Single-cell RNA-seq: advances and future challenges

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mRNA-Seq whole-transcriptome analysis of a single cell

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48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in Arabidopsis

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Here We Are, But Where Do We Go? A Systematic Review of Crustacean Transcriptomic Studies from 2014–2015

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Early Transcriptional Landscapes of Chlamydia trachomatis-Infected Epithelial Cells at Single Cell Resolution

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Applications of Single-Cell Sequencing for Multiomics

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SCDevDB: A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes

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DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments

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Integrating spatial transcriptomics and bulk RNA-seq: predicting gene expression with enhanced resolution through graph attention networks

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Comparison of third-generation sequencing approaches to identify viral pathogens under public health emergency conditions

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The Protective Role of TREM2 in the Heterogenous Population of Macrophages during Post-Myocardial Infarction Inflammation

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Dynamic mechanobiology of cardiac cells and tissues: Current status and future perspective

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Cell type-specific gene expression profiling in brain tissue: comparison between TRAP, LCM and RNA-seq

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Circulating Tumor Cells: The Importance of Single Cell Analysis

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Area cooling enables thermal positioning and manipulation of single cells

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Phylogenomics of the Epigenetic Toolkit Reveals Punctate Retention of Genes across Eukaryotes

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CoolMPS: evaluation of antibody labeling based massively parallel non-coding RNA sequencing

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Massive single-cell RNA-seq analysis and imputation via deep learningPreprint

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DREAMSeq: An Improved Method for Analyzing Differentially Expressed Genes in RNA-seq Data

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Progress in mimicking brain microenvironments to understand and treat neurological disorders

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Single-Cell Toolkits Opening a New Era for Cell Engineering

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A review on gene regulatory network reconstruction algorithms based on single cell RNA sequencing

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Mechanisms of fate decision and lineage commitment during haematopoiesis

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Intracellular Regulome Variability Along the Organ of Corti: Evidence, Approaches, Challenges, and Perspective

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Mass Cytometry Moving Forward in Support of Clinical Research: Advantages and Considerations

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Decoding brain memory formation by single-cell RNA sequencing

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Automation of sample preparation for mass cytometry barcoding in support of clinical research: protocol optimization

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Systems biology: perspectives on multiscale modeling in research on endocrine-related cancers

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Visualization and modeling of inhibition of IL-1β and TNF-α mRNA transcription at the single-cell level

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HIT-scISOseq: High-throughput and High-accuracy Single-cell Full-length Isoform Sequencing for Corneal EpitheliumPreprint

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Multi-level multi-view network based on structural contrastive learning for scRNA-seq data clustering

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Deconstruction of tophi and synovium defines SPP1+ macrophages involved in extracellular matrix remodelling in gout

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Single-Cell Expression Profiling and Proteomics of Primordial Germ Cells, Spermatogonial Stem Cells, Adult Germ Stem Cells, and Oocytes

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Transcriptome Architecture of Osteoblastic Cells Infected With Staphylococcus aureus Reveals Strong Inflammatory Responses and Signatures of Metabolic and Epigenetic Dysregulation

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Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data

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Single-cell RNA sequencing in the context of neuropathic pain: progress, challenges, and prospects

Chen, L., Li, Y., Zhu, L., Jin, H., Kang, X., & Feng, Z. (2022) · Translational research · doi:10.1016/j.trsl.2022.07.004 · Cited by 19

Beyond Basic Diversity Estimates—Analytical Tools for Mechanistic Interpretations of Amplicon Sequencing Data

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Immune landscape in rejection of renal transplantation revealed by high-throughput single-cell RNA sequencing

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Data-driven classification of individual cells by their non-Markovian motion

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PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization

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Does mouse embryo primordial germ cell activation start before implantation as suggested by single-cell transcriptomics dynamics?

