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 101–200 of 509

  1. A genetic disorder reveals a hematopoietic stem cell regulatory network co-opted in leukemia
    Richard A. Voit, Liming Tao, Fulong Yu, Liam D. Cato, Blake Cohen, Travis J. Fleming, Mateusz Antoszewski, Xiaotian Liao, Claudia Fiorini, Satish Kumar Nandakumar et al. · 2022 · Nature Immunology
  2. Weak interactions in higher-order chromatin organization
    Kantidze, Omar L, Razin, Sergey V · 2020 · Nucleic Acids Research
  3. Genetic perturbation of PU.1 binding and chromatin looping at neutrophil enhancers associates with autoimmune disease
    Watt, Stephen, Vasquez, Louella, Walter, Klaudia, Mann, Alice L., Kundu, Kousik, Chen, Lu, Sims, Ying, Ecker, Simone, Burden, Frances, Farrow, Samantha et al. · 2021 · Nature Communications
  4. Tissue-specific enhancer–gene maps from multimodal single-cell data identify causal disease alleles
    Saori Sakaue, Kathryn Weinand, Shakson Isaac, Kushal K. Dey, Karthik A. Jagadeesh, Masahiro Kanai, Gerald F. M. Watts, Zhu Zhu, Accelerating Medicines Partnership® RA/SLE Program and Network, Jennifer Albrecht et al. · 2024 · Nature Genetics
  5. High‐resolution mapping of cancer cell networks using co‐functional interactions
    Evan A. Boyle, Jonathan K. Pritchard, William James Greenleaf · 2018 · Molecular Systems Biology
  6. Endogenous Retrovirus-Derived lncRNA BANCR Promotes Cardiomyocyte Migration in Humans and Non-human Primates
    Kitchener D. Wilson, Mohamed Ameen, Hong-Chao Guo, Oscar J. Abilez, Lei Tian, Maxwell R. Mumbach, Sebastian Diecke, Xulei Qin, Yonggang Liu, Hua-Xiao Yang et al. · 2020 · Developmental Cell
  7. CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens
    Timothy Daley, Zhixiang Lin, Xueqiu Lin, Yanxia Liu, Wing Hung Wong, Lei S. Qi · 2018 · Genome biology
  8. Enhancer dependence of cell-type–specific gene expression increases with developmental age
    Wenqing Cai, Jialiang Huang, Qian Zhu, Bin E. Li, Davide Seruggia, Pingzhu Zhou, Minh Nguyen, Yuko Fujiwara, Huafeng Xie, Zhenggang Yang et al. · 2020 · Proceedings of the National Academy of Sciences
  9. Chromatin Conformation in Development and Disease
    Ilias Boltsis, Frank G. Grosveld, Guillaume Giraud, Petros Kolovos · 2021 · Frontiers in Cell and Developmental Biology
  10. The landscape of RNA polymerase II–associated chromatin interactions in prostate cancer
    Susmita Gurjar Ramanand, Yong Chen, Jiapei Yuan, Kelly Daescu, Maryou B.K. Lambros, Kathleen E. Houlahan, Suzanne Carreira, Wei Yuan, GuemHee Baek, Adam Sharp et al. · 2020 · Journal of Clinical Investigation
  11. Parsing multiomics landscape of activated synovial fibroblasts highlights drug targets linked to genetic risk of rheumatoid arthritis
    Haruka Tsuchiya, Mineto Ota, Shuji Sumitomo, Kazuyoshi Ishigaki, Akari Suzuki, Toyonori Sakata, Yumi Tsuchida, Hiroshi Inui, Jun Hirose, Yuta Kochi et al. · 2020 · Annals of the Rheumatic Diseases
  12. Gene regulation on extrachromosomal DNA
    King L. Hung, Paul S. Mischel, Howard Y. Chang · 2022 · Nature Structural & Molecular Biology
  13. A distal enhancer at risk locus 11q13.5 promotes suppression of colitis by Treg cells
    Rabab Nasrallah, Charlotte J. Imianowski, Lara Bossini‐Castillo, Francis M. Grant, Mikail Dogan, Lindsey Placek, Lina Kozhaya, Paula Kuo, Firas Sadiyah, Sarah K. Whiteside et al. · 2020 · Nature
  14. Three-dimensional genome organization in immune cell fate and function
