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Name：Ran Wang

Principal Investigator

Specially-appointed professor

Doctoral supervisor

Email：ran.wang@xjtu.edu.cn

2007 – 2011: Bachelor of Science, major in bioinformatics, College of Life Science, Northwest University.

2011 – 2017: Doctor of Philosophy, major in developmental biology and bioinformatics, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences.

2012 – 2013: Joint postgraduate studies, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology at Shanghai Institutes for Biological Sciences.

2017 – 2019: Postdoctoral fellow, Cancer Research UK Cambridge Institute, University of Cambridge.

2017 – 2019: Academic visitor, European Molecular Biology Laboratory, European Bioinformatics Institute.

2019 – 2023: Associate Professor, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences.

2019 – : Principal Investigator &. Specially-appointed professor, School of Life Science and Technology, Xi’an Jiaotong University.

Expertise in bioinformatics, developmental biology, single-cell and spatial multi-omics.

 

My lab focuses on the study of single-cell and spatial multi-omics, especially, using the frontier technologies to understand cell fate decisions. Recent technological advances in single-cell RNA-seq (scRNA-seq) and spatial transcriptomics have opened the door to profile tissues in greater depth - both with molecular profiling at the level of single cells and in more spatial detail. However, both single-cell and spatial transcriptomics have technical limitations. Most scRNA-seq technologies require tissue dissociation, resulting inevitably in the loss of spatial information related to tissue architecture and organization. The contemporary spatial technologies have yet to achieve a deep read of the transcriptome of the spatially registered cells, or a comprehensive 3D coverage of tissue architecture, which limit the knowledge gain on the molecular attributes of cell fate choice, lineage trajectory and tissue patterning. To solve these problems, we are now applying mathematical modeling, integrating these datasets and developing single-cell spatial algorithms, trying to build spatial molecular atlases of cells, tissues, and organs. Specifically, 1) combining scRNA-seq and spatial transcriptomics to construct single-cell resolution spatio-temporal molecular roadmaps of early organogenesis and body patterning of the mammalian embryo. 2) Using spatial transcriptomics, single-cell multi-omics technologies, in vivo and in vitro experimental strategies to study the molecular mechanisms of left-right patterning establishment during embryonic development.

First/Co-first author publication:

  1. Ran Wang #, Xianfa Yang #, Jiehui Chen #, Lin Zhang #, Jonathan A. Griffiths, Guizhong Cui, Yingying Chen, Yun Qian, Guangdun Peng, Jinsong Li, Liantang Wang, John C. Marioni, Patrick P.L. Tam *, Naihe Jing *. Time space and single-cell resolved tissue lineage trajectories and laterality of body plan at gastrulation. Nature Communications 2023, 14(1): 5675

  1. Ran Wang, Guangdun Peng, Patrick P L Tam, Naihe Jing *. Integration of Computational Analysis and Spatial Transcriptomics in Single-cell Study. Genomics, Proteomics & Bioinformatics 2023, 21(1): 13-23.

  1. Zhiping Rao #, Ran Wang # (co-first author), Sanlan Li #, Yuhan Shi, Licun Mo, Su'e Han, Jiacheng Yuan, Naihe Jing *, Leping Cheng *. Molecular Mechanisms Underlying Ascl1-Mediated Astrocyte-to-Neuron Conversion. Stem Cell Reports 2021, 16(3): 534-547.

  1. Wenqian Song #, Ran Wang # (co-first author), Weimin Jiang, Qi Yin, Guangdun Peng, Ruikai Yang, Qing Cissy Yu, Jianfeng Chen, Jingsong Li, Tom H Cheung, Naihe Jing, Yi Arial Zeng *. Hormones induce the formation of luminal-derived basal cells in the mammary gland. Cell Research 2019, 29(4): 206-220.

  1. Guang Yang #, Changyang Zhou #, Ran Wang # (co-first author), Shisheng Huang, Yu Wei, Xianfa Yang, Yajing Liu, Jianan Li, Zongyang Lu, Wenqin Ying, Xiajun Li, Naihe Jing, Xingxu Huang *, Hui Yang *, Yunbo Qiao *. Base-Editing-Mediated R17H Substitution in Histone H3 Reveals Methylation-Dependent Regulation of Yap Signaling and Early Mouse Embryo Development. Cell Reports 2019, 26(2): 302-312.

