The DOI matches its Crossref record; 87 of the 87 references it cites were found in a registry or an index.
Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion
Open accessPublished version of a preprint
Abstract
Understanding complex tissues requires single-cell deconstruction of gene regulation with precision and scale. Here, we assess the performance of a massively parallel droplet-based method for mapping transposase-accessible chromatin in single cells using sequencing (scATAC-seq). We apply scATAC-seq to obtain chromatin profiles of more than 200,000 single cells in human blood and basal cell carcinoma. In blood, application of scATAC-seq enables marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity and reconstruction of trajectories of cellular differentiation. In basal cell carcinoma, application of scATAC-seq reveals regulatory networks in malignant, stromal and immune cells in the tumor microenvironment. Analysis of scATAC-seq profiles from serial tumor biopsies before and after programmed cell death protein 1 blockade identifies chromatin regulators of therapy-responsive T cell subsets and reveals a shared regulatory program that governs intratumoral CD8+ T cell exhaustion and CD4+ T follicular helper cell development. We anticipate that scATAC-seq will enable the unbiased discovery of gene regulatory factors across diverse biological systems.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Note that these features were originally developed for scATAC-seq data on non-perturbed cells, with goals such as the identification of cell type, discovery of cell type-specific regulatory elements, or reconstruction of cellular differentiation trajectories43,61.”
From scPerturb: harmonized single-cell perturbation data (2024) · cites this paper as [61]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
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
Massively parallel digital transcriptional profiling of single cells
Zheng, G. X. Y., Terry, J. M., Belgrader, P., Ryvkin, P., Bent, Z. W., Wilson, R., Ziraldo, S. B., Wheeler, T. D., McDermott, G. P., Zhu, J., et al. (2017) · Nature Communications · doi:10.1038/ncomms14049 · Cited by 7,353
Self-citationHighly parallel genome-wide expression profiling of individual cells using nanoliter droplets.
Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A. R., Kamitaki, N., Martersteck, E. M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.002 · Cited by 7,110
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
Cancer immunotherapy using checkpoint blockade
Ribas, A., & Wolchok, J. D. (2018) · Science · doi:10.1126/science.aar4060 · Cited by 6,791
Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013) · Nature Methods · doi:10.1038/nmeth.2688 · Cited by 6,422
Self-citationIntegrative analysis of 111 reference human epigenomes
Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368 · cited 9×
“We identified 31 scATAC-seq clusters, which we classified using three parallel approaches: (1) chromatin accessibility of individual cis-elements (ATAC-seq peaks), (2) gene activity scores, which were computed from the accessibility of several enhancers linked to a single gene promoter20, and (3) TF activity, as compu…”
BackgroundMethodInfluentialSelf-citationTGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells
