Zhongming Zhao
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View article: Single-nucleus multiomics reveals the disrupted regulatory programs in three brain regions of sporadic early-onset Alzheimer’s disease
Single-nucleus multiomics reveals the disrupted regulatory programs in three brain regions of sporadic early-onset Alzheimer’s disease Open
Sporadic early-onset Alzheimer’s disease (sEOAD) represents a substantial but less-studied subtype of Alzheimer’s disease (AD). Here, we generated a single-nucleus multiome atlas derived from the postmortem prefrontal cortex, entorhinal co…
View article: FADVI: disentangled representation learning for robust integration of single-cell and spatial omics data
FADVI: disentangled representation learning for robust integration of single-cell and spatial omics data Open
Integrating single-cell and spatial omics data remains challenging due to strong batch effects across experiments and platforms. Existing methods focus on minimizing these effects but cannot disentangle technical variation from true biolog…
View article: DDDR-43. Oncogenic miRNA-155 modulates copper homeostasis to attenuate oncolytic virus efficacy in Glioblastoma
DDDR-43. Oncogenic miRNA-155 modulates copper homeostasis to attenuate oncolytic virus efficacy in Glioblastoma Open
Glioblastoma (GBM) is an aggressive and lethal form of primary brain tumor that rapidly progresses and infiltrates into adjacent normal brain areas. Despite extensive research and aggressive treatments with surgical resection, radiation, c…
View article: DDDR-66. Leveraging protease-resistant IGFBP2 to sensitize glioblastoma to oncolytic HSV therapy
DDDR-66. Leveraging protease-resistant IGFBP2 to sensitize glioblastoma to oncolytic HSV therapy Open
The prognosis for Glioblastoma (GBM) remains grim despite remarkable advances in gene- and immune-targeted therapies, underscoring the urgent need for novel approaches. Oncolytic herpes simplex virus-1 (oHSV) has shown promise in clinical …
View article: GRPa‐PRS: A risk stratification method to identify genetically‐regulated pathways in polygenic diseases
GRPa‐PRS: A risk stratification method to identify genetically‐regulated pathways in polygenic diseases Open
INTRODUCTION Polygenic risk score (PRS) assesses genetic risk for diseases, yet some high‐risk individuals avoid illness while low‐risk individuals develop it. We hypothesize that unknown counterfactors may reverse PRS predictions, offerin…
View article: Fructose and glucose from sugary drinks enhance colorectal cancer metastasis via SORD
Fructose and glucose from sugary drinks enhance colorectal cancer metastasis via SORD Open
The consumption of sugar-sweetened beverages (SSBs), which contain high levels of fructose and glucose, has been causally and mechanistically linked to an increased risk of colorectal cancer (CRC). However, the effects of SSB consumption o…
View article: miR147 promotes mucosal integrity and healing in intestinal inflammation
miR147 promotes mucosal integrity and healing in intestinal inflammation Open
The intestinal mucosal epithelium forms a barrier between luminal contents and the body. MicroRNAs (miRNAs) regulate mucosal homeostasis by controlling inflammatory responses and structural integrity. Here, we discovered a protective role …
View article: Multi-scale Data Improves Performance of Machine Learning Model for Long COVID Prediction
Multi-scale Data Improves Performance of Machine Learning Model for Long COVID Prediction Open
Long COVID affects a substantial proportion of the over 778 million individuals infected with SARS-CoV-2, yet predictive models remain limited in scope. While existing efforts, such as the National COVID Cohort Collaborative (N3C), have le…
View article: BrainGeneBot: a framework for variant prioritization and generative pretrained transformer-informed interpretation across polygenic risk score studies
BrainGeneBot: a framework for variant prioritization and generative pretrained transformer-informed interpretation across polygenic risk score studies Open
Polygenic risk scores (PRS) are widely used to assess genetic susceptibility in Alzheimer’s disease (AD) research. However, the rapid expansion of PRS studies has led to dataset-specific biases—stemming from factors like population makeup,…
View article: Cytoplasmic dynamics are overlooked in single nuclei RNA-seq but can be rescued by CytoRescue, a generative AI model to recover cytoplasm enriched gene
Cytoplasmic dynamics are overlooked in single nuclei RNA-seq but can be rescued by CytoRescue, a generative AI model to recover cytoplasm enriched gene Open
Single-nucleus RNA sequencing (snRNA-seq) generates single cell data from nuclei. It provides valuable compatibility with frozen or difficult-to-dissociate tissues while avoiding stress responses in fresh samples. However, cytoplasmic depl…
View article: Estrogen-related receptor alpha promotes skeletal muscle regeneration and mitigates muscular dystrophy
Estrogen-related receptor alpha promotes skeletal muscle regeneration and mitigates muscular dystrophy Open
Skeletal muscle regeneration in chronic muscle diseases such as Duchenne Muscular Dystrophy (DMD) has remained clinically unsurmountable. Estrogen-related receptor alpha (ERRα) plays a critical role in adult skeletal muscle metabolism and …
