Construction of a human cell landscape at single-cell level

Cytoscape: A software Environment for integrated models of biomolecular interaction networks

Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888

STAR: ultrafast universal RNA-seq aligner

Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709

SCANPY: large-scale single-cell gene expression data analysis

Wolf, F. A., Angerer, P., & Theis, F. J. (2018) · Genome Biology · doi:10.1186/s13059-017-1382-0 · Cited by 8,881

Highly 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

Scenic: single-cell regulatory network inference and clustering.

Aibar, S., González-Blas, C. B., Moerman, T., Huynh-Thu, V. A., Imrichova, H., Hulselmans, G., Rambow, F., Marine, J.-C., Geurts, P., Aerts, J., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4463 · Cited by 6,520

The single-cell transcriptional landscape of mammalian organogenesis

Cao, J., Spielmann, M., Qiu, X., Huang, X., Ibrahim, D. M., Hill, A. J., Zhang, F., Mundlos, S., Christiansen, L., Steemers, F. J., et al. (2019) · Nature · doi:10.1038/s41586-019-0969-x · Cited by 4,490

circlize implements and enhances circular visualization in R

Gu, Z., Gu, L., Eils, R., Schlesner, M., & Brors, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu393 · Cited by 4,290

RNA velocity of single cells

La Manno, G., Soldatov, R., Zeisel, A., Braun, E., Hochgerner, H., Petukhov, V., Lidschreiber, K., Kastriti, M. E., Lönnerberg, P., Furlan, A., et al. (2018) · Nature · doi:10.1038/s41586-018-0414-6 · Cited by 4,118

mRNA-Seq whole-transcriptome analysis of a single cell

Tang, F., Barbacioru, C., Wang, Y., Nordman, E., Lee, C., Xu, N., Wang, X., Bodeau, J., Tuch, B. B., Siddiqui, A., et al. (2009) · Nature Methods · doi:10.1038/nmeth.1315 · Cited by 3,969

Pathophysiology and pharmacological management of pulmonary and cardiovascular features of COVID-19

Hamouche, W., Bisserier, M., Brojakowska, A., Eskandari, A., Fish, K. M., Goukassian, D. A., & Hadri, L. (2020) · Journal of Molecular and Cellular Cardiology · doi:10.1016/j.yjmcc.2020.12.009 · Cited by 18

Between Fate Choice and Self-Renewal—Heterogeneity of Adult Neural Crest-Derived Stem Cells

Höving, A. L., Windmöller, B. A., Knabbe, C., Kaltschmidt, B., Kaltschmidt, C., & Greiner, J. F. W. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.662754 · Cited by 18

Thyroid cancer under the scope of emerging technologies

Tarabichi, M., Demetter, P., Craciun, L., Maenhaut, C., & Detours, V. (2021) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2021.111491 · Cited by 18

Spatiotemporal transcriptome atlas of human embryos after gastrulation

Pan, J., Li, Y., Lin, Z., Lan, Q., Zhang, Y., Chen, H., Sui, S., Zhai, M., Zhang, G., Cheng, Y., et al. (2026) · Nature · doi:10.1038/s41586-026-10545-0 · Cited by 19

The prospects of tumor chemosensitivity testing at the single-cell level

Yang, C., Yang, C., Yarden, Y., To, K. K. W., & Fu, L. (2020) · Drug Resistance Updates · doi:10.1016/j.drup.2020.100741 · Cited by 16

Single Cell Technologies: Beyond Microfluidics

Li, H., & Humphreys, B. D. (2021) · Kidney360 · doi:10.34067/kid.0001822021 · Cited by 18

PCGA: a comprehensive web server for phenotype-cell-gene association analysis

Xue, C., Jiang, L., Zhou, M., Long, Q., Chen, Y., Li, X., Peng, W., Yang, Q., & Li, M. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac425 · Cited by 16

Approaches to benchmark and characterize in vitro human model systems

Childs, C. J., Eiken, M. K., & Spence, J. R. (2022) · Development · doi:10.1242/dev.200641 · Cited by 17

RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding

Komatsu, J., Cico, A., Poncin, R., Bohec, M. L., Morf, J., Lipin, S., Graindorge, A., Eckert, H., Saffarian, A., Cathaly, L., et al. (2023) · Scientific Reports · doi:10.1038/s41598-023-31915-y · Cited by 17

