Wenji Ma, Ph.D., Professor

 School of Public Health

 Shanghai Jiao Tong University School of Medicine

 Phone: +86-21-63846590

 Email: wenjimacs@sjtu.edu.cn

Dr. Ma received a bachelor's degree in software engineering from Shandong University in 2009. She completed her Ph.D. in bioinformatics from the Department of Computer Science at City University of Hong Kong in 2013. From 2014 to 2019, she worked as a postdoctoral research scientist in the Department of Systems Biology in Columbia University Medical Center and was promoted to associate research scientist in July 2018. Before she joined Shanghai Jiao Tong University School of Medicine as a principal investigator in early 2023, she had been a research professor at the institute of Biophysics, Chinese Academy of Sciences since late 2019. She is interested in developing and applying computational methods to solve important biomedical problems. She has papers published in top journals such as Cell, Nature Immunology, and Cell Reports. Three of them were selected as highly cited papers by ESI. She was selected for the Young Elite Scientist Sponsorship Program by the China Association for Science and Technology in 2020 and received the Top 10 Advances in Bioinformatics award in 2021. Currently, she is supported by grants from the National Natural Science Foundation of China, the Ministry of Science and Technology of China, and so on.

Current research directions：

1. Identify the differentiation trajectory and key orchestrating transcriptional factors for cell subpopulations in health and disease by leveraging the large-scale single cell multi-omics data.

2. Develop innovative single cell multi-omics data analysis tools and databases.

Selected publications：

1. G. Jia*, W. Ma*, Z. Wu, S. Li, X. Zhang, Z. He, S.Wu, H. Tao, Y. Fang, X. Wang^#, and Q. Yang^# . Molecular landscape at the embryo-maternal interface for conceptus elongation and implantation. Cell Reports, Accepted.2023.

2. M. Wang*, L. Zhuo*, W. Ma*, Q. Wu^#, Y. Zhuo^#, X. Wang^#. AllenDigger, a Tool for Spatial Expression Data Visualization, Spatial Heterogeneity Delineation, and Single-Cell Registration Based on the Allen Brain Atlas. The Journal of Physical Chemistry A. 2023.

3. Q. Ma*, W. Ma*, T.Z. Song*, Z. Wu*, Z. Liu, Z. Hu, J.B. Han, L. Xu, B. Zeng, B. Wang, Y. Sun, D.D. Yu, Q. Wu, Y.G. Yao^#, Y.T. Zheng^#, X. Wang^#. Single-nucleus transcriptomic profiling of multiple organs in a rhesus macaque model of SARS-CoV-2 infection. Zoological Research. 2022;43(6):1041-62.

4. X. Ren*, W. Wen*, X. Fan*, W. Hou*, B. Su*, P. Cai*, J. Li*, Y. Liu*, F. Tang*, F. Zhang*, Y. Yang*, J. He*, W. Ma*, J. He*, P. Wang*, …., P. Zhou^#, Q. Jiang^#, Z. Huang^#, J.X. Bei^#, L. Wei^#, X.W. Bian^#, X. Liu^#, T. Cheng^#, X. Li^#, P. Zhao^#, F.S. Wang^#, H. Wang^#, B. Su^#, Z. Zhang^#, K. Qu^#, X. Wang^#, J. Chen^#, R. Jin^#, Z. Zhang^#. COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas. Cell. 2021;184(7):1895-913 e19.

5. P. Dogra, C. Rancan, W. Ma, M. Toth, T. Senda, D.J. Carpenter, M. Kubota, R. Matsumoto, P. Thapa, P.A. Szabo, M.M. Li Poon, J. Li, J. Arakawa-Hoyt, Y. Shen, L. Fong, L.L. Lanier, D.L. Farber. Tissue Determinants of Human NK Cell Development, Function, and Residence. Cell. 2020;180(4):749-63 e13.

6. W. Ma, J. Lee, D. Backenroth, Y.J. Zhou, E. Bush, P. Sims, K. Liu^#, Y. Shen^#. Single cell RNA-Seq reveals pre-cDCs fate determined by transcription factor combinatorial dose. BMC molecular and cell biology. 2019;20(1):20.

7. J. Lee*, Y.J. Zhou*, W. Ma*, W. Zhang, A. Aljoufi, T. Luh, K. Lucero, D. Liang, M. Thomsen, G. Bhagat, Y. Shen^#, K. Liu^#. Lineage specification of human dendritic cells is marked by IRF8 expression in hematopoietic stem cells and multipotent progenitors. Nature Immunology. 2017;18(8):877-88.

8. B.V. Kumar*, W. Ma*, M. Miron, T. Granot, R.S. Guyer, D.J. Carpenter, T. Senda, X. Sun, S.H. Ho, H. Lerner, A.L. Friedman, Y. Shen^#, D.L. Farber^#. Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites. Cell Reports. 2017;20(12):2921-34.

9. W. Ma, C. McAnulla, L. Wang. Protein complex prediction based on maximum matching with domain-domain interaction. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 2012;1824(12):1418-24.

10. W. Ma, Y. Yang, Z.-Z. Chen, L. Wang. Mutation region detection for closely related individuals without a known pedigree. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2011;9(2):499-510.

For a full publication list, please check: https://scholar.google.com/citations?user=U1fGKxYAAAAJ&hl=en

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