Changxin Wan

Pseudotimecascade visualizes multi-gene expression cascades along pseudotime and links them to biological functions in hematopoietic stem cell differentiation.

EpiFoundation is a foundation model for scATAC-seq that learns cell representations through peak-to-gene alignment, achieving state-of-the-art performance in downstream tasks.

The paper identifies Vcam1+ fibro-adipogenic progenitors as markers of fatty infiltration in chronic limb threatening ischemia using single-cell transcriptomics in mouse models.

MetaTiME identifies data-driven meta-components in tumor immune microenvironment scRNA-seq data to annotate cell states and reveal transcriptional regulators.

Smmit integrates multi-sample single-cell multi-omics data across samples and modalities, effectively removing batch effects and improving computational efficiency.

The paper identifies two classes of transcription factors based on their regulatory range and shows that long-range TFs' activity depends on chromatin state.

Lisa predicts transcriptional regulators of gene sets by integrating chromatin accessibility and ChIP-seq data to identify relevant regulators.