    Sergi Cuartero, Grégoire Stik, Ralph Stadhouders · 2022 · Nature reviews. Immunology
  15. Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network
    Wanwen Zeng, Yong Wang, Rui Jiang · 2019 · Bioinformatics
  16. Rewiring of 3D Chromatin Topology Orchestrates Transcriptional Reprogramming and the Development of Human Dilated Cardiomyopathy
    Yu-Liang Feng, Liuyang Cai, Wan-Zi Hong, Chun-Xiang Zhang, Ning Tan, Min Wang, Cheng Wang, Feng Liu, Xiao-Hong Wang, Jian-Yong Ma et al. · 2022 · Circulation
  17. 3D Enhancer–promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages
    Dylan Murphy, Eralda Salataj, Dafne Campigli Di Giammartino, Javier Rodriguez-Hernaez, Andreas Kloetgen, Vidur Garg, Erin Char, Christopher M. Uyehara, Ly-Sha Ee, UkJin Lee et al. · 2023 · Nature Structural & Molecular Biology
  18. Time course regulatory analysis based on paired expression and chromatin accessibility data
    Zhana Duren, Xi Xian Chen, Jingxue Xin, Yong Wang, Wing Hung Wong · 2020 · Genome Research
  19. Decoding the Human Face: Progress and Challenges in Understanding the Genetics of Craniofacial Morphology
    Sahin Naqvi, Hanne Hoskens, Franziska Wilke, Seth Michael Weinberg, John R. Shaffer, Susan Walsh, Mark D. Shriver, Joanna Wysocka, Peter D. Claes · 2022 · Annual Review of Genomics and Human Genetics
  20. Identification of cis-regulatory elements by chromatin structure
    Zefu Lu, William A. Ricci, Robert J. Schmitz, Xiaoyu Zhang · 2018 · Current Opinion in Plant Biology
  21. FoxP3 associates with enhancer-promoter loops to regulate Treg-specific gene expression
    Ricardo N. Ramírez, Kaitavjeet Chowdhary, Juliette Léon, Diane J. Mathis, Christophe O. Benoist · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  22. H3K27ac HiChIP in prostate cell lines identifies risk genes for prostate cancer susceptibility
    Claudia Giambartolomei, Ji-Heui Seo, Tommer Schwarz, Malika Kumar Freund, Ruth Johnson, Sándor Spisák, Sylvan C. Baca, Alexander Gusev, Nicholas Mancuso, Bogdan Paşaniuc et al. · 2021 · The American Journal of Human Genetics
  23. Profiling Chromatin Accessibility at Single-Cell Resolution
    Sarthak Sinha, Ansuman T. Satpathy, Weiqiang Zhou, Hongkai Ji, Jo Anne Stratton, Arzina Jaffer, Nizar Jacques Bahlis, A. Sorana Morrissy, Jeff A. Biernaskie · 2021 · Genomics Proteomics & Bioinformatics
  24. Epigenetics: An opportunity to shape innate and adaptive immune responses
    Antonietta Liotti, Anne Lise Ferrara, Stefania Loffredo, Maria Rosaria Galdiero, Gilda Varricchi, Francesca Di Rella, Giorgia Teresa Maniscalco, Martina Belardo, Roberta Vastano, Rosaria Prencipe et al. · 2022 · Immunology
  25. Chromatin Accessibility and Interactions in the Transcriptional Regulation of T Cells
    Peng Li, Warren J. Leonard · 2018 · Frontiers in Immunology
  26. Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9
    Xin Liu, Yong Chen, Yuannyu Zhang, Yuxuan Liu, Nan Liu, Giovanni A. Botten, Hui Cao, Stuart H. Orkin, Michael Q. Zhang, Jian Xu · 2020 · Genome biology
  27. Decoding enhancer complexity with machine learning and high-throughput discovery
    Gabrielle D Smith, Wan Hern Ching, Paola Cornejo‐Páramo, Emily S. W. Wong · 2023 · Genome biology
  28. The macro and micro of chromosome conformation capture
    Viraat Y. Goel, Anders S. Hansen · 2020 · Wiley Interdisciplinary Reviews Developmental Biology
  29. The three-dimensional landscape of the genome in human brain tissue unveils regulatory mechanisms leading to schizophrenia risk
    Mah, Won, Won, Hyejung · 2020 · Schizophrenia Research
