publications

Published work, manuscripts in preparation, and conference posters.

Publications

  1. F1000
    SpotSweeper-py: spatially-aware quality control metrics for spatial omics data in the Python ecosystem
    Xingyi Chen, Michael Totty, and Stephanie C. Hicks
    F1000Research, 2026
    HTML PDF Code Website

Manuscripts in preparation

  1. Evaluation design shapes estimates of cross-donor generalization in single-cell cell-type classification
    Xingyi Chen, Jiabei Li, and Alexis Battle
    Manuscript in preparation
    Code
  2. IsoVita: Interpretable detection of temporal variation in isoform composition
    Xingyi Chen and Stephanie Hicks
    Manuscript in preparation

Conference poster

  1. BoG
    Machine learning reveals tissue-agnostic and region-specific isoform aging markers in the human hippocampus
    Xingyi Chen, Beril Erdogdu, Mihaela Pertea, and 1 more author
    2026
    Poster presented at Biology of Genomes, Cold Spring Harbor Laboratory
    Poster