Xiang Zhou

Exposure to p,p'-dichlorodiphenyldichloroethylene (p,p'-DDE) Perturbs Cell State and Stem Cell Markers and Induces an Epidermal Phenotype in Human Breast Cells

This study shows that DDE exposure alters cell state and stem cell markers in breast cells, inducing an epidermal phenotype and upregulating keratinization pathways.

SVC: A Vision Transformer-based Spatially and Virtually Embedded Cell Model for Deciphering Subcellular Spatial Transcriptomic Heterogeneity

SVC predicts subcellular transcript localization and co-organization using a Vision Transformer model, revealing disease patterns and spatial biology not accessible at the cell level.

Accessible and reproducible deployment reveals the practical boundaries of single-cell foundation models

Across 13 single-cell foundation models and 94 datasets, PCA and established methods usually match or beat them; pretrained embeddings help mainly with scarce labels, rare cells and open-set detection.

SPICE: A Robust Computational Framework for Identifying Copy Number Variations in Spatial Transcriptomics

SPICE identifies somatic CNVs and ASCN profiles from spatial transcriptomics data by integrating gene expression, spatial coordinates, and SNPs to improve CNV detection accuracy.

Calibrated Prediction Intervals for Polygenic Scores: Updated Comparisons, Contextual Calibration, and Data Normalization

This paper compares two methods for creating calibrated prediction intervals for polygenic scores, showing their performance and the importance of normalization and preprocessing.

Exploring the Influence of Chemical Exposures in Breast Cancer Disparities: High-Throughput Transcriptomic Analysis in Normal Breast Cells from Diverse Donors

This study investigates how chemical exposures affect biological processes linked to aggressive breast cancer using transcriptomic analysis of normal breast cells from diverse donors.

A reference panel for linkage disequilibrium and genotype imputation using whole-genome sequencing data from 2,680 participants across India

The paper constructs a large-scale LD and genotype imputation reference panel using whole-genome sequencing data from 2,680 Indian participants, improving imputation accuracy and polygenic risk score performance.

FastCCC: A permutation-free framework for scalable, robust, and reference-based cell-cell communication analysis in single cell transcriptomics studies

FastCCC provides a permutation-free framework for reference-based cell-cell communication analysis, demonstrating robust performance across complex datasets and uncovering biologically relevant interactions.

ELLA: Modeling Subcellular Spatial Variation of Gene Expression within Cells in High-Resolution Spatial Transcriptomics.

ELLA models subcellular spatial variation of gene expression in high-resolution spatial transcriptomics, identifying genes with distinct localization patterns and associating them with mRNA characteristics.

Optimal transport modeling uncovers spatial domain dynamics in spatiotemporal transcriptomics studies

SpaDOT identifies spatial domains and their temporal dynamics in spatiotemporal transcriptomics data, revealing key developmental processes like valvulogenesis.

Region-based analysis with functional annotation identifies genes associated with cognitive function in South Asians from India

The paper identifies AD-associated genes in South Asians using whole-genome sequence data and variant analysis, finding associations for APOE, PICALM, and TSPOAP1 with cognitive function.

An alternative framework for transcriptome-wide association studies to detect and decipher gene-trait associations

VINTAGE improves gene-trait association detection by integrating genetic variance and local genetic correlation tests, outperforming SKAT and TWAS in power and mediation effect identification.

Multi-ancestry transcriptome-wide association studies of cognitive function, white matter hyperintensity, and Alzheimer's disease

This paper conducts multi-ancestry transcriptome-wide association studies to identify genes associated with cognitive function, white matter hyperintensity, and Alzheimer's disease using gene expression data from European and African ancestry individuals.

Proteome-Wide Association Studies for Blood Lipids and Comparison with Transcriptome-Wide Association Studies

The paper conducts proteome-wide and transcriptome-wide association studies for blood lipids, finding high-level consistency between proteome and transcriptome-lipid associations across tissues.

