I am a senior research professor of bioinformatics, brain science, and oncology at CAS and BGI-Research. Graduated from South China University of Technology with a bachelor’s degree in <Applied Physics>, and a Ph.D. in <Genetics>.
I have been involved in numerous significant international genomics research projects, including the giant panda genome, polar bear population genomics, the Genome 10K (G10K) project, the Cancer Single Cell Project, and the Human Cell Atlas. And I am also a co-founder of the Spatial and Temporal Omics Neuroscience Consortium (STOC-Neuro) and a member of the secretariat for the Major International Brain Mapping Initiative (MBCP).
I have published over 50 SCI papers, with a total citation count exceeding 10,000 times and an H-index greater than 30. Among these publications, I have authored 21 papers as the primary author (first author/co-first author/corresponding author), including 6 articles in top-tier journals such as Cell, Nature, and Science.
Research Areas
We are dedicated to integrating interdisciplinary theoretical knowledge from physics, computer science, and mathematics to conduct research on multi-omics big data in life sciences. Our aim is to understand complex biological systems such as brain science, tumor immunology, and the dynamic changes in organ and function evolution across species. We welcome you to join our research group to explore the frontiers of science and promote advancements in life sciences. Join us as we embark on this exciting journey of scientific discovery.
<1>: Biocomputing. Applying interdisciplinary scientific knowledge and cutting-edge AI large model technologies, integrating multi-omics big data such as genomics, single-cell analysis, spatial transcriptomics, and epigenomics, to decipher the molecular and cellular dynamics mechanisms underlying critical life processes.
<2>: Evolutionary Developmental Studies at Cellular and Functional Levels. Focusing on understanding the spatiotemporal dimensions of the central dogma (from the central dogma to spatiotemporal principles), we develop novel computational methods for studying evolutionary development at molecular, cellular, and structural levels. This includes exploring the mechanisms of tissue and organ development and investigating the principles of structure and function evolution.
<3>: Brain Science and Cancer Disease Research. We construct cell atlases of brain tissues and tumor microenvironments, study the diversity of cell types and spatial structures in the nervous and immune systems, and explore the regulatory mechanisms of cell migration and differentiation.
<4>: Comparative Genomics. Through genomic and population genetic analyses, we investigate the genetic mechanisms underlying species adaptability and changes in population structure.
Education
Sept. 2010-Jun. 2015 Ph.D.
Genetics, School of Biology, South China University of Technology
Sept. 2006-Jul. 2010 Bachelor
Applied Physics, School of Sciences, South China University of Technology
Experience
Since 2016
Senior Scientist, CAS and Institute of Super Cell, BGI-research
2016-2018
Adjunct Assistant Professor, Bio-computing, Chinese University of Hong Kong
2015-2017
Professor, School of Life Sciences, Sun Yat-sen University
2015-2016
Senior Researcher Scientist in Bioinformatics, Precision Medicine Center, BGI-Shenzhen
2009- 2015
Bioinformatics Engineer, BGI-Shenzhen.
Teaching Experience
Computational Biology
Genomics
Bio-computing
Scientific Paper Writing
Publications
Papers
1. Tang, Z.; Bai, Y.; Fang, Q.; Yuan, Y.; Zeng, Q.; Chen, S.; Xu, T.; Chen, J.; Tan, L.; Wang, C.; Li, Q.; Lin, J.; Yang, Z.; Wu, X.; Shi, G.; Wang, J.; Yin, C.; Guo, J.; Liu, S.; Peng, S.; Kuang, M. Spatial Transcriptomics Reveals Tryptophan Metabolism Restricting Maturation of Intratumoral Tertiary Lymphoid Structures. Cancer Cell 2025, S1535610825001126. https://doi.org/10.1016/j.ccell.2025.03.011.
