Population Variation and Genetic Control of Modular Chromatin Architecture in Humans
Waszak, Sebastian M., Delaneau, Olivier, Gschwind, Andreas R., Kilpinen, Helena, Raghav, Sunil K., Witwicki, Robert M., Orioli, Andrea, Wiederkehr, Michael, Panousis, Nikolaos I., Yurovsky, Alisa, Romano-Palumbo, Luciana, Planchon, Alexandra, Bielser, Deborah, Padioleau, Ismael, Udin, Gilles, Thurnheer, Sarah, Hacker, David, Hernandez, Nouria, Reymond, Alexandre, Deplancke, Bart, Dermitzakis, Emmanouil T.·2015·Cell
Cited by (219)
Items 101–200 of 219
- ESCC ATLAS: A population wide compendium of biomarkers for Esophageal Squamous Cell CarcinomaAsna Tungekar, Sumana Mandarthi, Pooja R. Mandaviya, Veerendra P. Gadekar, Ananthajith Tantry, Sowmya Kotian, Jyotshna Reddy, Divya Prabha, Sushma Bhat, Sweta Sahay et al. · 2018 · Scientific Reports
- A Novel Multivariate Approach to Phenotyping and Association Mapping of Multi-Locus Gametophytic Self-Incompatibility Reveals S, Z, and Other Loci in a Perennial Ryegrass (Poaceae) PopulationDaniel Thorogood, Steven Andrew Yates, Chloé Manzanares, Leif Skøt, Matthew Hegarty, Tina M. Blackmore, Susanne Barth, Bruno Studer · 2017 · Frontiers in Plant Science
- Cis -acting variation is common across regulatory layers but is often buffered during embryonic developmentSwann Floc’hlay, Emily S. W. Wong, Bingqing Zhao, Rebecca R. Viales, Morgane Thomas‐Chollier, Denis Thieffry, David A. Garfield, Eileen E. M. Furlong · 2020 · Genome Research
- The complexity of epigenetic diseasesAilbhe Jane Brazel, Douglas Vernimmen · 2015 · The Journal of Pathology
- Functional Characterization of Genetic Variant Effects on ExpressionElise D. Flynn, Tuuli Lappalainen · 2022 · Annual Review of Biomedical Data Science
- Extensive epigenetic and transcriptomic variability between genetically identical human B-lymphoblastoid cells with implications in pharmacogenomics researchLilla Ozgyin, Attila Horváth, Zsuzsanna Hevessy, Bálint L. Bálint · 2019 · Scientific Reports
- Brain Banks Spur New Frontiers in Neuropsychiatric Research and Strategies for Analysis and ValidationLe Wang, Yan Xia, Yu Chen, Rujia Dai, Wenying Qiu, Qingtuan Meng, Liz Kuney, Chao Chen · 2019 · Genomics Proteomics & Bioinformatics
- HMGNs: The enhancer charmersAlexia Martínez de Paz, Juan Ausió · 2015 · BioEssays
- Genome-wide uniformity of human ‘open’ pre-initiation complexesWilliam Lai, B. Franklin Pugh · 2016 · Genome Research
- Principles of microRNA Regulation Revealed Through Modeling microRNA Expression Quantitative Trait LociStefan Budach, Matthias Heinig, Annalisa Marsico · 2016 · Genetics
- The multifaceted interplay between lipids and epigeneticsKoen F. Dekkers, P. Eline Slagboom, J. Wouter Jukema, Bastiaan T. Heijmans · 2016 · Current Opinion in Lipidology
- Chromatin Hubs: A biological and computational outlookAntonio Mora, Xiaowei Huang, Shaurya Jauhari, Qin Li Jiang, Xuri Li · 2022 · Computational and Structural Biotechnology Journal
- Shaping immunity: The influence of natural selection on population immune diversityHaley E. Randolph, Katherine A Aracena, Yen‐Lung Lin, Zepeng Mu, Luis Bruno Barreiro · 2024 · Immunological Reviews
- MMARGE: Motif Mutation Analysis for Regulatory Genomic ElementsVerena M. Link, Casey E. Romanoski, Dirk Metzler, Christopher K. Glass · 2018 · Nucleic Acids Research
