Publications

† indicates equal contribution. * indicates corresponding author.

2026

Benchmarking cell type annotation in spatial transcriptomics: resolving cellular hierarchies, biological fidelity, and dynamic cell states
Zhu Y.^†, Hu Y.^†, Xie M. B.^†, Qin H., Szul Z. J., Young D. M., Yuan W., Wang Q., Liu Y. H., Meltzer S.*, Zhou X. M.*
Nature Biomedical Engineering, 2026 (under revision)

Atlas

Spatial transcriptomics reveals organizational properties of mouse spinal cord and alterations in neuropathic pain
Wang Q.^†, Hu Y.^†, Zhu Y., Peng J., Chelliah G., Sobanko M., Sanchez B., Ginty D. D., Zhou X. M., Meltzer S.
PNAS, 2026 · bioRxiv

SpaMV

Interpretable spatial multi-omics data integration and dimensionality reduction with SpaMV
Liu Y., Ma K., Xu H., Xu K., Hu Y., Lin Z., Lin J., Han B., Li S., Lin Z., Zhou X. M., Zhang L.
Nature Communications, 2026

CSsingle

CSsingle: a unified tool for robust decomposition of bulk and spatial transcriptomic data across diverse single-cell references
Shen W.*, Hu Y., Liu C., Lei Y., Wong H.-S., Wu S.*, Zhou X. M.*
Nucleic Acids Research, 2026

SCGclust: single-cell graph clustering using graph autoencoders integrating SNVs and CNAs
Potu T.^†, Hu Y.^†, Khan R., Dharani S., Ni J., Zhang L.*, Zhou X. M.*, Mallory X.*
Mathematics, 2026

ResGAT: sample-efficient graph attention for appendiceal cancer subtypes whole slide image analysis
Lin Z., Tong H., Hu Y., Gui X. S., Shen J., Lee B., Zhang L., Moyer D., Zhou M., Zhou X. M.*, Votanopoulos K.
MIDL, 2026

2025

MaskGraphene

MaskGraphene: an advanced framework for interpretable joint representation for multi-slice, multi-condition spatial transcriptomics
Hu Y., Lin Z., Xie M., Yuan W., Rao M., Liu Y. H., Shen W., Zhang L.*, Zhou X. M.*
Genome Biology, 2025

An interpretable framework for decoding transcriptomic foundation models
Hu Y.^†, Wen Z.^†, Lin Z., Qin H., Yuan W., Liu Y. H., Klindt D., Zhang L., Carja O., Zhou X. M.
Manuscript under review, 2025

From features to slice: parameter-cloud modeling of spatial transcriptomics for simulation and 3D interpolatory augmentation
Chen Y., Xie M., Hu Y., Yuan W., Sarkar H., Li B., Zhang L., Zhou X. M.
Preprint, 2025 (manuscript under review)

BioLACE: unifying spatial geometry and marker priors for cohesive cell-type clustering in spatial transcriptomics
Qin H., Hu Y., Zhu Y., Baek J., Yuan W., Meltzer S., Zhou X. M.
Preprint, 2025 (manuscript under review)

CNVeil enables accurate and robust tumor subclone identification and copy number estimation from single-cell DNA sequencing data
Yuan W.^†, Luo C.^†, Hu Y., Zhang L., Wen Z.-H., Liu Y. H., Mallory X.*, Zhou X. M.*
Preprint, 2025

2024

BenchmarkST

Benchmarking clustering, alignment, and integration methods for spatial transcriptomics
Hu Y., Xie M., Li Y., Rao M., Shen W., Luo C., Qin H., Baek J., Zhou X. M.
Genome Biology, 2024

2023

ADEPT

ADEPT: Autoencoder with differentially expressed genes and imputation for robust spatial transcriptomics clustering
Hu Y., Zhao Y., Schunk C. T., Ma Y., Derr T., Zhou X. M.
iScience, 2023

The hidden patient connections: predicting hormonal therapy medication discontinuation using hypergraph neural networks on clinical communications
Song Q.^†, Hu Y.^†, Ni C., Yin Z.
AMIA Summits on Translational Science Proceedings, 2023

Haplotyping-assisted diploid assembly and variant detection with linked reads
Hu Y., Yang C., Zhang L., Zhou X. M.
Methods in Molecular Biology, 2023

2022

Automated filtering of genome-wide large deletions through an ensemble deep learning framework
Hu Y., Mangal S., Zhang L., Zhou X. M.
Methods, 2022

2021

Text mining of gene–phenotype associations reveals new phenotypic profiles of autism-associated genes
Li S., Guo Z., Ioffe J. B., Hu Y., Zhen Y., Zhou X. M.
Scientific Reports, 2021