Hello, I'm Yafi.

Research Interest

My goal is to bridge the gap between computer science and life sciences by developing accessible, high-impact tools. My research interests lie in Computational Biology, with a focus on single-cell RNA sequencing, spatial transcriptomics and high-dimensional data visualization. I am particularly interested in building algorithms that can:

• Solve complex biological mysteries through multi-omics integration.
• Generate valuable insights for medical diagnosis and treatment.
• Empower researchers and clinicians with interpretable software.

scGIST: Gene Panel Design for Spatial Transcriptomics with Prioritized Gene Sets

Published in Genome Biology on February 2024

The initial goal of the project was to modify a simple linear programming algorithm to include prioritized genes which we achieved in a short period of time. After that, we challenged ourselved to achieve even better results. Through several iterations and experiments, we developed scGIST.

• Developed a deep-learning tool for designing single-cell spatial transcriptomics (sc-ST) gene panels.
• Created a custom loss function for constrained feature selection, optimizing both cell type detection and inclusion of prioritized genes.
• Achieved high accuracy in cell type identification across multiple datasets, outperforming existing methods, especially for small panel sizes.
• Enabled researchers to systematically prioritize genes of interest, including easy-to-target genes and receptor-ligand complexes, without sacrificing accuracy.

Publications

• Yafi, M., Hisham, M., Grisanti, F. et al. scGIST: gene panel design for spatial transcriptomics with prioritized gene sets. Genome Biol 25, 57 (2024). https://doi.org/10.1186/s13059-024-03185-y
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