Yuankai Huo

THiRST: Computer Vision Empowered Three-dimensional High-Resolution Spatial Transcriptomics Analytics

THiRST reconstructs 3D spatial transcriptomic data from serial 2D sections, improving cross-section consistency and enabling 3D gene expression analysis.

Genetic architecture of the limbic white matter microstructure in aging and Alzheimer's Disease.

This study identifies genetic loci and pathways associated with limbic white matter microstructure in aging and Alzheimer's Disease using multi-cohort diffusion MRI and bulk RNA-seq data.

TRaP: An Open-source, Reproducible Framework for Raman Spectral Preprocessing across Heterogeneous Systems

TRaP provides an open-source framework for reproducible Raman spectral preprocessing across different systems, enabling consistent and transparent analysis workflows.

scCotag: Diagonal integration of single-cell multi-omics data via prior-informed co-optimal transport and regularized barycentric mapping

scCotag improves single-cell multi-omics integration by using co-optimal transport and regularized barycentric mapping, outperforming existing methods in alignment and embedding accuracy.

Computer Vision Methods for Spatial Transcriptomics: A Survey

This paper surveys computer vision methods for spatial transcriptomics, categorizing models and discussing challenges and future directions.

A Specialized Epithelial Cell Type Regulating Mucosal Immunity and Driving Human Crohn's Disease

The paper identifies a novel epithelial cell type, LND, in Crohn's disease that is associated with immune dysregulation and disease activity.

Sex, racial, and APOE-ϵ4 allele differences in longitudinal white matter microstructure in multiple cohorts of aging and Alzheimer's disease

The paper examines how sex, race, and APOE-ε4 allele status affect white matter microstructure across multiple aging and Alzheimer's disease cohorts.

Superficial white matter across the lifespan: volume, thickness, change, and relationship with cortical features

This study quantifies superficial white matter volume and thickness across the lifespan using large datasets, finding unique age-related changes and relationships with cortical features.

Tractography Reproducibility Challenge with Empirical Data (TraCED): The 2017 ISMRM Diffusion Study Group Challenge

The paper evaluates tractography reproducibility using empirical data from a single healthy volunteer scanned on two scanners, finding high consistency among top algorithms but variability due to tract volume containment.