Cole Trapnell

Cole Trapnell developed Monocle, the pioneering computational tool for trajectory inference and pseudotime analysis of single-cell RNA-seq data, enabling researchers to reconstruct the dynamic paths of cell state transitions in cancer without time-series experiments. His algorithms have been widely adopted to map differentiation hierarchies within tumors, identify branch points where cancer cells diverge toward drug-resistant or metastatic states, and characterize the cell state transitions underlying epithelial-mesenchymal plasticity. He has extended trajectory methods to multi-omics data, integrating transcriptomic and epigenomic trajectories to reveal the regulatory programs driving cancer cell state transitions.