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EpiMogrify Models H3K4me3 Data to Identify Signaling Molecules that Improve Cell Fate Control and Maintenance

Kamaraj, U. S., Chen, J., Katwadi, K., Ouyang, J. F., Sun, Y., Lim, Y. M., Liu, X., Handoko, L., Polo, J. M., Petretto, E. G., et al. (2020) · Cell Systems · doi:10.1016/j.cels.2020.09.004 · Cited by 19 · see citing works

Asymmetric Histone Inheritance: Establishment, Recognition, and Execution

Urban, J. A., Ranjan, R., & Chen, X. (2022) · Annual Review of Genetics · doi:10.1146/annurev-genet-072920-125226 · Cited by 18 · see citing works

Photoselective sequencing: microscopically guided genomic measurements with subcellular resolution

Mangiameli, S. M., Chen, H., Earl, A., Dobkin, J. A., Lesman, D., Buenrostro, J. D., & Chen, F. (2023) · Nature Methods · doi:10.1038/s41592-023-01845-8 · Cited by 18 · see citing works

Efficient and strand-specific profiling of replicating chromatin with enrichment and sequencing of protein-associated nascent DNA in mammalian cells

Li, Z., Hua, X., Serra‐Cardona, A., Xu, X., & Zhang, Z. (2021) · Nature Protocols · doi:10.1038/s41596-021-00520-6 · Cited by 18 · see citing works

scPCOR-seq enables co-profiling of chromatin occupancy and RNAs in single cells

Pan, L., Ku, W. L., Tang, Q., Cao, Y., & Zhao, K. (2022) · Communications Biology · doi:10.1038/s42003-022-03584-6 · Cited by 18 · see citing works

CUT&RUN Profiling of the Budding Yeast Epigenome

Brahma, S., & Henikoff, S. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2257-5_9 · Cited by 15 · see citing works

Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns

Tost, J. (2022) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-11454-0_16 · Cited by 15 · see citing works

Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input

Handa, T., Harada, A., Maehara, K., Sato, S., Nakao, M., Gotō, N., Kurumizaka, H., Ohkawa, Y., & Kimurâ, H. (2020) · Nature Protocols · doi:10.1038/s41596-020-0375-8 · Cited by 16 · see citing works

Selective inhibitors of bromodomain <scp>BD1</scp> and <scp>BD2</scp> of <scp>BET</scp> proteins modulate radiation‐induced profibrotic fibroblast responses

Liu, C., Rioja, I., Bakr, A., Veldwijk, M. R., Sperk, E., Herskind, C., Weichenhan, D., Prinjha, R. K., Plass, C., Schmezer, P., et al. (2022) · International Journal of Cancer · doi:10.1002/ijc.33989 · Cited by 17 · see citing works

Genome-Wide Native R-Loop Profiling by R-Loop Cleavage Under Targets and Tagmentation (R-Loop CUT&Tag)

Wang, H., Li, C., & Liang, K. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2477-7_23 · Cited by 15 · see citing works

Single-cell profiling of histone modifications in the mouse brainPreprint

Bartošovič, M., Kabbe, M., & Castelo‐Branco, G. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.02.279703 · Cited by 15 · see citing works

Tn5 DNA Transposase in Multi-Omics Research

Penkov, D., Zubkova, E., & Parfyonova, Y. V. (2023) · Methods and Protocols · doi:10.3390/mps6020024 · Cited by 14 · see citing works

Genome-wide Interrogation of Protein-DNA Interactions in Mammalian Cells Using ChIPmentation

Xu, W. Q., Ye, Y., Sharrocks, A. D., Zhang, W., & Chen, X. X. (2020) · STAR Protocols · doi:10.1016/j.xpro.2020.100187 · Cited by 14 · see citing works

FFPE‐ATAC: A Highly Sensitive Method for Profiling Chromatin Accessibility in Formalin‐Fixed Paraffin‐Embedded Samples

Yadav, R. P., Polavarapu, V. K., Xing, P., & Chen, X. (2022) · Current Protocols · doi:10.1002/cpz1.535 · Cited by 14 · see citing works

Epigenetics and tissue immunity—Translating environmental cues into functional adaptations*

Tuong, Z. K., Stewart, B. J., Guo, S. A., & Clatworthy, M. R. (2021) · Immunological Reviews · doi:10.1111/imr.13036 · Cited by 13 · see citing works

Retrospective and multifactorial single-cell profiling reveals sequential chromatin reorganization during X inactivation

Kefalopoulou, S., Rullens, P. M. J., de Luca, K. L., de Vries, S. S., Korthout, T., van Oudenaarden, A., Zeller, P. J., & Kind, J. (2025) · Nature Cell Biology · doi:10.1038/s41556-025-01687-w · Cited by 12 · see citing works

Epigenomic technologies for precision oncology

Weichenhan, D., Lipka, D. B., Lutsik, P., Goyal, A., & Plass, C. (2020) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2020.08.004 · Cited by 13 · see citing works

Nanobody-tethered transposition allows for multifactorial chromatin profiling at single-cell resolutionPreprint

Stuart, T., Hao, S., Zhang, B., Mekerishvili, L., Landau, D. A., Maniatis, S., Satija, R., & Raimondi, I. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.08.483436 · Cited by 13 · see citing works

Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencingPreprint

Zhang, Y.-J., Tang, Y., Sun, Z.-X., Jia, J.-Q., Fang, Y., Wan, X., & Fang, D. (2023) · Genome Research · doi:10.1101/gr.277213.122 · Cited by 11 · see citing works

