Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

Model-based Analysis of ChIP-Seq (MACS)

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Massively parallel digital transcriptional profiling of single cells

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Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets.

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Spatial reconstruction of single-cell gene expression data

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Cancer immunotherapy using checkpoint blockade

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Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

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Integrative analysis of 111 reference human epigenomes

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TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells

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Dimensionality reduction for visualizing single-cell data using UMAP

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Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

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Engineering next-generation microfluidic technologies for single-cell phenomics

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Regulatory T cell therapies: from patient data to biological insights

Rodrigues, K. B., Eggenhuizen, P. J., Bacchetta, R., & Good, Z. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1675114 · Cited by 18

Dissecting neuroblastoma heterogeneity through single-cell multi-omics: insights into development, immunity, and therapeutic resistance

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Extensive evaluation of ATAC-seq protocols for native or formaldehyde-fixed nuclei

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Highly sensitive single-cell chromatin accessibility assay and transcriptome coassay with METATAC

Wu, H., Li, X., Jian, F., Yisimayi, A., Zheng, Y., Tan, L., Xing, D., & Xie, X. S. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2206450119 · Cited by 14

Temporally specific gene expression and chromatin remodeling programs regulate a conserved Pdyn enhancer

Phillips, R. A., Wan, E., Tuscher, J. J., Reid, D., Drake, O. R., Ianov, L., & Day, J. J. (2023) · eLife · doi:10.7554/elife.89993 · Cited by 17

Cell-free DNA from germline TP53 mutation carriers reflect cancer-like fragmentation patterns

Wong, D., Tageldein, M. M., Luo, P., Ensminger, E., Bruce, J. P., Oldfield, L. E., Gong, H., Fischer, N. W., Laverty, B., Subasri, V., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-51529-w · Cited by 20

Defining the regulatory logic of breast cancer using single-cell epigenetic and transcriptome profiling

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Single‐cell sequencing in translational cancer research and challenges to meet clinical diagnostic needs

Pfisterer, U., Bräunig, J., Brattås, P. L., Heidenblad, M., Karlsson, G., & Fioretos, T. (2021) · Genes Chromosomes and Cancer · doi:10.1002/gcc.22944 · Cited by 17

CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data

Thibodeau, A., Khetan, S., Eroğlu, A., Tewhey, R., Stitzel, M. L., & Ucar, D. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009670 · Cited by 16

Enzalutamide-induced signatures revealed by epigenetic plasticity using single-cell multi-omics sequencing in prostate cancer

Fan, H., Li, J., Manuel, A. M., & Zhao, Z. (2023) · Molecular Therapy - Nucleic Acids · doi:10.1016/j.omtn.2023.02.022 · Cited by 14

Single‐cell multi‐omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK‐positive lung cancer

Baek, S., Sung, E., Kim, G., Hong, M. H., Lee, C. Y., Shim, H. S., Park, S. Y., Kim, H. R., & Lee, I. (2025) · 癌症：英文版 · doi:10.1002/cac2.12658 · Cited by 16

The Epigenetics of Sepsis: How Gene Modulation Shapes Outcomes

Pignataro, G., Triunfo, C., Piccioni, A., Racco, S., Fuorlo, M., Forte, E., Franceschi, F., & Candelli, M. (2025) · Biomedicines · doi:10.3390/biomedicines13081936 · Cited by 15

Integrating transcription-factor abundance with chromatin accessibility in human erythroid lineage commitment

Baskar, R., Chen, A. F., Favaro, P. M. B., Reynolds, W. D., Müller, F., Borges, L., Jiang, S., Park, H. S., Kool, E. T., Greenleaf, W. J., et al. (2022) · Cell Reports Methods · doi:10.1016/j.crmeth.2022.100188 · Cited by 14

Complexity of enhancer networks predicts cell identity and disease genes revealed by single-cell multi-omics analysis

Hong, D., Lin, H., Liu, L., Shu, M., Dai, J., Lu, F., Tong, M., & Huang, J. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac508 · Cited by 15

Synergism Between IL21 and Anti-PD-1 Combination Therapy is Underpinned by the Coordinated Reprogramming of the Immune Cellular Network in the Tumor Microenvironment

Wu, S., Huang, H., Sun, R., Gao, D. S., Ye, F., Huang, J., Li, E., Ni, A., Lu, K. G., Chen, K., et al. (2023) · Cancer Research Communications · doi:10.1158/2767-9764.crc-23-0012 · Cited by 17