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Molecular phenotyping of infection-associated small non-coding RNAs

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Single-Cell Non-coding RNA in Embryonic Development

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An integrated enrichment system to facilitate isolation and molecular characterization of single cancer cells from whole blood

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

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Experimental approaches to identify small RNA s and their diverse roles in bacteria – what we have learnt in one decade of MicA research

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Identification of gene expression changes in rabbit uterus during embryo implantation

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Bioinformatics for RNA‐Seq Data Analysis

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Mrc1+ macrophage-derived IGF1 mitigates crystal nephropathy by promoting renal tubule cell proliferation via the AKT/Rb signaling pathway

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Efficient Production of On-Target Reads for Small RNA Sequencing of Single Cells Using Modified Adapters

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Quantitative single cell gene expression profiling in the avian embryo

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Reverse Transcription Errors and RNA–DNA Differences at Short Tandem Repeats

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Single cell RNA sequencing improves the next generation of approaches to AML treatment: challenges and perspectives

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Next-generation sequencing applications in food science: fundamentals and recent advances

Tigrero-Vaca, J., Díaz, B., Gu, G., & Cevallos‐Cevallos, J. M. (2025) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2025.1638957 · Cited by 21

Exploring the Complexity of Cortical Development Using Single-Cell Transcriptomics

Jeong, H., & Tiwari, V. K. (2018) · Frontiers in Neuroscience · doi:10.3389/fnins.2018.00031 · Cited by 16

Respiratory epithelial cell types, states and fates in the era of single-cell RNA-sequencing

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Single-Cell Transcriptomics Revealed White Matter Repair Following Subarachnoid Hemorrhage

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Single-cell SNP analyses and interpretations based on RNA-Seq data for colon cancer research

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E xploring G lucocorticoid R eceptor A gonists M echanism of A ction T hrough M ass C ytometry and R adial V isualizations

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Identification of cell type specific ACE2 modifiers by CRISPR screening

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Expansion of human pluripotent stem cells

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The vagal ganglia transcriptome identifies candidate therapeutics for airway hyperreactivity

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Toward uncharted territory of cellular heterogeneity: advances and applications of single-cell RNA-seq

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SLRRSC: Single-Cell Type Recognition Method Based on Similarity and Graph Regularization Constraints

Zhang, N.-N., Liu, J., Zheng, C.-H., & Wang, J. (2022) · IEEE Journal of Biomedical and Health Informatics · doi:10.1109/jbhi.2022.3148286 · Cited by 16

Physiological and immune profiling of tilapia Oreochromis niloticus gills by high-throughput single-cell transcriptome sequencing

Zheng, S., & Wang, W. (2023) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2023.109070 · Cited by 15

Emergence of Bias During the Synthesis and Amplification of cDNA for scRNA-seq

Luo, Q., & Zhang, H. (2018) · Advances in experimental medicine and biology · doi:10.1007/978-981-13-0502-3_12 · Cited by 15

RNA Regulatory Networks as a Control of Stochasticity in Biological Systems

Vandevenne, M. S., Delmarcelle, M., & Galleni, M. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00403 · Cited by 16

mRNA detection in budding yeast with single fluorophores

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Dimensionality reduction for single cell RNA sequencing data using constrained robust non-negative matrix factorization

Zhang, S., Liu, Y., Yang, J., Lin, Z., & Ng, M. K. (2020) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqaa064 · Cited by 15

A gentle introduction to understanding preclinical data for cancer pharmaco-omic modeling

Piyawajanusorn, C., Nguyen, L. C., Ghislat, G., & Ballester, P. J. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab312 · Cited by 18

Directed yeast genome evolution by controlled introduction of trans-chromosomic structural variations

Jia, B., Jin, J., Han, M., Li, B., & Yuan, Y. (2022) · Science China Life Sciences · doi:10.1007/s11427-021-2084-1 · Cited by 15

Single cells get together: High-resolution approaches to study the dynamics of early mouse development

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Analysis of Genome-Wide Monoallelic Expression Patterns in Three Major Cell Types of Mouse Visual Cortex Using Laser Capture Microdissection

Lin, C., Huang, S.-C., Tung, C.-C., Chou, C., Gau, S. S., & Huang, H. (2016) · PLoS ONE · doi:10.1371/journal.pone.0163663 · Cited by 15

