Jacquelyn W. Zimmerman

Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal

The paper introduces dominoSignal, a software tool that statistically tests differential cell signaling from single-cell data to infer changes in cell-cell communication networks.

Automated Quality Control of Time-Course Imaging from 3D in vitro cultures

The paper introduces an algorithm to correct mislabeling and align object positions in longitudinal 3D cell culture imaging, improving data integrity and reproducibility.

Digitize your Biology! Modeling multicellular systems through interpretable cell behavior

The paper introduces a framework for mathematical modeling of multicellular systems using interpretable cell behavior rules derived from biological knowledge and multi-omics data.

Cancer associated fibroblasts drive epithelial to mesenchymal transition and classical to basal change in pancreatic ductal adenocarcinoma cells with loss of IL-8 expression

The paper investigates how cancer-associated fibroblasts (CAF) influence tumor cell behavior in pancreatic ductal adenocarcinoma by driving EMT and altering cell subtypes, with IL-8 playing a key modulatory role.

Comparison of Different Approaches to Single Cell RNA Sequencing of Cancer Associated Fibroblasts

This study compares scRNA-seq of unenriched and CAF-enriched samples from PDAC tumors, finding that CAF enrichment better captures heterogeneity but loses other TME cells.

Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R, and GenePattern Notebook implementations of CoGAPS

The paper introduces computational tools for NMF analysis of single-cell RNA-seq data, demonstrating their use in quantifying cell state transitions in pancreatic cancer.