Mariathasan, S., Turley, S. J., Nickles, D., Castiglioni, A., Yuen, K., Wang, Y., Kadel III, E. E., Koeppen, H., Astarita, J. L., Cubas, R., et al. (2018) · Nature · doi:10.1038/nature25501 · Cited by 5,400
Dimensionality reduction for visualizing single-cell data using UMAP
Becht, E., McInnes, L., Healy, J., Dutertre, C.-A., Kwok, I. W. H., Ng, L. G., Ginhoux, F., & Newell, E. W. (2019) · Nature Biotechnology · doi:10.1038/nbt.4314 · Cited by 5,358
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
Tirosh, I., Izar, B., Prakadan, S. M., Wadsworth, M. H., Treacy, D., Trombetta, J. J., Rotem, A., Rodman, C., Lian, C., Murphy, G., et al. (2016) · Science · doi:10.1126/science.aad0501 · Cited by 4,944
Self-citation
Cited by
Sorted by citations
Items 901–999 of 999
Advances in epigenetic techniques to study development and diseases
Dzobo, K. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-26759-8.00019-9
CD39 defines a cytotoxic tumor-associated NK cell state responsive to NKG2A blockade in lung cancerPreprint
Serger, C., Rebuffet, L., Sandholzer, M., Rackwitz, W., Fusi, I., Herzig, P., Brüggemann, A., Pawlow, C., Chichelnitskiy, E., Hajnal, D., et al. (2026) · bioRxiv · doi:10.1101/2025.08.26.672316
shinyUMAP: an online tool for promoting understanding of single cell omics data visualizationPreprint
Misra, R., O’Leary, K., Chen, W., & Zheng, D. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.27.672621
Integrating Graph Convolutional Networks for Missing Gene Expression Imputation
Zhang, Y., Yu, H., Yan, Z., Pan, T., Zhang, Y., Liu, Y., Li, S., Guo, Y., Song, J., & Yu, D. (2025) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbbio.2025.3605719 · Cited by 1
Ding, T., Schweickart, G., Kaiser, K., Rivaldi, A., Marchal, N., Harrington, C. A., Varghese, A., Qin, K., Kelly, B., Sunkel, B. D., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.21.677597 · Cited by 1
Zhang, Y., Chen, C., Zhu, T., Luo, W., Zhou, R.-R., & Tan, W.-L. (2025) · PLoS ONE · doi:10.1371/journal.pone.0334104 · Cited by 1
Han, X. M., Wang, B., Xiang, W., Lin, F. Y., Sun, B., Yang, B., Ruan, Z., Liu, S., Li, S., Liu, H., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.14.682233
Yang, Z., Liu, S., & Chen, C. (2025) · Blood Science · doi:10.1097/bs9.0000000000000258
Advances in dietary bioactives: Unlocking chromatin accessibility
Huang, W., Lin, S., Yuan, Y., Farag, M. A., Wang, H., & Xiao, J. (2025) · Phytochemistry Reviews · doi:10.1007/s11101-025-10196-5
Xu, Y., Fleming, S. J., Wang, B., Schoenbeck, E. G., Babadi, M., & Huo, B. (2025) · SSRN Electronic Journal · doi:10.1101/2025.11.29.691308
Chen, C., Chen, X., Yang, Y., Cai, Y., Chen, N., Jiang, D., & Weng, Y. (2025) · Journal of Applied Genetics · doi:10.1007/s13353-025-01029-4 · Cited by 1
Liu, N., Sadlon, T. J., Wong, Y. Y., Pederson, S., Breen, J., & Barry, S. C. (2022) · Figshare · doi:10.6084/m9.figshare.20206400
Additional file 1 of simATAC: a single-cell ATAC-seq simulation framework
Navidi, Z., Zhang, L., & Wang, B. (2021) · Figshare · doi:10.6084/m9.figshare.14168506
Thibodeau, A., Eroğlu, A., McGinnis, C. S., Lawlor, N. T., Nehar-Belaid, D., Kursawe, R., Marcheş, R., Conrad, D. N., Kuchel, G. A., Gartner, Z. J., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16551025
Additional file 7 of MEDALT: single-cell copy number lineage tracing enabling gene discovery
