Construction of a human cell landscape at single-cell level

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The single-cell transcriptional landscape of mammalian organogenesis

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RNA velocity of single cells

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mRNA-Seq whole-transcriptome analysis of a single cell

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Spatial transcriptomic analyses highlight distinct erythroid niches in mice and humans

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RefTM: reference-guided topic modeling of single-cell chromatin accessibility data

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Tumor-derived Endothelial Cell: Important Etiological Factors in Endometriosis

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New generative methods for single-cell transcriptome data in bulk RNA sequence deconvolution

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SinCWIm: An imputation method for single-cell RNA sequence dropouts using weighted alternating least squares

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Peripheral mononuclear cells and systemic lupus erythematosus association: Integrated study of single-cell sequencing and mendelian randomization analysis

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The pan-cancer landscape of aldo-keto reductase1B10 reveals that its expression is diminished in gastric cancer

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scMoE: single-cell mixture of experts for learning hierarchical, cell-type-specific, and interpretable representations from heterogeneous scRNA-seq data

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PreDigs: A Database of Context-specific Cell Type Markers and Precise Cell Subtypes for Digestive Cell Annotation

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Full-length spatial transcriptome strategy based on robust and low-cost target tissue capture

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Decoding cell fate: integrated experimental and computational analysis at the single-cell level

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Deconvolution of Focal Segmental Glomerulosclerosis Pathophysiology Using Transcriptomics Techniques

Deleersnijder, D., Craenenbroeck, A. H. V., & Sprangers, B. (2021) · Glomerular Diseases · doi:10.1159/000518404 · Cited by 4

Single cell and immunity: Better understanding immune cell heterogeneities with single‐cell sequencing

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Hypoxia controls expression of kidney-pathogenic MUC1 variants

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Understanding Macrophage‐Tumor Interactions: Insights from Single‐Cell Behavior Monitoring in a Sessile Microdroplet System

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Single-cell analysis reveals conserved regulons shaping muscle stem cell behavior during development and aging in mammals

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Prognostic prediction and immune infiltration analysis based on lysosome and senescence state identifies MMP12 as a novel therapy target in gastric cancer

He, K., & Gong, G. (2024) · International Immunopharmacology · doi:10.1016/j.intimp.2024.113344 · Cited by 3

SIngle cell level Genotyping Using scRna Data (SIGURD)

Graßhoff, M., Kalmer, M., Chatain, N., Kricheldorf, K., Maurer, A., Weiskirchen, R., Koschmieder, S., & Costa, I. G. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae604 · Cited by 3

Comparative evaluation of ACetic - MEthanol high salt dissociation approach for single-cell transcriptomics of frozen human tissues

Utkina, M. V., Shcherbakova, A. S., Deviatiiarov, R. M., Ryabova, A., Loguinova, M. Y., Trofimov, V., Kuznetsova, A. A., Petropavlovskiy, M., Salimkhanov, R. K., Maksimov, D. O., et al. (2025) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2024.1469955 · Cited by 4

Next-Generation Barcoding for Single-Cell Omics

Li, T., Gu, Z., & Zhou, G. (2025) · Analytical Chemistry · doi:10.1021/acs.analchem.5c03587 · Cited by 3

Bioinformatics mining for gene expression data

Guo, A. (2020) · Scientia Sinica Vitae · doi:10.1360/ssv-2020-0260 · Cited by 3

Insights from Initial Variant Detection by Sequencing Single Sperm in Cattle

Yang, L., Gao, Y., Boschiero, C., Li, L., Zhang, H., Ma, L., & Liu, G. E. (2021) · Dairy · doi:10.3390/dairy2040050 · Cited by 3

Characterizing collaborative transcription regulation with a graph-based deep learning approach

Zhang, Z., Feng, F., Yao, Y., & Liu, J. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010162 · Cited by 3

Peripheral Blood Transcripts Predict Preoperative Obstructive Total Anomalous Pulmonary Venous Connection

Wan, Z., Li, X., Sun, J., Li, X., Liu, Z., Dong, H., Zhou, Q., Qiu, H., Xu, J., Yang, T., et al. (2022) · Frontiers in Cardiovascular Medicine · doi:10.3389/fcvm.2022.892000 · Cited by 3

Kidney Development: Recent Insights from Technological Advances

Röck, R., Rizzo, L., & Lienkamp, S. S. (2022) · Physiology · doi:10.1152/physiol.00041.2021 · Cited by 4