Application of single-cell omics in inflammatory bowel disease

Zheng, H. B. (2023) · World Journal of Gastroenterology · doi:10.3748/wjg.v29.i28.4397 · Cited by 16

Concepts and new developments in droplet-based single cell multi-omics

Chow, A., & Lareau, C. A. (2024) · Trends in biotechnology · doi:10.1016/j.tibtech.2024.07.006 · Cited by 16

Droplet-based single-cell sequencing: Strategies and applications

Shang, Y., Wang, Z., Xi, L., Wang, Y., Liu, M., Feng, Y., Wang, J., Wu, Q., Xiang, X., Chen, M., et al. (2024) · Biotechnology Advances · doi:10.1016/j.biotechadv.2024.108454 · Cited by 18

Topological identification and interpretation for single-cell epigenetic regulation elucidation in multi-tasks using scAGDE

Hao, G., Yi, F., Yu, Z., Su, Y., Zhu, H., Wang, F., Chen, X., Yang, Y., Wang, G., Wong, K., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-57027-x · Cited by 15

Cancer subclone detection based on DNA copy number in single-cell and spatial omic sequencing data

Wu, C.-Y., Rong, J., Sathe, A., Hess, P. R., Lau, B. T., Grimes, S. M., Huang, S., Ji, H. P., & Zhang, N. R. (2025) · Nature Methods · doi:10.1038/s41592-025-02773-5 · Cited by 15

Single-Cell Epigenomics in Cancer: Charting a Course to Clinical Impact

Bond, D. R., Uddipto, K., Enjeti, A. K., & Lee, H. J. (2020) · Epigenomics · doi:10.2217/epi-2020-0046 · Cited by 15

Single-cell technologies and analyses in hematopoiesis and hematological malignancies

Campillo‐Marcos, I., Álvarez‐Errico, D., Alandes, R. A., Mereu, E., & Esteller, M. (2021) · Experimental Hematology · doi:10.1016/j.exphem.2021.05.001 · Cited by 14

Coevolving JAK2V617F+relapsed AML and donor T cells with PD-1 blockade after stem cell transplantation: an index case

Penter, L., Gohil, S. H., Huang, T., Thrash, E. M., Schmidt, D., Li, S., Severgnini, M., Neuberg, D. S., Hodi, F. S., Livak, K. J., et al. (2021) · Blood Advances · doi:10.1182/bloodadvances.2021004335 · Cited by 15

The role of epigenetics in T-cell lymphoma

Yamagishi, M. (2022) · International Journal of Hematology · doi:10.1007/s12185-022-03470-1 · Cited by 16

The tumor microenvironment across four dimensions: assessing space and time in cancer biology

Larson, C. R., Mandloi, A., Acharyya, S., & Carstens, J. L. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1554114 · Cited by 16

Single-cell gene regulation network inference by large-scale data integration

Dong, X., Tang, K., Xu, Y., Wei, H., Han, T., & Wang, C. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac819 · Cited by 14

Single-cell multiomic understanding of HIV-1 reservoir at epigenetic, transcriptional, and protein levels

Wong, M., Wei, Y., & Ho, Y. (2023) · Current Opinion in HIV and AIDS · doi:10.1097/coh.0000000000000809 · Cited by 15

BET inhibition reforms the immune microenvironment and alleviates T cell dysfunction in chronic lymphocytic leukemia

Smith, A. L., Skupa, S. A., Eiken, A. P., Reznicek, T. E., Schmitz, E. G., Williams, N., Moore, D. Y., D'Angelo, C. R., Kallam, A., Lunning, M. A., et al. (2024) · JCI Insight · doi:10.1172/jci.insight.177054 · Cited by 14

CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression

Lewis, M. W., King, C. M., Wiśniewska, K., Regner, M. J., Coffey, A. R., Kelly, M. R., Méndez-Giráldez, R., Davis, E. S., Phanstiel, D. H., & Franco, H. L. (2024) · Cancer Research · doi:10.1158/0008-5472.can-23-3995 · Cited by 16

Single-Cell Sequencing: High-Resolution Analysis of Cellular Heterogeneity in Autoimmune Diseases

Tang, X., Zhang, Y., Zhang, H., Zhang, N., Dai, Z., Cheng, Q., & Li, Y. (2024) · Clinical Reviews in Allergy & Immunology · doi:10.1007/s12016-024-09001-6 · Cited by 15

