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CTGF promotes the repair and regeneration of alveoli after acute lung injury by promoting the proliferation of subpopulation of AEC2s

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LSD1 modulates the non-canonical integrin β3 signaling pathway in non-small cell lung carcinoma cells

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Preparation of Cells from Embryonic Organs for Single‐Cell RNA Sequencing

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Learning Low-Dimensional Latent Graph Structures: A Density Estimation Approach

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Dropout imputation and batch effect correction for single-cell RNA sequencing data

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In silico analysis of inner ear development using public whole embryonic body single-cell RNA-sequencing data

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Differential LysoTracker Uptake Defines Two Populations of Distal Epithelial Cells in Idiopathic Pulmonary Fibrosis

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Pulmonary Vascular Development

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Contribution of Single-Cell Transcriptomics to the Characterization of Human Spermatogonial Stem Cells: Toward an Application in Male Fertility Regenerative Medicine?

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Development of methods for detecting the fate of mesenchymal stem cells regulated by bone bioactive materials

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A single-cell atlas of West African lungfish respiratory system reveals evolutionary adaptations to terrestrialization

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Modeling single cell trajectory using forward-backward stochastic differential equations

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Mark1 regulates distal airspace expansion through type I pneumocyte flattening in lung development

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Looking at the developing lung in single-cell resolution

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scDA: Single cell discriminant analysis for single-cell RNA sequencing data

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A Personalized Low-Rank Subspace Clustering Method Based on Locality and Similarity Constraints for scRNA-seq Data Analysis

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A molecular circuit regulates fate plasticity in emerging and adult AT2 cells

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PRODUCTION OF A PRELIMINARY QUALITY CONTROL PIPELINE FOR SINGLE NUCLEI RNA-SEQ AND ITS APPLICATION IN THE ANALYSIS OF CELL TYPE DIVERSITY OF POST-MORTEM HUMAN BRAIN NEOCORTEX

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A Clustering Ensemble Method for Cell Type Detection by Multiobjective Particle Optimization

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Zero-inflated quantile rank-score based test (ZIQRank) with application to scRNA-seq differential gene expression analysis

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Decoding the IGF1 signaling gene regulatory network behind alveologenesis from a mouse model of bronchopulmonary dysplasia

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MTGDC: A Multi-Scale Tensor Graph Diffusion Clustering for Single-Cell RNA Sequencing Data

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NLRRC: A Novel Clustering Method of Jointing Non-Negative LRR and Random Walk Graph Regularized NMF for Single-Cell Type Identification

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Insect Insights at the Single-Cell Level: Technologies and Applications

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A critical role for miR-142 in alveolar epithelial lineage formation in mouse lung development

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Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression

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CPS analysis: self-contained validation of biomedical data clustering

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Expression of Carcinoembryonic Cell Adhesion Molecule 6 and Alveolar Epithelial Cell Markers in Lungs of Human Infants with Chronic Lung Disease

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Modeling heterogeneity in the pluripotent state: A promising strategy for improving the efficiency and fidelity of stem cell differentiation

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Immune cell type ‘fingerprints’ at the basis of outcome diversity of human infection

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ccImpute: an accurate and scalable consensus clustering based algorithm to impute dropout events in the single-cell RNA-seq data

Malec, M., Kurban, H., & Dalkilic, M. M. (2022) · BMC Bioinformatics · doi:10.1186/s12859-022-04814-8 · Cited by 10

MCRIP1 promotes the expression of lung-surfactant proteins in mice by disrupting CtBP-mediated epigenetic gene silencing

Weng, J. S., Nakamura, T., Moriizumi, H., Takano, H., Yao, R., & Takekawa, M. (2019) · Communications Biology · doi:10.1038/s42003-019-0478-3 · Cited by 10

Single-cell transcriptomics in dermatology

Deutsch, A., McLellan, B. N., & Shinoda, K. (2020) · JAAD International · doi:10.1016/j.jdin.2020.08.001 · Cited by 9

Regulation of Immune Responses by Nonhematopoietic Cells in Asthma

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Differentiation of mouse fetal lung alveolar progenitors in serum-free organotypic cultures

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Developmental basis of evolutionary lung loss in plethodontid salamanders

Lewis, Z., Kerney, R. R., & Hanken, J. (2022) · Science Advances · doi:10.1126/sciadv.abo6108 · Cited by 9

scBKAP: A Clustering Model for Single-Cell RNA-Seq Data Based on Bisecting K-Means

Wang, X., Gao, H., Qi, R., Zheng, R., Gao, X., & Yu, B. (2022) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2022.3230098 · Cited by 9

Voltage-gated ion channels as novel regulators of epithelial ion transport in the osmoregulatory organs of insects

Dates, J., & Kolosov, D. (2024) · Frontiers in Insect Science · doi:10.3389/finsc.2024.1385895 · Cited by 9

Single-Cell Genomics Unravels Brain Cell-Type Complexity

Guillaumet-Adkins, A., & Heyn, H. (2017) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-53889-1_20 · Cited by 9