  30. Dynamic 3D Chromatin Reorganization during Establishment and Maintenance of Pluripotency
    Bobbie Pelham‐Webb, Dylan Murphy, Effie Apostolou · 2020 · Stem Cell Reports
  31. Multi-omic insights into Parkinson's Disease: From genetic associations to functional mechanisms
    Brian M. Schilder, Elisa Navarro, Towfique Raj · 2021 · Neurobiology of Disease
  32. The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation
    Jordan M. Meyers, Muthukumar Ramanathan, Ronald L. Shanderson, Aimee Beck, Laura Donohue, Ian Ferguson, Margaret G. Guo, Deepti S. Rao, Weili Miao, David L. Reynolds et al. · 2021 · PLoS Pathogens
  33. Analysis of blood methylation quantitative trait loci in East Asians reveals ancestry-specific impacts on complex traits
    Qianqian Peng, Xinxuan Liu, Wenran Li, Han Jing, Jiarui Li, Xingjian Gao, Qi Luo, Charles E. Breeze, Siyu Pan, Qiwen Zheng et al. · 2024 · Nature Genetics
  34. cLoops2: a full-stack comprehensive analytical tool for chromatin interactions
    Yaqiang Cao, Shuai Liu, Gang Ren, Qingsong Tang, Keji Zhao · 2021 · Nucleic Acids Research
  35. Insights into rheumatic diseases from next-generation sequencing
    Laura T. Donlin, Sung Ho Park, Ευγενία Γιαννοπούλου, Aleksandra Ivovic, Kyung‐Hyun Park‐Min, Richard M. Siegel, Lionel B. Ivashkiv · 2019 · Nature Reviews Rheumatology
  36. Super-Enhancer Redistribution as a Mechanism of Broad Gene Dysregulation in Repeatedly Drug-Treated Cancer Cells
    Qi Ma, Feng Yang, Carlos Mackintosh, Ranveer Singh Jayani, Soohwan Oh, Chunyu Jin, Sreejith J. Nair, Daria Merkurjev, Wubin Ma, Stephanie Allen et al. · 2019 · Cell Reports
  37. Functional studies of lung cancer GWAS beyond association
    Erping Long, Harsh Patel, Jinyoung Byun, Christopher Ian Amos, Jiyeon Choi · 2022 · Human Molecular Genetics
  38. Hi-TrAC reveals division of labor of transcription factors in organizing chromatin loops
    Shuai Liu, Ya-Qiang Cao, Kai-Rong Cui, Qing-Song Tang, Ke-Ji Zhao · 2022 · Nature Communications
  39. Genome-Wide Association Studies of Endometrial Cancer: Latest Developments and Future Directions
    Tracy A. O’Mara, Dylan M. Glubb, Pik Fang Kho, Deborah J. Thompson, Amanda B. Spurdle · 2019 · Cancer Epidemiology Biomarkers & Prevention
  40. Transcriptional dysregulation by aberrant enhancer activation and rewiring in cancer
    Atsushi Okabe, Atsushi Kaneda · 2021 · Cancer Science
  41. CRISPRi links COVID-19 GWAS loci to LZTFL1 and RAVER1
    Iris M. Fink-Baldauf, William D. Stuart, John J. Brewington, Minzhe Guo, Yutaka Maeda · 2022 · EBioMedicine
  42. Exploring noncoding variants in genetic diseases: from detection to functional insights
    Ke Wu, Fengxiao Bu, Yang Wu, Gen Zhang, Xin Wang, Shunmin He, Mo‐Fang Liu, Runsheng Chen, Huijun Yuan · 2024 · Journal of genetics and genomics/Journal of Genetics and Genomics
  43. Genetic association and Mendelian randomization for hypothyroidism highlight immune molecular mechanisms
    Samuel Mathieu, Mewen Briend, Erik Abner, Christian Yves Couture, Zhonglin Li, Yohan Bossé, Sébastien Thériault, Tõnu Esko, Benoît J. Arsenault, Patrick Mathieu · 2022 · iScience
  44. multiDGD: A versatile deep generative model for multi-omics data
    Viktoria Schuster, Emma Dann, Anders Krogh, Sarah Amalia Teichmann · 2024 · Nature Communications
  45. Genetic Insights Into Smooth Muscle Cell Contributions to Coronary Artery Disease
    Doris Wong, Adam W. Turner, Clint L. Miller · 2019 · Arteriosclerosis Thrombosis and Vascular Biology
