Explanipedia

BrainBridge Characterizes Key Factors affecting Alzheimer’s Disease and Associated Phenotypes Open

Tianyu Liu, Minsheng Hao, Eric Sun, Yaroslav Markov, Le Zhang , et al. · 2025

Single-cell RNA sequencing (scRNA-seq) has significantly advanced our understanding of Alzheimer’s disease and aging by revealing cellular heterogeneity and shifts in cell-type composition between diseased/old and healthy/young individuals…

A unified framework for identification of cell-type-specific spatially variable genes in spatial transcriptomic studies Open

Y. Q. Zeng, Zhuohong Tan, Yuheng Chen, Xinrui Huang, Hongyu Zhao , et al. · 2025

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…

Recessive genomic and phenotypic variation in consanguineous families with cerebral palsy Open

Pritha Bisarad, Yung-Chun Wang, Peter T. Skidmore, Carolina Galaz-Montoya, Sara A. Lewis , et al. · 2025

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…

Spatial dynamics of brain development and neuroinflammation Open

Di Zhang, Leslie A. Kirby, Yingxin Lin, Wenqi Wang, Mengyi Song , et al. · 2025

The ability to spatially map multiple layers of omics information across developmental timepoints enables exploration of the mechanisms driving brain development¹, differentiation, arealization and disease-related alterations. H…

PRIME: a database for 16S rRNA microbiome data with phenotypic reference and comprehensive metadata Open

Zhizhuo Zhang, Hongyu Zhao, Tao Wang · 2025

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…

Pdgfrα deficiency in islet β-cells up-regulates apoptosis of beta-cells and disturbs glucose metabolism in B6 mice Open

Luyao Zhang, Yanpeng Xing, Pai Wang, Jianlei Gu, Jian Peng , et al. · 2025

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…

UNICORN: Towards universal cellular expression prediction with a multi-task learning framework Open

Tianyu Liu, Tinglin Huang, Lijun Wang, Yingxin Lin, Rex Ying , et al. · 2025

Sequence-to-function analysis is a challenging task in human genetics, especially in predicting cell-type-specific multi-omic phenotypes from biological sequences such as individualized gene expression. Here, we present UNICORN, a computat…

Beyond the Genotype: A Multi-Omic Analysis of APOEe4’s Role in Alzheimer’s Disease Open

Yaroslav Markov, Ahana Priyanka, Leqi Xu, Weiwei Wang, Kyra Thrush , et al. · 2025

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…

VISTA Uncovers Missing Gene Expression and Spatial-induced Information for Spatial Transcriptomic Data Analysis Open

Hongyu Zhao, Tianyu Liu, Xiao Luo, Yingxin Lin, Yizhou Sun · 2025

Characterizing cell activities within a spatially resolved context is essential to enhance our understanding of spatially-induced cellular states and features. While single-cell RNA-seq (scRNA-seq) offers comprehensive profiling of cells w…

scGPD: single-cell informed gene panel design for targeted spatial transcriptomics Open

Yunshan Guo, Jia Zhao, Rui B. Chang, Hongyu Zhao · 2025

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…

Incorporating additive genetic effects and linkage disequilibrium information to discover gene-environment interactions using BV-LDER-GE Open

Zihan Dong, Wei Jiang, Jiangnan Shen, Hongyu Li, Yuhan Xie , et al. · 2025

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…

Radiomics-based machine learning for glioma grade classification: a multicenter study with SHapley Additive exPlanations interpretability analysis Open

Yumeng Shi, Wei Jiang, Li Zhou, Yu Shi, Xinran Ji , et al. · 2025

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, …

HSP90 inhibitors in cancer immunotherapy: Therapeutic opportunities and challenges Open

Chao Zhang, Wenying Nie, Qiang Tu, Youming Zhang, Hongyu Zhao , et al. · 2025

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…

Thrombotic microangiopathy multidisciplinary assessment team: demographics, final diagnosis, treatment, and outcomes Open

Matthew Nguyen, Gayathri Dileep, Samir Patel, Fawaz Al Ammary, Minh‐Ha Tran , et al. · 2025

Brain Functional-Structural Gradient Coupling Reflects Development, Behavior and Genetic Influences Open

Simiao Gao, Zhiling Gu, Shengxian Ding, Gefei Wang, Zhengwu Zhang , et al. · 2025

