elsevier eBooks
- Genetic determinants of breast cancer riskJuliet D. French, Stacey L. Edwards · 2020 · Current Opinion in Endocrine and Metabolic Research
- Identification of Fkh1 and Fkh2 binding site variants associated with dynamically bound DNA elements including replication originsA. Zachary Ostrow, Oscar M. Aparicio · 2017 · Nucleus
- Unified theory of human genome reveals a constrained spatial chromosomal arrangement in interphase nucleiS. N. Fatakia, Ishita S. Mehta, Basuthkar Jagadeeshwar Rao · 2015 · arXiv (Cornell University)
- Entropic Tug of War: Topological Constraints Spontaneously Rectify the Dynamics of a Polymer with Heterogeneous FluctuationsAdam H. T. P. Höfler, Iurii Chubak, Christos N. Likos, Jan Smrek · 2026 · Physical Review X
- Cell line-specific features of 3D chromatin organization in hepatocellular carcinomaYeonwoo Kim, Hyeok-Jun Yang, Daeyoup Lee · 2023 · Genomics & Informatics
- Insights from Space: Potential Role of Diet in the Spatial Organization of ChromosomesJustin Martin O'Sullivan, Malina Doynova, Jisha Antony, Florian Pichlmueller, Julia A. Horsfield · 2014 · Nutrients
- New Genes Born-In or Invading Vertebrate GenomesCarlos Herrera-Úbeda, Jordi García‐Fernàndez · 2021 · Frontiers in Cell and Developmental Biology
- Investigation of FTO Gene-BMI Association in a Romanian Sample: a Functional Genomic Interpretation2022 · Biointerface Research in Applied Chemistry
- Maintaining transcriptional homeostasis during cell cycleLucía Ramos-Alonso, Pierre Chymkowitch · 2023 · Transcription
- The identification of hematopoietic-specific regulatory elements for WASp gene expressionJun Zhan, Irudayam Maria Johnson, Matthew M. Wielgosz, Arthur W. Nienhuis · 2016 · Molecular Therapy — Methods & Clinical Development
- Islet Epigenetic Impacts on β‐Cell Identity and FunctionMaria L. Golson · 2021 · Comprehensive physiology
- Revisiting Assessment of Computational Methods for Hi-C Data AnalysisJing Yang, Xingxing Zhu, Rui Wang, Mingzhou Li, Qianzi Tang · 2023 · International Journal of Molecular Sciences
- Peculiar k-mer Spectra Are Correlated with 3D Contact Frequencies and Breakpoint Regions in the Human GenomeWisam Mohammed Hikmat, Aaron Sievers, Michael Hausmann, Georg Lars Hildenbrand · 2024 · Genes
- DeepExDC interprets genomic compartmentalization changes in single-cell Hi-C dataHongqiang Lv, Pei Cao, Wenyao Long, Xiaoran Yin, Shengjun Xu, Laiyi Fu · 2025 · Briefings in Bioinformatics
- Chain Conformation and Packing Structure of Interlocked Ring Polymers in Semidilute Solutions: The Role of Topological CatenationWen-Yuan Song, Lijun Ma, Yingxiang Li, Hong Liu, Guojie Zhang · 2025 · Macromolecules
- Regulation and dysregulation of spatial chromatin structure in the central nervous systemYuki Fujita · 2021 · Anatomical Science International
- Spatial Organization of EpigenomesJonathan Dube, Xue Qing David Wang, Josée Dostie · 2016 · Current Molecular Biology Reports
- In trans promoter activation by enhancers in transient transfectionN. A. Smirnov, С. Б. Акопов, D. A. Didych, Л. Г. Николаев · 2016 · Gene
- Genomic Environments and Their Influence on Transposable Element CommunitiesBrent Saylor, Stefan C. Kremer, T. Ryan Gregory, Karl Cottenie · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- Androgen receptor acts as the transcriptional repressor of the nuclear receptor LRH-1 via the androgen-driven chromatin looping conformation in prostate cancerWenxing You, Tiantian Gao, Haolong Li, Daniel Hau Tak Lam, Wenjuan Xie, Lijia Xiao, Weijie Gao, Dinglan Wu, Junjian Wang, Yuliang Wang et al. · 2025 · Genes & Diseases
- Epigenetic gene regulation and stem cell functionAissa Benyoucef, Marjorie Brand · 2015 · Elsevier eBooks
- On the Concept Of Retrotransposons: Controlling Genome and Making Stress MemoriesDimitrios Noutsopoulos · 2016 · Journal of Biochemistry and Molecular Biology Research
- Chromatin ArchitectureCarsten Carlberg, Ferdinand Molnár · 2016 · Springer eBooks
- Dissecting the Immune System through Gene RegulationHideyuki Yoshida · 2024 · Advances in experimental medicine and biology
- GWAS and 3D chromatin mapping identifies multicancer risk genes associated with hormone-dependent cancersS. Rivera, Juliet D. French, Mainá Bitar, Haran Sivakumaran, Sneha Nair, Susanne Kaufmann, Kristine M. Hillman, Mahdi Moradi Marjaneh, Jonathan Beesley, Stacey L. Edwards · 2024 · PLoS Genetics