Acute and persistent responses after H5N1 vaccination in humans

Apps, R., Biancotto, A., Candia, J., Kotliarov, Y., Perl, S., Cheung, F., Farmer, R., Mulè, M. P., Rachmaninoff, N., Chen, J., et al. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114706 · Cited by 14

scATAnno: Automated Cell Type Annotation for Single-cell ATAC-seq Data

Jiang, Y., Hu, Z., Lu, F., Lynch, A. W., Jiang, J., Zhu, A., Zeng, Z., Zhang, Y., Wu, G., Xie, Y., et al. (2025) · Genomics Proteomics & Bioinformatics · doi:10.1093/gpbjnl/qzaf108 · Cited by 19

Discovering single nucleotide variants and indels from bulk and single-cell ATAC-seq

Massarat, A. R., Sen, A., Jaureguy, J., Tyndale, S. T., Fu, Y., Erikson, G. A., & McVicker, G. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab621 · Cited by 15

Genome editing to define the function of risk loci and variants in rheumatic disease

Baglaenko, Y., Macfarlane, D., Marson, A., Nigrovic, P. A., & Raychaudhuri, S. (2021) · Nature Reviews Rheumatology · doi:10.1038/s41584-021-00637-8 · Cited by 12

Evolution of plant cell-type-specific cis -regulatory elementsPreprint

Yan, H., Mendieta, J. P., Zhang, X., Marand, A. P., Liang, Y. Q., Luo, Z., Minow, M. A. A., Jang, H., Li, X., Roulé, T., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.01.08.574753 · Cited by 14

An Updated Model for the Epigenetic Regulation of Effector and Memory CD8+ T Cell Differentiation

Xu, T., Pereira, R. M., & Martínez, G. (2021) · The Journal of Immunology · doi:10.4049/jimmunol.2100633 · Cited by 14

GAGAM v1.2: An Improvement on Peak Labeling and Genomic Annotated Gene Activity Matrix Construction

Martini, L., Bardini, R., Savino, A., & Carlo, S. D. (2022) · Genes · doi:10.3390/genes14010115 · Cited by 12

Fast and flexible profiling of chromatin accessibility and total RNA expression in single nuclei using Microwell-seq3

Ye, F., Zhang, S., Fu, Y., Yang, L. X., Zhang, G., Wu, Y., Pan, J., Chen, H., Wang, X., Ma, L., et al. (2024) · Cell Discovery · doi:10.1038/s41421-023-00642-z · Cited by 13

Single-nucleus transcriptional and chromatin accessible profiles reveal critical cell types and molecular architecture underlying chicken sex determination

Li, J., Zhang, X., Wang, X., Wang, Z., Li, X., Zheng, J., Li, J., Xu, G., Sun, C., Yi, G., et al. (2024) · Journal of Advanced Research · doi:10.1016/j.jare.2024.05.007 · Cited by 14

FRA1 controls acinar cell plasticity during murine KrasG12D induced pancreatic acinar to ductal metaplasia

Li, A. L., Sugiura, K., Nishiwaki, N., Suzuki, K., Sadeghian, D., Zhao, J., Maitra, A., Falvo, D., Chandwani, R., Pitarresi, J. R., et al. (2024) · Developmental Cell · doi:10.1016/j.devcel.2024.07.021 · Cited by 12

Changes in conjunctival mononuclear phagocytes and suppressive activity of regulatory macrophages in desiccation induced dry eye

Alam, J., Yaman, E., de Paiva, C. S., Li, D., Silva, G. C. V., Zuo, Z. C., & Pflugfelder, S. C. (2024) · The Ocular Surface · doi:10.1016/j.jtos.2024.09.003 · Cited by 14

BCOR and ZC3H12A suppress a core stemness program in exhausted CD8+ T cells

Xu, J., Jia, Z., Zhao, X., Wang, L., Jin, G., Li, Z., Yin, N., Li, Y., & Peng, M. (2025) · The Journal of Experimental Medicine · doi:10.1084/jem.20241133 · Cited by 14

Application of single cell genomics to focal epilepsies: A call to action

Khoshkhoo, S., Lal, D., & Walsh, C. A. (2021) · Brain Pathology · doi:10.1111/bpa.12958 · Cited by 16

