Single-cell DNA methylation profiling: technologies and biological applications
Karemaker, Ino D., Vermeulen, Michiel·2018·Trends in Biotechnology
Cited by (172)
Items 101–172 of 172
- Aging of common carp (Cyprinus carpio L.) sperm induced by short-term storage does not alter global DNA methylation and specific histone modifications in offspringYu Cheng, Swapnil Gorakh Waghmare, Songpei Zhang, Pavlína Věchtová, Fabian Schumacher, Burkhard Kleuser, Azin Mohagheghi Samarin, Azadeh Mohagheghi Samarin, Zuzana Linhartová, Abhipsha Dey et al. · 2023 · Aquaculture
- Redefining Mucosal Inflammation with Spatial GenomicsAna J Caetano, Paul Thomas Sharpe · 2024 · Journal of Dental Research
- Single-cell classification, analysis, and its application using deep learning techniquesR. Premkumar, Arthi Srinivasan, Kanika Devi, M Deepika, E Gaayathry, Pramod Jadhav, Abhishek Futane, Vigneswaran Narayanamurthy · 2024 · Biosystems
- Short history of 5-methylcytosine: from discovery to clinical applicationsOlga Taryma‐Leśniak, Katarzyna Ewa Sokolowska, Tomasz Kazimierz Wojdacz · 2021 · Journal of Clinical Pathology
- Identifying Readers for (hydroxy)methylated DNA Using Quantitative Interaction Proteomics: Advances and Challenges AheadVelin Marita Sequeira, Michiel Vermeulen · 2019 · Journal of Molecular Biology
- Mapping DNA Methylation in Mammals: The State of the ArtAntonio Lentini, Colm E. Nestor · 2020 · Methods in molecular biology
- Single-cell RNA sequencing to study vascular diversity and functionFeiyang Ma, Gloria E. Hernandez, Milagros C. Romay, M. Luisa Iruela‐Arispe · 2021 · Current Opinion in Hematology
- Integration of spatial and single-cell data across modalities with weak linkageShuxiao Chen, Bokai Zhu, Sijia Huang, John W. Hickey, Kevin Lin, Michael P. Snyder, William James Greenleaf, Garry P. Nolan, Nancy Ruonan Zhang, Zongming Ma · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- Determinants, mechanisms, and functional outcomes of myeloid cell diversity in cancerCaronni, Nicoletta, Montaldo, Elisa, Mezzanzanica, Luca, Cilenti, Francesco, Genua, Marco, Ostuni, Renato · 2021 · Immunological Reviews
- Strengthening Rigor and Reproducibility in Epigenome-Wide Association Studies of Social Exposures and Brain-Based Health OutcomesBrooke G. McKenna, Alexandre A. Lussier, Matthew J Suderman, Esther Walton, Andrew J. Simpkin, Anke Hüls, Erin C. Dunn · 2025 · Current Environmental Health Reports
- The emerging trends and prospects of DNA methylomics for abiotic stress tolerance in legumesSheel Yadav, Ambika Baldev Gaikwad, Gopal Kalwan, Laxmi Sharma, Pradeep Kumar Jain · 2025 · Journal of Plant Biochemistry and Biotechnology
- DNA Methylation of Fibroblast Phenotypes and Contributions to Lung FibrosisPoojitha Rajasekar, Jamie K. Patel, Rachel L. Clifford · 2021 · Cells
- Epigenome-wide association study (EWAS): Methods and applicationsMiljana Tanić · 2020 · Elsevier eBooks
- Designing studies for epigenetic biomarker development in autoimmune rheumatic diseasesCarlos de la Calle‐Fabregat, Javier Rodríguez‐Ubreva, Juan de Dios Cañete, Esteban Ballestar · 2022 · Rheumatology and Immunology Research
- Metric learning enables synthesis of heterogeneous single-cell modalitiesRohit Singh, Brian Hie, Ashwin Narayan, Bonnie Berger · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- SINBAD: a flexible tool for single cell DNA methylation dataYasin Uzun, Wenbao Yu, Changya Chen, Kai Tan · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
- Epigenetics in AquacultureFrancesc Piferrer · 2023 · Wiley eBooks
