Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

Mumbach, Maxwell R, Satpathy, Ansuman T, Boyle, Evan A, Dai, Chao, Gowen, Benjamin G, Cho, Seung Woo, Nguyen, Michelle L, Rubin, Adam J +19 more·2017·Nature Genetics

Cited by (509)

Items 201–300 of 509

  1. Characterization of sequence determinants of enhancer function using natural genetic variation
    Marty G. Yang, Emi Ling, Christopher J. Cowley, Michael E. Greenberg, Thomas Vierbuchen · 2022 · eLife
  2. ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms
    Qiangwei Zhou, Cheng Sheng, Shanshan Zheng, Zhenji Wang, Pengpeng Guan, Zhixian Zhu, Xingyu Huang, Cong Zhou, Guoliang Li · 2022 · Nucleic Acids Research
  3. Reference panel guided topological structure annotation of Hi-C data
    Yanlin Zhang, Mathieu Blanchette · 2022 · Nature Communications
  4. 3D genome organization during lymphocyte development and activation
    Anne Onrust-van Schoonhoven, Danny Huylebroeck, Rudi W. Hendriks, Ralph Stadhouders · 2019 · Briefings in Functional Genomics
  5. Predicting unrecognized enhancer-mediated genome topology by an ensemble machine learning model
    Li Tang, Matthew C. Hill, Jun Wang, Jian-Xin Wang, James F. Martin, Min Li · 2020 · bioRxiv
  6. Enhancer Connectome Nominates Target Genes of Inherited Risk Variants from Inflammatory Skin Disorders.
    Mark Y. Jeng, Maxwell R. Mumbach, Jeffrey M. Granja, Ansuman T. Satpathy, Howard Y. Chang, A. Chang · 2019 · Journal of Investigative Dermatology
  7. Cancer systems immunology
    Nathan Edward Reticker-Flynn, Edgar G. Engleman · 2020 · eLife
  8. A computational framework for identifying the transcription factors involved in enhancer-promoter loop formation
    Li Liu, Lirong Zhang, Fanny Dao, Yanchao Yang, Hao Lin · 2020 · Molecular Therapy — Nucleic Acids
  9. Understanding three-dimensional chromatin organization in diploid genomes
    Jing Li, Yu Lin, Qianzi Tang, Mingzhou Li · 2021 · Computational and Structural Biotechnology Journal
  10. From association to mechanism in complex disease genetics: the role of the 3D genome
    Yao Fu, Kandice L. Tessneer, Chuang Li, Patrick M. Gaffney · 2018 · Arthritis Research & Therapy
  11. The contribution of active and passive mechanisms of 5mC and 5hmC removal in human T lymphocytes is differentiation‐ and activation‐dependent
    Lucia Vincenzetti, Cristina Leoni, Michele Chirichella, Ivo Kwee, Silvia Monticelli · 2019 · European Journal of Immunology
  12. Activity-by-Contact model of enhancer specificity from thousands of CRISPR perturbations
    Charles P. Fulco, Joseph Nasser, Thouis R. Jones, Glen Munson, Drew T. Bergman, Vidya Subramanian, Sharon R. Grossman, Rockwell Anyoha, Tejal A. Patwardhan, Tung H. Nguyen et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  13. 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
  14. Decoding the epigenetics and chromatin loop dynamics of androgen receptor-mediated transcription
    Umut Berkay Altıntaş, Ji-Heui Seo, C. Giambartolomei, Dogancan Ozturan, B. Fortunato, Geoffrey M. Nelson, Seth R. Goldman, Karen Adelman, Faraz Hach, M. Freedman et al. · 2024 · Nature Communications
  15. Genome-wide chromatin contacts of super-enhancer-associated lncRNA identify LINC01013 as a regulator of fibrosis in the aortic valve
    Arnaud Chignon, Deborah Argaud, Marie-Chloé Boulanger, G. Mkannez, V. Bon-Baret, Zhong-Lin Li, S. Thériault, Y. Bossé, P. Mathieu · 2022 · PLoS Genetics
