Mapping Cell Atlases at the Single‐Cell Level
Source abstract
Abstract
Abstract Recent advancements in single‐cell technologies have led to rapid developments in the construction of cell atlases. These atlases have the potential to provide detailed information about every cell type in different organisms, enabling the characterization of cellular diversity at the single‐cell level. Global efforts in developing comprehensive cell atlases have profound implications for both basic research and clinical applications. This review provides a broad overview of the cellular diversity and dynamics across various biological systems. In addition, the incorporation of machine learning techniques into cell atlas analyses opens up exciting prospects for the field of integrative biology.
Source: crossref · Quality: baseline
Research context
OpenAlex topics: Single-cell and spatial transcriptomics · Cell Image Analysis Techniques · Advanced Fluorescence Microscopy Techniques
SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.
Affiliations
Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine Zhejiang University School of Medicine Hangzhou Zhejiang 310000 China
Liangzhu Laboratory Zhejiang University Hangzhou Zhejiang 311121 China
Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine Hangzhou Zhejiang 310058 China
Institute of Hematology Zhejiang University Hangzhou Zhejiang 310000 China
Funding
National Natural Science Foundation of China · National Key Research and Development Program of China
References (100+)
Show source-provided references
1. 10.1016/j.cell.2018.05.01210.1016/j.cell.2018.05.012 ↗
2. S. T.Aviv Regev O.Rozenblatt‐Rosen M.Stubbington K.Ardlie I.Amit P.Arlotta G.Bader C.Benoist M.Biton B.Bodenmiller B.Bruneau P.Campbell M.Carmichael P.Carninci L.Castelo‐Soccio M.Clatworthy H.Clevers C.Conrad R.Eils J.Freeman L.Fugger B.Goettgens D.Graham A.Greka N.Hacohen M.Haniffa I.Helbig R.Heuckeroth S.Kathiresan S.Kim et al. Human Cell Atlas Organizing Committee arxiv 2018.10.1101/121202 ↗
3. 10.1126/science.abl519710.1126/science.abl5197 ↗
4. 10.1038/s41586-021-03549-510.1038/s41586-021-03549-5 ↗
5. 10.1016/j.cell.2020.01.01510.1016/j.cell.2020.01.015 ↗
6. 10.1038/nmeth.131510.1038/nmeth.1315 ↗
7. 10.1038/nmeth.263910.1038/nmeth.2639 ↗
8. 10.1186/s13059-016-0938-810.1186/s13059-016-0938-8 ↗
9. 10.1126/science.124765110.1126/science.1247651 ↗
10. Soumillon M. · bioRxiv · 2014
11. 10.1186/gb-2013-14-4-r3110.1186/gb-2013-14-4-r31 ↗
12. 10.1016/j.cell.2015.05.00210.1016/j.cell.2015.05.002 ↗
13. 10.1016/j.cell.2015.04.04410.1016/j.cell.2015.04.044 ↗
14. Baysoy A. · Nat Rev Mol Cell Biol · 2023 · 1
15. 10.1038/s41576-023-00580-210.1038/s41576-023-00580-2 ↗
16. 10.1038/ncomms1404910.1038/ncomms14049 ↗
17. 10.1038/s41467-023-38409-510.1038/s41467-023-38409-5 ↗
18. Liu C. · bioRxiv · 2019
19. 10.1186/s13059-018-1603-110.1186/s13059-018-1603-1 ↗
20. 10.1038/s41592-021-01153-z10.1038/s41592-021-01153-z ↗
21. 10.1186/s12864-017-3893-110.1186/s12864-017-3893-1 ↗