Year of 2024 and before:
1. Qiu X*, Zhu D*, Yao J*, …, Xu Xun #, Liu S#, Bai Y#. Spatiotemporal modeling of molecular holograms. Cell . 2024（Corresponding author）
2. Hao S*, Zhu X*, Huang Z*, …, Liu L#, Liu S#, Sun Y#, Liu C#. Cross-species single-cell spatial transcriptomic atlases of the cerebellar cortex. Science, 2024 (Corresponding author)
3. Ying Lei, Xian Liang, Yunong Sun, Ting Yao, …, Shiping Liu#, Zhi Zhang#, Tiemin Liu#. Region-specific transcriptomic responses to obesity and diabetes in macaque hypothalamus. Cell Metabolism, Volume 36, Issue 2, 2024, Pages 438-453.e6, ISSN 1550-4131, https://doi.org/10.1016/jNaNet.2024.01.003. (Corresponding author)
4. Qin, Pengfei, Huaxian Chen, Yuhang Wang, Liang Wu, …, Shiping Liu#, Hongcheng Lin#. “Cancer-Associated Fibroblasts Undergoing Neoadjuvant Chemotherapy Suppress Rectal Cancer Revealed by Single-Cell and Spatial Transcriptomics.” Cell Reports Medicine 4, no. 10 (October 2023): 101231. https://doi.org/10.1016/j.xcrm.2023.101231. (Corresponding author)
5. Liang Wu, Jiayan Yan, Yinqi Bai, Feiyu Chen, …, Shiping Liu#, …, Jian Zhou#. “An Invasive Zone in Human Liver Cancer Identified by Stereo-Seq Promotes Hepatocyte–Tumor Cell Crosstalk, Local Immunosuppression and Tumor Progression.” Cell Research, June 19, 2023. https://doi.org/10.1038/s41422-023-00831-1. (Corresponding author)
6. Lei Y*, Cheng M*, Li Z*, …, Liu S#, Xu X#. Spatially resolved gene regulatory and disease-related vulnerability map of the adult Macaque cortex. Nat Commun. 2022;13(1):6747. doi:10.1038/s41467-022-34413-3 （Corresponding author）
7. Wu L*, Jiang M, Wang Y, ..., Liu S#. scDPN for High-throughput Single-cell CNV Detection to Uncover Clonal Evolution During HCC Recurrence. Genomics Proteomics Bioinformatics. 2021;19. doi:10.1016/j.gpb.2021.03.008（Corresponding author）
8. Sun Y-F*, Wu L*, Liu S-P*, Jiang M-M*, et al. Dissecting spatial heterogeneity and the immune-evasion mechanism of CTCs by single-cell RNA-seq in hepatocellular carcinoma. Nat Commun. 2021;12(1):4091. doi:10.1038/s41467-021-24386-0 （Co-first author）
9. Sun, Y.*, Wu, L.*#, Zhong, Y.*, Zhou, K.*, Hou, Y.*, Wang, Z., … Liu, S.#, Yang, X.#, Fan, J.# (2020). Single-cell landscape of the ecosystem in early-relapse hepatocellular carcinoma. Cell, 1–18. （Co-first author）
10. Wang, W.*, Zhong, Y.*, Zhuang, Z.*, Xie, J.*, Lu, Y.*, Huang, C.*, … Liu, S.#, Ling, F.#, Yao, X.# (2021). Multiregion single‐cell sequencing reveals the transcriptional landscape of the immune microenvironment of colorectal cancer. Clinical and Translational Medicine, 11(1). （Corresponding author）
11. Natarajan, K. N.*, Miao, Z.*, Jiang, M.*, Huang, X.*, Zhou, H., Xie, J., … Shiping L.#, Teichmann, S. A.# (2019). Comparative analysis of sequencing technologies for single-cell transcriptomics. Genome Biology, 20(1), 70.（Corresponding author）
12. Yu, Q.*, Zhang, W.*, Zhang, X.*, Zeng, Y., Wang, Y., Wang, Y., … ,Shiping Liu#, Li, B.# (2017). Population-wide sampling of retrotransposon insertion polymorphisms using deep sequencing and efficient detection. GigaScience, 6(9), 1–11.（Corresponding author）
13. Zhao Z*, Goldin L*, Liu S*, Wu L*, Zhou W*, Lou H*, et al. Evolution of multiple cell clones over a 29-year period of a CLL patient. Nat Commun. 2016;7: 13765. doi:10.1038/ncomms13765（Co-first author）
14. Liu, S.*, Lorenzen, E. D.*, Fumagalli, M.*, Li, B.*, Harris, K., Xiong, Z., … Wang, J.# (2014). Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell, 157, 785–794. doi:10.1016/j.cell.2014.03.054（First author）
15. Jex, A. R.*, Liu, S.*, Li, B.*, Young, N. D.*, Hall, R. S., Li, Y., … Gasser, R. B. #(2011). Ascaris suum draft genome. Nature. doi:10.1038/nature10553（Co-first author）
16. Dobrynin, P.*，Shiping Liu*, et al. Genomic legacy of the African cheetah, Acinonyx jubatus. Genome Biol. 16, 277 (2015). （Co-first author）
Books
1. Single Cell Biomedicine, Springer, June 2018, Co-author
2. Fundamentals of Single-cell Omics, Science Press, November 2024, Co-author