How developmental cell atlases inform stem cell embryo models

Haniffa, M. A., Maartens, A. P., & Teichmann, S. A. (2023) · Nature Methods · doi:10.1038/s41592-023-02072-x · Cited by 3

Deterministic scRNA-seq of individual intestinal organoids reveals new subtypes and coexisting distinct stem cell poolsPreprint

Bues, J., Biočanin, M., Pezoldt, J., Dainese, R., Chrisnandy, A., Rezakhani, S., Saelens, W., Gardeux, V., Gupta, R., Russeil, J., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.19.103812 · Cited by 3

Human Developmental Cell Atlas: milestones achieved and the roadmap aheadPreprint

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Single nucleus pituitary transcriptomic and epigenetic landscape reveals human stem cell heterogeneity with diverse regulatory mechanismsPreprint

Zhang, Z., Zamojski, M., Smith, G. R., Willis, T. L., Yianni, V., Mendelev, N., Pinças, H., Seenarine, N., Amper, M. A. S., Vasoya, M., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.06.18.449034 · Cited by 3

Hematopoiesis at single cell resolution spanning human development and maturationPreprint

Li, H., Ezike, J., Afanassiev, A., Greenstreet, L., Zhang, S. X., Whangbo, J., Butty, V. L., Moiso, E., Connelly, G. G., Morris, V., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.25.457678 · Cited by 4

Single-cell transcriptomic analysis unveils spinal motor neuron subtype diversity underpinning the water-to-land transition in vertebratesPreprint

Liau, E. S., Jin, S., Chen, Y., Liu, W.-S., Yong, L. W., Tsai, C.-T., Calon, M., Yu, J., Su, Y., Nedelec, S., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.09.29.462340 · Cited by 3

Embryoid bodies facilitate comparative analysis of gene expression in humans and chimpanzees across dozens of cell typesPreprint

Barr, K., Rhodes, K., & Gilad, Y. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.20.500831 · Cited by 3

Platform-Agnostic CellNet (PACNet) enables cross-study meta-analysis of cell fate engineering protocolsPreprint

Lo, E. K. W., Velazquez, J. J., Peng, D., Kwon, C., Ebrahimkhani, M. R., & Cahan, P. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.09.07.506886 · Cited by 3

How CRISPR Is Revolutionizing the Generation of New Models for Cancer ResearchPreprint

Rivera, F. J. S., & Dow, L. E. (2023) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a041384 · Cited by 4

ProjectSVR: Mapping single-cell RNA-seq data to reference atlases by supported vector regressionPreprint

Gao, J., Guo, S., & Zhang, Y.-W. (2023) · bioRxiv · doi:10.1101/2023.07.31.551202 · Cited by 6

Decoding cell identity with multi-scale explainable deep learningPreprint

Zhu, J., Zhang, Z., Xiang, Y., Xie, B., Dong, X., Xie, L., Zhou, P., Yao, R., Wang, X., Li, Y., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.05.578922 · Cited by 3

A spatial single-cell type multiplex map of human spermatogenesisPreprint

Hikmet, F., Méar, L., Gustavsson, J., Miranda, G., Zhang, C., Katona, B., Schutten, R., Oksvold, P., von Feilitzen, K., Forsberg, M., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.21.619380 · Cited by 3

Atrophy in multiple system atrophy relates to mitochondrial and oligodendrocytic processesPreprint

Chougar, L., Tremblay, C., Delva, A., Filiatrault, M., Vo, A., Hansen, J. Y., Farahani, A., Mišić, B., Khalafi, P., Castonguay, C.-E., et al. (2025) · medRxiv · doi:10.1101/2025.01.22.25320961 · Cited by 3

Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate pathogenic variants in age-related macular degenerationPreprint

Wang, S. K., Li, J., Nair, S., Korasaju, R., Chen, Y., Zhang, Y., Kundaje, A. B., Liu, Y., Wang, N., & Chang, H. Y. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.03.21.644670 · Cited by 3

A stem cell knockout village reveals lineage rewiring and a non-canonical islet cell fate in monogenic diabetesPreprint

Liu, D., Song, B., Li, Z., Zhang, S., Fabiha, T., Zhao, J., Inoki, A., Piccand, J., Soh, C.-L., Dixon, G., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.23.696311 · Cited by 4

Decipher the single-cell level responses to chemotherapy in pancreatic ductal adenocarcinoma by a cross-time context graph model

Li, X., Liu, Y., Zhou, F., Guo, W., Chen, G., Tao, J., Huang, J., Qiu, J., Chen, H., Ren, B. X., et al. (2025) · Cancer Letters · doi:10.1016/j.canlet.2025.217751 · Cited by 4

