Madeline E. Melzer

CIPHER uses gene co-fluctuations in unperturbed cells to predict transcriptome-wide responses to perturbations, outperforming existing methods and revealing key regulatory structures.

The paper investigates transcriptional adaptation in mammalian cells using computational analysis, mathematical modeling, and machine learning, identifying widespread prevalence and single-cell manifestations of compensatory gene networks.

singletCode uses synthetic barcodes to identify singlets in scRNA-seq and evaluates doublet detection methods' performance.