  16. 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
  17. Long Noncoding RNAs of the Arterial Wall as Therapeutic Agents and Targets in Atherosclerosis
    Lesca Miriam Holdt, Alexander Kohlmaier, Daniel Teupser · 2019 · Thrombosis and Haemostasis
  18. Multiomics dissection of molecular regulatory mechanisms underlying autoimmune-associated noncoding SNPs
    Xiaofeng Chen, Mingrui Guo, Yuan-Yuan Duan, Feng Jiang, Hao Wu, Shan‐Shan Dong, Xiaorong Zhou, Hlaing Nwe Thynn, Congcong Liu, Lin Zhang et al. · 2020 · JCI Insight
  19. Prioritizing transcriptional factors in gene regulatory networks with PageRank
    Hongxu Ding, Ying Yang, Yuanqing Xue, Lucas Seninge, Henry Z. Gong, Rojin Safavi, Andrea Califano, Joshua M. Stuart · 2020 · iScience
  20. 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
  21. HiChIP-Peaks: a HiChIP peak calling algorithm
    C. Shi, M. Rattray, G. Orozco · 2019 · bioRxiv
  22. Application of Hi-C and other omics data analysis in human cancer and cell differentiation research
    Haiyan Gong, Yi Yang, Sichen Zhang, Ming-Hong Li, Xiao-Tong Zhang · 2021 · Computational and Structural Biotechnology Journal
  23. Multi-omic Analysis of Primary Human Kidney Tissues Identifies Medulla-Specific Gene Expression Patterns
    Stefan Haug, Selvaraj Muthusamy, Yong Li, Galen Stewart, Xianwu Li, Martin Treppner, Anna Köttgen, Shreeram Akilesh · 2022 · Kidney International
  24. 3D chromatin hubs as regulatory units of identity and survival in human acute leukemia
    Giovanni Gambi, Francesco E. Boccalatte, Javier Rodriguez-Hernaez, Ziyan Lin, Bettina Nadorp, Alexander Polyzos, Jimin Tan, Kleopatra Avrampou, Giorgio Inghirami, Alex Kentsis et al. · 2024 · Molecular Cell
  25. The logic of native enhancer-promoter compatibility and cell-type-specific gene expression variation
    Takeo Narita, Yoshiki Higashijima, Sinan Kilic, Elina Maskey, Katrin Neumann, Chunaram Choudhary · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  26. DLoopCaller: A deep learning approach for predicting genome-wide chromatin loops by integrating accessible chromatin landscapes
    Siguo Wang, Qinhu Zhang, Ying He, Zhen Cui, Zhenghao Guo, Kyungsook Han, De-Shuang Huang · 2022 · PLoS Computational Biology
  27. Whole-genome sequencing uncovers two loci for coronary artery calcification and identifies ARSE as a regulator of vascular calcification
    Paul S. de Vries, Matthew P. Conomos, Kuldeep Singh, Christopher Nicholson, Deepti Jain, Natalie R. Hasbani, Wanlin Jiang, Sujin Lee, Christian Lacks Lino Cardenas, Sharon Marie Lutz et al. · 2023 · Nature Cardiovascular Research
  28. Nuclear microRNA 9 mediates G-quadruplex formation and 3D genome organization during TGF-β-induced transcription
    Julio Cordero, Guruprasadh Swaminathan, Diana G. Rogel-Ayala, Karla Rubio, Adel Elsherbiny, Samina Mahmood, Witold Szymański, J. Graumann, Thomas Braun, Stefan Günther et al. · 2024 · Nature Communications
  29. Focus on Causality in ESC/iPSC-Based Modeling of Psychiatric Disorders
    Anke Hoffmann, Michael J. Ziller, Dietmar Spengler · 2020 · Cells
  30. CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions
    William D. Stuart, Minzhe Guo, Iris M. Fink-Baldauf, Alan M. Coleman, John Paul Clancy, Marcus Alexander Mall, Foong‐Yen Y. Lim, John J. Brewington, Yutaka Maeda · 2020 · NAR Genomics and Bioinformatics
  31. U-FISH: a fluorescent spot detector for imaging-based spatial-omics analysis and AI-assisted FISH diagnosis
