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Peer-reviewedCC BY-NC 4.0Nucleic Acids Research

4D-atlas: a multi-species four-dimensional spatiotemporal transcriptomics database spanning development, regeneration, and disease

  • Hongying Zhao1
  • Wangyang Liu1
  • Haotian Xu2
  • Lu Wang1
  • Lina Yang1
  • Yanwu Sun1
  • Hongzheng Yu1
  • Mingming Wu2
  • Xiangtao Li3
  • Li Wang1
  1. 1College of Bioinformatics Science and Technology, Harbin Medical University , Harbin 150081 ,
  2. 2Departments of Cardiology and Critical Care Medicine, the First Affiliated Hospital of Harbin Medical University, NHC Key Laboratory of Cell Transplantation , Harbin 150081 ,
  3. 3School of Artificial Intelligence, Jilin University, Jilin 130012 ,
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Abstract

Four-dimensional (4D) spatial transcriptomics, which captures molecular landscapes across both three-dimensional (3D) tissue architecture and temporal progression, is essential for deciphering dynamic biological processes such as development, regeneration, and disease progression. Here, we present 4D-atlas (https://bio-bigdata.hrbmu.edu.cn/4D-Atlas or https://4d-atlas.bio-database.com/), the first publicly accessible database dedicated to multi-species 4D spatiotemporal transcriptomic atlases. 4D-atlas collects and standardizes 1629 spatial slices spanning 88 distinct time points with 2–41 per dataset and over 22.2 million cells or spatial spots from 15 representative datasets across six species, encompassing embryonic development, tissue regeneration, and disease progression. Beyond data collection, 4D-atlas provides seven interactive analytical modules that enable 4D (3D space + time) exploration of tissue morphogenesis, spatial gene modules, pathway activities, regulatory networks, cell–cell communication, developmental trajectories, and temporal expression patterns. Using a unified analytical pipeline to integrate 3D spatial architecture and molecular information across discrete biological stages, 4D-atlas enables systematic investigation of tissue morphogenesis and dynamic regulatory programs across time and space.

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Cite

BibTeXRIS
BibTeX
@article{zhao20264datlas,
  title = {{4D-atlas: a multi-species four-dimensional spatiotemporal transcriptomics database spanning development, regeneration, and disease}},
  author = {Hongying Zhao and Wangyang Liu and Haotian Xu and Lu Wang and Lina Yang and Yanwu Sun and Hongzheng Yu and Mingming Wu and Xiangtao Li and Li Wang},
  journal = {Nucleic Acids Research},
  year = {2026},
  month = oct,
  doi = {10.1093/nar/gkag1039},
  url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1039/8986575},
  note = {CC BY-NC 4.0},
}
RIS
TY  - JOUR
TI  - 4D-atlas: a multi-species four-dimensional spatiotemporal transcriptomics database spanning development, regeneration, and disease
AU  - Hongying Zhao
AU  - Wangyang Liu
AU  - Haotian Xu
AU  - Lu Wang
AU  - Lina Yang
AU  - Yanwu Sun
AU  - Hongzheng Yu
AU  - Mingming Wu
AU  - Xiangtao Li
AU  - Li Wang
PY  - 2026
DA  - 2026/10/23
JO  - Nucleic Acids Research
DO  - 10.1093/nar/gkag1039
UR  - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1039/8986575
AB  - Four-dimensional (4D) spatial transcriptomics, which captures molecular landscapes across both three-dimensional (3D) tissue architecture and temporal progression, is essential for deciphering dynamic biological processes such as development, regeneration, and disease progression. Here, we present 4D-atlas (https://bio-bigdata.hrbmu.edu.cn/4D-Atlas or https://4d-atlas.bio-database.com/), the first publicly accessible database dedicated to multi-species 4D spatiotemporal transcriptomic atlases. 4D-atlas collects and standardizes 1629 spatial slices spanning 88 distinct time points with 2–41 per dataset and over 22.2 million cells or spatial spots from 15 representative datasets across six species, encompassing embryonic development, tissue regeneration, and disease progression. Beyond data collection, 4D-atlas provides seven interactive analytical modules that enable 4D (3D space + time) exploration of tissue morphogenesis, spatial gene modules, pathway activities, regulatory networks, cell–cell communication, developmental trajectories, and temporal expression patterns. Using a unified analytical pipeline to integrate 3D spatial architecture and molecular information across discrete biological stages, 4D-atlas enables systematic investigation of tissue morphogenesis and dynamic regulatory programs across time and space.
SN  - 0305-1048
SN  - 1362-4962
ER  -