  46. The contribution of non-coding regulatory elements to cardiovascular disease
    Diego Villar, Stephanie Frost, Panos Deloukas, Andrew Tinker · 2020 · Open Biology
  47. Integration of Enhancer-Promoter Interactions with GWAS Summary Results Identifies Novel Schizophrenia-Associated Genes and Pathways
    Chong Wu, Wei Pan · 2018 · Genetics
  48. Analysis of Promoter-Associated Chromatin Interactions Reveals Biologically Relevant Candidate Target Genes at Endometrial Cancer Risk Loci
    O’Mara, Tracy A., Spurdle, Amanda B., Glubb, Dylan M., Endometrial Cancer Association Consortium · 2019 · Cancers
  49. Revisiting 3D chromatin architecture in cancer development and progression
    Yuliang Feng, Siim Pauklin · 2020 · Nucleic Acids Research
  50. Genetic Variants in Transcription Factor Binding Sites in Humans: Triggered by Natural Selection and Triggers of Diseases
    Chia‐Chun Tseng, Man-Chun Wong, Wei‐Ting Liao, Chung‐Jen Chen, Su‐Chen Lee, Jeng‐Hsien Yen, Shun‐Jen Chang · 2021 · International Journal of Molecular Sciences
  51. Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures
    Raquel García-Pérez, Paula Esteller-Cucala, Glòria Mas Martín, Irene Lobón, Valerio Di Carlo, Meritxell Riera, Martin Kuhlwilm, Arcadi Navarro, Antoine Blancher, Luciano Di Croce et al. · 2021 · Nature Communications
  52. Unravelling the molecular basis for regulatory T‐cell plasticity and loss of function in disease
    Timothy J. Sadlon, Cheryl Y. Brown, Veronika Bandara, Christopher M. Hope, John Even Schjenken, Stephen Pederson, James Breen, Alistair R. R. Forrest, Marc Beyer, Sarah Anne Robertson et al. · 2018 · Clinical & Translational Immunology
  53. Most chromatin interactions are not in linkage disequilibrium
    Sean Whalen, Katherine S. Pollard · 2019 · Genome Research
  54. Enhancer reprogramming in tumor progression: a new route towards cancer cell plasticity
    Luca Fagnocchi, Vittoria Poli, Alessio Zippo · 2018 · Cellular and Molecular Life Sciences
  55. Measurement of differential chromatin interactions with absolute quantification of architecture (AQuA-HiChIP)
    Gryder, Berkley E., Khan, Javed, Stanton, Benjamin Z. · 2020 · Nature Protocols
  56. CRISPR screens identify gene targets at breast cancer risk loci
    Tuano, Natasha K., Beesley, Jonathan, Manning, Murray, Shi, Wei, Perlaza-Jimenez, Laura, Malaver-Ortega, Luis F., Paynter, Jacob M., Black, Debra, Civitarese, Andrew, McCue, Karen et al. · 2023 · Genome Biology
  57. GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization
    Da-Inn Lee, Sushmita Roy · 2021 · Genome biology
  58. 3D chromatin reprogramming primes human memory T H 2 cells for rapid recall and pathogenic dysfunction
    Anne Onrust-van Schoonhoven, Marjolein J. W. de Bruijn, Bernard Stikker, Rutger W. W. Brouwer, Gert‐Jan Braunstahl, Wilfred F. J. van IJcken, Thomas Graf, Danny Huylebroeck, Rudi W. Hendriks, Grégoire Stik et al. · 2023 · Science Immunology
  59. BRD9-SMAD2/3 Orchestrates Stemness and Tumorigenesis in Pancreatic Ductal Adenocarcinoma
    Yuliang Feng, Liuyang Cai, Martin Pook, Feng Liu, Chao‐Hui Chang, Mai Abdel Mouti, Reshma Nibhani, Stefania Militi, James E. Dunford, Martin Philpott et al. · 2023 · Gastroenterology
  60. Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function
    Gabriel B. Loeb, Pooja Kathail, Richard W. Shuai, Ryan Chung, Reinier J. Grona, Sailaja Peddada, Volkan Sevi̇m, Scot Federman, Karl Mader, Audrey Y. Chu et al. · 2024 · Nature Genetics
