Single-Cell Technologies: From Research to Application

Topic Information

Dear Colleagues,

Recent advancements in single-cell sequencing, imaging, and analytical technologies have revolutionized our understanding of cellular heterogeneity, providing unparalleled insights into biological processes such as development, differentiation, and disease progression. These innovations enable researchers to analyze cellular dynamics with remarkable precision, uncovering critical mechanisms and biomarkers essential for health and disease. Additionally, single-cell technologies are driving transformative progress in personalized medicine, oncology, and immunology through precise diagnostics, targeted therapies, and innovative data analysis tools. Furthermore, the development of sophisticated computational and bioinformatics tools is vital for managing and interpreting the complex data generated from single-cell studies. These tools facilitate data integration, visualization, and interpretation, making them indispensable for extracting meaningful biological insights. This Topic seeks contributions from leading researchers across various disciplines to foster innovative applications and collaborative efforts. By integrating technological advancements with biological and clinical challenges, this Topic aims to drive progress in basic, translational, and clinical research. The ultimate goal is to enhance our understanding of cellular processes, improve diagnostic and therapeutic strategies, and translate these insights into improved health outcomes. Original research papers and review articles related to this Topic are welcomed.

Dr. Ken-Hong Lim
Prof. Dr. Chung-Der Hsiao
Prof. Dr. Pei-Ming Yang
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
BioTech biotech	3.1	4.8	2012	21.6 Days	CHF 1800
Current Issues in Molecular Biology cimb	3.0	3.7	1999	16.3 Days	CHF 2200
DNA dna	-	-	2021	36 Days	CHF 1000
Genes genes	2.8	5.5	2010	14.6 Days	CHF 2600
International Journal of Molecular Sciences ijms	4.9	9.0	2000	17.8 Days	CHF 2900

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Published Papers (2 papers)

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All BioTech DNA Genes IJMS CIMB

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18 pages, 6891 KB  

Open AccessArticle

Single-Nucleus Transcriptional Profiling Revealed Cell Diversity and Albino Mutation Mechanism in the Skin of Channa argus

by Lu Zhang, Jian Zhou, Qiang Li, Hongyu Ke, Zhipeng Huang, Zhongmeng Zhao, Han Zhao, Chengyan Mou, Wei Fan and Yuanliang Duan

Int. J. Mol. Sci. 2026, 27(2), 1023; https://doi.org/10.3390/ijms27021023 - 20 Jan 2026

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Abstract

Body color is the most prominent phenotypic trait in animals. To investigate the molecular regulatory mechanisms underlying skin pigmentation and body color in Channa argus, single-nucleus RNA sequencing technology was employed to analyze cell diversity and functional changes in the skin of [...] Read more.

Body color is the most prominent phenotypic trait in animals. To investigate the molecular regulatory mechanisms underlying skin pigmentation and body color in Channa argus, single-nucleus RNA sequencing technology was employed to analyze cell diversity and functional changes in the skin of normal and albino C. argus. Three pigment-related cell types, seven immune-related cell types, and nine other skin-related structural and functional cell types were identified. The skin of albino C. argus, which appears white to the naked eye, contains numerous melanocytes and iridophores with reflective silver properties. Compared to normal C. argus, melanocytes in albino individuals contained fewer melanin granules, while iridophores exhibited increased chromogenic substances. Melanocyte-specific genes—kitlg, myo5a, and scarb1—were significantly downregulated in albino melanocytes (p < 0.05). Conversely, iridophore-specific genes alk, pnp, and gpnmb were significantly upregulated in albino skin, whereas mlph was significantly downregulated (p < 0.05). Weighted gene co-expression network analysis revealed that scarb1 was associated with the melanocyte module, alk was identified as a core gene, and pnp was linked to the iridophore module. Functionally, scarb1 is involved in pigment transport, pnp in purine synthesis, and alk is essential for iridophore development. Therefore, scarb1, pnp, and alk may be correlated to albinism in C. argus. Overall, this study constructed a single-cell transcriptional atlas of C. argus skin, providing valuable reference data for further research into the regulatory mechanisms governing body color formation and maintenance in this species. Full article

(This article belongs to the Topic Single-Cell Technologies: From Research to Application)

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15 pages, 2509 KB  

Open AccessArticle

A New Tool to Decrease Interobserver Variability in Biomarker Annotation in Solid Tumor Tissue for Spatial Transcriptomic Analysis

by Sravya Palavalasa, Emily Baker, Jack Freeman, Aditri Gokul, Weihua Zhou, Dafydd Thomas, Wajd N. Al-Holou, Meredith A. Morgan, Theodore S. Lawrence and Daniel R. Wahl

Curr. Issues Mol. Biol. 2025, 47(7), 531; https://doi.org/10.3390/cimb47070531 - 9 Jul 2025

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Abstract

Integrating spatial transcriptomic data with immunofluorescence image data is challenging using existing tools due to their differences in spatial resolution. Immunofluorescence provides information about protein expression at the cellular or subcellular level, whereas spatial transcriptomic platforms typically rely on multicellular “spots” for RNA [...] Read more.

Integrating spatial transcriptomic data with immunofluorescence image data is challenging using existing tools due to their differences in spatial resolution. Immunofluorescence provides information about protein expression at the cellular or subcellular level, whereas spatial transcriptomic platforms typically rely on multicellular “spots” for RNA profiling. Our study coupled spatial transcriptomics of irradiated glioblastoma tissues with immunofluorescence for γH2AX, a marker of DNA damage within the nuclei of cells. We then compared gene expression in γH2AX-positive and negative regions within the tissue. There was significant interobserver variability in manual annotation of γH2AX positivity in multicellular spots by three different researchers (Kappa statistic = 0.345), despite all of them being familiar with γH2AX immunofluorescence and having predefined imaging parameters for annotation. This variability led to different researchers nominating different genes as being associated with DNA repair. To overcome this problem, we have developed a new tool using MATLAB. This tool performs “spot”-wise image analysis and uses researcher-defined parameters such as immunofluorescent marker intensity threshold and number of positive cells to annotate the “spots” as γH2AX positive or negative. The tissue with the most variability in manual annotation was annotated reproducibly by our MATLAB tool, leading to reproducible downstream analysis. Full article

(This article belongs to the Topic Single-Cell Technologies: From Research to Application)

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