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Because atlases differ in biological focus, species coverage, and dataset scale, a systematic comparison is required. This review analyzes current atlases by scope, strengths, and limitations, highlights gaps, and offers recommendations for future expansion, integration, and standardization to improve translational utility.",{"@graph":14,"@context":73},[15,34,56],{"@type":16,"itemListElement":17},"BreadcrumbList",[18,23,27,31],{"item":19,"name":20,"@type":21,"position":22},"https://docshare.wps.com","Home","ListItem",1,{"item":24,"name":25,"@type":21,"position":26},"https://docshare.wps.com/document/","Document",2,{"item":28,"name":29,"@type":21,"position":30},"https://docshare.wps.com/document/research-report/","Research & 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future atlas efforts?",{"text":72,"@type":64},"Expanding, integrating, and standardizing single-cell atlas initiatives to improve translational impact.","https://schema.org",{"og:url":32,"og:type":75,"og:title":10,"og:site_name":45,"og:description":12},"article",{"robots":77,"canonical":32},"index,follow",{"doc_id":79,"site_id":7},450358,1790796139,{"code":4,"msg":82,"data":83},"success",[84,88,92,96,101,105,110,114,119,122,126],{"id":22,"doc_module":4,"doc_module_name":25,"category_name":85,"show_sort_weight":86,"slug":87},"Story & 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\n[https://doi.org/10.1007/s00018-025-05952-x](https://doi.org/10.1007/s00018-025-05952-x) Cellular and Molecular Life Sciences  \nREVIEW  \nA comparative review of single-cell atlases: mapping cellular diversity across species and tissues  \nKeyun Look1 · Pei En Goh1 · Long Chiau Ming1,2 · Shi Hui Law3 · Sang Loon Tan3 · Ee Wern Tan3 · Hooi Leng Ser1 · Bey Hing Goh3,4,5  \nReceived: 20 June 2025 / Revised: 24 September 2025 / Accepted: 8 October 2025 © The Author(s) 2025  \nAbstract  \nSingle-cell sequencing (sc-seq) technologies have revolutionized biomedical research by enabling high-resolution analysis of cellular heterogeneity across multiple dimensions, including transcriptomics, epigenomics, and spatial profiling. These advances have led to the development of comprehensive single-cell atlases—reference maps of cell types and states across tissues and organisms, such as the Human Cell Atlas and Mouse Cell Atlas. These resources are foundational frameworks for investigating gene regulation, tissue architecture, and disease mechanisms. However, variations in biological focus, species representation, and dataset scale among available atlases necessitate a systematic comparative evaluation. This review provides an in-depth analysis of current single-cell atlases, assessing their scope, strengths, and limitations based on an updated framework derived from Hrovatin et al. We discuss the transformative role of sc-seq in oncology, immunology, and infectious disease research and highlight critical gaps in atlas development, including underrepresented species and tissue types. Finally, we propose key recommendations to guide future efforts in expanding, integrating, and standardizing single-cell atlas initiatives for enhanced translational impact.  \nKeywords Single-cell sequencing (sc-seq) · Single-cell atlases · Human cell atlas (HCA) · Mouse cell atlas (MCA) · Cellular heterogeneity  \n􀀍 Bey Hing Goh  \n[beyhingg@sunway.edu.my](beyhingg@sunway.edu.my); [goh.beyhing@uts.edu.au](goh.beyhing@uts.edu.au)  \nShi Hui Law  \n[chloelsh@sunway.edu.my](chloelsh@sunway.edu.my)  \n1 Sir Jeffrey Cheah Sunway Medical School, Faculty of Medical and Life Sciences, Sunway University, Bandar Sunway 47500, Malaysia  \n2 Datta Meghe College of Pharmacy, Datta Meghe Institute of Higher Education and Research (Deemed to Be University), Sawangi (M), Wardha, India  \n3 Sunway Biofunctional Molecules Discovery Centre, Faculty of Medical and Life Sciences, Sunway University, Bandar Sunway 47500, Malaysia  \n4 Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, Australia  \n5 Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan  \nIntroduction  \nLiving organisms are intricate systems composed of diverse cell types, each with distinct functions and characteristics [1] . Understanding cellular diversity is fundamental to unravelling the complexities of life and addressing critical clinical questions. Humans, for instance, are highly complex organisms with approximately 37 trillion cells [2] and an estimated 200 cell types in adulthood [3] . Even within the same cell population or organism, individual cells exhibit unique cell characteristics, including biochemical composition, quantitative variations, morphology, and physiological activity, leading to different disease susceptibility [4] . In particular, tumor cells display significant cancer heterogeneity, driven by distinct somatic genetic alterations, transcriptional regulations, epigenetic modifications, and tumor microenvironment interactions [5, 6] .  \nHistorically, bulk RNA sequencing has been a cornerstone of gene expression analysis, enabling biomarker identification, gene fusion discovery, and cancer classification [5] . However, this approach generates an average  \n1 3  \ngene expression profile acro","cbCaimzqyqtCZQCV","https://ap.wps.com/l/cbCaimzqyqtCZQCV","pdf",1359201,"English","# Abstract\n# Introduction\n## Cellular diversity and clinical relevance\n## From bulk RNA-seq to single-cell sequencing\n## Applications in oncology and infectious disease\n# Recent advances and reference atlas development","[{\"question\":\"What is the main purpose of this review?\",\"answer\":\"To provide an in-depth comparative analysis of current single-cell atlases by evaluating their scope, strengths, and limitations across species and tissues.\"},{\"question\":\"Why is a systematic comparison of single-cell atlases necessary?\",\"answer\":\"Because available atlases vary in biological focus, species representation, and dataset scale, which affects how they can be used to study gene regulation, tissue architecture, and disease mechanisms.\"},{\"question\":\"What key recommendation does the review emphasize for future atlas efforts?\",\"answer\":\"Expanding, integrating, and standardizing single-cell atlas initiatives to improve translational impact.\"}]","A comparative review of single-cell atlases: mapping cellular diversity across species and tissues - Review | PDF",1790732966,48]