Profiling chromatin states using single-cell itChIP-seq

Fast gapped-read alignment with Bowtie 2

Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400

Model-based Analysis of ChIP-Seq (MACS)

Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs017 · Cited by 9,049

deepTools2: a next generation web server for deep-sequencing data analysis

Ramírez, F., Ryan, D. P., Grüning, B., Bhardwaj, V., Kilpert, F., Richter, A. S., Heyne, S., Dündar, F., & Manke, T. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw257 · Cited by 8,096

Spatial reconstruction of single-cell gene expression data

Satija, R., Farrell, J. A., Gennert, D., Schier, A. F., & Regev, A. (2015) · Nature Biotechnology · doi:10.1038/nbt.3192 · Cited by 7,055

A robust and high-throughput Cre reporting and characterization system for the whole mouse brain

Madisen, L., Zwingman, T. A., Sunkin, S. M., Oh, S. W., Zariwala, H. A., Gu, H., Ng, L. L., Palmiter, R. D., Hawrylycz, M. J., Jones, A. R., et al. (2010) · Nature Neuroscience · doi:10.1038/nn.2467 · Cited by 6,907

Reversed graph embedding resolves complex single-cell trajectories

Qiu, X., Mao, Q., Tang, Y., Wang, L., Chawla, R., Pliner, H. A., & Trapnell, C. (2017) · Nature Methods · doi:10.1038/nmeth.4402 · Cited by 5,070

The ground state of embryonic stem cell self-renewal

Ying, Q.-L., Wray, J., Nichols, J., Batlle-Morera, L., Doble, B., Woodgett, J., Cohen, P., & Smith, A. (2008) · Nature · doi:10.1038/nature06968 · Cited by 3,442

ATAC-seq: a method for assaying chromatin accessibility genome-wide

Buenrostro, J. D., Wu, B., Chang, H. Y., & Greenleaf, W. J. (2015) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb2129s109 · Cited by 3,289

Single-cell chromatin accessibility reveals principles of regulatory variation

Buenrostro, J. D., Wu, B., Litzenburger, U. M., Ruff, D., Gonzales, M. L., Snyder, M. P., Chang, H. Y., & Greenleaf, W. J. (2015) · Nature · doi:10.1038/nature14590 · Cited by 2,308

Polycomb regulates sleep homeostasis in a specific group of cells in Drosophila brain

Zhao, X., Yang, X., & Du, J. (2025) · FEBS Journal · doi:10.1111/febs.70314 · Cited by 3

Single-cell protein-DNA interactomics and multiomics tools for deciphering genome regulation

Xiong, H., Wang, R., & He, A. (2023) · National Science Open · doi:10.1360/nso/20220057 · Cited by 3

Understanding single-cell multi-omics for high resolution cellular interactome mapping

Joshi, S., Kumari, A., & Joshi, R. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-23736-2.00002-2 · Cited by 2

SingleScan: a comprehensive resource for single-cell sequencing data processing and mining

Wang, K., Zhang, X., Cheng, H., Ma, W., Bao, G., Dong, L., Gou, Y., Yang, J., & Cai, H. (2023) · BMC Bioinformatics · doi:10.1186/s12859-023-05590-9 · Cited by 2

Diverse biological and engineering strategies towards organ regeneration

Hou, J., Zhou, Q., Zhu, X., Peng, J., & Xiong, J. (2021) · Cell Regeneration · doi:10.1186/s13619-021-00098-0 · Cited by 2

Emerging Roles of Epigenetic Regulators in Maintaining Hematopoietic Stem Cell Homeostasis

Wang, H., Han, Y., & Qian, P. (2023) · Advances in experimental medicine and biology · doi:10.1007/978-981-99-7471-9_3 · Cited by 2

Best practices for ChIP-seq and its data analysis

Hou, H., Hudson, M., & Liang, M. (2024) · Elsevier eBooks · doi:10.1016/b978-0-12-817218-6.00019-x · Cited by 1

Low-input CUT&Tag for efficient epigenomic profiling of zebrafish stage I oocytes

Zheng, Q., Wu, X., Li, X., Mo, X., Xiang, B., & Chen, J. (2024) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2024.1475912 · Cited by 1

A Single-Cell Omics Technical Guide for Advancing Neuropsychiatric Research

Casmey, K., Zimmermann, M., Xie, Y., Codeluppi-Arrowsmith, S. A., & Turecki, G. (2025) · Genes · doi:10.3390/genes16121394 · Cited by 3

Small noncoding RNAs play superior roles in maintaining hematopoietic stem cell homeostasis

Wang, H., Qian, W., Han, Y., & Qian, P. (2022) · Blood Science · doi:10.1097/bs9.0000000000000123 · Cited by 1

