Dr. Ning Shen
Address:
1369 Wenyi Xi Rd, Yuhang District, Hangzhou, Zhejiang Province, China
Academic Metrics
- h-index: 13
- i10-index: 13
- Total Citations: 509
Research Interests:
- Computational Biology and Bioinformatics
- Regulatory Genomics and Transcriptional Regulation
- Genomic Expression Regulation
- Cancer Genetics and Driver Mutations
- Targeted Drug Discovery (Rare Genetic Diseases)
- High-throughput Data Analysis
Biography:
Dr. Ning Shen is an Assistant Professor specializing in Computational Biology, Genomics, and Regulatory Genomics. Her primary research involves investigating genomic expression regulation by integrating high-throughput experimental and computational methodologies, with a focus on understanding transcription factor specificity and regulatory element function. Dr. Shen has applied her expertise to translational drug discovery, notably serving as the computational biology lead for multiple muscular dystrophy diseases and contributing critical IND-enabling data for therapeutic development. She currently studies the mechanisms of tissue specificity in cancer driver mutations.
Education Details
- Ph.D. (Pharmacology & Certificate in Computational Biology), Duke University, USA (2011–2016)
- B.S. (Biological Sciences), Fudan University, China (2006–2010)
Professional Background
- Assistant Professor (Current), Zhejiang University Medical Center, China (since March 2021).
- Research Fellow (Postdoctoral), Park Lab, Department of Biomedical Informatics, Harvard Medical School, USA (2019–2020).
- Computational Biology Lead, Fulcrum Therapeutics, USA (2017–2019).
- Postdoctoral Associate, Department of Biostatistics and Bioinformatics, Duke University, USA (2016–2017).
Achievements
- Computational Biology Lead contributing to IND-enabling data for a drug candidate (FTX-1821) in the treatment of Facioscapulohumeral Muscular Dystrophy (FSHD).
- Recipient of a Certificate in Computational Biology and Bioinformatics from Duke University.
Current Research Projects
Dr. Shen is focused on applying computational and genomic approaches to address human disease:
- Understanding the molecular mechanisms and tissue specificity driven by different cancer mutations through the integration of multiple large-scale genomic datasets.
- Investigating sequence and structural determinants governing the DNA binding specificity of paralogous transcription factors.
- Developing new computational methodologies for the analysis of gene expression and regulatory genomics.
Academic Profiles of Dr. Ning Shen
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Publications:
Dr. Shen maintains a prolific publication record focusing on the translational research of advanced nanomaterials for environmental and engineering applications.
- Shen, N., Zhang, Z., Baca, S., & Korthauer, K. (2025). decemedip: hierarchical Bayesian modeling for cell type deconvolution of immunoprecipitation-based DNA methylomes. bioRxiv. DOI: 10.1101/2025.05.09.653152.
- Shen, N. (2025). Invited Commentary on Validation of a CT-based model for early prediction of post pancreatectomy haemorrhage risk. Journal of Gastrointestinal Surgery.
- Shen, N., & Korthauer, K. (2024). vmrseq: probabilistic modeling of single-cell methylation heterogeneity. Genome Biology, 25(1), 321. DOI: 10.1186/s13059-024-03457-7.
- Rojas, L. A., Valentine, E., Accorsi, A., Maglio, J., Shen, N., Robertson, A., et al. (2020). p38$\alpha$ regulates expression of DUX4 in a model of facioscapulohumeral muscular dystrophy. The Journal of Pharmacology and Experimental Therapeutics, 374(3), 489-498.
- Shen, N., Zhao, J., Schipper, J. L., Zhang, Y., Bepler, T., Leehr, D., et al. (2018). Divergence in DNA specificity among paralogous transcription factors contributes to their differential in vivo binding. Cell systems, 6(4), 470-483.
Last Updated on October 03, 2025