Structure-preserving visualization for single-cell RNA-Seq profiles using deep manifold transformation with batch-correction

Xu, Y., Zang, Z., Xia, J., Tan, C., Geng, Y., & Li, S. Z. (2023) · Communications Biology · doi:10.1038/s42003-023-04662-z · Cited by 17

VT3D: a visualization toolbox for 3D transcriptomic data

Guo, L., Li, Y., Qi, Y., Huang, Z., Han, K., Liu, X., Liu, X., Xu, M., & Fan, G. (2023) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2023.04.001 · Cited by 17

A Framework Nucleic Acid-Mediated Multimodal Tandem Multivariate Signal Amplification Strategy for Simultaneous Absolute Quantification of Three Different MicroRNAs in a Single Cell

Xu, C., Chen, S.-Y., Hu, S., Li, R., Zhao, S., & Zhao, J. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.3c01335 · Cited by 17

Single-Cell RNA Sequencing Reveals Smooth Muscle Cells Heterogeneity in Experimental Aortic Dissection

Xu, C., Liu, X., Fang, X., Yu, L., Lau, H. C., Li, D., Liu, X., Li, H., Ren, J., Xu, B., et al. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.836593 · Cited by 18

Deep Learning Applications in Single-Cell Omics Data AnalysisPreprint

Erfanian, N., Heydari, A. A., Picazo, P. I., Derakhshani, A., GhasemiGol, M., Farahpour, M., Nasseri, S., Safarpour, H., & Sahebkar, A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.26.470166 · Cited by 17

Large language model consensus substantially improves the cell type annotation accuracy for scRNA-seq data

Chen, Y., Zhang, X., & Chen, J. (2026) · Communications Biology · doi:10.1038/s42003-026-10420-8 · Cited by 16

Federated Deep Learning Enables Cancer Subtyping by Proteomics

Cai, Z., Boys, E. L., Noor, Z., Aref, A. T., Xavier, D., Lucas, N., Williams, S. G., Koh, J. M. S., Poulos, R. C., Wu, Y., et al. (2025) · Cancer Discovery · doi:10.1158/2159-8290.cd-24-1488 · Cited by 20

Advanced Microfluidics for Single Cell‐Based Cancer Research

Carneiro, A., Palomer, M. A., Esteves, M., Rodrigues, C., Fernandes, J. M., Oliveira, F. A. D. S. D. S., Teixeira, A., Honrado, C., Diéguez, L., Abalde‐Cela, S., et al. (2025) · Advanced Science · doi:10.1002/advs.202500975 · Cited by 17

Modeling the vertebrate regulatory sequence landscape by UUATAC-seq and deep learning

Han, X., Wu, H., Wang, X., Liu, D., Fu, Y., Yang, L. X., Wang, R., Zhang, P., Wang, J., Ma, L., et al. (2025) · Cell · doi:10.1016/j.cell.2025.06.020 · Cited by 16

Multidimensional Immunophenotyping of Intraductal Papillary Mucinous Neoplasms Reveals Novel T Cell and Macrophage Signature

Eckhoff, A. M., Fletcher, A. A., Landa, K., Iyer, M. K., Nussbaum, D. P., Shi, C., Nair, S. K., & Allen, P. J. (2022) · Annals of Surgical Oncology · doi:10.1245/s10434-022-12157-0 · Cited by 16

Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Shen, R., Li, P., Zhang, B., Feng, L., & Cheng, S. (2022) · Journal of Translational Medicine · doi:10.1186/s12967-022-03661-8 · Cited by 16

Single-cell transcriptome analysis reveals the metabolic changes and the prognostic value of malignant hepatocyte subpopulations and predict new therapeutic agents for hepatocellular carcinoma

Han, C., Chen, J., Huang, J., Zhu, R., Zeng, J., Yu, H., & He, Z. (2023) · Frontiers in Oncology · doi:10.3389/fonc.2023.1104262 · Cited by 16

Generation of glucocorticoid-producing cells derived from human pluripotent stem cells