- A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleationGerard Llimos, Vincent Gardeux, Ute Koch, Judith F. Kribelbauer, Antonina Hafner, Daniel Alpern, Joern Pezoldt, Maria Litovchenko, Julie Russeil, Riccardo Dainese et al. · 2022 · Nature Communications
- Allelic imbalance reveals widespread germline-somatic regulatory differences and prioritizes risk loci in Renal Cell CarcinomaAlexander Gusev, Sándor Spisák, André P. Fay, Hallie A. Carol, Kevin C. Vavra, Sabina Signoretti, Viktória Tisza, Mark M. Pomerantz, Forough Abbasi, Ji-Heui Seo et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- Using Gene Expression to Annotate Cardiovascular GWAS LociMatthias Heinig · 2018 · Frontiers in Cardiovascular Medicine
- Shared genetic effects on chromatin and gene expression reveal widespread enhancer priming in immune responseKaur Alasoo, Julia Rodrigues, Subhankar Mukhopadhyay, Andrew J. Knights, Alice L. Mann, Kousik Kundu, Christine Hale, Gordon Dougan, Daniel J. Gaffney · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
- Genetic and epigenetic determinants of inter-individual variability in responses to toxicantsLauren Lewis, Gregory E. Crawford, Terrence S. Furey, Ivan Rusyn · 2017 · Current Opinion in Toxicology
- Regulatory grammar in human promoters uncovered by MPRA-based deep learningLucía Barbadilla-Martínez, Noud H.M. Klaassen, Vinícius H. Franceschini-Santos, Jérémie Breda, Hatice Yücel, Miguel Hernández-Quiles, Tijs van Lieshout, Carlos G. Urzúa-Traslaviña, Minh Chau Luong Boi, Maryam Akbarzadeh et al. · 2026 · Nature
- Transcription factor expression is the main determinant of variability in gene co‐activityLucas van Duin, Robert Krautz, Sarah Rennie, Robin Andersson · 2023 · Molecular Systems Biology
- Multiome-wide Association Studies: Novel Approaches for Understanding DiseasesMengting Shao, Kaiyang Chen, Shuting Zhang, Min Tian, Yan Shen, Chen Cao, Ning Gu · 2024 · Genomics Proteomics & Bioinformatics
- A Long-Distance Chromatin AffairAnnette Denker, Wouter L. de Laat · 2015 · Cell
- A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factorsRiccardo Dainese, Vincent Gardeux, Gerard Llimos, Daniel Alpern, Jia Yuan Jiang, Antonio C.A. Meireles-Filho, Bart Deplancke · 2020 · Proceedings of the National Academy of Sciences
- Genetic variation in cis-regulatory domains suggests cell type-specific regulatory mechanisms in immunityDiana Avalos, Guillaume Rey, Diogo M. Ribeiro, Anna Ramisch, Emmanouil T. Dermitzakis, Olivier Delaneau · 2023 · Communications Biology
- Gene expression models based on transcription factor binding events confer insight into functional cis -regulatory variantsWenqiang Shi, Oriol Fornés, Wyeth W. Wasserman · 2018 · Bioinformatics
- Epigenetic‐genetic chromatin footprinting identifies novel and subject‐specific genes active in prefrontal cortex neuronsFedor E. Gusev, Denis A. Reshetov, Amanda Mitchell, Т. В. Андреева, Aslihan Dincer, Anastasia P. Grigorenko, Gennady G. Fedonin, Tobias B. Halene, Maria Aliseychik, Andrey Yu. Goltsov et al. · 2019 · The FASEB Journal
- Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver modelBryan J. Matthews, Tisha Melia, David J. Waxman · 2021 · PLoS Genetics
- The high-resolution three-dimensional (3D) chromatin map of the tea plant (Camellia sinensis)Weilong Kong, Jiaxin Yu, Jingjing Yang, Yanbing Zhang, Xingtan Zhang · 2023 · Horticulture Research
- Modeling three-dimensional genomic organization in evolution and pathogenesisAlon Diament, Tamir Tuller · 2018 · Seminars in Cell and Developmental Biology
