Integrative analysis of 111 reference human epigenomes

Cited by (1,070)

Items 201–300 of 1,070

1. Using DNA methylation profiling to evaluate biological age and longevity interventions
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2. TERT rearrangements are frequent in neuroblastoma and identify aggressive tumors
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3. The cis-Regulatory Atlas of the Mouse Immune System
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4. Universal DNA methylation age across mammalian tissues
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5. Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation
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6. Towards a comprehensive catalogue of validated and target-linked human enhancers
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7. Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain
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8. AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model
   Avsec, Žiga, Latysheva, Natasha, Cheng, Jun, Novati, Guido, Taylor, Kyle R., Ward, Tom, Bycroft, Clare, Nicolaisen, Lauren, Arvaniti, Eirini, Pan, Joshua et al. · 2025
9. The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis
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10. Early life stress confers lifelong stress susceptibility in mice via ventral tegmental area OTX2
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11. Genome-wide association studies of cancer: current insights and future perspectives
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12. Global reference mapping of human transcription factor footprints
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13. Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases
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14. An atlas of dynamic chromatin landscapes in mouse fetal development
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15. Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia
    Sheng Li, Francine E. Garrett-Bakelman, Stephen S. Chung, Mathijs Arnoud Sanders, Todd Hricik, Franck Rapaport, Jay L. Patel, Richard James Dillon, Priyanka Vijay, Anna L Brown et al. · 2016 · Nature Medicine
16. Distinct viral reservoirs in individuals with spontaneous control of HIV-1
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17. Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels
    Xia Jiang, Paul F. O’Reilly, Hugues Aschard, Yi‐Hsiang Hsu, John Brent Richards, Josée Dupuis, Erik Ingelsson, David Karasik, Stefan Pilz, Diane J. Berry et al. · 2018 · Nature Communications
18. Active medulloblastoma enhancers reveal subgroup-specific cellular origins
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19. A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity
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20. The Three-Dimensional Organization of Mammalian Genomes
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21. A cross-disorder dosage sensitivity map of the human genome
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22. Whole genome sequencing analysis for cancer genomics and precision medicine
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23. RnBeads 2.0: comprehensive analysis of DNA methylation data
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24. DNA hypermethylation in disease: mechanisms and clinical relevance
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25. Advancing regulatory variant effect prediction with AlphaGenome
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26. SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation
    Xiaofeng Wang, Ryan S. Lee, B. Alver, Jeffrey R. Haswell, Su Wang, Jakub Mieczkowski, Yotam Drier, Shawn M. Gillespie, Tenley C. Archer, Jennifer N. Wu et al. · 2016 · Nature Genetics
27. Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells
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28. Mapping and characterization of structural variation in 17,795 human genomes
    NHGRI Centers for Common Disease Genomics, Abel, Haley J., Larson, David E., Regier, Allison A., Chiang, Colby, Das, Indraniel, Kanchi, Krishna L., Layer, Ryan M., Neale, Benjamin M., Salerno, William J. et al. · 2020 · Nature
29. Gilles de la Tourette syndrome
    Mary May Robertson, Valsamma Eapen, Harvey S. Singer, Davide Martino, Jeremiah M. Scharf, Peristera Paschou, Veit Roessner, Douglas W. Woods, Marwan I. Hariz, Carol A. Mathews et al. · 2017 · Nature Reviews Disease Primers
30. Genetic identification of cell types underlying brain complex traits yields insights into the etiology of Parkinson’s disease
    Julien Bryois, Nathan Skene, Thomas Folkmann Hansen, Lisette J. A. Kogelman, Hunna J. Watson, Zijing Liu, Roger A.H. Adan, Lars S. Alfredsson, Tetsuya Ando, Ole A. Andreassen et al. · 2020 · Nature Genetics
31. The GTEx Consortium atlas of genetic regulatory effects across human tissues
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32. Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis
    The BrainSeq Consortium, Jaffe, Andrew E., Straub, Richard E., Shin, Joo Heon, Tao, Ran, Gao, Yuan, Collado-Torres, Leonardo, Kam-Thong, Tony, Xi, Hualin S., Quan, Jie et al. · 2018 · Nature Neuroscience
33. Characterizing mutagenic effects of recombination through a sequence-level genetic map