Ruiz‐Babot, G., Eceiza, A., Abollo‐Jiménez, F., Malyukov, M., Carlone, D. L., Borges, K., Costa, A. R. D., Qarin, S., Matsumoto, T., Morizane, R., et al. (2023) · Cell Reports Methods · doi:10.1016/j.crmeth.2023.100627 · Cited by 17

Single‐Cell Transcriptome Landscape and Cell Fate Decoding in Human Brain Organoids after Transplantation

Xu, S., Li, X., Fan, P., Li, X., Hong, Y., Han, X. W., Wu, S., Chu, C., Chen, Y., Xu, M., et al. (2024) · Advanced Science · doi:10.1002/advs.202402287 · Cited by 16

The role of long non‐coding RNA Maternally Expressed Gene 3 in cancer‐associated fibroblasts at single cell pan‐cancer level

Zhou, T., Yan, H., Deng, Y., Zhu, Y., Xia, X., Wu, W., Zhang, W., Chen, H., Hu, J., Zhou, Z., et al. (2024) · Interdisciplinary medicine · doi:10.1002/inmd.20240018 · Cited by 17

Differential transcriptomic landscapes of multiple organs from SARS-CoV-2 early infected rhesus macaques

Gao, C., Li, M., Deng, W., Ma, C., Chen, Y., Sun, Y., Du, T., Liu, Q.-L., Li, W., Zhang, B., et al. (2022) · Protein & Cell · doi:10.1007/s13238-022-00915-5 · Cited by 16

Molecular atlas of the human brain vasculature at the single-cell levelPreprint

Wälchli, T., Ghobrial, M., Schwab, M., Takada, S., Zhong, H., Suntharalingham, S., Vetiska, S., Rodrigues, D. R., Rehrauer, H., Wu, R., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.10.18.464715 · Cited by 16

scLong: a billion-parameter foundation model for capturing long-range gene context in single-cell transcriptomics

Bai, D., Mo, S., Zhang, R., Luo, Y., Gao, J., Yang, J. P., Wu, Q., Rahmani, H., Amariuta, T., Grotjahn, D., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-69102-y · Cited by 15

Challenges and possible solutions for decoding extranasal olfactory receptors

Kalra, S., Mittal, A., Bajoria, M., Mishra, T., Maryam, S., Sengupta, D., & Ahuja, G. (2020) · FEBS Journal · doi:10.1111/febs.15606 · Cited by 15

Mechanisms regulating vascular and lymphatic regeneration in the heart after myocardial infarction

Berkeley, B., Tang, M. N. H., & Brittan, M. (2023) · The Journal of Pathology · doi:10.1002/path.6093 · Cited by 16

GTM-decon: guided-topic modeling of single-cell transcriptomes enables sub-cell-type and disease-subtype deconvolution of bulk transcriptomes

Swapna, L. S., Huang, M., & Li, Y. (2023) · Genome biology · doi:10.1186/s13059-023-03034-4 · Cited by 14

Sparse and Hierarchical Transformer for Survival Analysis on Whole Slide Images

Yan, R., Lv, Z., Yang, Z., Lin, S., Zheng, C.-H., & Zhang, F. (2023) · IEEE Journal of Biomedical and Health Informatics · doi:10.1109/jbhi.2023.3307584 · Cited by 16

Generating bulk RNA-Seq gene expression data based on generative deep learning models and utilizing it for data augmentation

Wang, Y., Chen, Q., Shao, H., Zhang, R., & Shen, H. (2023) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2023.107828 · Cited by 18

DANCE: a deep learning library and benchmark platform for single-cell analysis

Ding, J., Liu, R., Wen, H., Tang, W., Li, Z., Venegas, J., Su, R., Molho, D., Jin, W., Wang, Y., et al. (2024) · Genome biology · doi:10.1186/s13059-024-03211-z · Cited by 18

SIMS: A deep-learning label transfer tool for single-cell RNA sequencing analysis

Gonzalez-Ferrer, J., Lehrer, J., O’Farrell, A., Paten, B., Teodorescu, M., Haussler, D. H., Jönsson, V. D., & Mostajo-Radji, M. A. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100581 · Cited by 16