The role of single cell transcriptomics for efficacy and toxicity profiling of chimeric antigen receptor (CAR) T cell therapies

Thomas, M., Brabenec, R., Gregor, L., Andreu-Sanz, D., Carlini, E., Müller, P. J., Gottschlich, A., Simnica, D., Kobold, S., & Marr, C. (2025) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2025.110332 · Cited by 2

Dissecting cross‐lineage tumourigenesis under p53 inactivation through single‐cell multi‐omics and spatial transcriptomics

Wang, X., Mei, Y., Wang, X., Wu, H., Wang, R., Zhang, P., Zhang, G., Li, J., Jiang, M., Fang, X., et al. (2025) · Clinical and Translational Medicine · doi:10.1002/ctm2.70461 · Cited by 3

Network based simultaneous embedding of cells and marker genes from scRNA-seq studies

Bhattacharya, N., Chakraborti, S., Kumari, S., Mathew, B., Halder, A., Gujral, S., Gupta, K., Mittal, A., Sinha, D., Nelson, C. C., et al. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf537 · Cited by 2

Single cell omics identify an anti-inflammatory niche in macrophages of mild to moderate chronic obstructive pulmonary disease

Lv, B., Jiang, M., Zhang, G., Guo, D., Yu, J., Fang, X., Haoyu, T., Guo, H., Han, Y., Guo, Y., et al. (2025) · American Journal of Respiratory Cell and Molecular Biology · doi:10.1165/rcmb.2025-0134oc · Cited by 3

ProjectSVR: mapping single-cell RNA-seq data to reference atlases by supported vector regression

Gao, J., Fang, J., Zhu, Q., Li, G., Bi, Z., Hu, Y., Hong, B., Zhang, Y., Guo, S., & Wang, H. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf586 · Cited by 6

A systematic characterization of fibroblast subtypes and heterogeneity

Zhu, X. H., Kang, H., Zhao, Z., & Jia, P. (2025) · iScience · doi:10.1016/j.isci.2025.113915 · Cited by 2

ADAM5 is required for sperm-zona pellucida binding and sperm oviduct migration

Mashiko, D., Tonai, S., & Ikawa, M. (2025) · Biology of Reproduction · doi:10.1093/biolre/ioaf254 · Cited by 2

Integrative analysis of non-small cell lung cancer identifies Jumonji domain-containing 6/ETS homologous factor axis as a target to overcome radioresistance

Wang, M., Xu, L., Alu, A., Li, P., Liu, J., Chen, S., He, X., Han, X., Li, Y., Pu, Q., et al. (2025) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-025-02471-w · Cited by 2

MRI-derived atrophy in multiple system atrophy aligns with mitochondrial and glial gene expression patterns

Chougar, L., Tremblay, C., Delva, A., Filiatrault, M., Vo, A., Hansen, J. Y., Farahani, A., Mišić, B., Khalafi, P., Castonguay, C.-E., et al. (2025) · npj Parkinson s Disease · doi:10.1038/s41531-025-01227-1 · Cited by 5

Anti-TLR2 immunotherapy modulates neuron-to-oligodendrocyte propagation of α-synuclein in mouse and human models

Bae, E.-J., Ham, S., Jeong, Y. W., Yang, W. S., Shin, J., Lee, W.-J., Ahn, W. J., Yoon, Y.-S., Lee, H.-J., Lee, S. H., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-68870-x · Cited by 2

Dynamic lung single-cell atlas of domesticated and wild pigs

Huang, F., & Xiao, Y. (2026) · Science China Life Sciences · doi:10.1007/s11427-025-3150-6 · Cited by 3

circPLEKHM1 promotes tumor growth and metastasis through enhancing FXR1-mediated protein translation in PDAC

Yang, Y., Zhang, L., Gao, L., Ming, Y., Zhang, T., Ye, Z., Liu, W. K., Xiong, Q., Xu, X., Xu, F., et al. (2026) · Cancer Letters · doi:10.1016/j.canlet.2026.218414 · Cited by 2

Comprehensive Analysis of the Roles of the CCDC Protein Family Play in a Range of 58 Disease Processes

Jiang, S., Leng, P., Li, Y., Song, L., Xu, X., & Yang, L. (2026) · Applied Biochemistry and Biotechnology · doi:10.1007/s12010-026-05655-4 · Cited by 2