- Uncovering the lung cancer mechanisms through the chromosome structural ensemble characteristics and nucleation seedsWen‐Ting Chu, Jin Wang · 2024 · The Journal of Chemical Physics
- Geometric Diagrams of Genomes: constructing a visual grammar for 3D genomicsCarla Molins-Pitarch, Jonathan Khao, Santiago Bonet, Yolanda Justicia, Clementina Altube, Mike N. Goodstadt, Francesc Ribot, Erez Lieberman Aiden, Nicola Neretti, Gael G. McGill et al. · 2025 · Genome biology
- Acute Promyelocytic Leukaemia: Epigenetic Function of the PML-RARα OncogeneJulia P. Hofmann, Paolo Salomoni · 2016 · Springer eBooks
- Rapidly evolving in humans topologically associating domainsGennadi V. Glinsky · 2015 · arXiv (Cornell University)
- Functional Partition of a Bacterial Chromosome Through the Interplay of Nucleoid Associated Proteins and CondensinVirginia S. Lioy, Axel Cournac, Martial Marbouty, Stéphane Duigou, Julien Mozziconacci, Olivier Esppli, Frédéric Boccard, Romain Koszul · 2018 · SSRN Electronic Journal
- Multiparametric Signature of Glioblastoma Differentiation Revealed by Imaging of Cellular Epigenetic LandscapesChen Farhy, Santosh Hariharan, Jarkko Ylanko, Lotte van Woudenberg, Flavio Cimadamore, Fernando Ugarte, E. Camilla Forsberg, Chun‐Teng Huang, David William Andrews, Alexey V. Terskikh · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
- Magnetic Polymer Models for Epigenomic Organisation and Phase SeparationDavide Colì, Davide Michieletto, Davide Marenduzzo, Enzo Orlandini · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
- Physical Principles of Retroviral Integration in the Human GenomeDavide Michieletto, M. Lusic, Davide Marenduzzo, Enzo Orlandini · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
- Shaping Epigenetic Memory via Genomic Bookmarking: Supplementary InformationD. Michieletto, M. Chiang, D. Colì, Argyris Papantonis, Enzo Orlandini, P. R. Cook, D. Marenduzzo · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
- Multiscale Identification of Topological Domains in ChromatinDarya Filippova, Rob Patro, Geet Duggal, Carl Kingsford · 2013 · arXiv (Cornell University)
- Regulation of the Secretory PathwayAnita Capalbo, Jorge Cancino, Alberto Luini · 2015 · Elsevier eBooks
- Transvection is a plastic phenotypeXinyang Bing · 2013 · Lu Zone Ul (Laurentian University)
- Chromatin remodeling and dna topology in transcription and genome stabilityJenna Persson · 2013 · Figshare
- Chromatin Structure and DomainsFanny Izard, Charlotte Grimaud · 2017 · Encyclopedia of Life Sciences
- The Drosophila Interactions Database: Integrating The Interactome And TranscriptomeThilakam Murali · 2013 · Human Biology
- Design (and) principles of nuclear dynamics in StockholmYaron Shav‐Tal, Jan Lammerding · 2015 · Nucleus
- Organization of functional processes in the cell nucleus: The order emerging out of the disorderSergey V. Razin, Alexey A. Gavrilov · 2015 · Moscow University Biological Sciences Bulletin
- Mapping and Visualizing Spatial Genome OrganizationChristopher J. F. Cameron, James Fraser, Mathieu Blanchette, Josée Dostie · 2016 · Springer eBooks
- Emergence of FunctionIndika Rajapakse, Steve Smale · 2016 · arXiv (Cornell University)
- Energy-Dependent Intranuclear Movements: Role of Nuclear Actin and MyosinsGuillaume Huet, Maria Kristina Vartiainen · 2016 · Springer eBooks
- HBP: an integrative and flexible pipeline for the interaction analysis of Hi-C datasetChaobin He, Ping Li, Minglei Shi, Yan Zhang, Bingyu Ye, Dejian Xie, Wenlong Shen, Zhihu Zhao · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
- Repacking chromatin for therapyAlexandra Zidovska · 2017 · Nature Biomedical Engineering
- Systems Biology of Genome Structure and DynamicsZahra Fahmi, Sven A. Sewitz, Karen Lipkow · 2018 · RNA technologies
- Identification of Genomic Alterations Through Multilevel DNA Structural AnalysisRyan K. Shultzaberger, John Dresios · 2018 · Methods in molecular biology
- Analysis of Chromatin Interactions of BEAF-associated Promoters Using 4CShraddha Shrestha · 2018
- DNA Supercoil Unwinding by Variola Virus Type IB Topoisomerase is Accelerated by Superhelical Density and Hindered by Enzyme-DNA InteractionsBreeana G. Anderson · 2015
- Noncoding RNAs and Epigenetic Regulation in AgingAnnadurai Thangaraj, P. Periyasamy, Liang Chen, Naseer A Kutchy, Guo-Ku Hu, S. Buch · 2021 · Elsevier eBooks