Predicting the structural impact of human alternative splicing

Song, Y., Zhang, C., Omenn, G. S., O’Meara, M. J., & Welch, J. D. (2025) · Genome biology · doi:10.1186/s13059-025-03744-x · Cited by 16

Identification and Comprehensive Validation of a DNA Methylation-Driven Gene-Based Prognostic Model for Clear Cell Renal Cell Carcinoma

Zhang, D., Wang, Y., & Hu, X. (2020) · DNA and Cell Biology · doi:10.1089/dna.2020.5601 · Cited by 17

Cellular Tropism of SARS-CoV-2 across Human Tissues and Age-related Expression of ACE2 and TMPRSS2 in Immune-inflammatory Stromal Cells

Zheng, M. (2021) · Aging and Disease · doi:10.14336/ad.2021.0429 · Cited by 16

High-Dimensional Single-Cell Transcriptomics in Melanoma and Cancer Immunotherapy

Quek, C. Y. J., Bai, X., Long, G. V., Scolyer, R. A., & Wilmott, J. S. (2021) · Genes · doi:10.3390/genes12101629 · Cited by 16

Identification of the Thyrotropin-Releasing Hormone (TRH) as a Novel Biomarker in the Prognosis for Acute Myeloid Leukemia

Gao, Y., Zhou, J., Mao, J., Jiang, L., & Li, X. (2022) · Biomolecules · doi:10.3390/biom12101359 · Cited by 15

Lymphoma Heterogeneity Unraveled by Single-Cell Transcriptomics

Ysebaert, L., Quillet‐Mary, A., Tosolini, M., Pont, F., Laurent, C., & Fournié, J. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.597651 · Cited by 15

Concerted changes in Epithelium and Stroma: a multi-scale, multi-omics analysis of progression from Barrett’s Esophagus to adenocarcinoma

Strasser, M. K., Gibbs, D. L., Gascard, P. D., Bons, J., Hickey, J. W., Pan, D., Caruso, J. A., Wang, X., Chen‐Tanyolac, C., Bai, R., et al. (2025) · Developmental Cell · doi:10.1016/j.devcel.2025.06.034 · Cited by 39

Single-cell RNA Sequencing Reveals How the Aryl Hydrocarbon Receptor Shapes Cellular Differentiation Potency in the Mouse Colon

Yang, Y., Osorio, D., Davidson, L. A., Han, H., Mullens, D. A., Jayaraman, A., Safe, S. H., Ivanov, I. V., Cai, J. J., & Chapkin, R. S. (2021) · Cancer Prevention Research · doi:10.1158/1940-6207.capr-21-0378 · Cited by 14

Sterile Pancreas Inflammation during Preservation and after Transplantation

Kervella, D., Mesnard, B., Prudhomme, T., Bruneau, S., Masset, C., Cantarovich, D., Blancho, G., & Branchereau, J. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24054636 · Cited by 17

Biomarkers of reproductive health in wildlife and techniques for their assessment

Ghosal, R., Edwards, K. L., Chiarelli, T. L., Fanson, K. V., Ganswindt, A., Keeley, T., Koester, D. C., Roberts, B. M., Majelantle, T. L., Wauters, J., et al. (2023) · Theriogenology Wild · doi:10.1016/j.therwi.2023.100052 · Cited by 16

Microfluidic characterization of single‐cell biophysical properties and the applications in cancer diagnosis

Li, S., Xue, C., Li, Y., Chen, X., Zhao, Y., & Qin, K. (2023) · Electrophoresis · doi:10.1002/elps.202300177 · Cited by 14

Identification of Therapy-Induced Clonal Evolution and Resistance Pathways in Minimal Residual Clones in Multiple Myeloma through Single-Cell Sequencing

Cui, J., Li, X., Deng, S., Du, C., Fan, H., Yan, W., Xu, J., Li, X., Yu, T., Zhang, S., et al. (2024) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-24-0545 · Cited by 18

Single-cell sequencing in diabetic retinopathy: progress and prospects

Yang, T., Zhang, N., & Yang, N. (2025) · Journal of Translational Medicine · doi:10.1186/s12967-024-06066-x · Cited by 15

Single-cell transcriptome atlas of lamprey exploring Natterin- induced white adipose tissue browning