Role of histone acylation and related technical developments

Yan, H., & Zhang, H. (2023) · Scientia Sinica Vitae · doi:10.1360/ssv-2023-0226 · Cited by 1

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

Cayford, J., de la Mata, S. H., Schmiedel, B. J., Chandra, V. K., Vijayanad, P., & Seumois, G. (2020) · Journal of Visualized Experiments · doi:10.3791/61617 · Cited by 1

Genome-wide Analyses of Histone Modifications in the Mammalian Genome

Tian, S., Slager, S. L., Klee, E. W., & Yan, H. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-91909-8.00021-9 · Cited by 2

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

Cayford, J., de la Mata, S. H., Schmiedel, B. J., Chandra, V., Vijayanad, P., & Seumois, G. (2020) · Journal of Visualized Experiments · doi:10.3791/61617-v · Cited by 1

High-throughput single-cell joint analysis of histone modifications and gene expression by Paired-TagPreprint

Zhu, C., Zhang, Y., Li, Y. E., Lucero, J. D., Behrens, M. M., & Ren, B. (2021) · Research Square · doi:10.21203/rs.3.pex-1301/v1 · Cited by 1

Ultra-high-throughput microbial single-cell whole genome sequencing for genome-resolved metagenomicsPreprint

Li, J., Zhang, R., Li, T., Shi, Q., Song, Z., Jiang, L., Shi, Y., Ma, C., Liang, X., Zhang, J., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.08.485055 · Cited by 1

High-throughput single-cell joint analysis of histone modifications and gene expression by Paired-TagPreprint

Zhu, C., Zhang, Y., Li, Y. E., Lucero, J. D., Behrens, M. M., & Ren, B. (2021) · Research Square · doi:10.21203/rs.3.pex-1301/v2 · Cited by 1

Transcriptome analysis of blastocysts acquiring implantation competency in mice

Kong, S., & Wang, H. (2020) · Bioscientifica Proceedings · doi:10.1530/biosciprocs.10.010

New tools for ‘ZEBRA-FISHING’

Bergo, V., & Trompouki, E. (2021) · Briefings in Functional Genomics · doi:10.1093/bfgp/elab001

Other omics approaches to the study of rare diseases

Gatta, G. D. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-820140-4.00008-9

Evaluation of ChIC-based data requires normalization that properly retains signal-to-noise ratiosPreprint

Liu, B., Chen, F., & Xie, W. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.14.456176

Evolution of genome wide approaches to unveil transcriptional networks

Chan, N. T., & Xu, W. (2023) · Elsevier eBooks · doi:10.1016/b978-0-12-824010-6.00024-1

CHIP-seq: The evolution of genome-wide approaches to unveil the transcriptional network

Chan, N. T., & Xu, W. (2023) · Elsevier eBooks · doi:10.1016/b978-0-12-824010-6.00014-9

Next generation sequencing in toxicology

Vavilis, T., Stamoula, Ε., Sachinidis, A., Lamprinou, M., Dardalas, I., Ainatzoglou, A., Drakoulis, N., & Anagnostopoulos, A. K. (2023) · Elsevier eBooks · doi:10.1016/b978-0-12-824315-2.01188-x

CUT&RUN and CUT&Tag: Low-input methods for genome-wide mapping of chromatin proteins

Gopalan, S., & Fazzio, T. G. (2023) · Elsevier eBooks · doi:10.1016/b978-0-12-823376-4.00010-0

Deciphering the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression with single-nucleus CUT&RUNPreprint

Womersley, H. J., Muliaditan, D., DasGupta, R., & Cheow, L. F. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.14.580230

Additional file 2 of BIND&MODIFY: a long-range method for single-molecule mapping of chromatin modifications in eukaryotes

Weng, Z., Ruan, F., Chen, W., Chen, Z., Xie, Y., Luo, M., Xie, Z., Zhang, C., Wang, J., Sun, Y., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22623493

DMF-ChIP-seq for Highly Sensitive and Integrated Epigenomic Profiling of Low-Input Cells

Li, M., Xing, N., Lin, F., Liang, S., Huang, Y., Song, J. T., Xu, X. J., & Yang, C. J. (2024) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.4c11280

Advances and breakthroughs in single-cell nucleic acid omics

Sun, Z., Li, Z., Tang, Y., & Dong, F. (2025) · Scientia Sinica Vitae · doi:10.1360/ssv-2025-0107

Single-cell epigenomics: Methods and translation

Yadav, R. P., Pan, G., & Chen, X. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-26759-8.00029-1

Additional file 1 of SingleScan: a comprehensive resource for single-cell sequencing data processing and mining