  1. Xianfa Yang #, Ran Wang # (co-first author), Xiongjun Wang #, Guoqing Cai, Yun Qian, Su Feng, Fangzhi Tan, Kun Chen, Ke Tang, Xingxu Huang *, Naihe Jing *, Yunbo Qiao *. TGFbeta signaling hyperactivation-induced tumorigenicity during the derivation of neural progenitors from mouse ESCs. Journal of Molecular Cell Biology 2018, 10(3): 216-228.

  1. Yuanyuan Li #, Ran Wang # (co-first author), Nan Qiao, Guangdun Peng, Ke Zhang, Ke Tang, Jing-Dong J Han *, Naihe Jing *. Transcriptome analysis reveals determinant stages controlling human embryonic stem cell commitment to neuronal cells. Journal of Biological Chemistry 2017, 292(48): 19590-19604.

  1. Yunbo Qiao #, Ran Wang # (co-first author), Xianfa Yang, Ke Tang, Naihe Jing *. Dual roles of histone H3 lysine 9 acetylation in human embryonic stem cell pluripotency and neural differentiation. Journal of Biological Chemistry 2015, 290(4): 2508-2520.

Co-author publication:

  1. Xiaoxiao Wang #, Yunlong Xiang #, Yang Yu #, Ran Wang, Yu Zhang, Qianhua Xu, Hao Sun, Zhen-Ao Zhao, Xiangxiang Jiang, Xiaoqing Wang, Xukun Lu, Dandan Qin, Yujun Quan, Jiaqi Zhang, Ng Shyh-Chang, Hongmei Wang, Naihe Jing, Wei Xie *, Lei Li *. Formative pluripotent stem cells show features of epiblast cells poised for gastrulation. Cell Research 2021, 31(5): 526-541.

  1. Ke Zhang #, Fang Yu #, Jian Zhu #, Sue Han #, Jiehui Chen #, Xuanyuan Wu #, Yingying Chen, Tingyu Shen, Jiaoyang Liao, Wenke Guo, Xianfa Yang, Ran Wang, Yun Qian, Jiaxin Yang, Leping Cheng, Yun Zhao, Chi-Chung Hui, Jinsong Li, Guangdun Peng, Shuijin He *, Naihe Jing *, Ke Tang *. Imbalance of Excitatory/Inhibitory Neuron Differentiation in Neurodevelopmental Disorders with an NR2F1 Point Mutation. Cell Reports 2020, 31(3): 107521.

  1. Guangdun Peng #, Shengbao Suo #, Guizhong Cui #, Fang Yu #, Ran Wang, Jun Chen, Shirui Chen, Zhiwen Liu, Guoyu Chen, Yun Qian, Patrick P L Tam, Jing-Dong J Han *, Naihe Jing *. Molecular architecture of lineage allocation and tissue organization in early mouse embryo. Nature 2019, 572(7770): 528-532.

  1. Ting Zhang #, Wei Ke #, Xuan Zhou #, Yun Qian, Su Feng, Ran Wang, Guizhong Cui, Ran Tao, Wenke Guo, Yanhong Duan, Xiaobing Zhang, Xiaohua Cao, Yousheng Shu, Chunmei Yue *, Naihe Jing *. Human Neural Stem Cells Reinforce Hippocampal Synaptic Network and Rescue Cognitive Deficits in a Mouse Model of Alzheimer's Disease. Stem Cell Reports 2019, 13(6): 1022-1037.

  1. Xianfa Yang #, Boqiang Hu #, Jiaoyang Liao #, Yunbo Qiao #, Yingying Chen, Yun Qian, Su Feng, Fang Yu, Ji Dong, Yu Hou, He Xu, Ran Wang, Guangdun Peng, Jinsong Li *, Fuchou Tang *, Naihe Jing *. Distinct enhancer signatures in the mouse gastrula delineate progressive cell fate continuum during embryo development. Cell Research 2019, 29(11): 911-926.

