Computational biologist specializing in single-cell genomics, multi-omics integration, and cancer biology. I build and apply tools to understand the molecular underpinnings of disease at single-cell resolution.
My background is in cancer biology, with a focus on fibrolamellar carcinoma (FLC) and the tumor microenvironment. The analytical frameworks I've developed are broadly applicable across biomedical research, and I'm well equipped to bring these skills to new disease areas.
Currently seeking postdoc and industry positions in computational biology and single-cell genomics.
📍 Cornell University | 🔗 LinkedIn | 🎓 Google Scholar | 🔬 ORCID
- Single-nucleus and single-cell RNA-seq (snRNA-seq / scRNA-seq)
- Chromatin accessibility profiling (scATAC-seq)
- Multi-omics data integration
- Cell-cell communication analysis
- Tumor microenvironment characterization
I code with:
Bioinformatics: Seurat, ArchR, CellChat, Harmony, bioHPC / HPC clusters
Farghli, A. R., Sherman, M. S., Shui, B., Stephanou, A., Pepe-Mooney, B. J., et al. (2026). Single-nucleus ATAC-seq analysis resolves chromatin and transcriptional features of fibrolamellar carcinoma. Scientific Reports.
Carter, J. A., Dickerson, L. K., Stephanou, A., et al. (2026). Overcoming CXCR4-mediated T-cell exclusion potentiates antitumor cytotoxicity in fibrolamellar carcinoma. Gastroenterology.
Nukaya, M., Carney, P. R., Cafferty, C., et al. (2025). CDK7 is a novel therapeutic target in fibrolamellar carcinoma. iScience.
DiPietro, E., Bharath, N., Karski, M., ..., Farghli, A. R., et al. (2025). Expression of DNAJB1-PRKACA oncogene suppresses the differentiation potential of liver progenitor organoids towards a hepatocyte lineage. Scientific Reports.
Ma, R. K., Tsai, P.-Y., Farghli, A. R., et al. (2024). DNAJB1-PRKACA fusion protein-regulated LINC00473 promotes tumor growth and alters mitochondrial fitness in fibrolamellar carcinoma. PLoS Genetics, 20(3), e1011216.
Liu, S., Benito-Martin, A., Pelissier Vatter, F. A., ..., Farghli, A. R., et al. (2023). Breast adipose tissue-derived extracellular vesicles from obese women alter tumor cell metabolism. EMBO Reports, 24(12). (23 citations)