Wang, F., Wang, Q., Mohanty, V., Liang, S., Dou, J., Han, J., Minussi, D. C., Gao, R., Ding, L., Navin, N., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14100270
Qiu, X., Yu, H., Wu, H., Hu, Z., Zhou, J., Lin, H., Xue, W., Cai, W., Chen, J., Yan, Q., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14889648
Zong, D., Huang, B., Li, Y., Lu, Y., Xiang, N., Guo, C., Liu, Q., Sha, Q., Du, P., Yu, Q., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14443077
Zhang, H., Mulqueen, R. M., Iannuzo, N., Farrera, D. O., Polverino, F., Galligan, J. J., Ledford, J. G., Adey, A., & Cusanovich, D. A. (2024) · Figshare · doi:10.6084/m9.figshare.26696667
Zhang, W., Jiang, R., Chen, S., & Wang, Y. (2023) · Figshare · doi:10.6084/m9.figshare.24277169
Additional file 1 of Joint analysis of scATAC-seq datasets using epiConv
Lin, L., & Zhang, L. (2022) · Figshare · doi:10.6084/m9.figshare.20407420
Yu, W., Uzun, Y., Zhu, Q., Chen, C., & Tan, K. (2020) · Figshare · doi:10.6084/m9.figshare.12160050
Zhang, X., Marand, A. P., Yan, H., & Schmitz, R. J. (2024) · Figshare · doi:10.6084/m9.figshare.25566288
Zhang, H., Mulqueen, R. M., Iannuzo, N., Farrera, D. O., Polverino, F., Galligan, J. J., Ledford, J. G., Adey, A., & Cusanovich, D. A. (2024) · Figshare · doi:10.6084/m9.figshare.26696679
Zhang, H., Mulqueen, R. M., Iannuzo, N., Farrera, D. O., Polverino, F., Galligan, J. J., Ledford, J. G., Adey, A., & Cusanovich, D. A. (2024) · Figshare · doi:10.6084/m9.figshare.26696682
Additional file 6 of MEDALT: single-cell copy number lineage tracing enabling gene discovery
Wang, F., Wang, Q., Mohanty, V., Liang, S., Dou, J., Han, J., Minussi, D. C., Gao, R., Ding, L., Navin, N., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14100267
Additional file 1 of MEDALT: single-cell copy number lineage tracing enabling gene discovery
Wang, F., Wang, Q., Mohanty, V., Liang, S., Dou, J., Han, J., Minussi, D. C., Gao, R., Ding, L., Navin, N., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14100249
Thibodeau, A., Eroğlu, A., McGinnis, C. S., Lawlor, N. T., Nehar-Belaid, D., Kursawe, R., Marcheş, R., Conrad, D. N., Kuchel, G. A., Gartner, Z. J., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16551022
Zhang, H., Mulqueen, R. M., Iannuzo, N., Farrera, D. O., Polverino, F., Galligan, J. J., Ledford, J. G., Adey, A., & Cusanovich, D. A. (2024) · Figshare · doi:10.6084/m9.figshare.26696676
Zhang, H., Mulqueen, R. M., Iannuzo, N., Farrera, D. O., Polverino, F., Galligan, J. J., Ledford, J. G., Adey, A., & Cusanovich, D. A. (2024) · Figshare · doi:10.6084/m9.figshare.26696673
Yu, W., Uzun, Y., Zhu, Q., Chen, C., & Tan, K. (2020) · Figshare · doi:10.6084/m9.figshare.12160044
Additional file 4 of simATAC: a single-cell ATAC-seq simulation framework
Navidi, Z., Zhang, L., & Wang, B. (2021) · Figshare · doi:10.6084/m9.figshare.14168524
Zhang, X., Marand, A. P., Yan, H., & Schmitz, R. J. (2024) · Figshare · doi:10.6084/m9.figshare.25566386
Zhang, H., Mulqueen, R. M., Iannuzo, N., Farrera, D. O., Polverino, F., Galligan, J. J., Ledford, J. G., Adey, A., & Cusanovich, D. A. (2024) · Figshare · doi:10.6084/m9.figshare.26696670
Zhang, X., Marand, A. P., Yan, H., & Schmitz, R. J. (2024) · Figshare · doi:10.6084/m9.figshare.26703730
Zhang, W., Jiang, R., Chen, S., & Wang, Y. (2024) · Figshare · doi:10.6084/m9.figshare.24277238
