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, Hugnot, Jean-Philippe, Tanay, Amos, Cavalli, Giacomo·2017·Cell
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Items 401–500 of 999
- Temporally Correlated Active Forces Drive Segregation and Enhanced Dynamics in Chromosome PolymersSumitabha Brahmachari, Tomer Markovich, F. C. MacKintosh, José N. Onuchic · 2024 · PRX Life
- ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-CYousra Ben Zouari, Anne Molitor, N. Sikorska, V. Pancaldi, Tom Sexton · 2018 · Genome Biology
- Characterizing the 3D structure and dynamics of chromosomes and proteins in a common contact matrix frameworkRichard J. Lindsay, Bill Pham, Tongye Shen, Rachel Patton McCord · 2018 · Nucleic Acids Research
- Evolution and function of chromatin domains across the tree of lifeMichael-Florian Szalay, Blanka Majchrzycka, Ivana Jerković, Giacomo Cavalli, Daniel M. Ibrahim · 2024 · Nature Structural & Molecular Biology
- Functional maps of a genomic locus reveal confinement of an enhancer by its target geneMathias Eder, Christina J. I. Moene, Lise Dauban, Mikhail D. Magnitov, James A. Drayton, Marcel de Haas, Christ Leemans, Martijn Verkuilen, Elzo de Wit, Anders S. Hansen et al. · 2025 · Science
- Many facades of CTCF unified by its coding for three-dimensional genome architectureQiang Wu, Peifeng Liu, Leyang Wang · 2020 · Journal of genetics and genomics/Journal of Genetics and Genomics
- Controlled X‐chromosome dynamics defines meiotic potential of female mouse in vitro germ cellsJacqueline Severino, Moritz Bauer, Tom Mattimoe, Niccolò Arecco, Luca Cozzuto, Patricia Lorden, Norio Hamada, Yoshiaki Nosaka, So I Nagaoka, Pauline N. C. B. Audergon et al. · 2022 · The EMBO Journal
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- Three‐dimensional chromatin re‐organization during muscle stem cell agingBenjamin A. Yang, Jacqueline A. Larouche, K. Sabin, Paula M. Fraczek, Stephen C.J. Parker, Carlos A. Aguilar · 2023 · Aging Cell
- Enhancer-promoter interactions are reconfigured through the formation of long-range multiway hubs as mouse ES cells exit pluripotencyDavid Lando, Xiaoyan Ma, Yang Cao, Aleksandra Jartseva, Tim J. Stevens, Wayne Boucher, Nicola Reynolds, Bertille Montibus, Dominic Hall, Andreas Lackner et al. · 2024 · Molecular Cell
- Extrusion fountains are restricted by WAPL-dependent cohesin release and CTCF barriersNing Qing Liu, Mikhail D. Magnitov, Marijne M. G. A. Schijns, Tom van Schaik, Hans Teunissen, Bas van Steensel, Elzo de Wit · 2025 · Nucleic Acids Research
- Genomic analysis of transcriptional networks directing progression of cell states during MGE developmentMagnus Sandberg, Leila Taher, Jianxin Hu, Brian L. Black, Alex S. Nord, John L.R. Rubenstein · 2018 · Neural Development
- HiCNN2: Enhancing the Resolution of Hi-C Data Using an Ensemble of Convolutional Neural NetworksTong Liu, Zheng Wang · 2019 · Genes
- The Interplay between Phase Separation and Gene-Enhancer Communication: A Theoretical StudyAndrea M. Chiariello, Federico Corberi, Mario Salerno · 2020 · Biophysical Journal
- Three-dimensional interactions between enhancers and promoters during intestinal differentiation depend upon HNF4Chen, Lei, Cao, Weihuan, Aita, Rohit, Aldea, Dennis, Flores, Juan, Gao, Nan, Bonder, Edward M., Ellison, Christopher E., Verzi, Michael P. · 2021 · Cell Reports
- Coding and noncoding variants in EBF3 are involved in HADDS and simplex autismEvin M. Padhi, Tristan J. Hayeck, Zhang Cheng, Sumantra Chatterjee, Brandon J. Mannion, Marta S. Byrska‐Bishop, Marjolaine Willems, Lucile Pinson, Sylvia Redon, Caroline Bénech et al. · 2021 · Human Genomics