    Bjarni V. Halldórsson, Gunnar Pálsson, Ólafur Andri Stefánsson, Hákon Jónsson, Marteinn Thor Hardarson, Hannes P. Eggertsson, Bjarni Gunnarsson, Ásmundur Oddsson, Gisli Hreinn Halldorsson, Florian Zink et al. · 2019 · Science
34. Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues
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35. Titin-truncating variants affect heart function in disease cohorts and the general population
    Sebastian Schäfer, Antonio de Marvao, Eleonora Adami, Lorna R. Fiedler, Benjamin Ng, Ester Sandar Win Khin, Owen J. L. Rackham, Sebastiaan van Heesch, Chee Jian Pua, Miao Kui et al. · 2016 · Nature Genetics
36. Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens
    David W. Morgens, Michael Wainberg, Evan A. Boyle, Oana Ursu, Carlos L. Araya, C. Kimberly Tsui, Michael Seamus Haney, Gaelen T. Hess, Kyuho Han, Edwin E. Jeng et al. · 2017 · Nature Communications
37. Comparative transcriptomics in human and mouse
    Alessandra Breschi, T Gingeras, Roderic Guigó · 2017 · Nature Reviews Genetics
38. Epigenetics of Stress-Related Psychiatric Disorders and Gene × Environment Interactions
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39. 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
40. Transcription factor binding dynamics during human ES cell differentiation
    Alexander M. Tsankov, Hongcang Gu, Veronika Akopian, Michael J. Ziller, Julie Donaghey, Ido Amit, Andreas Gnirke, Alexander Meissner · 2015 · Nature
41. Genome-wide meta-analysis of problematic alcohol use in 435,563 individuals yields insights into biology and relationships with other traits
    Hang Zhou, Julia Sealock, Sandra Sanchez‐Roige, Toni‐Kim Clarke, Daniel F. Levey, Zhongshan Cheng, Boyang Li, Renato A Polimanti, Rachel L. Kember, Rachel Vickers‐Smith et al. · 2020 · Nature Neuroscience
42. Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases
    Elle M. Weeks, Jacob C. Ulirsch, Nathan Cheng, Brian L. Trippe, Rebecca S. Fine, Jenkai Miao, Tejal A. Patwardhan, Masahiro Kanai, Joseph Nasser, Charles P. Fulco et al. · 2023 · Nature Genetics
43. Epigenetic regulatory functions of DNA modifications: 5-methylcytosine and beyond
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44. Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome
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45. An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder
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46. A road map for understanding molecular and genetic determinants of osteoporosis
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47. Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior
    Ryan N. Doan, Byoung-Il Bae, Beatriz Cubelos, Cindy Y. Chang, Amer A. Hossain, Samira Al-Saad, Nahit Motavallı Mukaddes, Özgür Öner, Muna Al‐Saffar, Soher Balkhy et al. · 2016 · Cell
48. Genome-wide association study of glioma subtypes identifies specific differences in genetic susceptibility to glioblastoma and non-glioblastoma tumors
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49. Association of Body Mass Index with DNA Methylation and Gene Expression in Blood Cells and Relations to Cardiometabolic Disease: A Mendelian Randomization Approach
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50. Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers
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51. Genome-wide mapping and analysis of chromosome architecture
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52. Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis
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53. Pioneer transcription factors, chromatin dynamics, and cell fate control
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54. Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data
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55. Functional Enhancers Shape Extrachromosomal Oncogene Amplifications
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56. Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci
    Eilis J. Hannon, Helen Spiers, Joana F. Viana, Ruth Pidsley, Joe Burrage, Therese M. Murphy, Claire Troakes, Gustavo Turecki, Michael C. O’Donovan, Leonard C. Schalkwyk et al. · 2015 · Nature Neuroscience
57. Genetic mapping of cell type specificity for complex traits
    Kyoko Watanabe, Maša Umićević Mirkov, Christiaan de Leeuw, Martijn P. van den Heuvel, Daniëlle Posthuma · 2019 · Nature Communications
58. Genomic Patterns of De Novo Mutation in Simplex Autism
    Tychele N. Turner, Bradley P. Coe, Diane E. Dickel, Kendra Hoekzema, Bradley J. Nelson, Michael C. Zody, Zev N. Kronenberg, Fereydoun Hormozdiari, Archana Natarajan Raja, Len A. Pennacchio et al. · 2017 · Cell
59. Common genetic variants and modifiable risk factors underpin hypertrophic cardiomyopathy susceptibility and expressivity
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60. Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation
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61. Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks
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62. Parent-of-origin-specific signatures of de novo mutations
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63. Loci associated with skin pigmentation identified in African populations
    Crawford, Nicholas G., Kelly, Derek E., Hansen, Matthew E. B., Beltrame, Marcia H., Fan, Shaohua, Bowman, Shanna L., Jewett, Ethan, Ranciaro, Alessia, Thompson, Simon, Lo, Yancy et al. · 2017 · Science
