Zhaorong's CV

Education

• Ph.D in Bioinformatics, Boston University, 2026
• M.S. in Bioinformatics, Boston University, 2019
• B.S. in Applied Mathematics, Stony Brook University, 2018
• B.S. in Biology, Stony Brook University, 2018

Work experience

• August 2019 - Present: Bioinformatic Scientist
  • Harvard Medical School
• August 2022 - April 2023: Bioinformatics Co-op
  • Merck
• January 2019 - August 2020: Research Assistant
  • Boston University
• August 2018 - January 2019: Research Assistant
  • Koch Institute

Skills

• Programming Language:
  • Java
  • C
  • Python
  • R
  • Perl
  • SQL
• Pipeline system
  • Snakemake
  • Nextflow
• Bioinformatics analysis
  • Spatial Transcriptome analysis
    • Cell segmentation calling
    • Clustering and Cell type annotation
    • NICHE detection
    • Intercellular ligand-receptor communication
  • Single cell Transcriptome
    • Alignment and quantification
    • Clustering and Cell type annotation
    • Trajectory analysis (Pseudo-time and RNA velocity)
    • Intercellular ligand-receptor communication
    • Cell Atlas Construction
  • Bulk RNA-Seq
    • Alignment and Quantification
    • Differential expression analysis
    • WGCNA
    • Biomarker signature extractions
    • Virus detection and viral gene expression quantification
  • Epigenetic Data (ATAC/ChIP-Seq/CUT&RUN)
    • Alignment, QC and Peak calling
    • Differential accessibility/methylation/acetylation analysis
  • Multi-ome data integration and analysis
    • Integration transcriptome and epigeome data

Publications

Retargeted oncolytic viruses engineered to remodel the tumor microenvironment for glioblastoma immunotherapy

Giovannoni, F., Strathdee, C. A., Faust Akl, C., Andersen, B. M., Li, Z., Lee, H. G., ... & Quintana, F. J. (2025). Retargeted oncolytic viruses engineered to remodel the tumor microenvironment for glioblastoma immunotherapy. Nature Cancer, 6(12), 1994-2010.

Eradicating Drug-tolerant Persister Cells in EGFR-Mutated Non–Small Cell Lung Cancer by Targeting TROP2 with CAR-T Cellular Therapy

Baldacci, S., Brea, E. J., Facchinetti, F., Li, Z., Ngo, K., Malhotra, S., ... & Barbie, D. A. (2025). Eradicating Drug-tolerant Persister Cells in EGFR-Mutated Non–Small Cell Lung Cancer by Targeting TROP2 with CAR-T Cellular Therapy. Cancer discovery, 15(11), 2235-2250.

Glioblastoma-instructed astrocytes suppress tumour-specific T cell immunity

Faust Akl, C., Andersen, B. M., Li, Z., Giovannoni, F., Diebold, M., Sanmarco, L. M., ... & Quintana, F. J. (2025). Glioblastoma-instructed astrocytes suppress tumour-specific T cell immunity. Nature, 643(8070), 219-229.

Barcoded viral tracing identifies immunosuppressive astrocyte–glioma interactions

Andersen, B. M., Faust Akl, C., Wheeler, M. A., Li, Z., Diebold, M., Kilian, M., ... & Quintana, F. J. (2025). Barcoded viral tracing identifies immunosuppressive astrocyte–glioma interactions. Nature, 644(8078), 1097-1106.

ICARus: a pipeline to extract robust gene expression signatures from transcriptome datasets

Li, Z., & Fuxman Bass, J. I. (2025). ICARus: a pipeline to extract robust gene expression signatures from transcriptome datasets. Frontiers in Bioinformatics, 5, 1604418.

CLEC16A in astrocytes promotes mitophagy and limits pathology in a multiple sclerosis mouse model

Kadowaki, A., Wheeler, M. A., Li, Z., Andersen, B. M., Lee, H. G., Illouz, T., ... & Quintana, F. J. (2025). CLEC16A in astrocytes promotes mitophagy and limits pathology in a multiple sclerosis mouse model. Nature Neuroscience, 28(3), 470-486.

Droplet-based functional CRISPR screening of cell–cell interactions by SPEAC-seq

Faust Akl, C., Linnerbauer, M., Li, Z., Lee, H. G., Clark, I. C., Wheeler, M. A., & Quintana, F. J. (2025). Droplet-based functional CRISPR screening of cell–cell interactions by SPEAC-seq. Nature protocols, 20(2), 440-461.

Identification of environmental factors that promote intestinal inflammation

Sanmarco, L. M., Chao, C. C., Wang, Y. C., Kenison, J. E., Li, Z., Rone, J. M., ... & Quintana, F. J. (2022). Identification of environmental factors that promote intestinal inflammation. Nature, 611(7937), 801-809.

Disease-associated astrocyte epigenetic memory promotes CNS pathology

Lee, H. G., Rone, J. M., Li, Z., Akl, C. F., Shin, S. W., Lee, J. H., ... & Quintana, F. J. (2024). Disease-associated astrocyte epigenetic memory promotes CNS pathology. Nature, 627(8005), 865-872.

AHR signaling is induced by infection with coronaviruses

Giovannoni, F., Li, Z., Remes-Lenicov, F., Davola, M. E., Elizalde, M., Paletta, A., ... & Quintana, F. J. (2021). AHR signaling is induced by infection with coronaviruses. Nature communications, 12(1), 5148.