- Integration of DNA damage responses with dynamic spatial genome organizationMia Stanić, Karim Mekhail · 2021 · Trends in Genetics
- Precise measurements of chromatin diffusion dynamics by modeling using Gaussian processesGuilherme Monteiro Oliveira, Attila Oravecz, Dominique Kobi, Manon Maroquenne, Kerstin Bystricky, Tom Sexton, Nacho Molina · 2021 · Nature Communications
- 3D genome organization in the epithelial-mesenchymal transition spectrumQing You Pang, Tuan Zea Tan, Vignesh Sundararajan, Yi-Chia Chiu, Edward Yu Wing Chee, Vin Yee Chung, Mahesh Arjandas Choolani, Ruby Yun‐Ju Huang · 2022 · Genome biology
- Predicting 3D chromatin interactions from DNA sequence using Deep LearningRobert S. Piecyk, Luca Schlegel, Frank M. Johannes · 2022 · Computational and Structural Biotechnology Journal
- Painters in chromatin: a unified quantitative framework to systematically characterize epigenome regulation and memoryAmith Z. Abdulla, Cédric Vaillant, Daniel Jost · 2022 · Nucleic Acids Research
- CTCF and cohesin promote focal detachment of DNA from the nuclear laminaTom van Schaik, Ning Qing Liu, Stefano Giustino Manzo, Daan Peric‐Hupkes, Elzo de Wit, Bas van Steensel · 2022 · Genome biology
- 3D genome organization links non-coding disease-associated variants to genesGisela Orozco, Stefan Schoenfelder, Nicolas J. Walker, S. Eyre, Peter Fraser · 2022 · Frontiers in Cell and Developmental Biology
- ERK1/2 signalling dynamics promote neural differentiation by regulating chromatin accessibility and the polycomb repressive complexClaudia I. Semprich, Lindsay Davidson, Adriana Amorim Torres, Harshil Patel, James Briscoe, Vicki Metzis, Kate G. Storey · 2022 · PLoS Biology
- Spatial clustering and common regulatory elements correlate with coordinated gene expressionJingyu Zhang, Hengyu Chen, Ruoyan Li, David A. Taft, Guang Yao, Fan Bai, Jianhua Xing · 2019 · PLoS Computational Biology
- H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactionsYichao Cai, Ying Zhang, Yan Ping Loh, Jia Qi Tng, Mei Chee Lim, Zhendong Cao, Anandhkumar Raju, Erez Lieberman Aiden, Shang Li, Lakshmanan Manikandan et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- Hypoxia-induced phase separation of ZHX2 alters chromatin looping to drive cancer metastasisChuan Gao, Ang Gao, Yulong Jiang, Ronghui Gao, Yan Guo, Zirou Peng, Weiwei Jiang, Mengyao Zhang, Zirui Zhou, Chaojun Yan et al. · 2025 · Molecular Cell
- Into the Fourth Dimension: Dysregulation of Genome Architecture in Aging and Alzheimer’s DiseaseWarren Winick‐Ng, Rebecca Jane Rylett · 2018 · Frontiers in Molecular Neuroscience
- Heterogeneous Loop Model to Infer 3D Chromosome Structures from Hi-CLei Liu, Min Hyeok Kim, Changbong Hyeon · 2019 · Biophysical Journal
- Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networksMiguel Madrid-Mencía, Emanuele Raineri, T. B. Ngoc Cao, Véra Pancaldi · 2020 · Nucleic Acids Research
- Condensin I subunit Cap-G is essential for proper gene expression during the maturation of post-mitotic neuronsAmira Hassan, Pablo Araguas Rodriguez, Stefan K. Heidmann, Emma L Walmsley, Gabriel Aughey, Tony D. Southall · 2020 · eLife
- Epigenetic regulation of cortical neurogenesis; orchestrating fate switches at the right time and placeManal A. Adam, Corey C. Harwell · 2020 · Current Opinion in Neurobiology