Single-Cell Sequencing Technologies for Cardiac Stem Cell Studies

Liu, T., Wu, H., Wu, S., & Wang, C. (2017) · Stem Cells and Development · doi:10.1089/scd.2017.0050 · Cited by 9

Preamplification with dUTP and Cod UNG Enables Elimination of Contaminating Amplicons

Andersson, D., Švec, D., Pedersen, C., Henriksen, J. R., & Ståhlberg, A. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19103185 · Cited by 9

VPAC: Variational projection for accurate clustering of single-cell transcriptomic data

Chen, S., Hua, K., Cui, H., & Jiang, R. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-2742-4 · Cited by 10

Reconstructing the Developmental Trajectories of Multiple Subtypes in Pulmonary Parenchymal Epithelial Cells by Single-Cell RNA-seq

Huang, Y., Zheng, Y., Yin, J., Lu, T., Li, M., Liang, J., Hu, Z., Bi, G., Zhan, C., Xue, L., et al. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.573429 · Cited by 9

Gene Selection and Classification of scRNA‐seq Data Combining Information Gain Ratio and Genetic Algorithm with Dynamic Crossover

Feng, J., Niu, X., Zhang, J., & Wang, J. (2022) · Wireless Communications and Mobile Computing · doi:10.1155/2022/9639304 · Cited by 9

Characterization of a flexible AAV-DTR/DT mouse model of acute epithelial lung injury

Griesser, E., Schönberger, T., Stierstorfer, B., Wyatt, H., Rist, W., Lamla, T., Thomas, M. J., Lamb, D. J., & Geillinger‐Kästle, K. E. (2022) · American Journal of Physiology-Lung Cellular and Molecular Physiology · doi:10.1152/ajplung.00364.2021 · Cited by 9

A single-cell atlas reveals shared and distinct immune responses and metabolic profiles in SARS-CoV-2 and HIV-1 infections

Pan, T., Cao, G., Tang, E., Zhao, Y., Penaloza‐MacMaster, P., Fang, Y. H., & Huang, J. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1105673 · Cited by 10

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Overexpressing dominant-negative FGFR2-IIIb impedes lung branching morphogenesis in pigs

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Paradigms That Define Lung Epithelial Progenitor Cell Fate in Development and Regeneration

Sivakumar, A., & Frank, D. B. (2019) · Current Stem Cell Reports · doi:10.1007/s40778-019-00166-x · Cited by 9

Leaf Trichome Distribution Pattern in Arabidopsis Reveals Gene Expression Variation Associated with Environmental Adaptation

Okamoto, S., Negishi, K., Toyama, Y., Ushijima, T., & Morohashi, K. (2020) · Plants · doi:10.3390/plants9070909 · Cited by 9

Single-Cell Transcriptional Profiling of the Intestinal Epithelium

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EC-PGMGR: Ensemble Clustering Based on Probability Graphical Model With Graph Regularization for Single-Cell RNA-seq Data

Zhu, Y., Zhang, D., Zhang, X.-F., Yi, M., Ou-Yang, L., & Wu, M. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.572242 · Cited by 9

Ensemble Classification through Random Projections for Single-Cell RNA-Seq Data

Vrahatis, A. G., Tasoulis, S. K., Georgakopoulos, S. V., & Plagianakos, V. P. (2020) · Information · doi:10.3390/info11110502 · Cited by 9

The diversity of adult lung epithelial stem cells and their niche in homeostasis and regeneration

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Solving the Tyranny of PipettingPreprint

Quake, S. R. (2018) · arXiv (Cornell University) · doi:10.48550/arxiv.1802.05601 · Cited by 9

Improved ClickTags enable live-cell barcoding for highly multiplexed single cell sequencing

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Intrarenal Single-Cell Sequencing of Hepatitis B Virus Associated Membranous Nephropathy

Yu, L., Lin, W., Shen, C., Meng, T., Jin, P., Ding, X., Eggenhuizen, P. J., Ooi, J. D., Tang, R., Nie, W., et al. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.869284 · Cited by 9

Alveolar type 2 cells marker gene SFTPC inhibits epithelial-to-mesenchymal transition by upregulating SOX7 and suppressing WNT/β-catenin pathway in non-small cell lung cancer

Zhang, Q., An, N., Liu, Y., Zhu, Y., Pan, W., Gu, P., Zhao, J., Pu, Q., & Zhu, W. (2024) · Frontiers in Oncology · doi:10.3389/fonc.2024.1448379 · Cited by 8

Cellular plasticity and regenerative mechanisms in the lung

Zaragosi, L., Salwig, I., Wasnick, R. M., Lehmann, M., & Pardo–Saganta, A. (2026) · European Respiratory Review · doi:10.1183/16000617.0168-2025 · Cited by 8

Epithelial cells in chronic obstructive pulmonary disease exacerbations: Targets for lung repair

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De Novo Gene Expression Reconstruction in Space

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RFCell: A Gene Selection Approach for scRNA-seq Clustering Based on Permutation and Random Forest

Zhao, Y., Fang, Z., Lin, C., Deng, C., Xu, Y., & Li, H. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.665843 · Cited by 8

Complex biological questions being addressed using single cell sequencing technologies

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Leveraging data-driven self-consistency for high-fidelity gene expression recovery

Islam, M. T., Wang, J., Ren, H., Li, X., Khuzani, M. B., Sang, S., Yu, L., Shen, L., Zhao, W., & Xing, L. (2022) · Nature Communications · doi:10.1038/s41467-022-34595-w · Cited by 8

Activity‐Based Protein Profiling of Oxidases and Reductases

Krammer, L., & Breinbauer, R. (2023) · Israel Journal of Chemistry · doi:10.1002/ijch.202200086 · Cited by 8

Lung patterning: Is a distal‐to‐proximal gradient of cell allocation and fate decision a general paradigm?