Wang, K., Zhang, X., Cheng, H., Ma, W., Bao, G., Dong, L., Gou, Y., Yang, J., & Cai, H. (2023) · Figshare · doi:10.6084/m9.figshare.24770447

Additional file 1 of Profiling the transcriptomic signatures and identifying the patterns of zygotic genome activation – a comparative analysis between early porcine embryos and their counterparts in other three mammalian species

Zhai, Y., Yu, H., An, X., Zhang, Z., Zhang, M., Zhang, S., Li, Q., & Li, Z. (2022) · Figshare · doi:10.6084/m9.figshare.21629002

Additional file 3 of BIND&MODIFY: a long-range method for single-molecule mapping of chromatin modifications in eukaryotes

Weng, Z., Ruan, F., Chen, W., Chen, Z., Xie, Y., Luo, M., Xie, Z., Zhang, C., Wang, J., Sun, Y., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22623496

Additional file 1 of BIND&MODIFY: a long-range method for single-molecule mapping of chromatin modifications in eukaryotes

Weng, Z., Ruan, F., Chen, W., Chen, Z., Xie, Y., Luo, M., Xie, Z., Zhang, C., Wang, J., Sun, Y., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22623490

Matched single-cell chromatin, transcriptome, and surface marker profiling captures in vivo epigenomic reprogramming during basal-to-luminal transition in the mammary glandPreprint

Karpukhina, A. A., Moutaux, E., Durand, A., Keymeulen, A. V., Viaene, A., Miranda, M., Abed, L. H., Besson‐Girard, S., Lambault, M., Dupré, D., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.16.706078

Molecular basis of transcriptional dysregulations in the spinocerebellar ataxia type 7, a neurodegenerative polyglutamine disorder

Hache, A. (2020) · theses.fr (ABES) · doi:10.70675/2bbb827bzf007z47abz8f7azf1cb83d78ba6

Protocol update to: Genome-wide interrogation of protein-DNA interactions in mammalian cells using ChIPmentation

Li, X., Xu, W., Ye, Y., Sharrocks, A. D., Zhang, W., & Chen, X. X. (2026) · STAR Protocols · doi:10.1016/j.xpro.2026.104495

Single-cell chromatin landscapes visualize epigenetic barriers and reveal lineage-specific Polycomb-mediated repressionPreprint

Пирогов, С. А., Purik, A., Ilin, A., Barcenas-Walls, J. R., Bartošovič, M., & Mannervik, M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.04.722686

Microfluidics for single cell detection

Kaloni, A., Ganatra, S., Pandya, A., & Modi, A. (2026) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2026.06.008

Simultaneous single-cell profiling of chromatin, transcriptome and surface markers with OneCell CUT&Tag captures epigenomic reprogramming

Karpukhina, A. A., Moutaux, E., Durand, A., Keymeulen, A. V., Viaene, A., Miranda, M., Abed, L. H., Besson‐Girard, S., Lambault, M., Dupré, D., et al. (2026) · Nature Biotechnology · doi:10.1038/s41587-026-03259-1

Evolution, application and clinical significance of profiling chromatin interactions at a genome-wide scale

Qian, Q., Xu, Y., & Wei, L. (2026) · Acta Biochimica et Biophysica Sinica · doi:10.3724/abbs.2026165

ItChIP-simultaneous indexing and tagmentation-based ChIP-seqPreprint

Ai, S., Xiong, H., Li, C. C., Luo, Y., Liu, Y., Yu, X., & He, A. (2019) · doi:10.21203/rs.2.11366/v1 · Cited by 1

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

Rotem, A., Ram, O., Shoresh, N., Sperling, R. A., Goren, A., Weitz, D. A., & Bernstein, B. E. (2015) · Nature Biotechnology · doi:10.1038/nbt.3383 · Cited by 854

IT-scC&T-seq streamlines scalable, parallel profiling of protein–DNA interactions in single cells

Ma, J., Jin, W., Rong, L., Gao, Z., Zaman, H., Shakhawat, H. M., Long, F., Zhang, Z., Huang, J., Lu, X., et al. (2025) · Genome biology · doi:10.1186/s13059-025-03661-z · Cited by 5

A chromatin integration labelling method enables epigenomic profiling with lower input

Harada, A., Maehara, K., Handa, T., Arimura, Y., Nogami, J., Hayashi‐Takanaka, Y., Shirahige, K., Kurumizaka, H., Kimurâ, H., & Ohkawa, Y. (2018) · Nature Cell Biology · doi:10.1038/s41556-018-0248-3 · Cited by 154

Dropping in on single-cell epigenetic profiles

Swami, M. (2015) · Nature Reviews Genetics · doi:10.1038/nrg4036 · Cited by 4