- Adding another dimension to gene regulationLinda Koch · 2015 · Nature Reviews Genetics
- Estimating the proportion of disease heritability mediated by gene expression levelsLuke Jen O’Connor, Alexander Gusev, Xuanyao Liu, Po‐Ru Loh, Hilary K. Finucane, Alkes L. Price · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
- GRaNIE and GRaNPA: Inference and evaluation of enhancer-mediated gene regulatory networks applied to study macrophagesKamal, Aryan, Arnold, Christian, Claringbould, Annique, Moussa, Rim, Servaas, Nila H., Kholmatov, Maksim, Daga, Neha, Nogina, Daria, Mueller-Dott, Sophia, Reyes-Palomares, Armando et al. · 2021
- Accurate identification of genes associated with brain disorders by integrating heterogeneous genomic data into a Bayesian frameworkDan He, Ling Li, Huasong Zhang, Feiyi Liu, Shaoying Li, Xuehao Xiu, Cong Fan, Mengling Qi, Meng Meng, Junping Ye et al. · 2024 · EBioMedicine
- Mining the topography and dynamics of the 4D Nucleome to identify novel CNS drug pathwaysGerald A. Higgins, Ari Allyn-Feuer, Patrick E. Georgoff, Vahagn C. Nikolian, Hasan Badre Alam, Brian D. Athey · 2017 · Methods
- Allele-specific epigenetic activity in prostate cancer and normal prostate tissue implicates prostate cancer risk mechanismsAnamay H. Shetty, Ji-Heui Seo, Connor A. Bell, Edward P. O’Connor, Mark M. Pomerantz, Matthew L. Freedman, Alexander Gusev · 2021 · The American Journal of Human Genetics
- Towards the Genetic Architecture of Complex Gene Expression Traits: Challenges and Prospects for eQTL Mapping in HumansChaeyoung Lee · 2022 · Genes
- Adaptive Evolution and EpigeneticsIlkka Kronholm · 2017 · Elsevier eBooks
- Druggable Transcriptional Networks in the Human Neurogenic EpigenomeGerald A. Higgins, Aaron M. Williams, Alex S. Ade, Hasan Badre Alam, Brian D. Athey · 2019 · Pharmacological Reviews
- Blood cell traits’ GWAS loci colocalization with variation in PU.1 genomic occupancy prioritizes causal noncoding regulatory variantsRaehoon Jeong, Martha L. Bulyk · 2023 · Cell Genomics
- Making Biological Sense of Genetic Studies of Age-Related Macular DegenerationSingh, Nivedita, Swaroop, Anand, Ratnapriya, Rinki · 2021 · Advances in Experimental Medicine and Biology
- ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learningWouter Saelens, Olga Pushkarev, Bart Deplancke · 2025 · Nature Communications
- Role of Non-Coding Variants in Brugada SyndromeAdrian Pérez-Agustín, Mel·lina Pinsach‐Abuin, Sara Pagans · 2020 · International Journal of Molecular Sciences
- The regulatory grammar of human promoters uncovered by MPRA-trained deep learningLucía Barbadilla-Martínez, Noud H.M. Klaassen, Vinícius H. Franceschini-Santos, Jérémie Breda, Miguel Hernández-Quiles, Tijs van Lieshout, Carlos G. Urzúa-Traslaviña, Hatice Yücel, Minh Chau Luong Boi, Celia Hermana-Garcia-Agullo et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Emerging Roles for Epigenetic Programming in the Control of Inflammatory Signaling Integration in Heath and DiseaseYiqun Hu, Feng Yan, Le Ying, Dakang Xu · 2017 · Advances in experimental medicine and biology
- A cell-specific regulatory region of the human ABO blood group gene regulates the neighborhood gene encoding odorant binding protein 2BRie Sano, Yōichirō Takahashi, Haruki Fukuda, Megumi Harada, Akira Hayakawa, Takafumi Okawa, Rieko Kubo, Haruo Takeshita, Junichi Tsukada, Yoshihiko Kominato · 2021 · Scientific Reports