22. 10.1007/978-1-4939-9240-9_1010.1007/978-1-4939-9240-9_10 ↗
23. 10.1126/science.125836710.1126/science.1258367 ↗
24. 10.1038/nmeth0717-752c10.1038/nmeth0717-752c ↗
25. 10.1007/978-1-0716-2756-3_210.1007/978-1-0716-2756-3_2 ↗
26. 10.1038/s41467-021-22801-010.1038/s41467-021-22801-0 ↗
27. 10.1038/nmeth.415410.1038/nmeth.4154 ↗
28. 10.1126/science.aam894010.1126/science.aam8940 ↗
29. 10.1126/science.aam899910.1126/science.aam8999 ↗
30. 10.1038/s41586-019-0969-x10.1038/s41586-019-0969-x ↗
31. 10.1038/s41421-021-00333-710.1038/s41421-021-00333-7 ↗
32. 10.1038/s41587-019-0147-610.1038/s41587-019-0147-6 ↗
33. 10.1016/j.cell.2018.06.05210.1016/j.cell.2018.06.052 ↗
34. 10.1126/science.aba761210.1126/science.aba7612 ↗
35. 10.1038/s41592-022-01601-410.1038/s41592-022-01601-4 ↗
36. 10.1038/s41594-019-0323-x10.1038/s41594-019-0323-x ↗
37. 10.1126/science.aau073010.1126/science.aau0730 ↗
38. 10.1038/s41467-018-06355-210.1038/s41467-018-06355-2 ↗
39. 10.1038/nbt.411210.1038/nbt.4112 ↗
40. 10.1038/s41467-022-35374-310.1038/s41467-022-35374-3 ↗
41. 10.1038/s41586-020-03182-810.1038/s41586-020-03182-8 ↗
42. 10.1038/nmeth.438010.1038/nmeth.4380 ↗
43. 10.1038/nbt.397310.1038/nbt.3973 ↗
44. 10.1038/nm.348810.1038/nm.3488 ↗
45. 10.1126/science.abc626110.1126/science.abc6261 ↗
46. 10.1002/advs.20210122910.1002/advs.202101229 ↗
47. 10.1126/science.aaf240310.1126/science.aaf2403 ↗
48. 10.1038/s41592-019-0548-y10.1038/s41592-019-0548-y ↗
49. 10.1126/science.aaw121910.1126/science.aaw1219 ↗
50. 10.1016/j.cell.2021.05.01010.1016/j.cell.2021.05.010 ↗
51. 10.1016/j.cell.2022.10.02110.1016/j.cell.2022.10.021 ↗
52. 10.1016/j.cell.2022.04.00310.1016/j.cell.2022.04.003 ↗
53. Chen A. · Cell · 2023
54. 10.1016/j.cell.2020.10.02610.1016/j.cell.2020.10.026 ↗
55. 10.1038/s41586-023-05795-110.1038/s41586-023-05795-1 ↗
56. 10.1126/science.abb953610.1126/science.abb9536 ↗
57. 10.1038/s41586-023-06837-410.1038/s41586-023-06837-4 ↗
58. 10.1126/science.280.5363.58510.1126/science.280.5363.585 ↗
59. 10.1126/science.aaa609010.1126/science.aaa6090 ↗
60. 10.1016/j.neuron.2016.10.00110.1016/j.neuron.2016.10.001 ↗
61. 10.1038/s41586-019-1049-y10.1038/s41586-019-1049-y ↗
62. 10.1038/s41586-021-03705-x10.1038/s41586-021-03705-x ↗
63. 10.1038/s41586-021-03969-310.1038/s41586-021-03969-3 ↗
64. 10.1038/s41587-021-01006-210.1038/s41587-021-01006-2 ↗
65. Wang X. · Science · 2018 · 361
66. 10.1038/nprot.2014.19110.1038/nprot.2014.191 ↗
67. Z.Yao C. T. J. v.Velthoven M.Kunst M.Zhang D.McMillen C.Lee W.Jung J.Goldy A.Abdelhak P.Baker E.Barkan D.Bertagnolli J.Campos D.Carey T.Casper A. B.Chakka R.Chakrabarty S.Chavan M.Chen M.Clark J.Close K.Crichton S.Daniel T.Dolbeare L.Ellingwood J.Gee A.Glandon J.Gloe J.Gould J.Gray et al. bioRxiv2023 2023.03.06.531121.
68. S. M.Salas P.Czarnewski L. B.Kuemmerle S.Helgadottir C.Matsson‐Langseth S.Tismeyer C.Avenel H.Rehman K.Tiklova A.Andersson M.Chatzinikolaou F. J.Theis M. D.Luecken C.Wählby N.Ishaque M.Nilsson bioRxiv2023 2023.02.13.528102.