- In situ Chromatin Interaction Analysis Using Paired‐End Tag SequencingPing Wang, Yuliang Feng, Kun Zhu, Haoxi Chai, Ya‐Ting Chang, Xiaofei Yang, Xiyuan Liu, Chen Shen, Eva Gega, Byoungkoo Lee et al. · 2021 · Current Protocols
- Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivationGiancarlo Bonora, Vijay Ramani, Ritambhara Singh, He Fang, Dana L. Jackson, Sanjay R Srivatsan, Ruolan Qiu, Choli Lee, Cole Trapnell, Jay Shendure et al. · 2021 · Genome biology
- Neuron-specific chromosomal megadomain organization is adaptive to recent retrotransposon expansionsSandhya Chandrasekaran, Sergio Espeso‐Gil, Yong‐Hwee Eddie Loh, Behnam Javidfar, Bibi S. Kassim, Yueyan Zhu, Yuan Zhang, Yuhao Dong, Lucy K. Bicks, Haixin Li et al. · 2021 · Nature Communications
- DNA methylation in transposable elements buffers the connection between three-dimensional chromatin organization and gene transcription upon rice genome duplicationZhenfei Sun, Yunlong Wang, Zhaojian Song, Hui Zhang, Yuanda Wang, Kunpeng Liu, Min Ma, Pan Wang, Yaping Fang, Detian Cai et al. · 2022 · Journal of Advanced Research
- Contributions of 3D chromatin structure to cell-type-specific gene regulationMarie Schaeffer, Marcelo Nöllmann · 2023 · Current Opinion in Genetics & Development
- CEBPA Phase Separation Links Transcriptional Activity and 3D Chromatin HubsMarie Christou‐Kent, Sergi Cuartero, Carla Garcia‐Cabau, Julia Rühle, Julian Naderi, Julia Erber, Maria Victoria Neguembor, Marcos Plana-Carmona, Marc Alcoverro-Bertran, Luísa de Andrés-Aguayo et al. · 2022 · Cell Reports
- NicE-C efficiently reveals open chromatin–associated chromosome interactions at high resolutionZheng-Yu Luo, Ran Zhang, Teng-Fei Hu, Yu-Ting Zhu, Yue-Ming Wu, Wen-Fei Li, Zhi Zhang, Xue-Biao Yao, Hai-Yi Liang, Xiao-Yuan Song · 2022 · Genome Research
- Single cell Hi-C identifies plastic chromosome conformations underlying the gastrulation enhancer landscapeNimrod Rappoport, Elad Chomsky, Takashi Nagano, Charlie Seibert, Yaniv Lubling, Yael Baran, Aviezer Lifshitz, Wing‐Kit Leung, Zohar Mukamel, Ron Shamir A et al. · 2023 · Nature Communications
- DiffDomain enables identification of structurally reorganized topologically associating domainsDunming Hua, Ming Gu, Xiao Zhang, Yanyi Du, Hangcheng Xie, Li Qi, Xiangjun Du, Zhidong Bai, Xiaopeng Zhu, Dechao Tian · 2024 · Nature Communications
- Advances in the multimodal analysis of the 3D chromatin structure and gene regulationMan-Hyuk Han, Jihyun Park, Minhee Park · 2024 · Experimental & Molecular Medicine
- Exploring the roles of RNAs in chromatin architecture using deep learningShuzhen Kuang, Katherine S. Pollard · 2024 · Nature Communications
- Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping functionNarducci, Domenic N., Hansen, Anders S. · 2025 · Molecular Cell
- ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCFMikhail D. Magnitov, Michela Maresca, Noemí Alonso Saiz, Hans Teunissen, Jinhong Dong, Kizhakke Mattada Sathyan, Luca Braccioli, Michael J. Guertin, Elzo de Wit · 2024 · Molecular Cell
- OGT prevents DNA demethylation and suppresses the expression of transposable elements in heterochromatin by restraining TET activity genome-wideHugo Sepúlveda, Xiang Li, Leo J. Arteaga-Vazquez, Isaac F. López-Moyado, Melina Brunelli, Lot Hernández-Espinosa, Xiaojing Yue, J. Carlos Angel, Caitlin Brown, Zhen Dong et al. · 2025 · Nature Structural & Molecular Biology
- RETRACTED: Kinetic organization of the genome revealed by ultraresolution multiscale live imagingJoo Lee, Liangfu Chen, Simon Gaudin, Kavvya Gupta, Ana Novačić, Andrew J. Spakowitz, Alistair Nicol Boettiger · 2025 · Science · Retracted