- Shaping the human brain: evolutionary cis-regulatory plasticity drives changes in synaptic activity-controlled adaptive gene expressionPriit Pruunsild, Hilmar Bading · 2019 · Current Opinion in Neurobiology
- New approaches for archaeal genome-guided cultivationYinzhao Wang, Yoichi Kamagata, Meng Li, Feifei Han, Fengping Wang, Xiang Xiao · 2021 · Science China Earth Sciences
- Methods for fine-mapping with chromatin and expression dataMegan Roytman, Gleb Kichaev, Alexander Gusev, Bogdan Paşaniuc · 2018 · PLoS Genetics
- Chromatin accessibility variation provides insights into missing regulation underlying immune-mediated diseasesRaehoon Jeong, Martha L. Bulyk · 2024 · eLife
- EXTRA-seq: a genome-integrated extended massively parallel reporter assay to quantify enhancer-promoter communicationJudith F. Kribelbauer, Vincent Gardeux, Gerard Llimos, Kateřina Faltejsková, Julie Russeil, Nadia Grenningloh, Lucas Levassor, Clémence Steiner, Jiřı́ Vondrášek, Bart Deplancke · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Chromatin accessibility variation provides insights into missing regulation underlying immune-mediated diseasesRaehoon Jeong, Martha L. Bulyk · 2025 · eLife
- Quantitative Trait Loci Identify Functional Noncoding Variation in CancerHolger Heyn · 2016 · PLoS Genetics
- Epigenetic variation impacts ancestry-associated differences in the transcriptional response to influenza infectionKatherine A Aracena, Yen‐Lung Lin, Kaixuan Luo, Alain Pacis, Saideep Gona, Zepeng Mu, Vania Yotova, Renata Sindeaux, Albéna Pramatarova, Marie-Michelle Simon et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
- Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traitsKevin W. Currin, Hannah J. Perrin, Gautam Kumar Pandey, Abdalla A Alkhawaja, Swarooparani Vadlamudi, Annie E Musser, Amy S. Etheridge, K. Alaine Broadaway, Jonathan D. Rosen, Arushi Varshney et al. · 2025 · Genome Research
- Non-coding variants impact cis-regulatory coordination in a cell type-specific mannerOlga Pushkarev, Guido van Mierlo, Judith F. Kribelbauer, Wouter Saelens, Vincent Gardeux, Bart Deplancke · 2024 · Genome biology
- Genetic Risk Factors for EndometriosisJenny N. Fung, Yadav Sapkota, Dale R. Nyholt, Grant W. Montgomery · 2017 · Journal of Endometriosis and Pelvic Pain Disorders
- Adaptive evolution and epigeneticsIlkka Kronholm · 2022 · Elsevier eBooks
- Clinical applications of molecular genetic discoveriesAli J. Marian · 2015 · Translational research
- Enhanced methods to detect haplotypic effects on gene expressionRobert Brown, Gleb Kichaev, Nicholas Mancuso, James Boocock, Bogdan Paşaniuc · 2017 · Bioinformatics
- Allele specific binding of histone modifications and a transcription factor does not predict allele specific expression in correlated ChIP-seq peak-exon pairsClaire Prowse-Wilkins, Jianghui Wang, Josie B. Garner, Michael Edward Goddard, Amanda Jane Chamberlain · 2023 · Scientific Reports
- Genetic determinants of chromatin accessibility in T cell activation across humansRachel E. Gate, Christine S. Cheng, Aviva Presser Aiden, Atsede Siba, Marcin Tabaka, Dmytro Lituiev, Ido Machol, M. Grace Gordon, Meena Subramaniam, Muhammad Shamim et al. · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
- Genetic Determinants of Plasma Low-Density Lipoprotein Cholesterol Levels: Monogenicity, Polygenicity, and “Missing” HeritabilityJesús María Martín-Campos · 2021 · Biomedicines
- Detection of Regulator Genes and eQTLs in Gene NetworksLingfei Wang, Tom Michoel · 2016 · Springer eBooks