Yu, W., Uzun, Y., Zhu, Q., Chen, C., & Tan, K. (2020) · Figshare · doi:10.6084/m9.figshare.12160035
Feng, D., Liang, Z., Wang, Y., Yao, J., Yuan, Z., Hu, G., Qu, R., Xie, S. B., Li, D., Yang, L., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22613404
Coronado, M., Vincelle-Nieto, Á., Azcárate, I. G., Pérez-Benavente, S., Puyet, A., Díez, A., Bautista, J. M., & Reyes‐Palomares, A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.10.693423
TimeFlow 2: An Unsupervised Cell Lineage Detection Method for Flow Cytometry Data
Liarou, M., Matthes, T., & Marchand‐Maillet, S. (2026) · Cytometry Part A · doi:10.1002/cytoa.70006
Scoville, D. W., Grimm, S. A., Xu, X., Anchang, B., & Jetten, A. M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.06.697979
Single-nucleus chromatin accessibility and gene expression co-profiling by ISSAAC-seq
Xu, W., Hu, Y., Zhang, Y., Schnepp, P. M., Lo, L. M., Zhang, Q., Cheng, S. M., & Chen, X. X. (2026) · Nature Protocols · doi:10.1038/s41596-025-01304-y
Tulloch, A. J., Delgado, R. N., Catta-Preta, R., & Cepko, C. L. (2026) · eLife · doi:10.7554/elife.107565.2
Early exposure to PFAS disrupts neuro-muscular development in zebrafish embryosPreprint
Afzal, Z., Papas, B. N., Veershetty, V., Pittman, E. E., Hatcher, C., Li, J., Casey, W., & Kumar, D. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.19.700343
Tet2 modulates ER stress responses related to β-cell death and autoimmunity in diabetes
Rui, J., Kothari, M., Kursawe, R., Barkestani, M. N., Genosar, R., Clark, P. L., Stitzel, M. L., & Herold, K. C. (2026) · iScience · doi:10.1016/j.isci.2026.114818
Transcriptional and epigenetic control of human naïve CD8+ T cell activation
Hu, Y., Du, Y., Chen, X., Li, Y., & Yang, C. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1749526
Xue, J., Zhou, J., Li, Y. E., & Yu, Z. (2025) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm66473.2025.11356399
Precision CRISPR annotation of the functional enhancer landscape in primary human T cellsPreprint
Wang, P., Giles, J. R., Huang, H., Manne, S., Jordan, M. S., Huang, A. C. C., Shi, J., & Wherry, E. J. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.27.702006
A generic reference defined by consensus peaks for single-cell ATAC-seq data analysis
Meng, Q., Wu, X., Chen, W., Zhao, Y., Li, C., Wei, Z., Zeng, X., Li, J., Xi, X., Chen, S., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-69461-6 · Cited by 5
Angelis, M. T. D., Santamaria, G., Amaddeo, A., Iannello, A. M., Viglietto, G., & Rizzuto, A. (2026) · Surgical Oncology · doi:10.1016/j.suronc.2026.102382
A pipeline for single-cell chromatin accessibility data analysis
Zhang, M., & Chen, C. (2026) · Blood Science · doi:10.1097/bs9.0000000000000259
BARTsc identifies key transcriptional regulators from single-cell omics dataPreprint
Zhang, H., Kang, L., Wang, J., Liang, K., Wang, Z., Xu, K., & Zang, C. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.24.707729 · Cited by 1
Self-citationBlanco‐Luquin, I., Martinez‐de‐Morentin, X., Vilas‐Zornoza, A., Mouzo, D., Lopez, A. L., Macías, M., Alignani, D., Maillo, A., Alvarez, A. C. G., Ibrahim, L. A., et al. (2026) · Scientific Data · doi:10.1038/s41597-026-06971-4
Detection of mitochondrial DNA mutations in T cells following 5-FU or cisplatin exposure