- mRNA initiation and termination are spatially coordinatedEzequiel Calvo-Roitberg, Christine L. Carroll, Gyeungyun Kim, Valeria C. Sanabria, Sergey V. Venev, Steven T. Mick, Joseph D. Paquette, Maritere Urióstegui-Arcos, Job Dekker, Ana Fiszbein et al. · 2025 · Science
- Finding Friends in the Crowd: Three-Dimensional Cliques of Topological Genomic DomainsPhilippe Collas, Tharvesh M. Liyakat Ali, Annaël Brunet, Thomas Germier · 2019 · Frontiers in Genetics
- Advances in technologies for 3D genomics researchYan Zhang, Guoliang Li · 2020 · Science China Life Sciences
- Dbx2 regulation in limbs suggests inter TAD sharing of enhancersLeonardo L Beccari, Gabriel Jaquier, Lucille Lopez‐Delisle, Eddie Rodríguez-Carballo, Bénédicte Mascrez, Sandra Gitto, Joost M. Woltering, Denis Duboule · 2021 · Developmental Dynamics
- Enhancer and super-enhancer landscape in polycystic kidney diseaseRonak Lakhia, Abheepsa Mishra, Laurence Michael Biggers, Venkat S. Malladi, Patricia Cobo-Stark, Sachin S. Hajarnis, Vishal Patel · 2021 · Kidney International
- Joint epigenome profiling reveals cell-type-specific gene regulatory programmes in human cortical organoidsFlorian Noack, Silvia Vangelisti, Nora Ditzer, Faye Chong, Mareike Albert, Boyan Bonev · 2023 · Nature Cell Biology
- Long interspersed nuclear elements safeguard neural progenitors from precocious differentiationTomohisa Toda, Tracy A. Bedrosian, Simon T. Schafer, Michael S. Cuoco, Sara B. Linker, Saeed Ghassemzadeh, Lisa E. Mitchell, Jack T. Whiteley, Nicole Novaresi, Aidan H. McDonald et al. · 2024 · Cell Reports
- Genome-wide variability in recombination activity is associated with meiotic chromatin organizationXiaofan Jin, Geoffrey Fudenberg, Katherine S. Pollard · 2021 · Genome Research
- Competition Between Transcription and Loop Extrusion Modulates Promoter and Enhancer DynamicsAngeliki Platania, Cathie Erb, Mariano Barbieri, Bastien Molcrette, Erwan Grandgirard, Marit A. C. de Kort, Karen J. Meaburn, Tiegh Taylor, Virlana M. Shchuka, Silvia Kocanova et al. · 2023 · SSRN Electronic Journal
- SAFB restricts contact domain boundaries associated with L1 chimeric transcriptionYaqiang Hong, Luyao Bie, Tao Zhang, Xiaohan Yan, Guangpu Jin, Zhuo Chen, Yang Wang, Xiufeng Li, Gaofeng Pei, Yongyan Zhang et al. · 2024 · Molecular Cell
- 3D Chromosomal Landscapes in Hematopoiesis and ImmunityAndreas Kloetgen, Palaniraja Thandapani, Aristotelis Tsirigos, Iannis Aifantis · 2019 · Trends in Immunology
- Polycomb proteins as organizers of 3D genome architecture in embryonic stem cellsTomás Pachano, Giuliano Crispatzu, Álvaro Rada-Iglesias · 2019 · Briefings in Functional Genomics
- Chromatin Landscape During Skeletal Muscle DifferentiationÓscar Hernández‐Hernández, Rodolfo Daniel Ávila‐Avilés, J. Manuel Hernández‐Hernández · 2020 · Frontiers in Genetics
- Generation of onco-enhancer enhances chromosomal remodeling and accelerates tumorigenesisPeiwei Chai, Jie Yu, Ruobing Jia, Xuyang Wen, Tianyi Ding, Xiaoyu Zhang, Hongyan Ni, Renbing Jia, Shengfang Ge, He Zhang et al. · 2020 · Nucleic Acids Research
- HiC-ACT: improved detection of chromatin interactions from Hi-C data via aggregated Cauchy testTaylor M. Lagler, Armen Abnousi, Ming Hu, Yuchen Yang, Yun Li · 2021 · The American Journal of Human Genetics
