Hongyu Zhao
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View article: PERADIGM: Phenotype embedding similarity-based rare disease gene mapping
PERADIGM: Phenotype embedding similarity-based rare disease gene mapping Open
Identifying genes associated with rare diseases remains challenging due to the scarcity of patients and the limited statistical power of traditional association methods. Here, we introduce PERADIGM ( P henotype E mbedding similarity-based …
View article: Glis3 Is a Modifier of Cyst Progression in Autosomal Dominant Polycystic Kidney Disease
Glis3 Is a Modifier of Cyst Progression in Autosomal Dominant Polycystic Kidney Disease Open
Background: Autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations affecting polycystin-1 (PC1) or polycystin-2 (PC2). The existence of a ‘cilia-dependent cyst activation’ (CDCA) pathway has been identified by showing …
View article: A unified framework for identification of cell-type-specific spatially variable genes in spatial transcriptomic studies
A unified framework for identification of cell-type-specific spatially variable genes in spatial transcriptomic studies Open
Characterizing cell-type-specific spatially variable genes (SVGs) within tissue context is essential for exploring the landscape of complex biological systems in spatial transcriptomic (ST) studies. In this paper, we present a unified fram…
View article: Recessive genomic and phenotypic variation in consanguineous families with cerebral palsy
Recessive genomic and phenotypic variation in consanguineous families with cerebral palsy Open
Cerebral palsy (CP) is a neurodevelopmental disorder of motor function, with genetic etiologies, particularly de novo variants, identified in approximately one-third of cases. The contribution of consanguinity – long-recognized as a CP ris…
View article: IMMU-85. Uncovering differences in local and systemic immunity in human primary and metastatic brain tumors
IMMU-85. Uncovering differences in local and systemic immunity in human primary and metastatic brain tumors Open
While therapies targeting T cell immune checkpoint receptors have demonstrated clinical efficacy for patients with brain metastases, adults with high-grade gliomas fail to benefit. We comprehensively profiled intratumoral and circulating T…
View article: PRIME: a database for 16S rRNA microbiome data with phenotypic reference and comprehensive metadata
PRIME: a database for 16S rRNA microbiome data with phenotypic reference and comprehensive metadata Open
PRIME (Phenotypic Reference for Integrated Microbiome Enrichment) is a curated and standardized database of human microbiome 16S rRNA amplicon sequencing data, designed to facilitate cross-study analysis, reproducibility, and phenotype-dri…
View article: Pdgfrα deficiency in islet β-cells up-regulates apoptosis of beta-cells and disturbs glucose metabolism in B6 mice
Pdgfrα deficiency in islet β-cells up-regulates apoptosis of beta-cells and disturbs glucose metabolism in B6 mice Open
Introduction Pancreatic β-cell dysfunction is a key contributor to the development of Type 2 Diabetes. The platelet-derived growth factor receptor α (PDGFRα) is known to play a crucial role in β-cell proliferation and expansion. However, i…
View article: Beyond the Genotype: A Multi-Omic Analysis of APOEe4’s Role in Alzheimer’s Disease
Beyond the Genotype: A Multi-Omic Analysis of APOEe4’s Role in Alzheimer’s Disease Open
Alzheimer’s disease (AD) is characterized by widespread molecular dysregulation, with the APOEe4 allele recognized as its strongest genetic risk factor. However, the mechanisms by which APOEe4 drives distinct molecular changes – whether by…
View article: TS-Reasoner: Aligning Time Series Foundation Models with LLM Reasoning
TS-Reasoner: Aligning Time Series Foundation Models with LLM Reasoning Open
Time series reasoning is crucial to decision-making in diverse domains, including finance, energy usage, traffic, weather, and scientific discovery. While existing time series foundation models (TSFMs) can capture low-level dynamic pattern…
View article: scGPD: single-cell informed gene panel design for targeted spatial transcriptomics
scGPD: single-cell informed gene panel design for targeted spatial transcriptomics Open
In targeted spatial transcriptomics technologies, a key challenge is to select an informative gene panel that captures the complexity of cellular and spatial heterogeneity within tissues. Many existing methods use prior knowledge or heuris…
View article: Incorporating additive genetic effects and linkage disequilibrium information to discover gene-environment interactions using BV-LDER-GE
Incorporating additive genetic effects and linkage disequilibrium information to discover gene-environment interactions using BV-LDER-GE Open
Uncovering environmental factors interacting with genetic factors to influence complex traits is important in genetic epidemiology and disease etiology. We introduce BiVariate Linkage-Disequilibrium Eigenvalue Regression for Gene-Environme…