- Human PRE-PIK3C2B exhibits long-range intra- and inter-chromosomal interactions with genomic regions enriched in repressive marksJayant Maini, Ankit Kumar Pathak, Kausik Bhattacharyya, Narendra Kumar, Ankita Narang, N. F. Jain, Inderpreet Singh, Vanika Dhingra, Vani Brahmachari · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- Deciphering hierarchical organization of topologically associated domains through change-point testingHaipeng Xing, Yingru Wu, Chen, Yong, Zhang, Michael · 2019 · arXiv (Cornell University)
- Chromatin ArchitectureCarsten Carlberg, Ferdinand Molnár · 2013 · Springer eBooks
- Aspects of the normal genome2019 · Elsevier eBooks
- IntroductionDavide Michieletto · 2016 · Springer theses
- Aspects of the Normal Genome2015 · Elsevier eBooks
- Bibliography2019 · Elsevier eBooks
- Replication Labeling Methods for Super-Resolution Imaging of Chromosome Territories and Chromatin DomainsEzequiel Miron, Joseph Windo, Fena Ochs, Lothar Schermelleh · 2022 · Methods in molecular biology
- Uncovering the lung cancer mechanisms through the chromosome structural ensemble characteristicsWen‐Ting Chu, Jin Wang · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- Discovery of dynamic changes in 3D chromatin architecture through polymer physics modelAnubhooti, Abdul Wasim, Priyanka Kriti Narayan, Jagannath Mondal, Jagan M.R. Pongubala · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Genome structural dynamics: insights from Gaussian network analysis of Hi-C dataAnupam Banerjee, She Zhang, İvet Bahar · 2024 · Briefings in Functional Genomics
- BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundariesYangyang Liu, Bingqiang Liu, Juntao Liu · 2025 · Genome Research
- Islet Epigenetic Impacts on β‐Cell Identity and FunctionMaria L. Golson · 2021 · Comprehensive physiology
- Differential Expression of Lamins and Modulation of Chromatin Architecture in Carcinogenesis: tous pour un et un pour tousShreyasi Dey Sarkar, Duhita Sengupta, Kaushik Sengupta · 2025 · Sub-cellular biochemistry/Subcellular biochemistry
- Bibliography2025 · Elsevier eBooks
- Additional file 2 of Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patternsChengyi Wu, Huang, Jialiang · 2024 · Figshare
- Additional file 1 of Deciphering hierarchical organization of topologically associated domains through change-point testingHaipeng Xing, Wu, Yingru, Zhang, Michael Q., Chen, Yong · 2021 · Figshare
- Additional file 1 of Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patternsChengyi Wu, Huang, Jialiang · 2024 · Figshare
- Professor Emma Whitelaw, a pioneer of epigenetic inheritanceAlyson Ashe, Jessica J. Hawes · 2026 · Frontiers in Epigenetics and Epigenomics
- Predicting statistics of gene translocation events: Role of chromatin compaction and double-strand DNA breakAnirudh Jairam, Shuvadip Dutta, Sangram Kadam, Kiran Kumari, Ranjith Padinhateeri · 2026 · Physical review. E
- EpiTADformer: A Transformer-Based Model for High-Resolution TAD Boundary Detection Using Epigenomic Signal EmbeddingsMy Ngoc Ha Nguyen, Shaojun Tang, Joseph L. McClay, Joshua Chuck Harrell, Mikhail G. Dozmorov · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- Genome-wide identification and characterization of C. elegans DNA replication origins during developmentMarta Rodríguez‐Martínez · 2013 · theses.fr (ABES)
- Dynamique de l'organisation nucléaire des séquences d'ADN répétées centromériques humaines au cours du cycle cellulaireJean Ollion · 2014 · theses.fr (ABES)
- Engineering autonomous and programmable biosensors through synthetic biology : integrating multiplexed biomarker detection and biomolecular signal processing into next-generation diagnosticsAlexis Courbet · 2015
- Non-codings RNAs, regulators of gene expression in Arabidopsis thaliana root developmental plasticityNatali Romero-Barrios · 2016 · theses.fr (ABES)
- Dynamique et organisation supérieure de la chromatine : exploration des domaines d’association topologiqueVuthy Ea · 2014 · theses.fr (ABES)
- Le HRS-Seq : une nouvelle méthode d'analyse à haut-débit des séquences génomiques associées aux compartiments nucléairesMarie-Odile Baudement · 2015
- The functional and spatial organization of chromatin during Thymocyte developmentYousra Ben Zouari · 2018
- Exploring the structural and functional dynamics of the X-inactivation centre locus during developmentRafael Galupa · 2017 · theses.fr (ABES)
- 3D genome conformation and gene expression in fetal pig muscle at late gestationMaría Marti-Marimon · 2018 · theses.fr (ABES)
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