- A scalable Bayesian functional GWAS method accounting for multivariate quantitative functional annotations with applications for studying Alzheimer diseaseJunyu Chen, Lei Wang, Philip L. De Jager, David A. A Bennett, Aron S. Buchman, Jingjing Yang · 2022 · Human Genetics and Genomics Advances
- Leveraging molecular quantitative trait loci to comprehend complex diseases/traits from the omics perspectiveZijun Zhu, Xinyu Chen, Sainan Zhang, Rui Yu, Changlu Qi, Liang Cheng, Xue Zhang · 2023 · Human Genetics
- Epigenetics and Control of RNAsHenrike Maatz, Sebastiaan van Heesch, Franziska Kreuchwig, Allison B. Faber, Eleonora Adami, Norbert Hübner, Matthias Heinig · 2016 · Methods in molecular biology
- Chromatin accessibility variation provides insights into missing regulation underlying immune-mediated diseasesRaehoon Jeong, Martha L. Bulyk · 2024 · eLife
- Chromatin activity identifies differential gene regulation across human ancestriesKade P. Pettie, Maxwell R. Mumbach, Amanda J. Lea, Julien F. Ayroles, Howard Y. Chang, Maya M. Kasowski, Hunter B. Fraser · 2024 · Genome biology
- Focus on single-gene effects limits discovery and interpretation of complex-trait-associated variantsKathryn A. Lawrence, T. Gjorgjieva, D. Nachun, Stephen B. Montgomery · 2026 · American Journal of Human Genetics
- Genome supranucleosomal organization and genetic susceptibility to diseasesKim Philipp Jablonski, Christoph Fretter, Léopold Carron, Thierry Forné, M.‐Th. Hütt, Annick Lesne · 2017 · AIP conference proceedings
- Prioritization of enhancer mutations by combining allele-specific chromatin accessibility with deep learningZeynep Kalender Atak, Ibrahim Ihsan Taskiran, Christopher Flerin, David Mauduit, Liesbeth Minnoye, Gert Hulsemans, Valerie Christiaens, Ghanem-Elias Ghanem, Jasper Wouters, Stein Aerts · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- Cis acting variation is common, can propagates across multiple regulatory layers, but is often buffered in developmental programsSwann Floc’hlay, Emily S. W. Wong, Bingqing Zhao, Rebecca R. Viales, Morgane Thomas‐Chollier, Denis Thieffry, David A. Garfield, Eileen E. M. Furlong · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- The Biological Function of Genome OrganizationXin Yang, Hongni Zhu, Yajie Liu, Jinhong Wang, Yi Song, Shasha Liao, Peng Dong · 2025 · International Journal of Molecular Sciences
- Leveraging low-cost short-read sequencing: revolutionizing complex trait geneticsSarah N. Ruckman, Anthony D. Long · 2026 · Molecular Biology and Evolution
- AlleleHMM: a data-driven method to identify allele specific differences in distributed functional genomic marksShao-Pei Chou, Charles G. Danko · 2018 · bioRxiv
- Mitochondrial GenomicsVipin Kumar Singh, P. Gupta, Neeraj Kumar Rajput, Anshu Bhardwaj · 2016 · Elsevier eBooks
- Might E-cadherin promoter polymorphisms of rs16260 and rs5030625 associate with the risk of nephrolithiasis?Cigdem Donmez, Ece Konaç, Tahsin Batuhan Aydoğan, Cenk Y. Bilen · 2016 · SpringerPlus
- High resolution genetic mapping of causal regulatory interactions in the human genomeN. Kumasaka, A. Knights, D. Gaffney · 2017 · bioRxiv
- Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variationsYuwei Cao, Lauren Patel, Lauren Alcoser, Eric M. Mendenhall, Christopher W. Benner, Sven Heinz, Alon Goren · 2025 · Genome Research