Zhang, K., Aung, T., Yao, E., & Chuang, P. (2023) · BioEssays · doi:10.1002/bies.202300083 · Cited by 8

Glycogen Synthase Kinase-3 Inhibition by CHIR99021 Promotes Alveolar Epithelial Cell Proliferation and Lung Regeneration in the Lipopolysaccharide-Induced Acute Lung Injury Mouse Model

Fernandes, R., Barbosa-Matos, C., Borges-Pereira, C., de Carvalho, A. L. R. T., & Costa, S. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25021279 · Cited by 8

Strategies for the acquisition of transcriptional and epigenetic information in single cells

Li, G., Dzilic, E., Flores, N., Shieh, A., & Wu, S. M. (2017) · Journal of Thoracic Disease · doi:10.21037/jtd.2016.08.17 · Cited by 8

The alternative life of RNA —sequencing meets single molecule approaches

Moya, S. M. F., Ehses, J., & Kiebler, M. A. (2017) · FEBS Letters · doi:10.1002/1873-3468.12639 · Cited by 8

Nx1-Seq (Well Based Single-Cell Analysis System)

Hashimoto, S. (2019) · Advances in experimental medicine and biology · doi:10.1007/978-981-13-6037-4_4 · Cited by 8

Identifying progressive gene network perturbation from single-cell RNA-seq data

Mukherjee, S., Carignano, A., Seelig, G., & Lee, S. (2018) · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) · doi:10.1109/embc.2018.8513444 · Cited by 8

Single‐cell analysis of CD8 T lymphocyte diversity during adaptive immunity

Arsenio, J. (2019) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1475 · Cited by 9

EnClaSC: a novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes

Chen, X., Chen, S., & Jiang, R. (2020) · BMC Bioinformatics · doi:10.1186/s12859-020-03679-z · Cited by 8

Seq Your Destiny: Neural Crest Fate Determination in the Genomic Era

Gandhi, S., & Bronner-Fraser, M. E. (2021) · Annual Review of Genetics · doi:10.1146/annurev-genet-071719-020954 · Cited by 9

Feature Selection in Single-Cell RNA-seq Data via a Genetic Algorithm

Chatzilygeroudis, K. I., Vrahatis, A. G., Tasoulis, S. K., & Vrahatis, M. N. (2021) · Lecture notes in computer science · doi:10.1007/978-3-030-92121-7_6 · Cited by 8

Alternative Isoform Analysis of Ttc8 Expression in the Rat Pineal Gland Using a Multi-Platform Sequencing Approach Reveals Neural Regulation

Hartley, S. W., Mullikin, J. C., Klein, D. C., Park, M., Program, N. C. S., & Coon, S. L. (2016) · PLoS ONE · doi:10.1371/journal.pone.0163590 · Cited by 8

Deciphering Developmental Processes from Single-Cell Transcriptomes

Robson, P. (2014) · Developmental Cell · doi:10.1016/j.devcel.2014.04.032 · Cited by 1

Single cell transcriptomic profiling identifies molecular phenotypes of newborn human lung cellsPreprint

Bhattacharya, S., Myers, J. L., Baker, C. D., Guo, M., Danopoulos, S., Myers, J. R., Bandyopadhyay, G. K., Romas, S., Huyck, H. L., Misra, R. S., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.06.16.156042 · Cited by 6

A single-cell atlas of mouse lung development

Negretti, N. M., Plosa, E. J., Benjamin, J. T., Schuler, B. A., Habermann, A. C., Jetter, C. S., Gulleman, P. M., Bunn, C., Hackett, A. N., Ransom, M. A., et al. (2021) · Development · doi:10.1242/dev.199512 · Cited by 157

A Single Cell Atlas of Lung DevelopmentPreprint

Negretti, N. M., Plosa, E. J., Benjamin, J. T., Schuler, B. A., Habermann, A. C., Jetter, C. S., Gulleman, P. M., Taylor, C. J., Nichols, D. S., Matlock, B. K., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.21.427641 · Cited by 7

Identification and Characterization of Cellular Heterogeneity within Human Late Developmental Stage Dissociated Lung by CITE‐Seq

Bandyopadhyay, G. K., Lillis, J. A., Misra, R. S., Myers, J. R., Ashton, J. M., Huyck, H. L., Krenitsky, D. M., Romas, S., Poole, C., Holden‐Wiltse, J., et al. (2019) · The FASEB Journal · doi:10.1096/fasebj.2019.33.1_supplement.847.5 · Cited by 4