Family single-cell atlases reveal pig pregnancy and fetal growth restriction critical cell types

Cai, L., Zhang, Q., Yao, T., Zou, X., Xie, L., Yang, S., Xiao, Y., Huang, F., Peng, Z., Yang, J., et al. (2026) · Science · doi:10.1126/science.adu7265 · Cited by 2

AICellType: a large language model-based platform for accurate cell type annotation

Cheng, C., Fang, S., Zuo, Q., Sun, J., Hu, X., Liu, X., & Jin, M. (2026) · Briefings in Bioinformatics · doi:10.1093/bib/bbag151 · Cited by 2

Cross-species comparison of amniote single-cell transcriptomes reveals evolutionary conservation and divergence in the chicken immune system

Wang, F., Ren, J., Zhou, Y., Huo, W., Liu, H., Qin, M., Jing, Y., Yin, Z., Shi, T., Shan, H., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-72642-y · Cited by 2

Expression-based species deconvolution and realignment removes misalignment error in multispecies single-cell data

Choi, J., Lee, W., Yoon, J.-K., Choi, S. M., Lee, C., Moon, H., Cho, S., Chung, J.-H., Yang, H., & Kim, J. (2022) · BMC Bioinformatics · doi:10.1186/s12859-022-04676-0 · Cited by 2

Evolutionary innovations of human cerebral cortex viewed through the lens of high‐throughput sequencing

Suzuki, I. (2022) · Developmental Neurobiology · doi:10.1002/dneu.22893 · Cited by 2

Biomimetic hydrogel blanket for conserving and recovering intrinsic cell properties

Um, S., Seo, Y., Seo, H., Lee, K., Park, S. H., Jeon, J. H., Lim, J. Y., Ok, M., Kim, Y.-C., Kim, H., et al. (2022) · Biomaterials Research · doi:10.1186/s40824-022-00327-w · Cited by 2

Exploring the potential mechanisms of impairment on genitourinary system associated with coronavirus disease 2019 infection: Bioinformatics and molecular simulation analyses

Zhao, K., Zhang, D., Xu, X., Wang, S., Liu, Z., Ren, X., Zhang, X., Lü, Z., Ren, S., & Qin, C. (2023) · Asian journal of urology · doi:10.1016/j.ajur.2022.12.004 · Cited by 2

Revolutionizing the Life Sciences by Developing a Holographic Digital Mannequin

Cong, B., Liu, X., Zhang, S., Ni, Z., & Wang, L. (2023) · Engineering · doi:10.1016/j.eng.2023.05.004 · Cited by 2

Single-cell transcriptomics reveals tumor microenvironment remodeling in hepatocellular carcinoma with varying tumor subclonal complexity

Shi, J., Zhang, Y., Xu, L., & Wang, F. (2024) · Frontiers in Genetics · doi:10.3389/fgene.2024.1467682 · Cited by 2

collectNET: a web server for integrated inference of cell–cell communication network

Pan, Y., Gao, Z., Cui, X., Li, Z., & Jiang, R. (2024) · Database · doi:10.1093/database/baae098 · Cited by 2

IGFBP7+ subpopulation and IGFBP7 risk score in astrocytoma: insights from scRNA-Seq and bulk RNA-Seq

Zhao, L., Shao, W., Xiahou, Z., Ren, L., Liu, C., Song, Y., Xu, H. Y., Wang, Z., & Jin, X. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1434300 · Cited by 2

Senescent T Cells: The Silent Culprit in Acute Myeloid Leukemia Progression?

Zhang, X., & Liu, L. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms252312550 · Cited by 2

Deciphering the complex clonal heterogeneity of polycythemia vera and the response to interferon alfa

Kalmer, M., Graßhoff, M., Maié, T., Pannen, K., Toledo, M. A. S., Vieri, M., Olschok, K., Lemanzyk, R., Lazarevic, J., Junge, B., et al. (2025) · Blood Advances · doi:10.1182/bloodadvances.2024012600 · Cited by 4

Heterogeneity of the tumor immune cell microenvironment revealed by single-cell sequencing in head and neck cancer

Li, C., Liao, J., Chen, B., & Wang, Q. (2025) · Critical Reviews in Oncology/Hematology · doi:10.1016/j.critrevonc.2025.104677 · Cited by 2

Endothelial transcriptomic, epigenomic and proteomic data challenge the proposed role for TSAd in vascular permeability

Brash, J. T., Diez-Pinel, G., Rinaldi, L., Castellan, R. F. P., Fantin, A., & Ruhrberg, C. (2025) · Angiogenesis · doi:10.1007/s10456-025-09971-x · Cited by 2