    Weize Xu, Huaiyuan Cai, Qian Zhang, Zhengze Wang, Jiajun Yang, Xiaofeng Wu, Chengwen Li, Chenghua Cui, Changzhi Liu, He Jin et al. · 2025 · Genome biology
  32. 3D chromatin remodeling potentiates transcriptional programs driving cell invasion
    Benjamin Lebeau, Maïka Jangal, Tiejun Zhao, Cheng Kit Wong, Nolan Wong, Eduardo Cepeda Cañedo, Steven Hébert, Adriana Aguilar‐Mahecha, Catherine Chabot, Marguerite Buchanan et al. · 2022 · Proceedings of the National Academy of Sciences
  33. Enhancer remodeling drives MLL oncogene-dependent transcriptional dysregulation in leukemia stem cells
    Feng Pan, M. Iwasaki, Wenqi Wu, Ya-Nan Jiang, Xin Yang, Li Zhu, Zhigang Zhao, Michael L. Cleary · 2023 · Blood Advances
  34. Hi-TrAC detects active sub-TADs and reveals internal organizations of super-enhancers
    Yaqiang Cao, Shuai Liu, Kairong Cui, Qingsong Tang, Keji Zhao · 2023 · Nucleic Acids Research
  35. BAT Hi-C maps global chromatin interactions in an efficient and economical way.
    Jie Huang, Yong-Peng Jiang, Haonan Zheng, Xiong Ji · 2019 · Methods
  36. Complexity of enhancer networks predicts cell identity and disease genes revealed by single-cell multi-omics analysis
    Danni Hong, Hongli Lin, Lifang Liu, Muya Shu, Jianwu Dai, Falong Lu, Mengsha Tong, Jialiang Huang · 2022 · Briefings in Bioinformatics
  37. Impact of supraphysiologic MDM2 expression on chromatin networks and therapeutic responses in sarcoma
    Samantha M. Bevill, Salvador Casaní-Galdón, C. E. El Farran, Eli G Cytrynbaum, Kevin A. Macias, Sylvie E. Oldeman, Kayla J. Oliveira, Molly M. Moore, E. Hegazi, C. Adriaens et al. · 2023 · Cell Genomics
  38. Mapping the functional impact of non-coding regulatory elements in primary T cells through single-cell CRISPR screens
    Celia Alda-Catalinas, Ximena Ibarra-Soria, Christina Flouri, Jorge Esparza Gordillo, Diana L. Cousminer, Anna Hutchinson, Bin Sun, William G. Pembroke, Sebastian Ullrich, Adam Krejčí et al. · 2024 · Genome biology
  39. From GWAS variant to function: A study of ∼148,000 variants for blood cell traits
    Quan Sun, Cheynna Crowley, Le Huang, Jia Wen, Jiawen Carmen Chen, Erik L. Bao, Paul Livermore Auer, Guillaume Lettre, Alex P. Reiner, Vijay G. Sankaran et al. · 2021 · Human Genetics and Genomics Advances
  40. Integrative dissection of gene regulatory elements at base resolution
    Zeyu Chen, Nauman M. Javed, Molly M. Moore, Jingyi Wu, Gary Sun, Michael E. Vinyard, Alejandro Collins, Luca Pinello, Fadi J. Najm, B Bernstein · 2023 · Cell Genomics
  41. Single-cell profiling of histone modifications in the mouse brain
    Marek Bartošovič, Mukund Kabbe, Gonçalo Castelo‐Branco · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  42. Revolutionizing Implantation Studies: Uterine-Specific Models and Advanced Technologies
    Shuyun Li, Francesco John DeMayo · 2025 · Biomolecules
  43. Three-dimensional regulatory hubs support oncogenic programs in glioblastoma
    Sarah L. Breves, Dafne Campigli Di Giammartino, James Nicholson, Stéfano M. Cirigliano, Syed Raza Mahmood, Uk Jin Lee, Alexander Martinez‐Fundichely, Johannes Jungverdorben, Richa Singhania, Sandy Rajkumar et al. · 2024 · Molecular Cell
  44. A comprehensive review of bioinformatics tools for chromatin loop calling
    Li Liu, Kai-Yuan Han, Huimin Sun, Lu Han, Dong Gao, Qilemuge Xi, Li-Rong Zhang, Hao Lin · 2023 · Briefings Bioinform.