- Runx3 is required for oncogenic Myc upregulation in p53-deficient osteosarcomaShohei Otani, Yuki Date, Tomoya Ueno, Tomoko Ito, Shuhei Kajikawa, Keisuke Omori, Ichiro Taniuchi, Masahiro Umeda, Toshihisa Komori, Junya Toguchida et al. · 2021 · Oncogene
- Postmitotic differentiation of human monocytes requires cohesin-structured chromatinJulia Minderjahn, Alexander H. Fischer, Konstantin Maier, Karina Mendes, Margit Nuetzel, Johanna Raithel, Hanna Stanewsky, Ute Ackermann, Robert Månsson, Claudia Gebhard et al. · 2022 · Nature Communications
- A tour of 3D genome with a focus on CTCFDiane C. Wang, William Yang Wang, Linlin Zhang, Xiangdong Wang · 2018 · Seminars in Cell and Developmental Biology
- Organization of the Pluripotent GenomePatrick Siang Lin Lim, Eran Meshorer · 2020 · Cold Spring Harbor Perspectives in Biology
- Regulation of CTCF loop formation during pancreatic cell differentiationXiaowen Lyu, M. Jordan Rowley, Michael J. Kulik, Stephen Dalton, Victor G. Corces · 2023 · Nature Communications
- Global loss of promoter–enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesisYizhou Zhu, Hayan Lee, Shannon M. White, Annika K K Weimer, Emma Monte, Aaron M. Horning, Stephanie A. Nevins, Edward D. Esplin, Kristina Paul, Gat Krieger et al. · 2024 · Nature Cancer
- Non-backtracking walks reveal compartments in sparse chromatin interaction networksKirill Polovnikov, A. Gorsky, Sergei Nechaev, Sergey V. Razin, Sergey V. Ulianov · 2020 · Scientific Reports
- The dynamics of chromatin architecture in brain development and functionIzabela Harabula, Ana Pombo · 2021 · Current Opinion in Genetics & Development
- Extracting multi-way chromatin contacts from Hi-C dataLei Liu, Bokai Zhang, Changbong Hyeon · 2021 · PLoS Computational Biology
- Chromatin Structure and Dynamics: Focus on Neuronal Differentiation and Pathological ImplicationSophie Nothof, Frédérique Magdinier, Julien Van‐Gils · 2022 · Genes
- Understanding the function of regulatory DNA interactions in the interpretation of non-coding GWAS variantsWujuan Zhong, Weifang Liu, Jiawen Carmen Chen, Quan Sun, Ming Hu, Yun Li · 2022 · Frontiers in Cell and Developmental Biology
- The 3D genome and its impacts on human health and diseaseSiqi Wang, Zhengyu Luo, Weiguang Liu, Tengfei Hu, Zhongying Zhao, Michael G Rosenfeld, Xiaoyuan Song · 2023 · Life Medicine
- Remodeling of Il4-Il13-Il5 locus underlies selective gene expressionHiroyuki Nagashima, Justin Shayne, Kan Jiang, Franziska Petermann, Aleksandra Pękowska, Yuka Kanno, John J. O’Shea · 2024 · Nature Immunology
- A large CRISPR-induced bystander mutation causes immune dysregulationDimitre R. Simeonov, Alexander J. Brandt, Alice Y. K. Chan, Jessica T. Cortez, Zhongmei Li, Jonathan M. Woo, Youjin Lee, Claudia M.B. Carvalho, Alyssa C. Indart, Theodore L. Roth et al. · 2019 · Communications Biology
- Analyzing the 3D chromatin organization coordinating with gene expression regulation in B-cell lymphomaLuís Augusto Eijy Nagai, Sung‐Joon Park, Kenta Nakai · 2019 · BMC Medical Genomics
- Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome DuplicationsMaría Touceda‐Suárez, Elizabeth M Kita, Rafael D. Acemel, Panos Firbas, Marta Silvia Magri, Silvia Naranjo, Juan J. Tena, José Luis Gómez-Skármeta, Ignacio Maeso, Manuel Irimia · 2020 · Molecular Biology and Evolution
- Microscopic Chromosomal Structural and Dynamical Origin of Cell Differentiation and ReprogrammingXiakun Chu, Jin Wang · 2020 · Advanced Science
