The accessible chromatin landscape of the human genome

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Items 101–200 of 1,010

1. Identification of 153 new loci associated with heel bone mineral density and functional involvement of GPC6 in osteoporosis
   John P. Kemp, John A. Morris, Carolina Medina‐Gómez, Vincenzo Forgetta, Nicole M. Warrington, Scott E. Youlten, Jie Zheng, Celia Louise Gregson, Elin Grundberg, Katerina Trajanoska et al. · 2017 · Nature Genetics
2. EWS-FLI1 Utilizes Divergent Chromatin Remodeling Mechanisms to Directly Activate or Repress Enhancer Elements in Ewing Sarcoma
   Nicolò Riggi, Birgit Knoechel, Shawn M. Gillespie, Esther Rheinbay, Gaylor Boulay, Mario L. Suvà, Nikki E. Rossetti, Wannaporn E. Boonseng, Ozgur Oksuz, Edward Cook et al. · 2014 · Cancer Cell
3. Conduct disorder
   Graeme F. Fairchild, David John Hawes, Paul Joseph Frick, William Copeland, Candice L. Odgers, Barbara Franke, Christine Margarete Freitag, Stéphane A. De Brito · 2019 · Nature Reviews Disease Primers
4. A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer
   Ali Amin Al Olama, Zsofia Kote‐Jarai, Sonja I. Berndt, David V. Conti, Fredrick R. Schumacher, Ying Han, Sara Benlloch, Dennis J. Hazelett, Zhaoming Wang, Edward J. Saunders et al. · 2014 · Nature Genetics
5. Epigenetic programming and reprogramming during development
   Irene Cantone, Amanda G. Fisher · 2013 · Nature Structural & Molecular Biology
6. Role of non-coding sequence variants in cancer
   Ekta Khurana, Yao Fu, Dimple Chakravarty, Francesca Demichelis, Mark A. Rubin, Mark Gerstein · 2016 · Nature Reviews Genetics
7. Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin
   Whalen, Sean, Truty, Rebecca M, Pollard, Katherine S · 2016 · Nature Genetics
8. Defining the genetic, genomic, cellular, and diagnostic architectures of psychiatric disorders
   Sullivan, Patrick F., Geschwind, Daniel H. · 2019 · Cell
9. Identification of transcription factor binding sites using ATAC-seq
   Zhijian Li, Marcel H. Schulz, Thomas Look, Matthias Begemann, Martin Zenke, Ivan G. Costa · 2019 · Genome biology
10. CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome
    Klann, Tyler S, Black, Joshua B, Chellappan, Malathi, Safi, Alexias, Song, Lingyun, Hilton, Isaac B, Crawford, Gregory E, Reddy, Timothy E, Gersbach, Charles A · 2017 · Nature Biotechnology
11. The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts
    Wagner, James R, Busche, Stephan, Ge, Bing, Kwan, Tony, Pastinen, Tomi, Blanchette, Mathieu · 2014 · Genome biology
12. Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility
    Lareau, Caleb A., Duarte, Fabiana M., Chew, Jennifer G., Kartha, Vinay K., Burkett, Zach D., Kohlway, Andrew S., Pokholok, Dmitry, Aryee, Martin J., Steemers, Frank J., Lebofsky, Ronald et al. · 2019 · Nature Biotechnology
13. STT3-dependent PD-L1 accumulation on cancer stem cells promotes immune evasion
    Jung-Mao Hsu, Weiya Xia, Yi-Hsin Hsu, Li-Chuan Chan, Wen-Hsuan Yu, Jong‐Ho Cha, Chun‐Te Chen, Hsin-Wei Liao, Chu‐Wei Kuo, Kay‐Hooi Khoo et al. · 2018 · Nature Communications
14. Passive and active DNA methylation and the interplay with genetic variation in gene regulation
    Gutierrez-Arcelus, Maria, Lappalainen, Tuuli, Montgomery, Stephen B, Buil, Alfonso, Ongen, Halit, Yurovsky, Alisa, Bryois, Julien, Giger, Thomas, Romano, Luciana, Planchon, Alexandra et al. · 2013 · eLife
15. GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations
    Umadevi Paila, Brad Chapman, Rory Kirchner, Aaron R. Quinlan · 2013 · PLoS Computational Biology
16. Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells
    Gifford, Casey A., Ziller, Michael J., Gu, Hongcang, Trapnell, Cole, Donaghey, Julie, Tsankov, Alexander, Shalek, Alex K., Kelley, David R., Shishkin, Alexander A., Issner, Robbyn et al. · 2013 · Cell
17. The Ensembl Regulatory Build
    Zerbino, Daniel R, Wilder, Steven P, Johnson, Nathan, Juettemann, Thomas, Flicek, Paul R · 2015 · Genome Biology
18. Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape
    Richard I. Sherwood, Tatsunori Hashimoto, Charles W O'Donnell, Sophia Lewis, Amira A. Barkal, John Peter van Hoff, Vivek Karun, Tommi Jaakkola, David Kenneth Gifford · 2014 · Nature Biotechnology
19. Nucleosomes impede Cas9 access to DNA in vivo and in vitro
    Max A. Horlbeck, Lea B. Witkowsky, Benjamin Guglielmi, Joseph M. Replogle, Luke A. Gilbert, Jacqueline E. Villalta, Sharon E. Torigoe, Robert Tjian, Jonathan S. Weissman · 2016 · eLife
20. Identifying gene targets for brain-related traits using transcriptomic and methylomic data from blood
    Qi, Ting, Wu, Yang, Zeng, Jian, Zhang, Futao, Xue, Angli, Jiang, Longda, Zhu, Zhihong, Kemper, Kathryn, Yengo, Loic, Zheng, Zhili et al. · 2018 · Nature Communications
21. Functional implications of genome topology
    Cavalli, Giacomo, Misteli, Tom · 2013 · Nature Structural & Molecular Biology
22. YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers
    Stein, Claudia, Bardet, Anaïs Flore, Roma, Guglielmo, Bergling, Sebastian, Clay, Ieuan, Ruchti, Alexandra, Agarinis, Claudia, Schmelzle, Tobias, Bouwmeester, Tewis, Schübeler, Dirk et al. · 2015 · PLOS Genetics
23. A Reference Methylome Database and Analysis Pipeline to Facilitate Integrative and Comparative Epigenomics
    Qiang Song, Benjamin E. Decato, Elizabeth E. Hong, Meng Zhou, Fang Fang, Jianghan Qu, Tyler H. Garvin, Michael D. Kessler, Jun Zhou, Andrew D. Smith · 2013 · PLoS ONE
24. Genome-wide meta-analysis identifies new susceptibility loci for migraine
    North American Brain Expression Consortium, Anttila, Verneri, UK Brain Expression Consortium, the International Headache Genetics Consortium, Winsvold, Bendik S, Gormley, Padhraig, Kurth, Tobias, Bettella, Francesco, McMahon, George, Kallela, Mikko et al. · 2013 · Nature Genetics
25. Endogenous Retrotransposition Activates Oncogenic Pathways in Hepatocellular Carcinoma
    Ruchi Shukla, Kyle R. Upton, Martín Muñoz-López, Daniel J. Gerhardt, Malcolm E Fisher, Thu Nguyen, Paul Martin Brennan, John Kenneth Baillie, Agnese Collino, Serena Ghisletti et al. · 2013 · Cell
26. 3D Chromosome Regulatory Landscape of Human Pluripotent Cells
    Ji, Xiong, Dadon, Daniel B., Powell, Benjamin E., Fan, Zi Peng, Borges-Rivera, Diego, Shachar, Sigal, Weintraub, Abraham S., Hnisz, Denes, Pegoraro, Gianluca, Lee, Tong Ihn et al. · 2016 · Cell Stem Cell
27. Towards a comprehensive catalogue of validated and target-linked human enhancers
    Gasperini, Molly, Tome, Jacob M., Shendure, Jay · 2020 · Nature Reviews Genetics
28. dbSUPER: a database of super-enhancers in mouse and human genome
    Aziz Khan, Xuegong Zhang · 2015 · Nucleic Acids Research
29. Relationship Between Methylome and Transcriptome in Patients With Nonalcoholic Fatty Liver Disease
    Murphy, Susan K., Yang, Hyuna, Moylan, Cynthia A., Pang, Herbert, Dellinger, Andrew, Abdelmalek, Manal F., Garrett, Melanie E., Ashley–Koch, Allison, Suzuki, Ayako, Tillmann, Hans L. et al. · 2013 · Gastroenterology
30. The Spatial Organization of the Human Genome
    Bickmore, Wendy A. · 2013 · Annual Review of Genomics and Human Genetics
31. The role of enhancers in cancer
    Inderpreet Sur, Jussi Taipale · 2016 · Nature reviews. Cancer
32. The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation
    Iwafuchi-Doi, Makiko, Donahue, Greg, Kakumanu, Akshay, Watts, Jason A., Mahony, Shaun, Pugh, B. Franklin, Lee, Dolim, Kaestner, Klaus H., Zaret, Kenneth S. · 2016 · Molecular Cell
33. Global reference mapping of human transcription factor footprints
    Vierstra, Jeff, Lazar, John, Sandstrom, Richard, Halow, Jessica, Lee, Kristen, Bates, Daniel, Diegel, Morgan, Dunn, Douglas, Neri, Fidencio, Haugen, Eric et al. · 2020 · Nature
34. Genetic dissection of the α-globin super-enhancer in vivo
    Hay, Deborah, Hughes, Jim R, Babbs, Christian, Davies, James O J, Graham, Bryony J, Hanssen, Lars L P, Kassouf, Mira T, Oudelaar, A Marieke, Sharpe, Jacqueline A, Suciu, Maria C et al. · 2016 · Nature Genetics
35. Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites
    Jian Yan, Martin Enge, Thomas Whitington, Kashyap Dave, Jianping Liu, Inderpreet Sur, Bernhard Schmierer, Arttu Jolma, Teemu Kivioja, Minna Taipale et al. · 2013 · Cell
36. Active medulloblastoma enhancers reveal subgroup-specific cellular origins
    Charles Y. Lin, Serap Erkek, Yiai Tong, Linlin Yin, Alexander Joel Federation, Marc Zapatka, Parthiv Haldipur, Daisuke Kawauchi, Thomas Risch, Hans-Jörg Warnatz et al. · 2016 · Nature
37. The prevalence, evolution and chromatin signatures of plant regulatory elements
    Zefu Lu, Alexandre P. Marand, William A. Ricci, Christina L. Ethridge, Xiaoyu Zhang, Robert J. Schmitz · 2019 · Nature Plants
38. Mechanisms of enhancer action: the known and the unknown
    Anil Panigrahi, Bert W. O’Malley · 2021 · Genome biology
39. An atlas of dynamic chromatin landscapes in mouse fetal development
    David U. Gorkin, Iros Barozzi, Yuan Zhao, Yanxiao Zhang, Hui Huang, Ah Young Lee, Bin Li, Joshua Chiou, André Wildberg, Bo Ding et al. · 2020 · Nature
40. Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain
    Luo, Chongyuan, Lancaster, Madeline A., Castanon, Rosa, Nery, Joseph R., Knoblich, Juergen A., Ecker, Joseph R. · 2016 · Cell Reports
41. Rho-actin signaling to the MRTF coactivators dominates the immediate transcriptional response to serum in fibroblasts
    Cyril Esnault, Aengus Stewart, Francesco Gualdrini, Philip East, Stuart D. Horswell, Nik Matthews, Richard Treisman · 2014 · Genes & Development
42. The interaction landscape between transcription factors and the nucleosome
    Fangjie Zhu, Lucas Farnung, Eevi Kaasinen, Biswajyoti Sahu, Yimeng Yin, Bei Wei, Svetlana Dodonova, Kazuhiro R. Nitta, Ekaterina Yu. Morgunova, Minna Taipale et al. · 2018 · Nature
43. Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics
    Ekta Khurana, Yao Fu, Vincenza Colonna, Xinmeng Jasmine Mu, Hyun Min Kang, Tuuli Lappalainen, Andrea Sboner, Lucas Lochovsky, Jieming Chen, Arif O. Harmanci et al. · 2013 · Science
44. Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution
    Mayer, Andreas, di Iulio, Julia, Maleri, Seth, Eser, Umut, Vierstra, Jeff, Reynolds, Alex, Sandstrom, Richard, Stamatoyannopoulos, John A., Churchman, L. Stirling · 2015 · Cell
45. Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits
    Corradin, Olivia, Saiakhova, Alina, Akhtar-Zaidi, Batool, Myeroff, Lois, Willis, Joseph, Cowper-Sal·lari, Richard, Lupien, Mathieu, Markowitz, Sanford, Scacheri, Peter C. · 2014 · Genome Research
46. Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility
    Sarah K. Denny, Dian Yang, Chen-Hua Chuang, Brady Jennifer J, Jing Shan Lim, Barbara M. Grüner, Shin‐Heng Chiou, Alicia N. Schep, Jessika Baral, Cécile Hamard et al. · 2016 · Cell
47. Heritability and genomics of gene expression in peripheral blood
    Wright, Fred A, Sullivan, Patrick F, Brooks, Andrew I, Zou, Fei, Sun, Wei, Xia, Kai, Madar, Vered, Jansen, Rick, Chung, Wonil, Zhou, Yi-Hui et al. · 2014 · Nature Genetics
48. A compendium of promoter-centered long-range chromatin interactions in the human genome
    Jung, Inkyung, Schmitt, Anthony, Diao, Yarui, Lee, Andrew J., Liu, Tristin, Yang, Dongchan, Tan, Catherine, Eom, Junghyun, Chan, Marilynn, Chee, Sora et al. · 2019 · Nature Genetics
49. Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape
    Raluca Gordân, Ning Shen, Iris Dror, Tianyin Zhou, John Horton, Remo Rohs, Martha L. Bulyk · 2013 · Cell Reports
50. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project
    Leif Andersson, Alan L. Archibald, Cynthia D.K. Bottema, Rüdiger Bräuning, Shane C. Burgess, David W. Burt, Eduardo Casas, Hans H. Cheng, Laura Clarke, Christine Couldrey et al. · 2015 · Genome biology
51. Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates
    Hao Wu, Tianlei Xu, Hao Feng, Li Chen, Ben Li, Bing Yao, Zhaohui Steve Qin, Peng Jin, Karen N. Conneely · 2015 · Nucleic Acids Research
52. Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues
    Jason Ernst, M Kellis · 2015 · Nature Biotechnology
53. The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements
    Pierre‐Étienne Jacques, Justin Jeyakani, Guillaume Bourque · 2013 · PLoS Genetics
54. Architectural and Functional Commonalities between Enhancers and Promoters
    Tae-Kyung Kim, Ramin Shiekhattar · 2015 · Cell
55. 5mC Oxidation by Tet2 Modulates Enhancer Activity and Timing of Transcriptome Reprogramming during Differentiation
    Gary C. Hon, Chun‐Xiao Song, Tingting Du, Fulai Jin, Siddarth Selvaraj, Ah Young Lee, Chia‐An Yen, Zhen Ye, Shi-Qing Mao, Bang-An Wang et al. · 2014 · Molecular Cell
56. Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers
    Xiaoyang Zhang, Peter S. Choi, Joshua M. Francis, Marcin B. Imielinski, Hideo Watanabe, Andrew D. Cherniack, Matthew M. Meyerson · 2015 · Nature Genetics
57. Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity
    Alexander, Jeffrey M, Guan, Juan, Li, Bingkun, Maliskova, Lenka, Song, Michael, Shen, Yin, Huang, Bo, Lomvardas, Stavros, Weiner, Orion D · 2019 · eLife
58. Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development
    Falong Lu, Yuting Liu, Azusa Inoue, Tsukasa Suzuki, Keji Zhao, Yi Zhang · 2016 · Cell
59. The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers
    Christopher Ian Amos, Joe Dennis, Zhaoming Wang, Jinyoung Byun, Fredrick R. Schumacher, Simon A. Gayther, Graham Casey, David J. Hunter, Thomas A. Sellers, Stephen B. Gruber et al. · 2016 · Cancer Epidemiology Biomarkers & Prevention
60. Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes
    Andrew B. Stergachis, Shane J. Neph, Alex P. Reynolds, Richard Humbert, Brady Miller, Sharon L. Paige, Benjamin Vernot, Jeffrey B. Cheng, Robert E. Thurman, Richard S. Sandstrom et al. · 2013 · Cell
61. Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response
    HIPSCI Consortium, Alasoo, Kaur, Rodrigues, Julia, Mukhopadhyay, Subhankar, Knights, Andrew J., Mann, Alice L., Kundu, Kousik, Hale, Christine, Dougan, Gordon, Gaffney, Daniel J. · 2018 · Nature Genetics
62. Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation
    Kyong-Rim Kieffer-Kwon, Zhonghui Tang, Ewy A. Mathé, Jason Qian, Myong‐Hee Sung, Guoliang Li, Wolfgang Resch, Songjoon Baek, Nathanael D. Pruett, Lars Grøntved et al. · 2013 · Cell
63. Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices
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64. Genome-wide mapping of endogenous G-quadruplex DNA structures by chromatin immunoprecipitation and high-throughput sequencing
    Robert Hänsel‐Hertsch, Jochen Spiegel, Giovanni Marsico, David Tannahill, Shankar Balasubramanian · 2018 · Nature Protocols
65. Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation
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66. Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples
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67. Structural and functional diversity of Topologically Associating Domains
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68. Regulation of disease-associated gene expression in the 3D genome
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69. The origin of Metazoa: a unicellular perspective
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70. Index and biological spectrum of human DNase I hypersensitive sites
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71. Synergistic Activation of Inflammatory Cytokine Genes by Interferon-γ-Induced Chromatin Remodeling and Toll-like Receptor Signaling
    Qiao, Yu, Giannopoulou, Eugenia G., Chan, Chun Hin, Park, Sung-ho, Gong, Shiaoching, Chen, Janice, Hu, Xiaoyu, Elemento, Olivier, Ivashkiv, Lionel B. · 2013 · Immunity
72. Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq
    Sebé-Pedrós, Arnau, Saudemont, Baptiste, Chomsky, Elad, Plessier, Flora, Mailhé, Marie-Pierre, Renno, Justine, Loe-Mie, Yann, Lifshitz, Aviezer, Mukamel, Zohar, Schmutz, Sandrine et al. · 2018 · Cell
73. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA
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74. Exhaustion-associated regulatory regions in CD8 + tumor-infiltrating T cells
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75. Transcriptional landscape of repetitive elements in normal and cancer human cells
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76. Domains of genome-wide gene expression dysregulation in Down’s syndrome
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77. In Situ Capture of Chromatin Interactions by Biotinylated dCas9
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78. DNA double-strand-break complexity levels and their possible contributions to the probability for error-prone processing and repair pathway choice
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79. Dynamic Changes in Chromatin Accessibility Occur in CD8 + T Cells Responding to Viral Infection
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80. Risk SNP-Mediated Promoter-Enhancer Switching Drives Prostate Cancer through lncRNA PCAT19
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81. Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation
    François Le Dily, Davide Baù, Andy Pohl, Guillermo Pablo Vicent, François Serra, Daniel Soronellas, Giancarlo Castellano, Roni H. G. Wright, Cecilia Ballaré, Guillaume J. P. Filion et al. · 2014 · Genes & Development
82. Eukaryotic transcriptional dynamics: from single molecules to cell populations
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83. Genome-Wide Epigenetic Regulation of miRNAs in Cancer
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84. Deciphering the multi-scale, quantitative cis-regulatory code
    Seungsoo Kim, Joanna Wysocka · 2023 · Molecular Cell
85. Astrocytic abnormalities and global DNA methylation patterns in depression and suicide
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86. Statistical and integrative system-level analysis of DNA methylation data
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87. Biology and Mechanisms of Action of the Vitamin D Hormone
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88. Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data
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89. Single-cell epigenomics: techniques and emerging applications
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90. Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels
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91. Meta-analysis of Genome-wide Association Studies Identifies 1q22 as a Susceptibility Locus for Intracerebral Hemorrhage
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92. ENCODE explained
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93. Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution
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94. International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways
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95. Open chromatin reveals the functional maize genome
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96. Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
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97. The how and why of lncRNA function: An innate immune perspective
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98. Role of DNA Methylation in Modulating Transcription Factor Occupancy
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99. Genome-wide map of regulatory interactions in the human genome
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100. Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules
     Kelsey A. Maher, Marko Bajic, Kaisa Kajala, Mauricio Alberto Reynoso, Germain C. Pauluzzi, Donnelly A. West, Kristina Zumstein, Margaret Roth Woodhouse, Kerry L. Bubb, Michael W. Dorrity et al. · 2017 · The Plant Cell