Pervasive findings of directional selection realize the promise of ancient DNA to elucidate human adaptation

This paper detects widespread directional selection in ancient DNA data, identifying 347 genome-wide significant loci and linking them to traits like body fat, skin color, and cognitive performance.

An expression-directed linear mixed model (edLMM) discovering low-effect genetic variants

This paper introduces edLMM, a method that detects low-effect genetic variants using moderate sample sizes, improving missing heritability estimation.

Effect of APOE e4 and its modification by sociodemographic characteristics on cognitive measures in South Asians from LASI-DAD

The paper examines the effect of APOE ε4 and its interaction with sociodemographic factors on cognitive measures in South Asians from LASI-DAD, finding stronger associations in older adults and females.

Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single cell resolution

The paper uses single-cell RNA-seq to study how genetic variants influence the transcriptional response to glucocorticoids and immune stimuli in children, identifying treatment-specific gene regulation.

STAREG: an empirical Bayesian approach to detect replicable spatially variable genes in spatial transcriptomic studies

STAREG identifies replicable spatially variable genes across spatial transcriptomic studies using an empirical Bayesian approach with improved power and false discovery rate control.

The Michigan Genomics Initiative: a biobank linking genotypes and electronic clinical records in Michigan Medicine patients

The Michigan Genomics Initiative links genotypes with electronic clinical records in Michigan Medicine patients, showing higher disease prevalence and validating GWAS findings.

Spatially Aware Dimension Reduction for Spatial Transcriptomics

This paper introduces SpatialPCA, a spatially-aware dimension reduction method for spatial transcriptomics, enabling analysis with existing single-cell tools and revealing new biological insights in tumor and neuronal contexts.

SpaceX: Gene Co-expression Network Estimation for Spatial Transcriptomics

SpaceX identifies gene co-expression networks in spatial transcriptomics data, revealing spatially regulated genes in mouse hypothalamus and human breast cancer.

ExPRSweb - An Online Repository with Polygenic Risk Scores for Common Health-related Exposures

The paper develops ExPRSweb, an online repository of polygenic risk scores for common exposures, showing improved prediction of chronic conditions when combined with traditional PRSs.

Genome-wide association meta-analysis of spontaneous coronary artery dissection reveals common variants and genes related to artery integrity and tissue-mediated coagulation

This study identifies 17 genetic risk loci for spontaneous coronary artery dissection (SCAD), including 12 new ones, and highlights genes related to artery integrity and coagulation.

Statistical analysis of spatially resolved transcriptomic data by incorporating multi-omics auxiliary information

The paper develops a method to improve statistical power in spatial transcriptomic analysis by integrating multi-omics data while controlling false discovery rate.

Joint dimension reduction and clustering analysis for single-cell RNA-seq and spatial transcriptomics data

This paper introduces DR-SC, a method that jointly performs dimension reduction and spatial clustering for single-cell and spatial transcriptomics data, improving accuracy and biological relevance.

On Cross-ancestry Cancer Polygenic Risk Scores

This study evaluates the utility of breast and prostate cancer polygenic risk scores across different ancestry groups using UK Biobank data, showing significant enrichments in cancer cases within top PRS percentiles.

Multi-scale Inference of Genetic Trait Architecture using Biologically Annotated Neural Networks

This paper introduces BANNs, a probabilistic framework for GWA studies that improves association mapping and enrichment analysis by incorporating biological annotations and variational inference.

Cancer PRSweb - an Online Repository with Polygenic Risk Scores (PRS) for Major Cancer Traits and Their Phenome-wide Exploration in Two Independent Biobanks

The paper introduces Cancer-PRSweb, an online repository of polygenic risk scores for cancer traits, evaluated in two biobanks with predictive performance metrics and phenome-wide association studies.

Genetic association studies of fibromuscular dysplasia identify new risk loci and shared genetic basis with more common vascular diseases