- Reconstructing the 3D genome organization of Neanderthals reveals that chromatin folding shaped phenotypic and sequence divergenceEvonne McArthur, David C. Rinker, Yang Cheng, Qixuan Wang, Juan Wang, Erin N. Gilbertson, Geoffrey Fudenberg, Maureen Pittman, Kathleen C. Keough, Feng Yue et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
- When 3D genome changes cause disease: the impact of structural variations in congenital disease and cancerJoachim Weischenfeldt, Daniel M. Ibrahim · 2023 · Current Opinion in Genetics & Development
- Kdm1a safeguards the topological boundaries of PRC2-repressed genes and prevents aging-related euchromatinization in neuronsBeatriz del Blanco, S. Niñerola, Ana M. Martín-González, Juan Paraíso-Luna, Minji Kim, Rafael Muñoz-Viana, Carina Racovac, J. Sanchez-Mut, Yi-Jun Ruan, Ángel Barco · 2024 · Nature Communications
- Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic developmentChakraborty, Shreeta, Wenzlitschke, Nina, Anderson, Matthew J., Eraso, Ariel, Baudic, Manon, Thompson, Joyce J., Evans, Alicia A., Shatford-Adams, Lilly M., Chari, Raj, Awasthi, Parirokh et al. · 2025 · Developmental Cell
- Stochastic Gene Choice during Cellular DifferentiationTakeo Wada, Sandrine Wallerich, Attila Becskei · 2018 · Cell Reports
- From Loops to Looks: Transcription Factors and Chromatin Organization Shaping Terminal B Cell DifferentiationAlba Azagra, Ester Marina-Zárate, Almudena R. Ramiro, Biola M. Javierre, Maribel Parra · 2019 · Trends in Immunology
- Epigenetic Regulation of Neural Stem Cells: The Emerging Role of NucleoporinsClaudia Colussi, Claudio Grassi · 2021 · Stem Cells
- HiCRes: a computational method to estimate and predict the genomic resolution of Hi-C librariesClaire Marchal, Nivedita Singh, Ximena Corso‐Díaz, Anand Swaroop · 2021 · Nucleic Acids Research
- Reference panel guided topological structure annotation of Hi-C dataYanlin Zhang, Mathieu Blanchette · 2022 · Nature Communications
- 5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer designJi Hun Kim, Katelyn R. Titus, Wanfeng Gong, Jonathan A. Beagan, Zhendong Cao, Jennifer E. Phillips‐Cremins · 2018 · Methods
- Diverse gene regulatory mechanisms mediated by Polycomb group proteins during neural developmentMasafumi Tsuboi, Yusuke Hirabayashi, Yukiko Gotoh · 2019 · Current Opinion in Neurobiology
- Modeling Single-Molecule Conformations of the HoxD Region in Mouse Embryonic Stem and Cortical Neuronal CellsSimona Bianco, Carlo Annunziatella, Guillaume Andrey, Andrea M. Chiariello, Andrea Esposito, Luca Fiorillo, Antonella Prisco, Mattia Conte, Raffaele Campanile, Mario Nicodemi · 2019 · Cell Reports
- 3D genome organization during lymphocyte development and activationAnne Onrust-van Schoonhoven, Danny Huylebroeck, Rudi W. Hendriks, Ralph Stadhouders · 2019 · Briefings in Functional Genomics
- 4See: A Flexible Browser to Explore 4C DataYousra Ben Zouari, A. Platania, Anne Molitor, Tom Sexton · 2020 · Frontiers in Genetics
- BAZ2A safeguards genome architecture of ground‐state pluripotent stem cellsDamian Dalcher, Jennifer Y. Tan, Cristiana Bersaglieri, Rodrigo Peña‐Hernández, Eva Vollenweider, Stefan Zeyen, Marc W. Schmid, Valerio Bianchi, Stefan Butz, Marcin Roganowicz et al. · 2020 · The EMBO Journal
- Transcription-coupled changes in genomic region proximities during transcriptional burstingHiroaki Ohishi, Soya Shinkai, Hitoshi Owada, Takeru Fujii, Kazufumi Hosoda, Shuichi Onami, Takashi Yamamoto, Yasuyuki Ohkawa, Hiroshi Ochiai · 2024 · Science Advances
- Decoding the organization, dynamics, and function of the 4D genomeErin Aboelnour, Boyan Bonev · 2021 · Developmental Cell