Rongling Wu

Qian Li

Wednesday, October 21, 2026 4:00 PM - 5:30 PM

A3-4-301

Zoom 928 682 9093 (BIMSA)

High-resolution spatial transcriptomics (ST) enables subcellular spatially resolved transcript profiling but remains difficult to annotate in complex tissues because of gene coverage and super sparseness in expression. These challenges are amplified in cancer research, where neoplastic cell states and rare immune cells in tumor microenvironment are often poorly captured by generic references and/or cell typing tools exclusively built on molecular profile. Here, we present BiNVaST, a niche boundary-preserving and dual-branch variational autoencoder (VAE) fused with statistical simulator for reliable cell typing across multiple spatial platforms. It generates platform-adjusted in silico training data by integrating query spatial profile and user-defined pre-annotated single-cell reference through Singular Value Decomposition and Wasserstein-based Optimal Transport. The VAE framework combines molecular similarity and spatial proximity to predict the probabilities of pre-defined cellular identity for each segmented cell. We rigorously benchmarked BiNVaST against popular methods (e.g., Seurat, SingleR, CellTypist) across Xenium V1, Xenium Prime 5K, CosMx 6K, Stereo-seq, Visium HD platforms, using six tissues from four disease categories, e.g., Ovarian Cancer, Colon Cancer, Pediatric High-Grade Glioma. Our tool is sensitive in detecting divergent tumor cell states and significantly improves the cross-platform concordance, distinguishing disease-specific neoplastic and non-neoplastic cellular subpopulations and supporting robust cellular or niche inferences in heterogeneous tissues.

Dr. Li is an Assistant Professor in Biostatistics and Associate Member in Comprehensive Cancer Center at St. Jude Children’s Research Hospital. Her research focus on statistical and machine learning methods in multi-omics integration, cell type inference in bulk transcriptomics and spatial transcriptomics. She actively collaborated with researchers (i.e., pathologists, oncologists, basic scientists) in childhood cancers, especially in pediatric brain tumors. She has more than 40 publications, thirteen of which are first or (co-)corresponding authorship, such as Bioinformatics, Genome Biology, Genome Medicine. She has mentored two postdoc fellows as primary mentor, as well as co-mentored multiple undergraduate and graduate students during the past 5 years.