- An Optimized Method for the Construction of a DNA Methylome from Small Quantities of Tissue or Purified DNA from Arabidopsis EmbryoHyunjin Yoo, Kyunghyuk Park, Jaehoon Lee, Seunga Lee, Yeonhee Choi · 2021 · Molecules and Cells
- Experimental development of the epigenomic library construction method to elucidate the epigenetic diversity and causal relationship between epigenome and transcriptome at a single-cell levelKyunghyuk Park, Min Chul Jeon, Bokyung Kim, Bukyoung Cha, Jong‐Il Kim · 2022 · Genomics & Informatics
- Improve-RRBS: a novel tool to correct the 3′ trimming of reduced representation sequencing readsÁbel Fóthi, Hongbo Liu, Katalin Suszták, Tamás Arányi · 2024 · Bioinformatics Advances
- Interweaving Tumor Heterogeneity into the Cancer Epigenetic/Metabolic AxisJia Yu Leung, Kimberly Chia, Derrick Sek Tong Ong, Reshma Taneja · 2019 · Antioxidants and Redox Signaling
- Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding modelsJan Grau, Florian Schmidt, Marcel H. Schulz · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- Progress in single-cell sequencing of retinal vein occlusion or ischemic hypoxic retinopathyFeng, Yanbing, Wu, Yibo, Zhu, Yixing, He, Yanyan, Weng, Wenqing · 2025 · Experimental Eye Research
- Epigenetic Alterations in Age-Related Macular Degeneration: Mechanisms and ImplicationsDana Kisswani, Christina Carroll, Fátima Valdés‐Mora, Matt Rutar · 2025 · International Journal of Molecular Sciences
- Dissecting epigenetic heterogeneity in single-cell DNA methylomes with a unified frameworkSongming Tang, Siyu Li, Guangxin Zhang, Aoran Lyu, Han Li, Shengquan Chen · 2026 · Nature Communications
- scDMV: a zero–one inflated beta mixture model for DNA methylation variability with scBS-seq dataYan Zhou, Ying Zhang, Minjiao Peng, Yaru Zhang, Chenghao Li, Lianjie Shu, Yaohua Hu, Jianzhong Su, Jinfeng Xu · 2023 · Bioinformatics
- DNA Methylation and Bipolar DisorderZihao Yang, Sijie Zhang, Lijun Ouyang, Aijun Liao, Ying He, Zongchang Li, Xiaogang Chen · 2023 · Journal of Psychiatry and Brain Science
- vmrseq: probabilistic modeling of single-cell methylation heterogeneityNing Shen, Keegan D. Korthauer · 2024 · Genome biology
- A comparison of integration methods for single‐cell RNA sequencing data and ATAC sequencing dataYulong Kan, Weihao Wang, Yunjing Qi, Zhongxiao Zhang, Xikeng Liang, Shuilin Jin · 2025 · Quantitative Biology
- Cell-Type Heterogeneity in DNA Methylation Studies: Statistical Methods and GuidelinesAndrew Erich Teschendorff · 2022 · Springer eBooks
- Shining a light on cell biology of the nucleus with single-cell sequencingJeroen van den Berg, Peter J. Zeller · 2025 · Current Opinion in Cell Biology
- ExpressHeart: Web Portal to Visualize Transcriptome Profiles of Non-Cardiomyocyte CellsGang Li, Changfei Luan, Yanhan Dong, Yifang Xie, Scott C. Zentz, Robert Zelt, Jeffrey M. Roach, Jiandong Liu, Qian Li, Yun Li et al. · 2021 · International Journal of Molecular Sciences
- Whole-Genome Bisulfite Sequencing with a Small Amount of DNAHiroki Tsutsui, Ueli Grossniklaus · 2024 · Methods in molecular biology
- SuperGLUE facilitates an explainable training framework for multi-modal data analysisTianyu Liu, Jia Zhao, Hongyu Zhao · 2025 · Cell Reports Methods
- Single-cell aging clocks: A precision tool for dissecting and targeting the aging processYuduo Hao, Sijia Xie, Yijie Wei, Xiaoshuo Sun, Yu Xiao, Xueqin Xie, Kaiyuan Han, Ting Wang, Zhepeng Wang, Luqiang Zhang et al. · 2026 · Ageing Research Reviews
- MC profiling: a novel approach to analyze DNA methylation heterogeneity in genome-wide bisulfite sequencing dataGiulia De Riso, Antonella Sarnataro, Giovanni Scala, Mariella Cuomo, Rosa Della Monica, Stefano Amente, Lorenzo Chiariotti, Gennaro Miele, Sergio Cocozza · 2022 · NAR Genomics and Bioinformatics