Pang, Y., Qin, Y., Du, Z., Liu, Q., Zhang, J., Han, K., Lu, J., Yuan, Z., Li, J., Pan, S., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-56153-w · Cited by 14

scCobra allows contrastive cell embedding learning with domain adaptation for single cell data integration and harmonization

Zhao, B., Song, K., Wei, D., Xiong, Y., & Ding, J. (2025) · Communications Biology · doi:10.1038/s42003-025-07692-x · Cited by 18

Dissection of single-cell landscapes for the development of chimeric antigen receptor T cells in Hodgkin lymphoma

Gottschlich, A., Grünmeier, R., Hoffmann, G. V., Nandi, S., Kavaka, V., Müller, P. J., Jobst, J., Öner, A., Kaiser, R. W. J., Gärtig, J., et al. (2025) · Blood · doi:10.1182/blood.2023022197 · Cited by 15

Gene expression rearrangements denoting changes in the biological state

Gonzalez, A., Nieves, J., Leon, D. A., Vega, M. L. B., & Sosa, P. V. (2021) · Scientific Reports · doi:10.1038/s41598-021-87764-0 · Cited by 14

CoolMPS for robust sequencing of single-nuclear RNAs captured by droplet-based method

Hahn, O., Fehlmann, T., Zhang, H., Munson, C. N., Vest, R. T., Borcherding, A., Liu, S., Villarosa, C., Drmanac, S., Drmanac, R., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1127 · Cited by 16

Contemplating Dichotomous Nature of Gamma Delta T Cells for Immunotherapy

Bhat, J., Placek, K., & Faissner, S. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.894580 · Cited by 14

Addressing Cellular Heterogeneity in Cancer through Precision Proteomics

Waas, M., & Kislinger, T. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00338 · Cited by 13

The Good, The Bad and The Ugly: A Mathematical Model Investigates the Differing Outcomes Among CoVID-19 Patients

Sahoo, S., Hari, K., Jhunjhunwala, S., & Jolly, M. K. (2020) · Journal of the Indian Institute of Science · doi:10.1007/s41745-020-00205-1 · Cited by 22

Single-Cell RNA Sequencing Reveals Thoracolumbar Vertebra Heterogeneity and Rib-Genesis in Pigs

Li, J., Wang, L., Yu, D., Hao, J., Zhang, L., Adeola, A. C., Mao, B., Gao, Y., Wu, S., Zhu, C., et al. (2021) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2021.09.008 · Cited by 14

ELeFHAnt: A supervised machine learning approach for label harmonization and annotation of single cell RNA-seq dataPreprint

Thorner, K., Zorn, A. M., & Chaturvedi, P. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.09.07.459342 · Cited by 14

Deep learning using bulk RNA-seq data expands cell landscape identification in tumor microenvironment

Wang, X., Wang, H., Liu, D., Wang, N., He, D., Wu, Z., Zhu, X., Wen, X., Li, X., Li, J., et al. (2022) · OncoImmunology · doi:10.1080/2162402x.2022.2043662 · Cited by 13

Notch3 directs differentiation of brain mural cells from human pluripotent stem cell–derived neural crest

Gastfriend, B. D., Snyder, M. E., Holt, H., Daneman, R., Palecek, S. P., & Shusta, E. V. (2024) · Science Advances · doi:10.1126/sciadv.adi1737 · Cited by 16

Single-cell atlas of rainbow trout peripheral blood leukocytes and profiling of their early response to infectious pancreatic necrosis virus

Perdiguero, P., Jiménez‐Barrios, P., Morel, E., Abós, B., & Tafalla, C. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1404209 · Cited by 12

aKNNO: single-cell and spatial transcriptomics clustering with an optimized adaptive k-nearest neighbor graph

Li, J., Shyr, Y., & Liu, Q. (2024) · Genome biology · doi:10.1186/s13059-024-03339-y · Cited by 17

Clinical cell-surface targets in metastatic and primary solid cancers

Sharifi, M. N., Shi, Y., Chrostek, M. R., Callahan, S. C., Shang, T. A., Berg, T. J., Helzer, K. T., Bootsma, M. L., Sjöström, M., Josefsson, A., et al. (2024) · JCI Insight · doi:10.1172/jci.insight.183674 · Cited by 13