Kirkpatrick, C. A., Quick, C. M., Post, S. R., Leung, Y., Dings, R. P. M., Paulos, C. M., Burdine, L., & Lu, Y.-C. W. (2026) · Cell Reports Medicine · doi:10.1016/j.xcrm.2026.102663
Teng, Y., Li, H., Cheng, L., Jiang, Y., Jiang, H., & Liu, Y. (2026) · Biomedicines · doi:10.3390/biomedicines14030643
HitAnno: Atlas-level cell type annotation based on scATAC-seq data via a hierarchical language modelPreprint
Wang, Z., Chen, X., Cui, X., Gao, Z., Li, Z., Li, K., & Jiang, R. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.10.710729
Gerstner, N., Fröhlich, A. S., Matosin, N., Binder, E. B., & Arloth, J. (2026) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-026-06177-2
Wu, R., Ling, Y., He, Y., Yao, L., Shi, Q., Shen, W., Li, X., Liu, Y., & Li, J. (2026) · PeerJ · doi:10.7717/peerj.20704
Single cell multi-OMICS analysis of Treg biology in cancer
Richer, W. (2021) · theses.fr (ABES) · doi:10.70675/97f429e9z2993z4b78z88dezf46fae0d3a30
Unsupervised representation learning for single-cell transcriptomic and epigenomic data
Raimundo, F. (2022) · theses.fr (ABES) · doi:10.70675/760cd5d0z17c6z4f4ezb476z68bd387daf22
Huang, Z., Kong, W., & Wang, S. (2026) · Frontiers in Genetics · doi:10.3389/fgene.2026.1795752
Fan, H., Du, C., Xu, C., Wang, H., Wang, Y., Wu, Z., Zhao, B., Chen, C., Shang, S., Sun, M.-A., et al. (2026) · BMC Genomics · doi:10.1186/s12864-026-12854-0 · Cited by 3
Histone mark remodeling in cancer: an enhancer-centered perspective
Park, J., 전진하, Gim, S., & Chung, C. (2026) · Genes & Genomics · doi:10.1007/s13258-026-01768-6
Yu, L., Deary, L. T., Liu, Q., Zhang, Q., & Zhao, S. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.27.721080
Yu, C., Huang, J., Zhang, X., Wang, Y., Song, J., & Shen, W. (2026) · Journal of Molecular and Cellular Cardiology · doi:10.1016/j.yjmcc.2026.05.003
Tumor heterogeneity as a driver of drug resistance and its implications for personalized therapy
Da, E., Zhu, R., Xi, B., Zhang, L., & Tang, G. (2026) · Cancer Drug Resistance · doi:10.20517/cdr.2025.216
Variations in DNA Methylation Are Landmarks of Freshwater Adaptation in Three-Spined Sticklebacks
Starshin, A., Mazur, A., Mugue, N. S., Kaplun, D., Golden, A., Khrameeva, E. E., & Prokhortchouk, E. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27104265
Yerrabelli, R., Thibodeau, A., Nehar-Belaid, D., Marcheş, R., Ravichandran, S., Barnouin, Y., Sen, R., Paust, S., Stitzel, M. L., Ferrucci, L., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.08.723786
Liu, L., zhang, Z., Huang, Q., Liu, B., & 吴洪波 (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1822205
Emerging Technologies in Single-Cell Analysis
Thi, V. A. P., Nguyen, K. L., Thi, T.-H. N., & Chu, D.-T. (2026) · Springer eBooks · doi:10.1007/978-981-95-9789-5_2
ATACompass enables cross-species cell identity mapping for scATAC-seq without gene annotations
Jiang, J., Ding, Y., Jin, B., Liu, G., Wang, S., Zhang, Y., Wang, Y., Li, X., Liu, J., Li, W., et al. (2026) · Cell Reports Methods · doi:10.1016/j.crmeth.2026.101460
Zhang, S., Deng, Y., Deng, Y., Yin, X., Zhang, Y. M., Chen, Y., Zhang, M. Q., Wang, X., Li, H., Cao, Z., et al. (2026) · Briefings in Bioinformatics · doi:10.1093/bib/bbag265
TRIM71 suppresses cervical cancer progression by inhibiting Nectin4-mediated Wnt/β-catenin signaling
