Xiaoshu Chen

PASTRI: Resolving Stage-Specific Cell-State Dynamics from Annotated Cell Lineage Trees

PASTRI infers stage-specific cell-state transition rates from annotated cell lineages, revealing rate-limiting steps and attractor states in development and disease.

Stereotyped cell lineage trees support robust development

The paper uses single-cell transcriptomes and lineage trees to show that sub-CLTs are stereotyped across biological replicates, indicating a robust developmental program.

Transcriptome Analysis in Yeast Reveals the Externality of Position Effect

The paper analyzes transcriptome profiles of yeast strains with GFP insertions to show how genomic context affects gene expression and cellular growth.

Computational comparison of developmental cell lineage trees by alignments

This paper introduces DELTA, an algorithm for aligning developmental cell lineage trees to compare similarities in developmental programs and identify cell fate transformations and evolutionary correspondences.

Dosage sensitivity of X-linked genes in human embryonic single cells

The paper reanalyzes single-cell RNA-seq data to show X-linked genes are not upregulated in male human embryos and their expression ratio decreases, contradicting Ohno's hypothesis.

DNA local structure decreases mutation rates

The paper shows that DNA curvature affects mutation rates in yeast and human tumors, with lower curvature linked to higher mutation rates.