  45. Epromoters are new players in the regulatory landscape with potential pleiotropic roles
    Juliette Malfait, Jing Wan, Salvatore Spicuglia · 2023 · BioEssays
  46. Evolutionary Innovations in Conserved Regulatory Elements Associate With Developmental Genes in Mammals
    Severin Uebbing, Acadia A. Kocher, Marybeth Baumgartner, Yu Ji, Suxia Bai, Xiaojun Xing, Timothy Nottoli, James P. Noonan · 2024 · Molecular Biology and Evolution
  47. Multi-omics analysis in primary T cells elucidates mechanisms behind disease-associated genetic loci
    C. Shi, Dan-Yun Zhao, Jake Butler, A. Frantzeskos, S. Rossi, James Ding, C. Ferrazzano, Charlotte Wynn, R. Hum, E. Richards et al. · 2023 · Genome Biology
  48. Candidate long‐range regulatory sites acting on the IL17 pathway genes TRAF3IP2 and IL17RA are associated with psoriasis
    Joanne Nititham, Calum Fergusson, Colin Palmer, Wilson J. Liao, John Foerster · 2018 · Experimental Dermatology
  49. Identification of rheumatoid arthritis causal genes using functional genomics
    James Ding, Gisela Orozco · 2019 · Scandinavian Journal of Immunology
  50. XL-DNase-seq: improved footprinting of dynamic transcription factors
    Kyu-Seon Oh, Jisu Ha, Songjoon Baek, Myong-Hee Sung · 2019 · Epigenetics & Chromatin
  51. Using functional genomics to advance the understanding of psoriatic arthritis
    Chenfu Shi, Magnus Rattray, Anne C Barton, John Bowes, Gisela Orozco · 2020 · Rheumatology
  52. HiCoP, a simple and robust method for detecting interactions of regulatory regions
    Yan Zhang, Zhaoqiang Li, Shasha Bian, Hao Zhao, Delong Feng, Yanhong Chen, Yuhe Hou, Qifa Liu, Bingtao Hao · 2020 · Epigenetics & Chromatin
  53. System Genetics Including Causal Inference Identify Immune Targets for Coronary Artery Disease and the Lifespan
    Valentin Bon-Baret, Arnaud Chignon, Marie‐Chloé Boulanger, Zhonglin Li, Déborah Argaud, Benoît J. Arsenault, Sébastien Thériault, Yohan Bossé, Patrick Mathieu · 2021 · Circulation Genomic and Precision Medicine
  54. Filtering the Junk: Assigning Function to the Mosquito Non-Coding Genome
    Elise J. Farley, Heather Eggleston, Michelle M. Riehle · 2021 · Insects
  55. The 3D genome: From fundamental principles to disease and cancer
    David Umlauf, Raphaël Mourad · 2018 · Seminars in Cell and Developmental Biology
  56. Allele-Specific QTL Fine Mapping with PLASMA
    Austin T. Wang, Anamay H. Shetty, Edward P. O’Connor, Connor A. Bell, Mark M. Pomerantz, Matthew L. Freedman, Alexander Gusev · 2020 · The American Journal of Human Genetics
  57. Locus-specific chromatin profiling of evolutionarily young transposable elements
    Darren Taylor, Robert Lowe, Claude Philippe, Kevin C L Cheng, Olivia A. Grant, Nicolae Radu Zabet, Gaël Cristofari, Miguel Ramos Branco · 2021 · Nucleic Acids Research
  58. Enhancer-promoter activation by the Kaposi sarcoma-associated herpesvirus episome maintenance protein LANA
    Xiang Ye, Lindsey N. Guerin, Ziche Chen, Suba Rajendren, William Dunker, Yang Zhao, Ruilin Zhang, Emily C. Hodges, John J. Karijolich · 2024 · Cell Reports