  61. Osteoarthritis year in review 2024: Genetics, genomics, and epigenetics
    Cindy Germaine Boer · 2024 · Osteoarthritis and Cartilage
  62. Parkinson's disease genetic risk in a midbrain neuronal cell line.
    Steven E. Pierce, Trevor A. Tyson, Alix Booms, Jordan D Prahl, G. Coetzee · 2018 · Neurobiology of Disease
  63. Tri-omic single-cell mapping of the 3D epigenome and transcriptome in whole mouse brains throughout the lifespan
    Haoxi Chai, Xingyu Huang, Guangzhou Xiong, Jiaxiang Huang, Katarzyna Karolina Pels, Lingyun Meng, Jin Han, Dongmei Tang, Guanjing Pan, Liang Deng et al. · 2025 · Nature Methods
  64. BMI1 enhancer polymorphism underlies chromosome 10p12.31 association with childhood acute lymphoblastic leukemia
    Adam J. de Smith, Kyle M. Walsh, Stephen Starko Francis, Chenan Zhang, Helen M. Hansen, Ivan V. Smirnov, Libby M. Morimoto, Todd P. Whitehead, Alice Y. Kang, Xiaorong Shao et al. · 2018 · International Journal of Cancer
  65. Blood disease–causing and –suppressing transcriptional enhancers: general principles and GATA2 mechanisms
    Emery H. Bresnick, Kirby D. Johnson · 2019 · Blood Advances
  66. Chromatin Looping Links Target Genes with Genetic Risk Loci for Dermatological Traits
    Shi, Chenfu, Ray-Jones, Helen, Ding, James, Duffus, Kate, Fu, Yao, Gaddi, Vasanthi Priyadarshini, Gough, Oliver, Hankinson, Jenny, Martin, Paul, McGovern, Amanda et al. · 2021 · Journal of Investigative Dermatology
  67. Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31
    Ray-Jones, Helen, Duffus, Kate, McGovern, Amanda, Martin, Paul, Shi, Chenfu, Hankinson, Jenny, Gough, Oliver, Yarwood, Annie, Morris, Andrew P., Adamson, Antony et al. · 2020 · BMC Biology
  68. HiChIPdb: a comprehensive database of HiChIP regulatory interactions
    Wan-Wen Zeng, Qiao Liu, Qi-Jin Yin, Rui Jiang, Wing Hong Wong · 2022 · Nucleic Acids Res.