A tale of two strands: Decoding chromatin replication through strand-specific sequencing

Li, Z., & Zhang, Z. (2025) · Molecular Cell · doi:10.1016/j.molcel.2024.10.035 · Cited by 12 · see citing works

Combinatorial profiling of multiple histone modifications and transcriptome in single cells using scMTR-seq

Wang, Y., Li, J., Malcolm, A. A., Mansfield, W., Clark, S. J., Argelaguet, R., Biggins, L., Acton, R., Andrews, S., Reik, W., et al. (2025) · Science Advances · doi:10.1126/sciadv.adu3308 · Cited by 11 · see citing works

Single-Cell Profiling in Multiple Myeloma: Insights, Problems, and Promises

Samur, M., Szalat, R. E., & Munshi, N. C. (2023) · Blood · doi:10.1182/blood.2022017145 · Cited by 12 · see citing works

Advances in Epigenomic Sequencing and Their Applications in Cancer Diagnostics

Lin, L., & Liu, Y. (2025) · Precision Chemistry · doi:10.1021/prechem.5c00014 · Cited by 11 · see citing works

Natural and Experimental Rewiring of Gene Regulatory Regions

Downes, D. J., & Hughes, J. R. (2022) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-112921-010715 · Cited by 11 · see citing works

Epigenetic Modulation of Radiation-Induced Diacylglycerol Kinase Alpha Expression Prevents Pro-Fibrotic Fibroblast Response

Liu, C., Tóth, R., Bakr, A., Goyal, A., Islam, M. S., Breuer, K., Mayakonda, A., Lin, Y.-Y., Stepper, P., Jurkowski, T. P., et al. (2021) · Cancers · doi:10.3390/cancers13102455 · Cited by 12 · see citing works

In situ tools for chromatin structural epigenomics

Henikoff, S., & Ahmad, K. (2022) · Protein Science · doi:10.1002/pro.4458 · Cited by 10 · see citing works

Single-cell Technologies Provide Novel Insights into Liver Physiology and Pathology

Chen, G., Xu, W., Long, Z., Chong, Y., Lin, B., & Jie, Y. (2023) · Journal of Clinical and Translational Hepatology · doi:10.14218/jcth.2023.00224 · Cited by 10 · see citing works

Decoding Human Biology and Disease Using Single-Cell Omics Technologies

Shi, Q., Chen, X., & Zhang, Z. (2023) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2023.06.003 · Cited by 10 · see citing works

Long-range single-molecule mapping of chromatin modification in eukaryotesPreprint

Weng, Z., Ruan, F., Chen, W., Xie, Z., Xie, Y., Zhang, C., Chen, Z., Wang, J., Sun, Y., Fang, Y., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.08.451578 · Cited by 6 · see citing works

Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progressionPreprint

Womersley, H. J., Muliaditan, D., DasGupta, R., & Cheow, L. F. (2024) · Genome Research · doi:10.1101/gr.279105.124 · Cited by 8 · see citing works

DynaTag for efficient mapping of transcription factors in low-input samples and at single-cell resolution

Hunold, P., Pizzolato, G., Heramvand, N., Kaiser, L., Barbiera, G., van Ray, O., Thomas, R. K., George, J., Peifer, M., & Hänsel‐Hertsch, R. (2025) · Nature Communications · doi:10.1038/s41467-025-61797-9 · Cited by 8 · see citing works

Cystine import and oxidative catabolism fuel vascular growth and repair via nutrient-responsive histone acetylation.

Drekolia, M., Mettner, J., Wang, D., Lagos, F. A. D., Koch, C., Hecker, D., Eresch, J., Mao, Y.-F., Bähr, M., Weichenhan, D., et al. (2025) · Cell Metabolism · doi:10.1016/j.cmet.2025.10.003 · Cited by 8 · see citing works

Antibody-guided Chromatin Tagmentation (ACT-seq)

Carter, B., Zhao, K., Ku, W. L., Kang, J. Y., & Tang, Q. (2019) · Protocol Exchange · doi:10.1038/protex.2019.026

Antibody-guided Chromatin Tagmentation for Two or More Factors (ACT2-seq)Preprint

Carter, B. C., Ku, W. L., & Zhao, K. (2021) · Research Square · doi:10.21203/rs.3.pex-1695/v1

Enhancing sensitivity and versatility of Tn5-based single cell omics

Seufert, I., Sant, P., Bauer, K., Syed, A. P., Rippe, K., & Mallm, J. (2023) · Frontiers in Epigenetics and Epigenomics · doi:10.3389/freae.2023.1245879 · Cited by 8 · see citing works

CUT&amp;Tag for efficient epigenomic profiling of small samples and single cells

Kaya-Okur, H. S., Wu, S. J., Codomo, C. A., Pledger, E. S., Bryson, T. D., Henikoff, J. G., Ahmad, K., & Henikoff, S. (2019) · Nature Communications · doi:10.1038/s41467-019-09982-5 · Cited by 2,187 · see citing works

High-throughput single-cell epigenomic profiling by targeted insertion of promoters (TIP-seq)

Bartlett, D. A., Dileep, V., Handa, T., Ohkawa, Y., Kimurâ, H., Henikoff, S., & Gilbert, D. M. (2021) · The Journal of Cell Biology · doi:10.1083/jcb.202103078 · Cited by 46 · see citing works