Immune Sexual Dimorphism: Connecting the Dots

Gal-Oz, S. T., & Shay, T. (2021) · Physiology · doi:10.1152/physiol.00006.2021 · Cited by 13

Microfluidics for Cancer Biomarker Discovery, Research, and Clinical Application

Žvirblytė, J., & Mažutis, L. (2022) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-04039-9_20 · Cited by 13

Discovering Cellular Mitochondrial Heteroplasmy Heterogeneity with Single Cell RNA and ATAC Sequencing

Marshall, A. S., & Jones, N. S. (2021) · Biology · doi:10.3390/biology10060503 · Cited by 12

DeNOPA: decoding nucleosome positions sensitively with sparse ATAC-seq data

Xu, B., Li, X., Gao, X., Jia, Y., Liu, J., Li, F., & Zhang, Z. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab469 · Cited by 13

Neuromesodermal progenitor origin of trunk neural crest in vivoPreprint

Lukoseviciute, M., Mayes, S., & Sauka‐Spengler, T. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.10.430513 · Cited by 12

Applications of Single-Cell Sequencing Technology to the Enteric Nervous System

Guyer, R. A., Mueller, J. L., & Goldstein, A. M. (2022) · Biomolecules · doi:10.3390/biom12030452 · Cited by 12

Unraveling the Complexity of Liver Disease One Cell at a Time

Bader, G. D., McGilvray, I. D., MacParland, S. A., Atif, J., & Thoeni, C. E. (2022) · Seminars in Liver Disease · doi:10.1055/s-0042-1755272 · Cited by 12

Targeting epigenetic deregulations for the management of esophageal carcinoma: recent advances and emerging approaches

Ahuja, P., Yadav, R., Goyal, S., Yadav, C., Ranga, S., & Kadian, L. K. (2023) · Cell Biology and Toxicology · doi:10.1007/s10565-023-09818-5 · Cited by 12

Deep generative models in single-cell omics

Rivero-García, I., Torres, M., & Sánchez‐Cabo, F. (2024) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2024.108561 · Cited by 13

A multi-omic single-cell landscape of the aging mouse ovary

Zhang, J., Jia, S., Zheng, Z., Cao, L., Zhou, J., & Fu, X. (2025) · GeroScience · doi:10.1007/s11357-025-01556-2 · Cited by 13

Learning the cellular origins across cancers using single-cell chromatin landscapes

Bairakdar, M. D., Lee, W., Giotti, B., Kumar, A., Štancl, P., Wagenblast, E., Hambardzumyan, D., Polak, P. P., Karlić, R., & Tsankov, A. M. (2025) · Nature Communications · doi:10.1038/s41467-025-63957-3 · Cited by 13

Lipopolysaccharide increases bitter taste sensitivity via epigenetic changes in Tas2r gene clusters

Lin, C., Jyotaki, M., Quinlan, J., Feng, S., Zhou, M., Jiang, P., Matsumoto, I., Huang, L., Ninomiya, Y., Margolskee, R. F., et al. (2023) · iScience · doi:10.1016/j.isci.2023.106920 · Cited by 12

Gene-regulatory network analysis of ankylosing spondylitis with a single-cell chromatin accessible assay

Yu, H., Wu, H., Zheng, F., Zhu, C., Yin, L., Dai, W., Liu, D. J., Tang, D., Hong, X., & Dai, Y. (2020) · Scientific Reports · doi:10.1038/s41598-020-76574-5 · Cited by 12

Advances in Single-Cell Multi-Omics and Application in Cardiovascular Research

Zhang, X., Qiu, H., Zhang, F., & Ding, S. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.883861 · Cited by 14

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

Computational Analyses and Challenges of Single-cell ATAC-seq

Wang, C., Zhou, J., Zhang, H., Zhuang, Z., Bai, G., Tang, M., Liu, S., & Liu, T. (2025) · Genomics Proteomics & Bioinformatics · doi:10.1093/gpbjnl/qzaf115 · Cited by 13

Genomic Analysis of Foxp3 Function in Regulatory T Cells

Dolsten, G. A., & Pritykin, Y. (2023) · The Journal of Immunology · doi:10.4049/jimmunol.2200864 · Cited by 16

Construction of single-cell cross-species chromatin accessibility landscapes with combinatorial-hybridization-based ATAC-seq

Zhang, G., Fu, Y., Yang, L., Ye, F., Zhang, P., Zhang, S., Ma, L., Li, J., Wu, H., Han, X., et al. (2024) · Developmental Cell · doi:10.1016/j.devcel.2024.01.015 · Cited by 11