Connectivity Map Analysis of a Single-Cell RNA-Sequencing -Derived Transcriptional Signature of mTOR Signaling

Mahi, N. A., Zhang, E. Y., Sherman, S. G., Yu, J. J., & Medvedovic, M. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22094371 · Cited by 13

New insights empowered by single-cell sequencing: From neural crest to enteric nervous system

Li, Z., & Ngan, E. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.05.025 · Cited by 11

Unique expression of the atypical mitochondrial subunit NDUFA4L2 in cerebral pericytes fine tunes HIF activity in response to hypoxia

Mesa‐Ciller, C., Turiel, G., Guajardo-Grence, A., López-Rodríguez, A. B., Egea, J., Bock, K. D., Aragonés, J., & Urrutia, A. A. (2022) · Journal of Cerebral Blood Flow & Metabolism · doi:10.1177/0271678x221118236 · Cited by 13

CaSee: A lightning transfer-learning model directly used to discriminate cancer/normal cells from scRNA-seq

Shi, H., Zhang, X., Yang, Z., Dong, J., Wang, Y., Zhou, Y., Li, X., Guo, C., & Hu, Z. (2022) · Oncogene · doi:10.1038/s41388-022-02478-5 · Cited by 13

scAnno: a deconvolution strategy-based automatic cell type annotation tool for single-cell RNA-sequencing data sets

Liu, H., Li, H., Sharma, A., Huang, W., Pan, D., Gu, Y., Lin, L., Sun, X., & Liu, H. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad179 · Cited by 14

An analytical framework for decoding cell type-specific genetic variation of gene regulation

Xiao, Y., Wang, J., Li, J., Zhang, P., Li, J., Zhou, Y., Zhou, Q., Chen, M., Sheng, X., Liu, Z., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39538-7 · Cited by 13

Single-cell assignment using multiple-adversarial domain adaptation network with large-scale references

Ren, P., Shi, X., Yu, Z., Dong, X., Ding, X., Wang, J., Sun, L., Yan, Y., Hu, J., Zhang, P., et al. (2023) · Cell Reports Methods · doi:10.1016/j.crmeth.2023.100577 · Cited by 13

Stable Long-Term Culture of Human Distal Airway Stem Cells for Transplantation

Zhou, Y., Wang, Y., Li, D., Zhang, T., Ma, Y., & Zuo, W. (2021) · Stem Cells International · doi:10.1155/2021/9974635 · Cited by 13

Obesity-instructed TREM2 high macrophages identified by comparative analysis of diabetic mouse and human kidney at single cell resolutionPreprint

Subramanian, A., Vernon, K. A., Zhou, Y., Marshall, J. L., Alimova, M., Zhang, F., Slyper, M., Waldman, J., Montesinos, M. S., Dionne, D. A., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.30.446342 · Cited by 14

Single-cell analysis reveals novel clonally expanded monocytes associated with IL1β–IL1R2 pair in acute inflammatory demyelinating polyneuropathy

Li, M., Song, J., Yin, P., Chen, H., Wang, Y.-J., Xu, C., Jiang, F., Wang, H., Han, B., Du, X., et al. (2023) · Scientific Reports · doi:10.1038/s41598-023-32427-5 · Cited by 12

NMI Functions as Immuno-regulatory Molecule in Sepsis by Regulating Multiple Signaling Pathways

Zeng, J., Yang, Z., Xu, D., Song, J., Liu, Y., Qin, J., & Weng, Z. (2023) · Inflammation · doi:10.1007/s10753-023-01893-4 · Cited by 12

Single-cell profiling of the pig cecum at various developmental stages

Xiao, Y., 江西农业大学猪遗传改良与种质创新全国重点实验室, 江. 南. 3., Zhang, Q., Huang, F., Rao, L., Yao, T., Yang, S., Xie, L., Zou, X.-X., Cai, L., et al. (2023) · 动物学研究 · doi:10.24272/j.issn.2095-8137.2023.007 · Cited by 13

Housekeeping protein-coding genes interrogated with tissue and individual variations

Tung, K.-F., Pan, C., & Lin, W. (2024) · Scientific Reports · doi:10.1038/s41598-024-63269-4 · Cited by 12