  59. Hi-C, a chromatin 3D structure technique advancing the functional genomics of immune cells
    Ran Liu, Ruitang Xu, Siyu Yan, Peiyu Li, Changteng Jia, Haoqiang Sun, Kaiwen Sheng, Yongjie Wang, Qi Zhang, Jiao Guo et al. · 2024 · Frontiers in Genetics
  60. Functional genomics in autoimmune diseases
    James Ding, Antonios Frantzeskos, Gisela Orozco · 2020 · Human Molecular Genetics
  61. Deciphering the Complexity of 3D Chromatin Organization Driving Lymphopoiesis and Lymphoid Malignancies
    Laurianne Scourzic, Eralda Salataj, Effie Apostolou · 2021 · Frontiers in Immunology
  62. The two waves in single-cell 3D genomics
    Sergey V. Ulianov, Sergey V. Razin · 2021 · Seminars in Cell and Developmental Biology
  63. Leveraging cell-type-specific regulatory networks to interpret genetic variants in abdominal aortic aneurysm
    Shining Ma, Xi Chen, Xiang Zhu, Philip S. Tsao, Wing Hung Wong · 2021 · Proceedings of the National Academy of Sciences
  64. Enhancer RNA Transcription Is Essential for a Novel CSF1 Enhancer in Triple-Negative Breast Cancer
    Michael W. Lewis, Kamila Wiśniewska, Caitlin M. King, Shen Li, Alisha R. Coffey, Michael R. Kelly, Matthew J. Regner, Hector L. Franco · 2022 · Cancers
  65. The Landscape of Accessible Chromatin during Yak Adipocyte Differentiation
    Zhilong Zhang, Yongfeng Zhang, Qi Bao, Yarong Gu, Chunnian Liang, Min Chu, Xian Guo, Pengjia Bao, Ping Yan · 2022 · International Journal of Molecular Sciences
  66. Mustache: Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
    Abbas Roayaei Ardakany, Halil Tuvan Gezer, Stefano Lonardi, Ferhat Ay · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  67. Erythropoietin Regulates Transcription and YY1 Dynamics in a Pre-Established Chromatin Architecture
    Andrea A. Perreault, Jonathan D. Brown, Bryan J. Venters · 2020 · iScience
  68. CRISPR/Cas9 guided genome and epigenome engineering and its therapeutic applications in immune mediated diseases
    Desh Deepak Singh, R. David Hawkins, Riitta Lahesmaa, Subhash Kumar Tripathi · 2019 · Seminars in Cell and Developmental Biology
  69. Advances in higher-order chromatin architecture: the move towards 4D genome
    Namyoung Jung, Tae-Kyung Kim · 2021 · BMB Reports
  70. Advances in profiling chromatin architecture shed light on the regulatory dynamics underlying brain disorders
    Brandon M. Pratt, Hyejung Won · 2021 · Seminars in Cell and Developmental Biology
  71. Epigenetics, Enhancer Function and 3D Chromatin Organization in Reprogramming to Pluripotency
    Andreas Hörnblad, Silvia Remeseiro · 2022 · Cells
  72. Consensus guidelines on the construct validity of rodent models of restless legs syndrome
    Aaro V. Salminen, Stefan Clemens, Diego Garcı́a-Borreguero, Imad Ghorayeb, Yuqing Li, Mauro Manconi, William G. Ondo, David B. Rye, Jerome M. Siegel, Alessandro Silvani et al. · 2022 · Disease Models & Mechanisms
  73. Genomic Analysis of Foxp3 Function in Regulatory T Cells
    Gabriel A. Dolsten, Yuri Pritykin · 2023 · The Journal of Immunology
  74. Stage-specific dynamic reorganization of genome topology shapes transcriptional neighborhoods in developing human retinal organoids