View article: Genetic, Transcriptomic, and Epigenomic Insights into Sjögren’s Disease: An Integrative Network Investigation and Immune Diseases Comparison
Genetic, Transcriptomic, and Epigenomic Insights into Sjögren’s Disease: An Integrative Network Investigation and Immune Diseases Comparison Open
Sjögren’s disease (SjD) is a systemic autoimmune disorder primarily causing dry eyes and mouth. It frequently overlaps with other autoimmune diseases (AIDs), including rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). Howev…
View article: Figure S3 from Depletion of Adipose Stroma-Like Cancer-Associated Fibroblasts Potentiates Pancreatic Cancer Immunotherapy
Figure S3 from Depletion of Adipose Stroma-Like Cancer-Associated Fibroblasts Potentiates Pancreatic Cancer Immunotherapy Open
A, Fig. 4 schematic testing if D-CAN synergizes with immune checkpoint blockade (aPDL1) in male and female mice. B, Initial body weights in experimental mice. C, Tumor weight from an experiment in female mice investigating the effects of D…
View article: Figure S1 from Depletion of Adipose Stroma-Like Cancer-Associated Fibroblasts Potentiates Pancreatic Cancer Immunotherapy
Figure S1 from Depletion of Adipose Stroma-Like Cancer-Associated Fibroblasts Potentiates Pancreatic Cancer Immunotherapy Open
A, Fig. 1 schematic of testing the effect of Pdgfrb+ CAF depletion on PDAC progression. B, initial body weight in experiment A. C, experiment A tumor section H&E staining showing inflammation (i), necrosis (n), and well-differentiated tumo…
View article: Figure S2 from Depletion of Adipose Stroma-Like Cancer-Associated Fibroblasts Potentiates Pancreatic Cancer Immunotherapy
Figure S2 from Depletion of Adipose Stroma-Like Cancer-Associated Fibroblasts Potentiates Pancreatic Cancer Immunotherapy Open
The effects of Pdgfrb+ CAF vs ASC-like CAF depletion on the TME. A, tumor section immunofluorescence for CD3 (Red) expression to measure T-cell infiltration and nuclei (blue) (left), CD3+ cell quantification (right). B, tumor section immun…
View article: Dr. Kinase: predicting the drug-resistance hotspots of protein kinases
Dr. Kinase: predicting the drug-resistance hotspots of protein kinases Open
Protein kinases (PKs) regulate various cellular functions, and are targeted by small-molecule kinase inhibitors (KIs) in cancers and other diseases. However, drug resistance (DR) of KIs occurs through critical mutations in four types of re…
View article: iGTP: learning interpretable cellular embedding for inferring biological mechanisms underlying single-cell transcriptomics
iGTP: learning interpretable cellular embedding for inferring biological mechanisms underlying single-cell transcriptomics Open
Deep-learning models like Variational AutoEncoder have enabled low dimensional cellular embedding representation for large-scale single-cell transcriptomes and shown great flexibility in downstream tasks. However, biologically meaningful l…
View article: Key Ferroptosis Genes and their Predictive and Diagnostic Value in Fanconi Anemia
Key Ferroptosis Genes and their Predictive and Diagnostic Value in Fanconi Anemia Open
Fanconi anemia (FA) and ferroptosis both affect tumor-related processes. However, few studies have reported on genetic associations between FA and ferroptosis. Our study evaluated the usefulness of genes related to ferroptosis in predictin…
View article: Enhanced and Interpretable Prediction of Multiple Cancer Types Using a Stacking Ensemble Approach with SHAP Analysis
Enhanced and Interpretable Prediction of Multiple Cancer Types Using a Stacking Ensemble Approach with SHAP Analysis Open
Background: Cancer is a leading cause of death worldwide, and its early detection is crucial for improving patient outcomes. This study aimed to develop and evaluate ensemble learning models, specifically stacking, for the accurate predict…
View article: BMAL1–HIF2A heterodimer modulates circadian variations of myocardial injury
BMAL1–HIF2A heterodimer modulates circadian variations of myocardial injury Open
Acute myocardial infarction is a leading cause of morbidity and mortality worldwide 1 . Clinical studies have shown that the severity of cardiac injury after myocardial infarction exhibits a circadian pattern, with larger infarcts and poor…
View article: Enhancing the utility of polygenic scores in Alzheimer’s disease through systematic curation and annotation
Enhancing the utility of polygenic scores in Alzheimer’s disease through systematic curation and annotation Open
Introduction Polygenic Scores (PGSs) assess cumulative genetic risk variants that contribute to the association with complex diseases like Alzheimer’s Disease (AD). The PGS Catalog is a valuable repository of PGSs of various complex diseas…
View article: Figure S2 from Depletion of Adipose Stroma-Like Cancer-Associated Fibroblasts Potentiates Pancreatic Cancer Immunotherapy
Figure S2 from Depletion of Adipose Stroma-Like Cancer-Associated Fibroblasts Potentiates Pancreatic Cancer Immunotherapy Open
The effects of Pdgfrb+ CAF vs ASC-like CAF depletion on the TME. A, tumor section immunofluorescence for CD3 (Red) expression to measure T-cell infiltration and nuclei (blue) (left), CD3+ cell quantification (right). B, tumor section immun…