Peroxisome proliferator–activated receptor delta and liver diseases

Yamazaki, T., Cable, E. E., & Schnabl, B. (2025) · Hepatology Communications · doi:10.1097/hc9.0000000000000646 · Cited by 14

Cross-species imputation and comparison of single-cell transcriptomic profiles

Zhang, R., Yang, M., Schreiber, J. M., O’Day, D. R., Turner, J. M. A., Shendure, J., Distèche, C. M., Deng, X., & Noble, W. S. (2025) · Genome biology · doi:10.1186/s13059-025-03493-x · Cited by 13

scCompass: An Integrated Multi‐Species scRNA‐seq Database for AI‐Ready

Wang, P., Liu, W., Wang, J., Liu, Y., Li, P., Xu, P., Cui, W., Zhang, R., Long, Q., Hu, Z., et al. (2025) · Advanced Science · doi:10.1002/advs.202500870 · Cited by 17

Tissue-resident lymphocytes: weaponized sentinels at barrier surfaces

Belz, G. T., Denman, R., Seillet, C., & Jacquelot, N. (2020) · F1000Research · doi:10.12688/f1000research.25234.1 · Cited by 12

Single-Cell Analysis for Whole-Organism Datasets

Pisco, A. O., Tojo, B. M., & McGeever, A. (2021) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-092820-031008 · Cited by 11

The molecular and phenotypic makeup of fetal human skin T lymphocytes

Reitermaier, R., Ayub, T., Staller, J., Kienzl, P., Fortelny, N., Vieyra-Garcia, P. A., Worda, C., Fiala, C., Staud, C. J., Eppel, W., et al. (2021) · Development · doi:10.1242/dev.199781 · Cited by 12

The differential activity of biological processes in tissues and cell subsets can illuminate disease-related processes and cell-type identities

Sharon, M., Vinogradov, E., Argov, C. M., Lazarescu, O., Zoabi, Y., Hekselman, I., & Yeger‐Lotem, E. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btab883 · Cited by 12

Single-cell RNA sequencing revealed the liver heterogeneity between egg-laying duck and ceased-laying duck

Du, X., Lai, S., Zhao, W., Xu, X., Xu, W., Zeng, T., Tian, Y., & Lu, L. (2022) · BMC Genomics · doi:10.1186/s12864-022-09089-0 · Cited by 14

Single-Cell Analysis of the Adult Human Heart Across Health and Cardiovascular Disease Reveals the Cellular Landscape Underlying SARS-CoV-2 Invading Myocardial Tissue Through ACE2

Chen, C., Wang, J., Liu, Y., & Hu, J. J. (2022) · Journal of Translational Medicine · doi:10.1186/s12967-023-04224-1 · Cited by 13

Multi-batch single-cell comparative atlas construction by deep learning disentanglement

Lynch, A. W., Brown, M. A., & Meyer, C. A. (2023) · Nature Communications · doi:10.1038/s41467-023-39494-2 · Cited by 11

SLIT3-mediated fibroblast signaling: a promising target for antifibrotic therapies

Gong, L., & Si, M. (2023) · American Journal of Physiology-Heart and Circulatory Physiology · doi:10.1152/ajpheart.00216.2023 · Cited by 11

Single‐Cell RNA Sequencing for Precision Oncology: Current State-of-Art

Seow, J. J. W., Wong, R. M. M., Pai, R., & Sharma, A. (2020) · Journal of the Indian Institute of Science · doi:10.1007/s41745-020-00178-1 · Cited by 11

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

Analysis of the Tropism of SARS-CoV-2 Based on the Host Interactome of the Spike Protein

Bamberger, C., Pankow, S., Martínez‐Bartolomé, S., Diedrich, J. K., Park, S. K. R., & Yates, J. R. (2023) · Journal of Proteome Research · doi:10.1021/acs.jproteome.3c00387 · Cited by 12

The Host Interactome of Spike Expands the Tropism of SARS-CoV-2Preprint

Bamberger, C., Pankow, S., Martínez‐Bartolomé, S., Diedrich, J. K., Park, S. K. R., & Yates, J. R. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.16.431318 · Cited by 12

Mate-pair genome sequencing reveals structural variants for idiopathic male infertility