    Zepeng Qu, Zachary A. Batz, Nivedita Singh, Claire Marchal, Anand Swaroop · 2023 · Cell Reports
  75. KDM4C inhibition blocks tumor growth in basal breast cancer by promoting cathepsin L-mediated histone H3 cleavage
    Zheqi Li, Guillermo Peluffo, Laura E. Stevens, Xintao Qiu, Marco Seehawer, Amatullah Tawawalla, Xiao-Yun Huang, Shawn B. Egri, Shaunak Raval, Maeve McFadden et al. · 2025 · Nature Genetics
  76. Enhancer promoter interactome and Mendelian randomization identify network of druggable vascular genes in coronary artery disease
    Arnaud Chignon, Samuel Mathieu, Anne Rufiange, Déborah Argaud, Pierre Voisine, Yohan Bossé, Benoît J. Arsenault, Sébastien Thériault, Patrick Mathieu · 2022 · Human Genomics
  77. GWAS-associated variants, non-genetic factors, and transient transcriptome in multiple sclerosis etiopathogenesis: A colocalization analysis
    Gianmarco Bellucci, Renato Umeton, Rachele Bigi, Silvia Romano, Maria Chiara Buscarinu, Roberta Reniè, Virginia Rinaldi, Raffaella Pizzolato Umeton, Emanuele Morena, Carmela Romano et al. · 2021 · Journal of the Neurological Sciences
  78. Glucocorticoids unmask silent non-coding genetic risk variants for common diseases
    T. Nguyen, Huan-Yao Gao, Duan Liu, T. Philips, Zhen-Qing Ye, Jeong-Heon Lee, Geng-xian Shi, K. Copenhaver, Ling-Xin Zhang, Lixuan Wei et al. · 2021 · bioRxiv
  79. Approaching Shared Pathophysiology in Immune-Mediated Diseases through Functional Genomics
    David González‐Serna, Gonzalo Villanueva-Martín, Marialbert Acosta‐Herrera, Ana Márquez, Javier J. Martin · 2020 · Genes
  80. Detailed Regulatory Interaction Map of the Human Heart Facilitates Gene Discovery for Cardiovascular Disease
    Valerio Bianchi, Geert Geeven, Nathan R. Tucker, Catharina R.E. Hilvering, Amelia Weber Hall, Carolina Roselli, Matthew C. Hill, James F. Martin, Kenneth B. Margulies, Patrick T. Ellinor et al. · 2019 · SSRN Electronic Journal
  81. CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms
    Li, Yongge, Ju, Fusong, Chen, Zhiyuan, Qu, Yiming, Xia, Huanhuan, He, Liang, Wu, Lijun, Zhu, Jianwei, Shao, Bin, Deng, Pan · 2023 · Genome Biology
  82. EnContact: predicting enhancer-enhancer contacts using sequence-based deep learning model
    Mingxin Gan, Wenran Li, Rui Jiang · 2019 · PeerJ
  83. CharID: a two-step model for universal prediction of interactions between chromatin accessible regions
    Yin Shen, Quan Zhong, Liu Tian, Zi Wen, Wei Shen, Li Li · 2021 · Briefings in Bioinformatics
  84. Biology and Model Predictions of the Dynamics and Heterogeneity of Chromatin-Nuclear Lamina Interactions
    Julia Madsen-Østerbye, A. Bellanger, N. Galigniana, P. Collas · 2022 · Frontiers in Cell and Developmental Biology
  85. Functional genomic assays to annotate enhancer–promoter interactions genome wide
    Alden King-Yung Leung, Yao Li, Haiyuan Yu · 2022 · Human Molecular Genetics
  86. Untangling the genetics of beta cell dysfunction and death in type 1 diabetes
    Catherine C. Robertson, Ruth M. Elgamal, Belle A. Henry-Kanarek, Peter Arvan, Shuibing Chen, Sangeeta Dhawan, Decio Laks Eizirik, John S. Kaddis, Golnaz Vahedi, Stephen C.J. Parker et al. · 2024 · Molecular Metabolism
