Shengyuan Wang, Ph.D.

Summary

Computational biologist and data scientist with 10 years of research experience analyzing high-dimensional biological datasets to study gene regulation, disease mechanisms, biomarker-relevant biology, and clinical outcome associations. Strong background in statistical modeling, data mining, machine learning, multi-omics integration, NGS data analysis, functional genomics, and cancer genomics. Experienced in developing reproducible analytical workflows and scalable data resources using Python, R, Linux, Git, SQL, Nextflow, Docker, CI/CD, AWS, and HPC environments. Skilled at translating complex biological data into interpretable results, testable hypotheses, clear visualizations, and actionable scientific insights to support biomarker discovery and collaborative research.

Areas of Expertise

Education and Training

Publications

• Wang, S., Wu, Z., Zhong, Z., Zhou, X., & Zang, C. (2025). Transcriptional condensates at super-enhancers mediate pH-dependent transcriptional control in innate immunity. bioRxiv, 2025-10. https://doi.org/10.1101/2025.10.29.685293
• Wang, S., Wang, Z., & Zang, C. (2025). Genomic clustering tendency of transcription factors reflects phase-separated transcriptional condensates at super-enhancers. Nucleic Acids Research, 53(3), gkaf015. https://doi.org/10.1093/nar/gkaf015
• Wang, S., Wang, Z., Atwood, G., Xu, Y., & Zang, C. (2025). CTCFDB: a systematic framework and comprehensive data resource for CTCF binding in the human genome. Cancer Research, 85(8_Supplement_1), 1074-1074. https://doi.org/10.1158/1538-7445.AM2025-1074.
• Ma, Z., Liu, M., Wang, S., Wang, S., & Zang, C. (2026). Differential analysis of image-based chromatin tracing data with Dory. bioRxiv, 2026-02. https://doi.org/10.64898/2026.02.19.706897
• Prajapati, S. C., Meydan, C., Neelamraju, Y., Wang, Z., Atwood, G., Paudel, B. B., Fan, H., Dunham, N., Dillon, R., Gandara, J. A., Lee, T., Sheridan, C., Wang, S., Zumbo, P., Becker, M. W., Bullinger, L., Carroll, M. P., D’Andrea, R. J., Levine, R. L., Mason, C., Melnick, A. M., Zang, C., Bekiranov, S., & Garrett-Bakelman, F. E. CCAAT-enhancer binding protein delta functions as a tumor suppressor gene in acute myeloid leukemia. Neoplasia 74 (2026): 101293. https://doi.org/10.1016/j.neo.2026.101293
• Nguyen, Y., Sibley, L., Przanowski, P., Zhao, X. Y., Kovacs, M., Wang, S., ... & Zong, H (2024). Toxoplasma Gondii Infection Supports the Infiltration of T Cells into Brain Tumors. Journal of Neuroimmunology 393 (2024): 578402. https://doi.org/10.1016/j.jneuroim.2024.578402
• Wang, S., Wang, Z., Wang, Y. H., Li, H., Stukenburg, P. T., & Zang, C. (2024). Integration analysis of lncRNAs and R-loops in 3D genome organization and gene regulation in the cancer genome. Cancer Research, 84(6_Supplement), 7355-7355. https://doi.org/10.1158/1538-7445.AM2024-7355
• Al Awak, M.M., Wang, P., Wang, S., Tang, Y., Sun, Y.P. and Yang, L., 2017. Correlation of carbon dots' light-activated antimicrobial activities and fluorescence quantum yield. RSC advances, 7(48), pp.30177-30184. https://doi.org/10.1039/C7RA05397E
• Meziani, M.J., Dong, X., Zhu, L., Jones, L.P., LeCroy, G.E., Yang, F., Wang, S., Wang, P., Zhao, Y., Yang, L. and Tripp, R.A., 2016. Visible-light-activated bactericidal functions of carbon “Quantum” dots. ACS applied materials & interfaces, 8(17), pp.10761-10766. https://doi.org/10.1021/acsami.6b01765
• Wang, S., LeCroy, G.E., Yang, F., Dong, X., Sun, Y.P. and Yang, L., 2015. Carbon nanotube-assisted capturing of bacterial pathogens. RSC advances, 5(111), pp.91246-91253. https://doi.org/10.1039/C5RA16684E

Presentations

Oral Presentations

• Comprehensive integration of CTCF binding across cell types for cancer genomics and epigenetics research, Commonwealth of Virginia Cancer Research Conference, Richmond, VA, 2025
• Spatially clustered pattern of transcription factor binding reveals phase-separated transcriptional condensates at super-enhancers, invited speaker, 5th Annual Emerging Scholars in Genome Sciences Symposium 2024, University of Virginia, Charlottesville, VA, 2024
• Integration analysis of lncRNAs and R-loops in 3D genome organization and gene regulation in the cancer genome, 2024 Postdoctoral Research Symposium, University of Virginia, Charlottesville, VA, 2024

Poster Presentations

• Transcriptional condensates at super-enhancers mediate pH-dependent transcriptional regulation in innate immunity and human cancer, Cold Spring Harbor Laboratory Meeting on Systems Biology: Global Regulation of Gene Expression, Cold Spring Harbor, NY, 2026
• CTCFDB: a systematic framework and comprehensive data resource for CTCF binding in the human genome, AACR Annual Meeting, Chicago, IL, 2025
• An integrated data resource and comprehensive data-driven approach to study CTCF binding in the human genome, RNA Center Inaugural Retreat, University of Virginia, Charlottesville, VA, 2025
• Spatially clustered pattern of transcription factor binding reveals phase-separated transcriptional condensates at super-enhancers, NIH NCI Histone Modifications and Chromatin Structure Symposium, National Institutes of Health, Bethesda, MD, 2024
• Integration analysis of lncRNAs and R-loops in 3D genome organization and gene regulation in the cancer genome, AACR Annual Meeting, San Diego, CA, 2024
• Roles of lncRNAs and R-loops in 3D genome organization and gene regulation in the cancer genome, BMG Annual Retreat, University of Virginia, Charlottesville, VA, 2022
• Analysis of topological properties of cancer-causing synonymous mutations, Frontiers of Computing in Health and Society, George Mason University, Virtually, 2021
• ValgusHel: A novel method to identify and characterize kinked alpha-helices, The Protein Society - 35th Anniversary Symposium, Virtually, 2021
• Structural and topological variations in amino acid residues encoded by synonymous codons, AAAS Annual Meeting, Washington D.C., 2019
• Investigation of polymer-functionalized carbon nanotube-coated filters for removal of bacterial pathogens, Institute of Biological Engineering Annual Conference, Greenville, SC, 2016

Scholarships, Awards and Honors

Journal Reviews

Reviewer: Cancer Research, Nucleic Acid Research

Ad hoc reviewer: Nature Cancer, Bioinformatics, Genome Biology

Mentoring Experience

Certificates