Artificial Intelligence Revolution in Transcriptomics: From Single Cells to Spatial Atlases

	Artificial Intelligence Revolution in Transcriptomics: From Single Cells to Spatial Atlases
	Li, SX; Xiao, TX; Lan, YY; Wu, CX; Li, ZY; Liu, R; Fang, Q; Zhang, C
	2026
发表期刊	Adv. Sci.
卷号	13 期号:5
摘要	Single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) have revolutionized the study of cellular heterogeneity and tissue organization. However, the increasing scale and complexity of these data demand more powerful and integrative computational strategies. Although conventional statistical and machine learning methods remain effective in specific contexts, they face limitations in scalability, multimodal integration, and generalization. In response, artificial intelligence (AI) has emerged as a transformative force, enabling new modes of analysis and interpretation. In this review, we survey AI applications across the transcriptomic analysis workflow-from initial preprocessing through key downstream analyses such as trajectory inference, gene regulatory network reconstruction, and spatial domain detection. For each analytical task, we trace the developmental trajectory and evolving trends of AI models, summarize their advantages, limitations, and domain-specific applicability. We also highlight key innovations, ongoing challenges, and future directions. Furthermore, this review provides practical guidance to assist researchers in model selection and support developers in the design of novel AI tools. An online companion supplement providing an in-depth look at all methods discussed: https://zhanglab-kiz.github.io/review-ai-transcriptomics.
收录类别	SCIE
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/15013
专题	管理、支撑部门_大脑进化与生物信息学（张超）
推荐引用方式 GB/T 7714	Li, SX,Xiao, TX,Lan, YY,et al. Artificial Intelligence Revolution in Transcriptomics: From Single Cells to Spatial Atlases[J]. Adv. Sci.,2026,13(5).
APA	Li, SX.,Xiao, TX.,Lan, YY.,Wu, CX.,Li, ZY.,...&Zhang, C.(2026).Artificial Intelligence Revolution in Transcriptomics: From Single Cells to Spatial Atlases.Adv. Sci.,13(5).
MLA	Li, SX,et al."Artificial Intelligence Revolution in Transcriptomics: From Single Cells to Spatial Atlases".Adv. Sci. 13.5(2026).

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2026070701.pdf（5367KB）	期刊论文	出版稿	开放获取	CC BY-NC-SA	请求全文