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Bioinformatics Training and Education Program

november, 2020

30nov3:00 pm4:00 pmExamination of cell-lineage and inter-cell interactions from spatial transcriptomics data

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Meeting ID: 918 4307 1125
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Meeting ID: 918 4307 1125
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Abstract: The spatial transcriptomics (ST) technology has enabled geographical profiling of tumor gene expression. However, each ST spot may detect mixture signals from diverse immune or malignant cells of unknown lineages, and local tissue densities may vary significantly across regions. Therefore, the decomposition of ST cell lineages remains a challenge that cannot be resolved by previous decomposition methods for fixed cell types in bulk tumors. We developed the Spatial Cell Estimator (SpaCE) to infer the cell identities and intercellular interactions for tumor ST data. Based on reliable cell lineage inference, SpaCE can further reveal how intercellular interactions affect the pathway and gene activities in distinct regions to modulate the cancer progression.

Bio: Beibei Ru is a postdoctoral research fellow in Dr. Peng Jiang’s Lab at NCI/CDSL. He is developing tools to mining spatial transcriptomics data. Prior to joining Peng’s Lab, Beibei did his PhD at the University of Hong Kong where he investigated the aberrant epigenetic regulation in cancer development.

Time

(Monday) 3:00 pm - 4:00 pm

Location

Online

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