Deep-learning prediction of gene expression from personal genomes

Drusinsky S, Whalen S, Pollard KS. Deep-learning prediction of gene expression from personal genomes. bioRxiv. 2024. doi: 10.1101/2024.07.27.605449

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Cellular Behavior Analysis from Live-Cell Imaging of TCR T Cell-Cancer Cell Interactions

Verma A, Yu C, Bachl S, Lopez I, Schwartz M, Moen E, Kale N, Ching C, Miller G, Dougherty T, Pao E, Graf W, Ward C, Jena S, Marson A, Carnevale J, Van Valen D, Engelhardt BE. Cellular behavior analysis from live-cell imaging of TCR T cell-cancer cell interactions. bioRxiv. 2024. doi: 10.1101/2024.11.19.624390

Quantized Multi-Task Learning for Context-Specific Representations of Gene Network Dynamics

Chen H, Venkatesh MS, Ortega JG, Mahesh SV, Nandi TN, Madduri RK, Pelka K, Theodoris CV. Quantized multi-task learning for context-specific representations of gene network dynamics. bioRxiv. 2024. doi: 10.1101/2024.08.16.608180

Neighborhood Nonnegative Matrix Factorization Identifies Patterns and Spatially-Variable Genes in Large-Scale Spatial Transcriptomics Data

Laursen R, Chen H, Demaray J, Pelka K, Engelhardt BE. Neighborhood nonnegative matrix factorization identifies patterns and spatially-variable genes in large-scale spatial transcriptomics data. bioRxiv. 2025.