  69. Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data
    Xi Xian Chen, Yuan Wang, Antonio Cappuccio, Wan-Sze Cheng, Frederique Murielle Ruf-Zamojski, Venugopalan D. Nair, Clare M. Miller, Aliza B. Rubenstein, German Nudelman, Alicja Tadych et al. · 2023 · Nature Computational Science
  70. Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping
    Quanyi Zhao, Michael Dacre, Trieu Nguyen, Milos Pjanic, Boxiang Liu, Dharini Iyer, Paul P. Cheng, Robert C. Wirka, Juyong Brian Kim, Hunter B. Fraser et al. · 2020 · Genome biology
  71. Augmenting and directing long-range CRISPR-mediated activation in human cells
    Y. Esther Tak, Joy E. Horng, Nicholas Thomas Perry, Hayley T. Schultz, Sowmya Iyer, Qiuming Yao, Luli S. Zou, Martin J. Aryee, Luca Pinello, J. Keith Joung · 2021 · Nature Methods
  72. Functional characterization of human genomic variation linked to polygenic diseases
    Tania Fabo, Paul A. Khavari · 2023 · Trends in Genetics
  73. Breakage fusion bridge cycles drive high oncogene number with moderate intratumoural heterogeneity
    Siavash R. Dehkordi, Ivy Tsz-Lo Wong, Jing Ni, Jens Luebeck, Kaiyuan Zhu, Gino Prasad, Lena Krockenberger, Guanghui Xu, Biswanath Chowdhury, Utkrisht Rajkumar et al. · 2025 · Nature Communications
  74. CNEr: A toolkit for exploring extreme noncoding conservation
    Ge Tan, Dimitris Polychronopoulos, Boris Lenhard · 2019 · PLoS Computational Biology
  75. Determinants and role of chromatin organization in acute leukemia
    Celestia Fang, Sridhar Rao, John D. Crispino, Panagiotis Ntziachristos · 2020 · Leukemia
  76. High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection
    Pranitha Vangala, Rachel Murphy, Sofia A. Quinodoz, Kyle J. Gellatly, Patrick E. McDonel, Mitchell Guttman, Manuel G. Garber · 2020 · Molecular Cell
  77. From the Genetics of Ankylosing Spondylitis to New Biology and Drug Target Discovery
    Nancy Zaarour, Yan Li, Shi Hui, Bowness Paul, Liye Chen · 2021 · Frontiers in Immunology
  78. Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath
    Xingjie Ren, Mengchi Wang, Bingkun Li, Kirsty Jamieson, Lina Zheng, Ian Richard Jones, Bin Li, Maya Asami Takagi, Jerry Lee, Lenka Maliskova et al. · 2021 · Science Advances
  79. CRISPR Tools for Systematic Studies of RNA Regulation
    J Engreitz, Omar O. Abudayyeh, Jonathan S. Gootenberg, Feng Zhang · 2019 · Cold Spring Harbor Perspectives in Biology
  80. Three-dimensional genome landscape of primary human cancers
    Kathryn E. Yost, Yan-Ding Zhao, King L. Hung, Kai-Yuan Zhu, Duo Xu, M. Corces, Shadi Shams, Brian H Louie, Shahab Sarmashghi, Laksshman Sundaram et al. · 2025 · Nature Genetics
  81. Triangulating Molecular Evidence to Prioritize Candidate Causal Genes at Established Atopic Dermatitis Loci
    Maria Sobczyk, Tom G. Richardson, Verena Zuber, Josine L. Min, GoDMC, Tom R. Gaunt, Lavinia Paternoster · 2021 · Journal of Investigative Dermatology
  82. Spatial promoter–enhancer hubs in cancer: organization, regulation, and function
    Zhao, Jingru, Faryabi, Robert B. · 2023 · Trends in Cancer
  83. Integration site–dependent HIV-1 promoter activity shapes host chromatin conformation
    Jack A. Collora, Y. Ho · 2023 · Genome Research
  84. Diverse Molecular Mechanisms Contribute to Differential Expression of Human Duplicated Genes
    Colin J. Shew, P. Carmona-Mora, Daniela C. Soto, Mira Mastoras, E. Roberts, Joseph Rosas, D. Jagannathan, G. Kaya, H. O'Geen, M. Dennis · 2020 · bioRxiv
  85. A cis-regulatory lexicon of DNA motif combinations mediating cell-type-specific gene regulation
    L. Donohue, M. Guo, Yang Zhao, N. Jung, Rose T. Bussat, D. S. Kim, Poornima H. Neela, Laura N. Kellman, Omar S. Garcia, R. Meyers et al. · 2022 · Cell Genomics