64. Dynamic landscape of immune cell-specific gene regulation in immune-mediated diseases
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65. Systematic differences in discovery of genetic effects on gene expression and complex traits
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66. The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space
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67. Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits
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68. Genetic architecture of 11 major psychiatric disorders at biobehavioral, functional genomic and molecular genetic levels of analysis
    Andrew David Grotzinger, Travis T. Mallard, Wonuola A. Akingbuwa, Hill Fung Ip, Mark J. Adams, Cathryn M. Lewis, Andrew Mark McIntosh, Jakob Grove, Søren Dalsgaard, Klaus‐Peter Lesch et al. · 2022 · Nature Genetics
69. Erratum: Genome-wide association meta-analysis of 78,308 individuals identifies new loci and genes influencing human intelligence
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70. Regulation of disease-associated gene expression in the 3D genome
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71. Index and biological spectrum of human DNase I hypersensitive sites
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72. Genome-wide physical activity interactions in adiposity ― A meta-analysis of 200,452 adults
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73. A decade of genome-wide association studies for coronary artery disease: the challenges ahead
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74. H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions
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75. Cell fate control by pioneer transcription factors
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76. Genome-wide Association Analysis of Psoriatic Arthritis and Cutaneous Psoriasis Reveals Differences in Their Genetic Architecture
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77. Genome-wide analysis identifies 12 loci influencing human reproductive behavior
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78. The diverse origins of circulating cell‐free DNA in the human body: a critical re‐evaluation of the literature
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79. Modulation of tissue repair by regeneration enhancer elements
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80. PAX3–FOXO1 Establishes Myogenic Super Enhancers and Confers BET Bromodomain Vulnerability
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81. A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer
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82. Risk SNP-Mediated Promoter-Enhancer Switching Drives Prostate Cancer through lncRNA PCAT19
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83. DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome
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84. Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development
    Phanstiel, Douglas H., Van Bortle, Kevin, Spacek, Damek, Hess, Gaelen T., Shamim, Muhammad Saad, Machol, Ido, Love, Michael I., Aiden, Erez Lieberman, Bassik, Michael C., Snyder, Michael P. · 2017 · Molecular Cell
85. Comparison of computational methods for Hi-C data analysis
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86. A combined analysis of genetically correlated traits identifies 187 loci and a role for neurogenesis and myelination in intelligence
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87. DNA methylation dynamics during B cell maturation underlie a continuum of disease phenotypes in chronic lymphocytic leukemia
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88. TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
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89. Genome-wide association analysis of 19,629 individuals identifies variants influencing regional brain volumes and refines their genetic co-architecture with cognitive and mental health traits
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90. Transcriptome and epigenome landscape of human cortical development modeled in organoids
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91. A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples
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92. CRISPR/Cas9-based engineering of the epigenome
    Pulecio, Julian, Verma, Nipun, Mejía-Ramírez, Eva, Huangfu, Danwei, Raya, Angel · 2017 · Cell Stem Cell
93. DeepChrome: deep-learning for predicting gene expression from histone modifications
    Ritambhara Singh, Jack Lanchantin, Gabriel Robins, Yanjun Qi · 2016 · Bioinformatics
94. Genomics of disease risk in globally diverse populations
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95. Where Are the Disease-Associated eQTLs?
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96. EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species
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97. Genomic Analysis in the Age of Human Genome Sequencing
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98. Nucleotide excision repair is impaired by binding of transcription factors to DNA
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99. Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling
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100. Novel genetic loci associated with hippocampal volume
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