Shamilene Sivagnanam

ImmunoPheno designs and analyzes immunophenotyping experiments using single-cell proteo-transcriptomic data to improve accuracy and reproducibility.

The paper identifies resistance mechanisms to KRAS-MEK pathway targeting in PDAC by analyzing clinical trial data and multi-omics profiles, showing that KRAS/MYC co-gain correlates with resistance and that co-targeting these genes is synergistic.

This study shows that HuR promotes immune evasion in PDAC by inhibiting T cell infiltration and function, suggesting HuR as a therapeutic target with immunotherapy.

This study identifies immune mimicry in breast cancer cells, where neoplastic cells express leukocyte receptors, enhancing tumor aggressiveness and therapy resistance.

This study shows that MHC-II expression in pancreatic cancer cells correlates with immune infiltration and improves immunotherapy response in mouse models.

This study develops a novel pancreatic cancer mouse model by expressing Myc and mutant Kras in adult acinar cells, showing metastasis and therapeutic resistance similar to human PDAc.

This study uses machine learning to analyze spatial proteomic data from pancreatic cancer patients, linking T cell function and localization to neoadjuvant CD40 therapy and clinical outcomes.

This study creates a multimodal tumor atlas to analyze how metastatic HR+ breast cancers adapt to CDK4/6 inhibitors, revealing mechanisms like mTORC1 activation and immune microenvironment changes.

CASSATT processes cycIHC data to align images, segment nuclei, and analyze spatial cell interactions and neighborhoods.

Galaxy-ME is a web-based software hub for analyzing and visualizing multiplex tissue imaging datasets, demonstrating its utility on normal and cancerous tissue data.

MCMICRO processes multiplexed tissue images into single-cell data, demonstrating its versatility across different tissues and imaging platforms.

This paper develops a simple and adaptable chromosome preparation protocol for invertebrates, enabling karyotyping and downstream applications in species lacking cell lines.