  86. 3D genome organization links non-coding disease-associated variants to genes
    Gisela Orozco, Stefan Schoenfelder, Nicolas J. Walker, S. Eyre, Peter Fraser · 2022 · Frontiers in Cell and Developmental Biology
  87. Tissue-specific enhancer functional networks for associating distal regulatory regions to disease
    Xi Xian Chen, Jian Zhou, Ran Zhang, Aaron K. Wong, Christopher Y. Park, Chandra L. Theesfeld, Olga G. Troyanskaya · 2021 · Cell Systems
  88. Immune Regulation in Time and Space: The Role of Local- and Long-Range Genomic Interactions in Regulating Immune Responses
    Liam P. Devenish, Musa M. Mhlanga, Yutaka Negishi · 2021 · Frontiers in Immunology
  89. Altered regulation of DPF3, a member of the SWI/SNF complexes, underlies the 14q24 renal cancer susceptibility locus
    Leandro Machado Colli, Lea Jessop, Timothy A. Myers, Sabrina Yvonne Camp, Mitchell J. Machiela, Jiyeon Choi, Renato Cunha, Olusegun O. Onabajo, Grace C Mills, Virginia Schmid et al. · 2021 · The American Journal of Human Genetics
  90. Transcriptional enhancers at 40: evolution of a viral DNA element to nuclear architectural structures
    Sreejith J. Nair, Tom Suter, Susan Siyu Wang, Yang Lu, Feng Yang, Michael G. Rosenfeld · 2022 · Trends in Genetics
  91. Predict long-range enhancer regulation based on protein–protein interactions between transcription factors
    Hao Wang, Binbin Huang, Jianrong Wang · 2021 · Nucleic Acids Research
  92. Molecular Insights Into Regulatory T-Cell Adaptation to Self, Environment, and Host Tissues: Plasticity or Loss of Function in Autoimmune Disease
    Cheryl Y. Brown, Timothy J. Sadlon, Christopher M. Hope, Ying Y. Wong, Soon Wei Wong, Ning Liu, Holly Withers, Katherine A. Brown, Veronika Bandara, Batjargal Gundsambuu et al. · 2020 · Frontiers in Immunology
  93. Loss of the long non-coding RNA OIP5-AS1 exacerbates heart failure in a sex-specific manner
    Aowen Zhuang, Anna C. Calkin, Shannen Lau, Helen Kiriazis, Daniel G. Donner, Yingying Liu, Simon T. Bond, Sarah C. Moody, Eleanor A.M. Gould, Timothy D. Colgan et al. · 2021 · iScience
  94. Deciphering pathogenicity of variants of uncertain significance with CRISPR-edited iPSCs
    Hongchao Guo, Lichao Liu, Masataka Nishiga, Le Cong, Joseph C. Wu · 2021 · Trends in Genetics
  95. 3D Genome Organization as an Epigenetic Determinant of Transcription Regulation in T Cells
    George Papadogkonas, Dionysios-Alexandros Papamatheakis, Charalampos G. Spilianakis · 2022 · Frontiers in Immunology
  96. 3D chromosomal landscapes in hematopoiesis and immunity
    A. Kloetgen, Palaniraja Thandapani, A. Tsirigos, lannis Aifantis · 2019 · Trends in immunology
  97. Restriction enzyme selection dictates detection range sensitivity in chromatin conformation capture-based variant-to-gene mapping approaches
    Su, Chun, Pahl, Matthew C., Grant, Struan F. A., Wells, Andrew D. · 2021 · Human Genetics
  98. Exploring the genetic basis of coronary artery disease using functional genomics
    Maykel López Rodríguez, Uma Thanigai Arasu, Minna Unelma Kaikkonen · 2023 · Atherosclerosis
  99. Positive and Negative Control of Enhancer-Promoter Interactions by Other DNA Loops Generates Specificity and Tunability.
    Nan Hao, K. Shearwin, I. Dodd · 2019 · Cell Reports
  100. Genetic variation contributes to gene expression response in ischemic stroke: an eQTL study
    Hajar Amini, Natasha Shroff, Boryana S. Stamova, Eva Ferino, Paulina Carmona-Mora, Xinhua Zhan, Preston Sitorus, Heather Hull, Glen C. Jickling, Frank R. Sharp et al. · 2020 · Annals of Clinical and Translational Neurology