Integration of single-cell sequencing and mendelian randomization reveals novel causal pathways between monocytes and hepatocellular carcinoma

Jiang, Y., Yu, J., Kang, Z., & Peng, Y. (2025) · Discover Oncology · doi:10.1007/s12672-025-02357-x · Cited by 2

SC2Spa: a deep learning based approach to map transcriptome to spatial origins at cellular resolution

Liao, L., Madan, E., Palma, A. M., Kim, H., Kumar, A., Bhoopathi, P., Winn, R. A., Trevino, J., Fisher, P. B., Brakebusch, C., et al. (2025) · BMC Bioinformatics · doi:10.1186/s12859-025-06173-6 · Cited by 2

Ensemble machine learning-based pre-trained annotation approach for scRNA-seq data using gradient boosting with genetic optimizer

Elnahas, O., Ead, W. M., Qiu, Y., & Lu, J. G. (2025) · BMC Bioinformatics · doi:10.1186/s12859-025-06151-y · Cited by 2

Integrative single‐cell transcriptomic analysis deciphers heterogeneous characteristics of gastrointestinal tract cancer

Sun, C., Li, T., Jin, X., Xiu, Z., Su, H., Yang, H., Liu, M., & Wu, K. (2025) · Clinical and Translational Medicine · doi:10.1002/ctm2.70415 · Cited by 1

From impossible to possible: the lessons from the control of recent COVID-19 outbreaks in China

Tai, L., Wong, K., Wang, L., & Di, L. (2021) · International Journal of Biological Sciences · doi:10.7150/ijbs.58906 · Cited by 3

Identification of Genetic Predisposition in Noncirrhotic Portal Hypertension Patients With Multiple Renal Cysts by Integrated Analysis of Whole-Genome and Single-Cell RNA Sequencing

Wu, Y. J., Wu, Y., Liu, K., Liu, H., Wang, S., Huang, J., & Ding, H. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.775470 · Cited by 2

Towards the detection of copy number variation from single sperm sequencing in cattle

Yang, L., Gao, Y., Oswalt, A., Fang, L., Boschiero, C., Neupane, M., Sattler, C. G., Li, C., Seroussi, E., Xu, L., et al. (2022) · BMC Genomics · doi:10.1186/s12864-022-08441-8 · Cited by 2

DecOT: Bulk Deconvolution With Optimal Transport Loss Using a Single-Cell Reference

Liu, G., Liu, X., & Ma, L. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.825896 · Cited by 3

Associating pathways with diseases using single-cell expression profiles and making inferences about potential drugs

Sharma, M., Jha, I. P., Chawla, S., Pandey, N., Chandra, O., Mishra, S. V., & Kumar, V. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac241 · Cited by 2

In search of a Drosophila core cellular network with single-cell transcriptome data

Yang, M. Y., Harrison, B. R., & Promislow, D. (2022) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkac212 · Cited by 2

GateView: A Multi-Omics Platform for Gene Feature Analysis of Virus Receptors within Human Normal Tissues and Tumors

Sun, Y., Huang, Z., Chen, W., Zhang, Y., Lei, H.-T., Huang, Q.-J., Lun, Z., Qu, L., & Zheng, L. (2024) · Biomolecules · doi:10.3390/biom14050516 · Cited by 3

How to Use Online Tools to Generate New Hypotheses for Mammary Gland Biology Research: A Case Study for Wnt7b

van de Grift, Y. B. C., Heijmans, N., & van Amerongen, R. (2020) · Journal of Mammary Gland Biology and Neoplasia · doi:10.1007/s10911-020-09474-z · Cited by 2

Single-cell analysis reveals the function of lung progenitor cells in COVID-19 patientsPreprint

Zhao, Z., Zhao, Y., Zhou, Y., Wang, X., Zhang, T., & Zuo, W. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.13.200188 · Cited by 2

A global overview of single-cell type selectivity and pleiotropy in complex diseases and traitsPreprint

Xue, C., Jiang, L., Long, Q., Chen, Y., Li, X., & Li, M. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.18.388488 · Cited by 2

Single-cell RNA sequencing identifies heterogeneous cell subtypes within gingival tissuePreprint

Qian, S., Huang, Q., Shi, J., Zhou, L., Zhao, Y. C., Li, B., & Lai, H. (2020) · doi:10.21203/rs.3.rs-101475/v1 · Cited by 2