- Application of high dimensional flow cytometry and unsupervised analysis to define the immune cell landscape of early childhood respiratory and blood compartmentsShivanthan Shanthikumar, Sarath Ranganathan, Richard Saffery, Melanie R. Neeland · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
- High coverage of single cell genomes by T7-assisted enzymatic methyl-sequencingJuan Wang, Yitong Fang, Wenfang Chen, Chen Zhang, Zhichao Chen, Zhe Xie, Zhe Weng, Weitian Chen, Fengying Ruan, Yeming Xie et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
- vmrseq: probabilistic modeling of single-cell methylation heterogeneityNing Shen, Keegan D. Korthauer · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- scELMo: Embeddings from Language Models are Good Learners for Single-cell Data AnalysisHongyu Zhao, Tianyu Liu, Tianqi Chen, Wangjie Zheng, Xiao Luo · 2024 · Research Square
- Epigenome-wide association study (EWAS) methods and applicationsMiljana Tanić · 2025 · Elsevier eBooks
- Challenges and emerging strategies for genome-wide evaluation of loss of imprinting in cancerMuhammad Talal Amin, Louis Coussement, Tim De Meyer · 2026 · British Journal of Biomedical Science
- Advancing Genomics in Urologic Tumors: Navigating Precision Therapeutic PathwaysFawad Inayat, Imad Tariq, Nabiha Bashir, Fawad Ullah, Hadiqa Aimen · 2024 · annals of urologic oncology
- Tracking Somatic Mutations for Lineage ReconstructionYaara Neumeier, Ofir Raz, Liming Tao, Zipora Marx, Ehud Y. Shapiro · 2025 · Methods in molecular biology
- Epigenetic Impacts of Non‐Coding Mutations Deciphered Through Pre‐Trained DNA Language Model at Single‐Cell ResolutionZhe Liu, An Gu, Yihang Bao, Guan Ning Lin · 2025 · Advanced Science
- Methods for Analyzing DNA Cytosine Modifications Genome-wideTibor A. Rauch, Gerd P. Pfeifer · 2022 · Elsevier eBooks
- The Chromatin Interaction SystemSarah Kreuz, Stefan-Sebastian David, Lorena V. Cortés-Medina, Wolfgang Fischle · 2022 · Wiley eBooks
- Tracking induced pluripotent stem cells differentiation with a fluorescent genetically encoded epigenetic probeAfanasii I. Stepanov, Alexandra A. Shuvaeva, Lidia V. Putlyaeva, Adelya A. Galiakberova, Valeriya Pronina, Dmitry V. Dylov, Alexey V. Terskikh, Konstantin A. Lukyanov, Nadya G. Gurskaya · 2023 · Research Square
- Imputation approaches and quality standards for single-cell epigenetic age predictionsZian Liu, Md. Abul Hassan Samee · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- Deep learning predicts DNA methylation regulatory variants in specific brain cell types and enhances fine mapping for brain disordersJiyun Zhou, Daniel R. Weinberger, Shizhong Han · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Single‐Cell Transcriptomics and Epigenomics for CRISPR‐Mediated Perturbation StudiesSaumyaa Saumyaa, Ramy Elgendy, Alessandro Bonetti · 2022
- MC profiling: a novel approach to analyze DNA methylation heterogeneity from bulk bisulfite sequencing dataGiulia De Riso, Antonella Sarnataro, Giovanni Scala, Mariella Cuomo, Rosa Della Monica, Stefano Amente, Lorenzo Chiariotti, Gennaro Miele, Sergio Cocozza · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
- Epigenetic intratumoral heterogeneityShijie Zheng · 2023 · Elsevier eBooks
- Challenges for single-cell epigenetic analysisEyal Metzl-Raz, Samuel H. Kim, Catherine R. Zhang, William James Greenleaf · 2023 · Elsevier eBooks
- The Molecular Epigenetic LensVanessa Lux · 2024 · SpringerBriefs in psychology