Progress of Single-Cell RNA Sequencing Technology in Myocardial Infarction Research

Li, L., Wang, M., Ma, Q., Li, Y., Ye, J., Sun, X., & Sun, G. (2022) · Frontiers in Cardiovascular Medicine · doi:10.3389/fcvm.2022.768834 · Cited by 13

Advanced sequencing-based high-throughput and long-read single-cell transcriptome analysis

Huang, S., Shi, W., Li, S., Fan, Q., Yang, C. J., Cao, J., & Wu, L. (2024) · Lab on a Chip · doi:10.1039/d4lc00105b · Cited by 14

A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics

Pandey, A. C., Bezney, J., DeAscanis, D., Kirsch, E., Ahmed, F., Crinklaw, A., Choudhary, K. S., Mandala, T., Deason, J., Hamidi, J., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-59880-2 · Cited by 16

Las técnicas de secuenciación masiva en el estudio de la diversidad biológica

de Heredia, U. L. (2016) · Munibe Ciencias Naturales · doi:10.21630/mcn.2016.64.07 · Cited by 14

Single-cell RNA-seq reveals CD16- monocytes as key regulators of human monocyte transcriptional response to Toxoplasma

Patir, A., Gossner, A. G., Ramachandran, P., Alves, J., Freeman, T. C., Henderson, N. C., Watson, M., & Hassan, M. A. (2020) · Scientific Reports · doi:10.1038/s41598-020-78250-0 · Cited by 14

Single-Cell RNA-Seq Reveals Heterogeneous lncRNA Expression in Xenografted Triple-Negative Breast Cancer Cells

Pinkney, H. R., Black, M. A., & Diermeier, S. D. (2021) · Biology · doi:10.3390/biology10100987 · Cited by 14

A novel method for single-cell data imputation using subspace regression

Tran, D., Tran, B., Nguyen, H., & Nguyen, T. (2022) · Scientific Reports · doi:10.1038/s41598-022-06500-4 · Cited by 14

scCNC: a method based on capsule network for clustering scRNA-seq data

Wang, H., Zhao, J., Zheng, C.-H., & Su, Y. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac393 · Cited by 14

ISOdb: A Comprehensive Database of Full-Length Isoforms Generated by Iso-Seq

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Single cell RNA-seq reveals molecular pathways altered by 7, 12-dimethylbenz[a]anthracene treatment on pig oocytes

Yang, C., Song, Z.-Q., Pei, S., Yu, X., Miao, J., Liang, H., Miao, Y., & Du, Z. (2020) · Theriogenology · doi:10.1016/j.theriogenology.2020.08.020 · Cited by 13

Targeting individual cells by barcode in pooled sequence libraries

Ranu, N., Villani, A.-C., Hacohen, N., & Blainey, P. C. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky856 · Cited by 13

Understanding breast cancer heterogeneity through non-genetic heterogeneity

Barough, N. B., Sajjadian, F., Jalilzadeh, N., Shafaei, H., & Velaei, K. (2021) · Breast Cancer · doi:10.1007/s12282-021-01237-w · Cited by 13

Identification of phosphorylated tau protein interactors in progressive supranuclear palsy ( PSP ) reveals networks involved in protein degradation, stress response, cytoskeletal dynamics, metabolic processes, and neurotransmission

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Bacterial single-cell transcriptomics: Recent technical advances and future applications in dentistry

Moon, J.-H., Roh, D., Kwack, K. H., & Lee, J. (2023) · Japanese Dental Science Review · doi:10.1016/j.jdsr.2023.08.001 · Cited by 13

Unveiling the novel immune and molecular signatures of ovarian cancer: insights and innovations from single-cell sequencing

Li, Z., Gu, H., Xu, X., Tian, Y., Huang, X., & Du, Y. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1288027 · Cited by 14

Current Applications of Single-Cell RNA Sequencing in Glioblastoma: A Scoping Review

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Single-cell sequencing in cancer research

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