Integrative Computational Framework for Linking Cell Surface Proteins to Downstream Transcriptional Programs in Cells

The composition of tumor microenvironment has an important impact on treatment response. Hence, we aim to develop a “systems biology” approach where single-cell multi-omics data collected from patients’ tumors are combined with our novel computer framework for systems-level characterization of the tumor microenvironment and the underlying regulatory mechanisms associated with therapy resistance. To achieve this, we will link surface proteins to downstream transcriptional response through integration of transcriptomic and proteomic data from human cancer specimens at the single-cell level by utilizing single-cell multi-omics technologies and machine learning strategies. Together, these approaches will give us unprecedented knowledge of the underlying causes of therapy resistance and new combination therapy strategies.

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Manuscript: SPaRTAN, a computational framework for linking cell-surface receptors to transcriptional regulators