69. 10.1016/j.tig.2021.03.00710.1016/j.tig.2021.03.007 ↗
70. 10.1038/s41586-019-1629-x10.1038/s41586-019-1629-x ↗
71. 10.1038/s41586-020-2157-410.1038/s41586-020-2157-4 ↗
72. 10.1186/s13059-020-02210-010.1186/s13059-020-02210-0 ↗
73. 10.1126/science.abl489610.1126/science.abl4896 ↗
74. 10.1126/science.abl429010.1126/science.abl4290 ↗
75. 10.1016/j.cell.2021.10.02410.1016/j.cell.2021.10.024 ↗
76. 10.1038/s41591-022-02104-710.1038/s41591-022-02104-7 ↗
77. 10.1038/s41586-021-04345-x10.1038/s41586-021-04345-x ↗
78. 10.1038/s41586-021-03620-110.1038/s41586-021-03620-1 ↗
79. 10.1038/s41587-020-00762-x10.1038/s41587-020-00762-x ↗
80. 10.1016/j.stem.2017.03.00710.1016/j.stem.2017.03.007 ↗
81. 10.1038/s41556-018-0123-210.1038/s41556-018-0123-2 ↗
82. 10.1038/s41586-019-1500-010.1038/s41586-019-1500-0 ↗
83. a)F.Tian F.Zhou X.Li W.Ma H.Wu M.Yang A. R.Chapman D. F.Lee L.Tan D.Xing G.Yin A.Semayel J.Wang J.Wang W.Sun R.He S.Zhang Z.Cao L.Wei S.Lu D.Yang Y.Mao Y.Gao K.Chen Y.Zhang X.Liu J.Yong L.Yan Y.Huang J.Qiao et al. bioRxiv2020 2020.04.12.038000;
84. b)H.Yu N.Ai P.Peng Y.Ke X.Chen Y.Li T.Zhao S.Jiang J.Liu L.Jiang bioRxiv2021 2021.11.02.466852.
85. 10.1038/s41586-021-04158-y10.1038/s41586-021-04158-y ↗
86. 10.1038/s41556-023-01108-w10.1038/s41556-023-01108-w ↗
87. Cao J. · Science · 2020 · 370
88. J.Pan Y.Li Z.Lin Q.Lan H.Chen M.Zhai S.Sui G.Zhang Y.Cheng Y.Tang Q.Wang Y.Zhang F.Ma Y.Xu Y.Mao Q.Chen Y.Guan N.Meng H.Lu X.Li T.Zheng X.Yao Q.Qin B.Jiang Y.Ren M.Luo J.Nancuo X.Jin J.Sheng C.Xu et al. bioRxiv2023 2023.04.22.537909.
89. 10.1038/s41586-018-0394-610.1038/s41586-018-0394-6 ↗
90. 10.1164/rccm.201911-2199OC10.1164/rccm.201911-2199OC ↗
91. 10.1038/s41586-020-2922-410.1038/s41586-020-2922-4 ↗
92. 10.1038/s41588-022-01243-410.1038/s41588-022-01243-4 ↗
93. 10.1038/s41591-023-02327-210.1038/s41591-023-02327-2 ↗
94. Sountoulidis A. · Nat. Cell Biol. · 2023 · 25 · 351
95. 10.1016/j.cell.2022.11.00510.1016/j.cell.2022.11.005 ↗
96. 10.1038/s41467-018-04334-110.1038/s41467-018-04334-1 ↗
97. 10.1016/j.xcrm.2021.10021910.1016/j.xcrm.2021.100219 ↗
98. 10.1038/s41467-021-27895-010.1038/s41467-021-27895-0 ↗
99. a)A. D.Reed S.Pensa A.Steif J.Stenning D. J.Kunz P.He A.‐J.Twigger K.Kania R.Barrow‐McGee I.Goulding J. J.Gomm L.Jones J. C.Marioni W. T.Khaled bioRxiv2023 2023.04.21.537845;
100. 10.1038/s41586-023-06252-910.1038/s41586-023-06252-9 ↗