Temporal control of progenitor competence shapes maturation in GABAergic neuron development in mice

Bright, A. R., Kotlyarenko, Y., Neuhaus, F., Rodrigues, D., Feng, C., Peters, C., Vitali, I., Dönmez, E., Myoga, M. H., Dvoretskova, E., et al. (2025) · Nature Neuroscience · doi:10.1038/s41593-025-01999-y · Cited by 13

Combined single-cell profiling of chromatin–transcriptome and splicing across brain cell types, regions and disease state

Hu, W., Foord, C., Hsu, J., Fan, L., Corley, M. J., Lanjewar, S. N., Xu, S., Belchikov, N., He, Y., Pang, A. P. S., et al. (2025) · Nature Biotechnology · doi:10.1038/s41587-025-02734-5 · Cited by 14

The evolution of gene regulation in mammalian cerebellum development

Sarropoulos, I., Sepp, M., Yamada, T., Schäfer, P. S. L., Trost, N., Schmidt, J., Schneider, C., Drummer, C., Mißbach, S., Taskiran, I. I., et al. (2026) · Science · doi:10.1126/science.adw9154 · Cited by 13

The Application of Single-Cell Technologies in Cardiovascular Research

Chen, Y., Liu, Y., & Gao, X. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.751371 · Cited by 11

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 12

scAVENGERS: a genotype-based deconvolution of individuals in multiplexed single-cell ATAC-seq data without reference genotypes

Han, S.-B., Kim, K., Park, S.-W., Lee, A., Chun, H., & Jung, I. (2022) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqac095 · Cited by 10

Isolation of Adipose Tissue Nuclei for Single-Cell Genomic Applications

Benitez, G. J., & Shinoda, K. (2020) · Journal of Visualized Experiments · doi:10.3791/61230 · Cited by 11

Archetypes of checkpoint-responsive immunity

Im, K. W., Combes, A. J., Spitzer, M. H., Satpathy, A. T., & Krummel, M. F. (2021) · Trends in Immunology · doi:10.1016/j.it.2021.09.007 · Cited by 13

Current and Prospective Methods for Assessing Anti-Tumor Immunity in Colorectal Cancer

Nussbaum, Y. I., Manjunath, Y., Suvilesh, K. N., Warren, W. C., Shyu, C., Kaifi, J. T., Ciorba, M. A., & Mitchem, J. B. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22094802 · Cited by 11

Single-cell multimodal profiling of proteins and chromatin accessibility using PHAGE-ATACPreprint

Fiškin, E., Lareau, C. A., Eraslan, G., Ludwig, L. S., & Regev, A. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.01.322420 · Cited by 11

TEA-seq: a trimodal assay for integrated single cell measurement of transcription, epitopes, and chromatin accessibilityPreprint

Swanson, E. G., Lord, C., Reading, J., Heubeck, A. T., Savage, A. K., Green, R. R., Li, X., Torgerson, T. R., Bumol, T. F., Graybuck, L. T., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.04.283887 · Cited by 11

Single-cell analyses reveal a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancerPreprint

Becker, W. R., Nevins, S. A., Chen, D. C., Chiu, R., Horning, A. M., Laquindanum, R., Mills, M. A., Chaı̈b, H., Ladabaum, U., Longacre, T. A., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.24.436532 · Cited by 11

Integrative epigenetic analysis reveals AP-1 promotes activation of tumor-infiltrating regulatory T cells in HCC

Zhuo, B., Zhang, Q., Xie, T., Wang, Y., Chen, Z., Zuo, D., & Guo, B. (2023) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-023-04746-3 · Cited by 11

MOCHA’s advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human cohorts

Zaim, S. R., Pebworth, M.-P., McGrath, I., Okada, L. Y., Weiss, M. D. A., Reading, J., Czartoski, J., Torgerson, T. R., McElrath, M. J., Bumol, T. F., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-50612-6 · Cited by 10

Detecting copy-number alterations from single-cell chromatin sequencing data by AtaCNA

Wang, X.-C., Jin, Z., Shi, Y., & Xi, R. (2025) · Cell Reports Methods · doi:10.1016/j.crmeth.2024.100939 · Cited by 10

Restriction of innate Tγδ17 cell plasticity by an AP-1 regulatory axis

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Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

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