Xinyi E. Chen

This paper introduces a measure of transcriptional dyscoordination to quantify aging in single cells, showing it increases with age and is linked to cellular processes like senescence and genome instability.

CHASM detects chromosomal copy number alterations in single-cell data, revealing age-related genomic instability in specific cell types and states.

The paper identifies an inflammatory secretory progenitor cell state in Crohn's disease patients and shows its epigenetic regulation in stem cells.

Clonotrace integrates gene expression and clonotype data to infer cell state transitions and fate biases, improving understanding of lineage dynamics in various biological systems.

This study identifies inflammatory memory as a mechanism for cancer resistance to immunotherapy and shows that combining JAK and TBK1 inhibitors can prevent it.

The paper quantifies the gene regulatory activity of naive DNA in yeast and human cells, finding that naive DNA can produce transcripts and chromatin marks similar to evolved sequences, suggesting biochemical activity is the default state.

GIL designs custom indexing primers for multiplexed sequencing, offering customization and compatibility with existing primers.

This paper models SARS-CoV-2 spike protein evolution using a neural network and Gaussian process to predict future variants up to five months in advance.