- Beyond Integration: SuperGLUE Facilitates Explainable Training Framework for Multi-modal Data AnalysisTianyu Liu, Jia Zhao, Hongyu Zhao · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Single-cell epigenomics: Methods and translationRam Prakash Yadav, Gang Pan, Xingqi Chen · 2025 · Elsevier eBooks
- Advances in whole genome methylomic sequencingJessica Nordlund · 2025 · Elsevier eBooks
- Mapping the landscape of cell type-dependent genetic regulation of DNA methylation across human tissuesJames Li, Niyati Jain, Jason Kiat, Tong Lin, Meritxell Oliva, Kathryn Demanelis, Farzana Jasmine, Muhammad Ghulam Kibriya, Habibul Ahsan, Lin Chen et al. · 2025 · Research Square
- Long-term DNA methylation changes induced by age and elevated CO2 in skeletal muscleJoseph Balnis, Andy Madrid, Emily L. Jackson, Lisa A. Drake, Catherine E. Vincent, Harold A. Singer, Reid S. Alisch, Ariel Jaitovich · 2025 · Skeletal Muscle
- Additional file 1 of DAMEfinder: a method to detect differential allele-specific methylationStephany Orjuela, Dania Machlab, Mirco Menigatti, Giancarlo Marra, Mark D. Robinson · 2020 · Figshare
- Additional file 1 of Single-cell DNA methylation sequencing by combinatorial indexing and enzymatic DNA methylation conversionZac Chatterton, Praves Lamichhane, Diba Ahmadi Rastegar, Lauren Fitzpatrick, Hélène Lebhar, Christopher Peter Marquis, Halliday, Glenda, John B. Kwok · 2024 · Figshare
- Additional file 2 of MultiMAP: dimensionality reduction and integration of multimodal dataMika Sarkin Jain, Krzysztof Polański, Conde, Cecilia Dominguez, Chen, Xi, Park, Jongeun, Lira Mamanova, Andrew J. Knights, Rachel Anne Botting, Emily Stephenson, Haniffa, Muzlifah et al. · 2021 · Figshare
- Additional file 3 of MultiMAP: dimensionality reduction and integration of multimodal dataMika Sarkin Jain, Krzysztof Polański, Conde, Cecilia Dominguez, Chen, Xi, Park, Jongeun, Lira Mamanova, Andrew J. Knights, Rachel Anne Botting, Emily Stephenson, Haniffa, Muzlifah et al. · 2021 · Figshare
- Additional file 1 of MultiMAP: dimensionality reduction and integration of multimodal dataMika Sarkin Jain, Krzysztof Polański, Conde, Cecilia Dominguez, Chen, Xi, Park, Jongeun, Lira Mamanova, Andrew J. Knights, Rachel Anne Botting, Emily Stephenson, Haniffa, Muzlifah et al. · 2021 · Figshare
- Méthylation de l'ADN : fonctions et ciblage au cours du développement chez la sourisThomas Dahlet · 2019 · theses.fr (ABES)
- Modelling the geometry of high-dimensional omics data : dimensionality, subspaces, trajectoriesJonathan Bac · 2022 · theses.fr (ABES)
- An Integrated and Robust Deep Learning Framework for Denoising and Analyzing Single‐Cell Spatial TranscriptomicsYaxuan Cui, Yang Cui, Ruheng Wang, Xin Zeng, Zheyong Zhu, Ding Yi, Ruihua Guo, Tetsuya Sakurai, Kenta Nakai, Xiucai Ye et al. · 2026 · Advanced Intelligent Systems
- A scalable Tn5-based method for genome-wide DNA methylation profiling in development and diseaseHanrong Hu, Nahuel Simonet, Ece Naz Bilgic, Heather Murray, Regina Reimann, Markus Rechsteiner, Fides Lea Zenk · 2026 · Nature Communications
- Epigenetic Clocks: Biological Aging, Disease, and Clinical ApplicationsA. Baki Yildirim, Duygu T. Yildirim, Hilal Akalin, Satya Prakash, Ratnesh Lal, Ariola Bacu, Radke Kaneva, Lembit Nei, Mahmut Çerkez Ergören, Nikolai Zhelev et al. · 2026 · The EuroBiotech Journal
- MethyAnno: An Interpretable Automated Annotation Method Leveraging Multi‐Scale Information and Metric Learning Framework for scDNAm DataYuhang Jia, Siyu Li, Songming Tang, Keju Gu, Shengquan Chen · 2026 · Advanced Science
- Dataset for "Scalable screening of ternary-code DNA methylation dynamics associated with human traits."Wanding Zhou · 2025 · Zenodo (CERN European Organization for Nuclear Research)