Liu, T., Chen, J., Dai, B., Du, D., Chen, M., Zhao, N., Mai, H., Fan, H., Lin, L., Liang, Y., et al. (2026) · Biology Direct · doi:10.1186/s13062-026-00843-y
Lange, B., Graceffo, E., Stenzel, W., Biebermann, H., Schuelke, M., & Wilpert, N. (2026) · medRxiv · doi:10.64898/2026.06.04.26354648
Wang, D., Zhu, X., Hu, N., Wu, B., Dong, Y., Song, Y., Li, X., Wang, Z., Huang, Z., Li, Y., et al. (2026) · Genes & Diseases · doi:10.1016/j.gendis.2026.102272
scMTG reconstructs single-cell temporal dynamics with Markov transition generatorsPreprint
Cui, X., Wang, H., Gao, Z., Jiang, R., Wong, W. H., & Liu, Q. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.04.730241
Aleynick, M., Wang, Q., Wu, J. E., Lemus, S., Chaimowitz, M. G., Mir, H., Warsaw, J. J., Guo, C., Macdonald, L. E., Waite, J. C., et al. (2026) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-25-1420
Epigenetically tunable biomaterials for immune modulation
Foudah, A. I., Ahmad, A., & Alam, A. (2026) · Chinese Chemical Letters · doi:10.1016/j.cclet.2026.113069
GRHL and PGR control WNT4 expression via 3D looping of conserved and species-specific enhancers
van de Grift, Y. B. C., Aarts, M. T., Wiese, K. E., Heijmans, N., Hooijkaas, I. B., Pritchard, C. E. J., Henneman, L., Krimpenfort, P., van Boxtel, A. L., & van Amerongen, R. (2026) · Cell Reports · doi:10.1016/j.celrep.2026.117575 · Cited by 2
Wang, K., Lu, H., Deng, N., Tao, Y., Yang, X., Yuan, M., Gao, L., Jiang, S., Shang, W., Deng, J., et al. (2026) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2026.189642
Self-citationLuo, Z., & Greenleaf, W. J. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.29.735326
Self-citationElitz, A., Fernandes, S., Cook, K. C. S., Warheit-Niemi, H. I., Zhao, B., Tóth, A., Zacharias, A. L., & Zacharias, W. J. (2026) · JCI Insight · doi:10.1172/jci.insight.201739 · Cited by 1
Vessel Organoids Reveal FOXF1 Variant-Specific Regulation of Mesoderm and Capillary DevelopmentPreprint
Pek, N. M. Q., Thorner, K., Guo, M., Dennison, T. S. H., Rajaguru, T., Stan, G., Kishimoto, K., Rottier, R. J., Kotton, D. N., Zorn, A. M., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.07.12.737936
Filippidis, P., Lu, C., Orlinick, B. L., Pang, A. P. S., Nelson, A., Spudich, S., Roman, F. M., Zigáčková, D., Singareddy, N., Mehta, S. S., et al. (2026) · Science Advances · doi:10.1126/sciadv.aee1278
Omelchenko, A. A., Rahman, S. A., Wang, A., Tabib, T., Viswanadham, V., Yuen, G. J., Estrada, P. M. D. R., D’Onofrio, V., Chen, Y., Sun, N., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-75559-8
Chugh, S., Shim, H., & McCarthy, D. J. (2026) · Genome biology · doi:10.1186/s13059-026-04199-4
Complex subtelomeric architectures in a complete rhesus macaque reference genome
Zhang, S., Xu, N., Lu, Y., Nie, Y., Li, Z., de Gennaro, L., Torraca, A. L., Fu, L., Zhang, Z., Chen, J., et al. (2026) · Cell · doi:10.1016/j.cell.2026.02.018 · Cited by 3
Effective and Robust Single-cell Cross-omics Annotation via Vector-Quantized Autoencoders
Peng, H., Liu, W., Cai, Y., Li, W., Zhang, Y., Guan, J., & Zhou, S. (2026) · ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD) · doi:10.1145/3770855.3818995
Lu, X., Zhao, G., Tang, Y., Li, F., & Cheng, M. M. H. (2026) · Current Proteomics · doi:10.1016/j.curpro.2026.100139