View article: Radiomics-based machine learning for glioma grade classification: a multicenter study with SHapley Additive exPlanations interpretability analysis
Radiomics-based machine learning for glioma grade classification: a multicenter study with SHapley Additive exPlanations interpretability analysis Open
We successfully developed and validated a robust, interpretable radiomics-based model that accurately predicts glioma WHO grade preoperatively. Its promising performance across diverse datasets suggests potential for clinical translation, …
View article: HSP90 inhibitors in cancer immunotherapy: Therapeutic opportunities and challenges
HSP90 inhibitors in cancer immunotherapy: Therapeutic opportunities and challenges Open
Heat shock protein 90 (HSP90), a highly evolutionarily conserved molecular chaperone, plays critical roles in both physiological processes and disease pathogenesis, with particularly prominent involvement in cancer initiation and progressi…
View article: Thrombotic microangiopathy multidisciplinary assessment team: demographics, final diagnosis, treatment, and outcomes
Thrombotic microangiopathy multidisciplinary assessment team: demographics, final diagnosis, treatment, and outcomes Open
Rationale & objective Thrombotic Microangiopathies (TMAs) include an etiological diverse group of phenotypically similar disorders. While individually rare, they are seen as an aggregate with regularity. Prior reports suggested the importa…
View article: Brain Functional-Structural Gradient Coupling Reflects Development, Behavior and Genetic Influences
Brain Functional-Structural Gradient Coupling Reflects Development, Behavior and Genetic Influences Open
Gradients are increasingly used to characterize the brain’s macroscale organization, offering low-dimensional representations of structural and functional connectivity. However, how structural-functional gradient coupling evolves during de…
View article: Multi-Ancestry Transcriptome-wide Association Studies Uncover New Insights into Breast Cancer Genetics and Biology
Multi-Ancestry Transcriptome-wide Association Studies Uncover New Insights into Breast Cancer Genetics and Biology Open
Genome-wide association studies (GWAS) have identified over 200 genetic risk loci for breast cancer, yet the target genes in these loci remain largely unknown. To address this knowledge gap, we conducted a series of multi-ancestry transcri…
View article: spVelo: RNA velocity inference for multi-batch spatial transcriptomics data
spVelo: RNA velocity inference for multi-batch spatial transcriptomics data Open
RNA velocity has emerged as a powerful tool to interpret transcriptional dynamics and infer trajectory from snapshot datasets. However, current methods fail to utilize the spatial information inherent in spatial transcriptomics and lack sc…
View article: Improving polygenic risk prediction performance through integrating electronic health records by phenotype embedding
Improving polygenic risk prediction performance through integrating electronic health records by phenotype embedding Open
Large-scale biobanks provide comprehensive electronic health records (EHRs) that capture detailed clinical phenotypes, potentially enhancing disease risk prediction. However, traditional polygenic risk score (PRS) methods rely on simplifie…
View article: The relationship between sleep patterns and the risk of edentulism: evidence from the CHARLS
The relationship between sleep patterns and the risk of edentulism: evidence from the CHARLS Open
Background Edentulism is a common disease among the elderly. The relationship between sleep patterns and edentulism has not been fully explored. Methods This study utilized baseline and follow-up data from the China Health and Retirement L…
View article: Identification of multi-omic pleiotropy factors for peripheral artery disease
Identification of multi-omic pleiotropy factors for peripheral artery disease Open
Background: Peripheral artery disease (PAD) is prevalent and frequently co-occurs with type 2 diabetes (T2D) and coronary artery disease (CAD). Although shared genetic factors may contribute to these comorbidities, few studies have examine…
View article: spEMO: Leveraging Multi-Modal Foundation Models for Analyzing Spatial Multi-Omic and Histopathology Data
spEMO: Leveraging Multi-Modal Foundation Models for Analyzing Spatial Multi-Omic and Histopathology Data Open
Recent advances in pathology foundation models (PFMs), which are pretrained on large-scale histopathological images, have significantly accelerated progress in disease-centered applications. In parallel, spatial multi-omic technologies col…
View article: Incorporating local ancestry information to predict genetically associated DNA methylation in admixed populations
Incorporating local ancestry information to predict genetically associated DNA methylation in admixed populations Open
Methylome-wide association studies (MWASs) have identified many 5′-cytosine-phosphate-guanine-3′ (CpG) sites associated with complex traits. Several methods have been developed to predict CpG methylation levels from genotypes when the dire…