The high-dimensional data created by high-throughput technologies require visualization
tools that reveal data structure and patterns in an intuitive form. We present PHATE, a …

As the biomedical community produces datasets that are increasingly complex and high
dimensional, there is a need for more sophisticated computational tools to extract biological …

Current methods for comparing single-cell RNA sequencing datasets collected in multiple
conditions focus on discrete regions of the transcriptional state space, such as clusters of cells. …

Obesity is a major modifiable risk factor for pancreatic ductal adenocarcinoma (PDAC), yet
how and when obesity contributes to PDAC progression is not well understood. Leveraging …

Biology has become a data-intensive science. Recent technological advances in single-cell
genomics have enabled the measurement of multiple facets of cellular state, producing …

As Earth's climate warms, soil carbon pools and the microbial communities that process them
may change, altering the way in which carbon is recycled in soil. In this study, we used a …

Checkpoint inhibitors (CPIs) targeting programmed death 1 (PD-1)/programmed death
ligand 1 (PD-L1) and cytotoxic T lymphocyte antigen 4 (CTLA-4) have revolutionized cancer …

The evolution of uniquely human traits likely entailed changes in developmental gene
regulation. Human Accelerated Regions (HARs), which include transcriptional enhancers …

Cancer is a hyper-proliferative disease. Whether the proliferative state originates from the
cell-of-origin or emerges later remains difficult to resolve. By tracking de novo transformation …

Phenotypic plasticity describes the ability of cancer cells to undergo dynamic, nongenetic
cell state changes that amplify cancer heterogeneity to promote metastasis and therapy …