  87. CRISPR-based strategies for studying regulatory elements and chromatin structure in mammalian gene control
    Cia‐Hin Lau, Yousin Suh · 2017 · Mammalian Genome
  88. Loop Catalog: a comprehensive HiChIP database of human and mouse samples
    Joaquin Reyna, Kyra Fetter, Romeo Ignacio, Cemil Can Ali Marandi, Astoria Ma, Nikhil Rao, Zichen Jiang, D. Figueroa, Sourya Bhattacharyya, Ferhat Ay · 2025 · Genome Biology
  89. HPRep: Quantifying Reproducibility in HiChIP and PLAC-Seq Datasets
    Jonathan D. Rosen, Yu-Chen Yang, Armen Abnousi, Jia-Wen Chen, Michael Song, Ian R. Jones, Yin Shen, Ming Hu, Yun Li · 2020 · bioRxiv
  90. Predicting novel genomic regions linked to genetic disorders using GWAS and chromosome conformation data – a case study of schizophrenia
    Daniel S. Buxton, Declan J. Batten, Jonathan J. Crofts, Nadia A Chuzhanova · 2019 · Scientific Reports
  91. Bacon: a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies
    L. Tang, M. Hill, P. Ellinor, Min Li · 2022 · Genome Biology
  92. Using omics data and genome editing methods to decipher GWAS loci associated with coronary artery disease
    Arnaud Chignon, Guillaume Lettre · 2025 · Atherosclerosis
  93. DNMT3A-dependent DNA methylation shapes the endothelial enhancer landscape
    Stephanie Gehrs, Zuguang Gu, Joschka Hey, Dieter Weichenhan, Niklas Buckwalter, Moritz Jakab, Agnes Hotz‐Wagenblatt, Kersten Breuer, Maria Llamazares Prada, Daniel Hübschmann et al. · 2025 · Nucleic Acids Research
  94. Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation
    Yeqiao Zhou, Atishay Jay, Noah G. Burget, Tobias Friedrich, Sora Yoon, Jessica Alsing, Guy Nir, Rudolf Grosschedl, Golnaz Vahedi, Robert B. Faryabi · 2025 · Nature Cell Biology
  95. High-throughput CRISPRi and CRISPRa technologies in 3D genome regulation for neuropsychiatric diseases
    Ian Richard Jones, Xingjie Ren, Yin Shen · 2022 · Human Molecular Genetics
  96. Inferring regulatory element landscapes and gene regulatory networks from integrated analysis in eight hulless barley varieties under abiotic stress
    Qijun Xu, Shunmou Huang, Ganggang Guo, Chunbao Yang, Mu Wang, Xingquan Zeng, Yulin Wang · 2022 · BMC Genomics
  97. Single-cell chromatin accessibility and transcriptomic characterization of Behcet’s disease
    Wen Shi, Jinguo Ye, Zhuoxing Shi, Caineng Pan, Qikai Zhang, Yuheng Lin, Dan Liang, Yizhi Liu, Xianchai Lin, Yingfeng Zheng · 2023 · Communications Biology
  98. Integrative high-throughput enhancer surveying and functional verification divulges a YY2-condensed regulatory axis conferring risk for osteoporosis
    Xiaofeng Chen, Yuan-Yuan Duan, Yingying Jia, Qian-Hua Dong, Wei Shi, Yan Zhang, Shan‐Shan Dong, Meng Li, Zhongbo Liu, Fei Chen et al. · 2024 · Cell Genomics
  99. CD-Loop: a chromatin loop detection method based on the diffusion model
    Jiquan Shen, Yang Wang, Junwei Luo · 2024 · Frontiers in Genetics
  100. Enhancers and MYC interplay in hematopoiesis
    Leonidas Benetatos, Agapi Benetatou, George Vartholomatos · 2020 · Journal of Molecular Medicine