Lee, A., Neehus, A., Wahlster, L., Agarwal, G., Weng, C., Zhang, A., Liu, T., Shelton, S. D., Ye, T., della Volpe, L., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.06.743308
scAmp enables focal gene amplification analysis from single-cell data
Jones, M. G., Weiser, N. E., Hung, K. L., Yan, X., Agarwal, S., Luebeck, J., Gnanasekar, A., Zhang, S., Wong, I. T.-L., Tang, J., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-76417-3
Self-citationAggarwal, V., Sun, Y., Liu, C., Cui, J., Manne, S., Dou, Y., Chen, Q., Brunazzi, E. A., Vignali, K. M., Wang, H., et al. (2026) · The Journal of Experimental Medicine · doi:10.1084/jem.20241968
Epigenetic reprogramming in autoimmune and immune-mediated skin disease
Bilik, S. M., Kraft, G., Sharifi, I., Hanly‐Jorda, F. M., Antonevich, S., Jimenez, J. J., & Satoh, T. K. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1915200
A multi-layer framework for computational cancer epigenomics
Srivastava, M., Kumar, P., Chouhan, A., Maan, K., Singh, S., Banerjee, M., & Kushwah, A. S. (2026) · Academia molecular biology and genomics. · doi:10.20935/acadmolbiogen8483
Zevounou, J., Lo, K. S., McGinnis, C. S., Satpathy, A. T., & Lettre, G. (2026) · Biochemistry and Biophysics Reports · doi:10.1016/j.bbrep.2026.102786
Self-citationBai, Y., & Lu, Z. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1955428
Qu, Y., Sun, J., Wang, Z., Sun, Q., & Zhou, Y. (2026) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2026.189717
Unifying multimodal single-cell data with a mixture-of-experts β-variational autoencoder frameworkPreprint
Ashford, A. J., Enright, T., Somers, J., Nikolova, O. H., & Demir, E. (2026) · Genome Research · doi:10.1101/gr.281431.125
Metadata
- Authors
- Satpathy, A. T., Granja, J. M., Yost, K. E., Qi, Y., Meschi, F., McDermott, G. P., Olsen, B. N., Mumbach, M. R., Pierce, S. E., Corces, M. R., Shah, P., Bell, J. C., Jhutty, D., Nemec, C. M., Wang, J., Wang, L., Yin, Y., Giresi, P. G., Chang, A. L. S., Zheng, G. X. Y., Greenleaf, W. J., & Chang, H. Y.
- Affiliations
- Stanford Medicine (US)
- 10X Genomics (United States) (US)
- Chan Zuckerberg Biohub San Francisco (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Zheng, Grace X. Y.
- Greenleaf, William J.
- Chang, Howard Y.
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2019-08
- Volume
- 37
- Issue
- 8
- Pages
- 925-936
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC7299161
- OpenAlex
- W2965985232
- Cited by
- 980
- References
- 86
- Citations by year
- 2026: 121 · 2025: 170 · 2024: 145 · 2023: 162 · 2022: 137 · 2021: 157 · 2020: 75 · 2019: 12
- FWCI
- 33.66
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Locations
- Nature Biotechnology (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (K08CA23188-01, P50HG007735)
- Parker Foundation
- Howard Hughes Medical Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- single-cell ATAC-seq, immune cell development, basal cell carcinoma, tumor microenvironment, T cell exhaustion, CD8+ T cells, enhancer activity, anti-PD-1 therapy, gene regulatory networks, next-generation sequencing
- MeSH terms
- Bone Marrow Cells, Cell Line, Chromatin, Computer Simulation, Gene Expression Regulation, Hematopoiesis, Humans, Leukocytes, Mononuclear, T-Lymphocytes, Transcription Factors, Single-Cell Analysis, High-Throughput Nucleotide Sequencing
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