Dong, Z., Qian, J., Law, T. S. M., Chau, M. H. K., Cao, Y., Xue, S., Tong, S., Zhao, Y., Kwok, Y. K. Y., Ng, K., et al. (2022) · Human Genetics · doi:10.1007/s00439-022-02510-4 · Cited by 11

Single-Cell RNA-Sequencing Analysis of Colonic Lamina Propria Immune Cells Reveals the Key Immune Cell-Related Genes of Ulcerative Colitis

Hua, R., Qiao, G., Chen, G., Sun, Z., Jia, H., Li, P., Zhang, B., & Qi, F. (2023) · Journal of Inflammation Research · doi:10.2147/jir.s440076 · Cited by 11

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

The BulkECexplorer compiles endothelial bulk transcriptomes to predict functional versus leaky transcription

Brash, J. T., Diez-Pinel, G., Colletto, C., Castellan, R. F. P., Fantin, A., & Ruhrberg, C. (2024) · Nature Cardiovascular Research · doi:10.1038/s44161-024-00436-w · Cited by 10

A single-cell atlas of chromatin accessibility in mouse organogenesis

Sun, K., Liu, X., & Lan, X. (2024) · Nature Cell Biology · doi:10.1038/s41556-024-01435-6 · Cited by 11

The landscape of malignant transition: Unraveling cancer cell-of-origin and heterogeneous tissue microenvironment

Luo, R., Liu, J., Wang, T., Zhao, W., Wang, Y., Wen, J., Wang, H., Ding, S., & Zhou, X. (2025) · Cancer Letters · doi:10.1016/j.canlet.2025.217591 · Cited by 13

Kidney-resident macrophages limit toxin-induced inflammation through their hallmark functions

Hong, M., Yun, D., Hwang, J., Kang, C., Yoon, H., Shin, S.-K., Jang, B., Oh, J., Park, P. G., Shin, H. M., et al. (2025) · Kidney International · doi:10.1016/j.kint.2025.07.022 · Cited by 12

Construction of a Multitissue Cell Atlas Reveals Cell‐Type‐Specific Regulation of Molecular and Complex Phenotypes in Pigs

Chen, L., Li, H., Teng, J., Wang, Z., Qu, X., Chen, Z., Cai, X., Zeng, H., Bai, Z., Li, J., et al. (2025) · Advanced Science · doi:10.1002/advs.202504961 · Cited by 16

Automated and Dynamic Control of Chemical Content in Droplets for Scalable Screens of Small Animals

Aubry, G., Milisavljevic, M., & Lu, H. (2022) · Small · doi:10.1002/smll.202200319 · Cited by 11

KIF2C affects sperm cell differentiation in patients with Klinefelter syndrome, as revealed by RNA‐Seq and scRNA‐Seq data

He, H., Huang, T., Yu, F., Chen, K., Guo, S., Zhang, L., Tang, X., Yuan, X., Liu, J., & Zhou, Y. (2022) · FEBS Open Bio · doi:10.1002/2211-5463.13446 · Cited by 11

Charting the human cell landscape

Tang, L. (2020) · Nature Methods · doi:10.1038/s41592-020-0834-8

Single-cell atlases: shared and tissue-specific cell types across human organs

Elmentaite, R., Conde, C. D., Yang, L., & Teichmann, S. A. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00449-w · Cited by 174

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

The Tabula Sapiens Consortium*, Jones, R. C., Karkanias, J., Krasnow, M. A., Pisco, A. O., Quake, S. R., Salzman, J., Yosef, N., Bulthaup, B., Brown, P., et al. (2022) · Science · doi:10.1126/science.abl4896 · Cited by 1,056

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

Islam, S., Kjällquist, U., Moliner, A., Zajac, P., Fan, J.-B., Lönnerberg, P., & Linnarsson, S. (2011) · Genome Research · doi:10.1101/gr.110882.110 · Cited by 949

Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs

He, S., Wang, L.-H., Liu, Y., Li, Y., Chen, H.-T., Xu, J.-H., Peng, W., Lin, G.-W., Wei, P.-P., Li, B., et al. (2020) · Genome biology · doi:10.1186/s13059-020-02210-0 · Cited by 237