  1. Berna Sozen #, Gianluca Amadei #, Andy Cox, Ran Wang, Ellen Na, Sylwia Czukiewska, Lia Chappell, Thierry Voet, Geert Michel, Naihe Jing, David M Glover, Magdalena Zernicka-Goetz *. Self-assembly of embryonic and two extra-embryonic stem cell types into gastrulating embryo-like structures. Nature Cell Biology 2018, 20(8): 979-989.

  1. Neophytos Christodoulou #, Christos Kyprianou #, Antonia Weberling, Ran Wang, Guizhong Cui, Guangdun Peng, Naihe Jing, Magdalena Zernicka-Goetz *. Sequential formation and resolution of multiple rosettes drive embryo remodelling after implantation. Nature Cell Biology 2018, 20(11): 1278-1289.

  1. Xianfa Yang #, Boqiang Hu #, Yu Hou #, Yunbo Qiao #, Ran Wang, Yingying Chen, Yun Qian, Su Feng, Jun Chen, Chang Liu, Guangdun Peng, Fuchou Tang *, Naihe Jing *. Silencing of developmental genes by H3K27me3 and DNA methylation reflects the discrepant plasticity of embryonic and extraembryonic lineages. Cell Research 2018, 28(5): 593-596.

  1. Chang Liu, Ran Wang, Zhisong He, Pierre Osteil, Emilie Wilkie, Xianfa Yang, Jun Chen, Guizhong Cui, Wenke Guo, Yingying Chen, Guangdun Peng, Patrick P L Tam, Naihe Jing *. Suppressing Nodal Signaling Activity Predisposes Ectodermal Differentiation of Epiblast Stem Cells. Stem Cell Reports 2018, 11(1): 43-57.

  1. Guizhong Cui #, Shengbao Suo #, Ran Wang, Yun Qian, Jing-Dong J Han *, Guangdun Peng *, Patrick P L Tam *, Naihe Jing *. Mouse gastrulation: Attributes of transcription factor regulatory network for epiblast patterning. Development, Growth & Differentiation 2018, 60(8): 463-472.

  1. Xue Han #, Sai Luo #, Guangdun Peng #, J Yuyang Lu, Guizhong Cui, Lichao Liu, Pixi Yan, Yafei Yin, Wei Liu, Ran Wang, Jiejie Zhang, Shanshan Ai, Zai Chang, Jie Na, Aibin He, Naihe Jing *, Xiaohua Shen *. Mouse knockout models reveal largely dispensable but context-dependent functions of lncRNAs during development. Journal of Molecular Cell Biology 2018, 10(2): 175-178.

  1. Su Feng #, Can Xing #, Tingyu Shen #, Yunbo Qiao, Ran Wang, Jun Chen, Jiaoyang Liao, Zhuo Lu, Xiong Yang, Saber Mohamed Abd-Allah, Jinsong Li, Naihe Jing *, Ke Tang *. Abnormal Paraventricular Nucleus of Hypothalamus and Growth Retardation Associated with Loss of Nuclear Receptor Gene COUP-TFII. Scientific Reports 2017, 7(1): 5282

  1. Guangdun Peng #, Shengbao Suo #, Jun Chen #, Weiyang Chen, Chang Liu, Fang Yu, Ran Wang, Shirui Chen, Na Sun, Guizhong Cui, Lu Song, Patrick P L Tam, Jing-Dong J Han *, Naihe Jing *. Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo. Developmental Cell 2016, 36(6): 681-697.

  1. Yunbo Qiao #, Xiongjun Wang #, Ran Wang, Yuanyuan Li, Fang Yu, Xianfa Yang, Lu Song, Guoliang Xu, Y Eugene Chin *, Naihe Jing *. AF9 promotes hESC neural differentiation through recruiting TET2 to neurodevelopmental gene loci for methylcytosine hydroxylation. Cell Discovery 2015, 1: 15017.

  1. Lingyu Li #, Lu Song #, Chang Liu, Jun Chen, Guangdun Peng, Ran Wang, Pingyu Liu, Ke Tang, Janet Rossant, Naihe Jing *. Ectodermal progenitors derived from epiblast stem cells by inhibition of Nodal signaling. Journal of Molecular Cell Biology 2015, 7(5): 455-465.