دورية أكاديمية
أعرض في EDS

StaVia: spatially and temporally aware cartography with higher-order random walks for cell atlases.

التفاصيل البيبلوغرافية
العنوان: StaVia: spatially and temporally aware cartography with higher-order random walks for cell atlases.
المؤلفون: Stassen SV; Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong. shobana.venkat88@gmail.com., Kobashi M; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong., Lam EY; Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong.; AI Chip Center for Emerging Smart Systems, Hong Kong Science Park, Shatin, New Territories, Hong Kong., Huang Y; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.; Department of Statistics and Actuarial Science, The University of Hong Kong, Pokfulam, Hong Kong., Ho JWK; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.; Laboratory of Data Discovery for Health, Hong Kong Science Park, Shatin, New Territories, Hong Kong., Tsia KK; Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong. tsia@hku.hk.; Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong. tsia@hku.hk.
المصدر: Genome biology [Genome Biol] 2024 Aug 16; Vol. 25 (1), pp. 224. Date of Electronic Publication: 2024 Aug 16.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: BioMed Central Ltd Country of Publication: England NLM ID: 100960660 Publication Model: Electronic Cited Medium: Internet ISSN: 1474-760X (Electronic) Linking ISSN: 14747596 NLM ISO Abbreviation: Genome Biol Subsets: MEDLINE
أسماء مطبوعة: Publication: London, UK : BioMed Central Ltd
Original Publication: London : Genome Biology Ltd., c2000-
مواضيع طبية MeSH: Zebrafish* , Single-Cell Analysis*, Animals ; Gastrulation ; Computational Biology/methods
مستخلص: Single-cell atlases pose daunting computational challenges pertaining to the integration of spatial and temporal information and the visualization of trajectories across large atlases. We introduce StaVia, a computational framework that synergizes multi-faceted single-cell data with higher-order random walks that leverage the memory of cells' past states, fused with a cartographic Atlas View that offers intuitive graph visualization. This spatially aware cartography captures relationships between cell populations based on their spatial location as well as their gene expression and developmental stage. We demonstrate this using zebrafish gastrulation data, underscoring its potential to dissect complex biological landscapes in both spatial and temporal contexts.
(© 2024. The Author(s).)
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معلومات مُعتمدة: grant nos. 17208918 Research Grants Council of the Hong Kong Special Administrative Region of China; RFS2021-7S06 Research Grants Council of the Hong Kong Special Administrative Region of China; C7047-16G Research Grants Council of the Hong Kong Special Administrative Region of China
تواريخ الأحداث: Date Created: 20240816 Date Completed: 20240817 Latest Revision: 20240819
رمز التحديث: 20240819
مُعرف محوري في PubMed: PMC11328412
DOI: 10.1186/s13059-024-03347-y
PMID: 39152459
قاعدة البيانات: MEDLINE
الوصف
تدمد:1474-760X
DOI:10.1186/s13059-024-03347-y