Construction of continuously expandable single-cell atlases through integration of heterogeneous datasets in a generalized cell-embedding spacePreprint

Xiong, L., Tian, K., Li, Y., & Zhang, Q. C. (2021) · Research Square · doi:10.21203/rs.3.rs-398163/v1 · Cited by 2

Identification of Key Genes and Pathways Associated with Chemotherapy and Radiotherapy Sensitivity in Locally Advanced Cervical CancerPreprint

Zhang, Z., Zhang, Y., Ma, Y., Xiang, S., Shen, J., Zhao, Y., Wu, X., Li, M., Yang, X., Kaboli, P. J., et al. (2020) · Research Square · doi:10.21203/rs.3.rs-131689/v1 · Cited by 2

Multiview Graph Learning for single-cell RNA sequencing dataPreprint

Karaaslanli, A., Saha, S., Aviyente, S., & Maiti, T. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.05.467476 · Cited by 2

Comprehensive identification of fetal cis-regulatory elements in the human genome by single-cell multi-omics analysisPreprint

Yu, H., Ai, N., Peng, P., Ke, Y., Chen, X., Li, Y., Zhao, T., Jiang, S., Liu, J., & Jiang, L. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.02.466852 · Cited by 2

Inferring predictive genetic models and regulatory elements by deep learning of cross-species single-cell gene expression landscapesPreprint

Li, J., Wang, J., Zhang, P., Wang, R., Mei, Y., Sun, Z., Fei, L., Jiang, M., Ma, L., Weigao, E., et al. (2022) · Research Square · doi:10.21203/rs.3.rs-1544073/v1 · Cited by 2

Latent human herpesvirus 6 is reactivated in chimeric antigen receptor T cellsPreprint

Lareau, C. A., Yin, Y., Maurer, K., Sandor, K. D., Yagnik, G., Peña, J., Crawford, J. C., Spanjaart, A. M., Gutierrez, J. C., Haradhvala, N. J., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.12.503683 · Cited by 2

Single-cell and Spatial Transcriptomics Clustering with an Optimized Adaptive K-Nearest Neighbor GraphPreprint

Li, J., Shyr, Y., & Liu, Q. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.13.562261 · Cited by 2

A human commons cell atlas reveals cell type specificity for OAS1 isoformsPreprint

Gálvez-Merchán, Á., Booeshaghi, A. S., & Pachter, L. S. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.23.586412 · Cited by 4

scELMo: Embeddings from Language Models are Good Learners for Single-cell Data AnalysisPreprint

Zhao, H., Liu, T., Chen, T., Zheng, W., & Luo, X. (2024) · Research Square · doi:10.21203/rs.3.rs-4014784/v1 · Cited by 2

Global cell-state and gene-program representations reveal conserved and context-specific perturbation responses of cellsPreprint

Pan, X., Saunders, R. A., Replogle, J. M., Weissman, J. S., & Zhuang, X. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.16.725005 · Cited by 3

Chimeric antigen receptor‐engineered adoptive cell therapy for AML: Current status and future perspectives

Huang, Y., Shao, M., Wang, Y., & Huang, H. (2022) · ImmunoMedicine · doi:10.1002/imed.1031 · Cited by 1

Characterization and verification of CD81 as a potential target in lung squamous cell carcinoma

Ye, X., Deng, J., Dong, C., Pan, X., & Lu, Y. (2023) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2023.149344 · Cited by 1

scGAT: A Cell-Type Annotation Framework for Single-Cell Transcriptomics Using Graph Attention Network and Meta Learning

Dong, J., Li, M., & Wang, F. (2023) · IEEE International Conference on Medical Artificial Intelligence (MedAI) · doi:10.1109/medai59581.2023.00022 · Cited by 1

Developmental-status-aware transcriptional decomposition establishes a cell state panorama of human cancers

Luo, Y., & Liang, H. (2024) · Genome Medicine · doi:10.1186/s13073-024-01393-6 · Cited by 1

Annotation of single-cell clusters using marker genes within and across species

Kundu, S., Chau, T., Maroof, D. S., & Li, S. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-23736-2.00015-0 · Cited by 1

Identification and validation of a novel signature based on immune‑related genes from epithelial cells to predict prognosis and treatment response in patients with lung squamous cell cancer by integrated analysis of single‑cell and bulk RNA sequencing

Wu, J., Li, Z., Zhou, W., Hu, Z., Gao, K., Yang, J., & Zhang, W. (2025) · Oncology Letters · doi:10.3892/ol.2025.14904 · Cited by 1

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