- SWI/SNF complex-mediated ZNF410 cooperative binding maintains chromatin accessibility and enhancer activitySiyuan Xu, Chuxuan Peng, Ren Ren, Haowen Lu, Han Zhao, Sijian Xia, Yijie Shen, Bin Xu, Haoyue Zhang, Xiaodong Cheng et al. · 2025 · Cell Reports
- Genome-wide identification and analysis of recurring patterns of epigenetic variation across individualsJennifer Zou, Emily Maciejewski, Jason Ernst · 2025 · Communications Biology
- Analysis of long-range contacts across cell types outlines a core sequence determinant of 3D genome organizationLiezel Tamon, Zahra Fahmi, James Ashford, Rosana Collepardo‐Guevara, Aleksandr B. Sahakyan · 2025 · NAR Genomics and Bioinformatics
- PhAT-QTL: A Phase-Aware Test for QTL DetectionMeena Subramaniam, Noah Zaitlen, Chun Ye · 2017 · Lecture notes in computer science
- Deep Learning applied to computational biology and agricultural sciencesRenato Hidaka Torres, Fabrício Almeida Araújo, Edian Franklin Franco De Los Santos, Debmalya Barh, Rommel Thiago Jucá Ramos, Marcus de Barros Braga · 2022 · Elsevier eBooks
- The interaction between enhancer variants and environmental factors as an overlooked aetiological paradigm in human complex diseaseSarah Malika Robert, Álvaro Rada-Iglesias · 2023 · BioEssays
- The BRCA1 tumor suppressor: potential long-range interactions of the BRCA1 promoter and the risk of breast cancerBeata Bielińska · 2017 · Journal of Translational Science
- 基于基因组信息指导的古菌培养新策略Yinzhao Wang, Yoichi Kamagata, 猛 李, 菲菲 韩, 风平 王, 湘 肖 · 2021 · SCIENTIA SINICA Terrae
- Functional Interpretation of Genetic Variants Using Deep Learning Predicts Impact on EpigenomeGabriel E. Hoffman, Eric E. Schadt, Panos Roussos · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
- Variation in PU.1 binding and chromatin looping at neutrophil enhancers influences autoimmune disease susceptibilityStephen B. Watt, Louella J. Vasquez, Klaudia Walter, Alice Mann, Kousik Kundu, Lu Chen, Yan Yan, Simone Ecker, Frances Burden, Samantha Farrow et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- Genetic variation in correlated regulatory region of ImmunityDiana Avalos, Guillaume Rey, Diogo M. Ribeiro, Anna Ramisch, Emmanouil T. Dermitzakis, Olivier Delaneau · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
- Analysis of long-range contacts across cell types outlines a core sequence determinant of 3D genome organisationLiezel Tamon, Zahra Fahmi, James Ashford, Rosana Collepardo‐Guevara, Aleksandr B. Sahakyan · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Chromatin accessibility variation provides insights into missing regulation underlying immune-mediated diseasesRaehoon Jeong, Martha L. Bulyk · 2025 · eLife
- Fishing for Function in the Human Gene PoolIros Barozzi, Axel Visel, Diane E. Dickel · 2016 · Trends in Genetics
- The Human GenomeHuntington F. Willard · 2016 · Elsevier eBooks
- Predictive long-range allele-specific mapping of regulatory variants and target transcriptsKibaick Lee, Seulkee Lee, Hyoeun Bang, Jung Kyoon Choi · 2017 · PLoS ONE
- References2018 · Elsevier eBooks
- Faculty Opinions recommendation of The impact of rare variation on gene expression across tissues.Mohan Liu · 2018 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
- Genetic variation in correlated regulatory regions of immunityDiana Avalos, Guillaume Rey, Diogo M. Ribeiro, Anna Ramisch, Emmanouil T. Dermitzakis, Olivier Delaneau · 2022 · Research Square
- In Silico Evaluation of Biomarker Genes for Melanoma CarcinomaBharat Kwatra, Mohammed Moin Khan · 2023 · bioRxiv (Cold Spring Harbor Laboratory)