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…

Knockoff procedure improves susceptibility gene identifications in conditional transcriptome-wide association studies Open

Xiangyu Zhang, Lijun Wang, Jia Zhao, Hongyu Zhao · 2025

Multi-Ancestry Transcriptome-wide Association Studies Uncover New Insights into Breast Cancer Genetics and Biology Open

Jie Ping, Guochong Jia, Qiuyin Cai, Xingyi Guo, Jifeng Wang , et al. · 2025

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…

spVelo: RNA velocity inference for multi-batch spatial transcriptomics data Open

Wenxin Long, Tianyu Liu, Lingzhou Xue, Hongyu Zhao · 2025

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…

Improving polygenic risk prediction performance through integrating electronic health records by phenotype embedding Open

Leqi Xu, Wangjie Zheng, Jiaqi Hu, Yingxin Lin, Jia Zhao , et al. · 2025

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…

Correction: Latent profile analysis of anticipatory grief in family caregivers of patients with chronic heart failure and its influencing factors Open

Ting Chen, Li Su, Jiajie Yu, Hongyu Zhao, Haoran Xiao , et al. · 2025

Identification of multi-omic pleiotropy factors for peripheral artery disease Open

Jiaqi Hu, Cassius Iyad Ochoa Chaar, Hongyu Zhao, Andrew T. DeWan · 2025

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…

spEMO: Leveraging Multi-Modal Foundation Models for Analyzing Spatial Multi-Omic and Histopathology Data Open

Hongyu Zhao, Tianyu Liu, Tinglin Huang, Tong Ding, Hao Wu , et al. · 2025

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…

Incorporating local ancestry information to predict genetically associated DNA methylation in admixed populations Open

Youshu Cheng, Geyu Zhou, Hongyu Li, Xinyu Zhang, Amy C. Justice , et al. · 2025

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…

Multi - scale perspective on hydrothermal treatment dewatering of lignite: Synergistic regulation of structural evolution and lightening of pyrolysis tar Open

Shucheng Liu, Haojie Yang, Yichao Zhang, Qingzhou Zeng, Fugui Liu , et al. · 2025

Correction: Single-nucleus RNA sequencing reveals distinct pathophysiological trophoblast signatures in spontaneous preterm birth subtypes Open

Cherilyn Uhm, Jianlei Gu, Weina Ju, Stephanie Pizzella, Hande Oktay , et al. · 2025

Robust pleiotropy-decomposed polygenic scores identify distinct contributions to elevated coronary artery disease polygenic risk Open

Jiaqi Hu, Yixuan Ye, Chi Zhang, Yunfeng Ruan, Pradeep Natarajan , et al. · 2025

Background Polygenic risk score (PRS) have proved to offer robust risk prediction for coronary artery disease (CAD). However, the global CAD PRS summarizes the joint effects of all the markers in the genome, masking potential genetic heter…

Almost Free Enhancement of Multi-Population PRS: From Data-Fission to Pseudo-GWAS Subsampling Open

Leqi Xu, Yikai Dong, Xiaowei Zeng, Z Bian, Geyu Zhou , et al. · 2025

Many multi-population polygenic risk score (PRS) methods have been proposed to improve prediction accuracy in underrepresented populations; however, no single method outperforms other methods across all data scenarios. Although integrating…

Single-cell transcriptomic and chromatin dynamics of the human brain in PTSD Open

Ahyeon Hwang, Mario Škarica, Siwei Xu, Jensine Coudriet, Che-Yu Lee , et al. · 2025

Leveraging pleiotropy to improve genetic risk prediction across diseases Open

Jiaqi Hu, Geyu Zhou, Hongyu Zhao, Andrew T. DeWan · 2025

Background Polygenic scores (PGSs) have shown promise in predicting disease risk, but their predictive accuracy remains limited for many complex diseases. Leveraging the shared genetic architecture among correlated traits may improve predi…

A perspective on developing foundation models for analyzing spatial transcriptomic data Open

Tianyu Liu, Minsheng Hao, Xinhao Liu, Hongyu Zhao · 2025

Do we need a foundation model (FM) for spatial transcriptomic analysis? To answer this question, we prepared this perspective as a primer. We first review the current progress of developing FMs for modeling spatial transcriptomic data and …

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