Feixiong Cheng
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View article: PrevCardioOncAI: Machine Learning Algorithms for Predicting Cardiovascular Disease in Cancer Survivors
PrevCardioOncAI: Machine Learning Algorithms for Predicting Cardiovascular Disease in Cancer Survivors Open
Background Cardiovascular disease (CVD) is a leading cause of death in cancer survivors. Predicting CVD risk in this population remains challenging. Risk prediction models that use machine learning algorithms could provide an objective met…
View article: A Quantum Framework for Protein Binding‐Site Structure Prediction on Utility‐Level Quantum Processors
A Quantum Framework for Protein Binding‐Site Structure Prediction on Utility‐Level Quantum Processors Open
Accurate prediction of protein active‐site structures remains a central challenge in structural biology, especially for short and flexible peptide fragments where conventional and simulation‐based methods often fail. Here, we present a qua…
View article: Dysregulation of innate immunity and cellular metabolism through virus-induced deISGylation
Dysregulation of innate immunity and cellular metabolism through virus-induced deISGylation Open
SUMMARY Interferon-stimulated gene 15 (ISG15) regulates diverse cellular responses including antiviral immunity through its conjugation to proteins, a process known as ISGylation. Several pathogens, including SARS-CoV-2, subvert ISGylation…
View article: Analyses of GWAS and Sub‐Threshold Loci Lead to the Discovery of Dendrite Development and Morphology Dysfunction Underlying Schizophrenia Genetic Risk
Analyses of GWAS and Sub‐Threshold Loci Lead to the Discovery of Dendrite Development and Morphology Dysfunction Underlying Schizophrenia Genetic Risk Open
Schizophrenia (SCZ) is highly polygenic, and its biological underpinnings remain unclear. In this study, a cost‐effective strategy of including sub‐threshold GWAS (subGWAS) loci (i.e., 5 × 10 −8 < P ≤ 10 −6 ) in analysis is explored to inc…
View article: Systematic characterization of cell type-specific master metabolic regulators in Alzheimer's disease
Systematic characterization of cell type-specific master metabolic regulators in Alzheimer's disease Open
Alzheimer’s disease (AD) exhibits metabolic heterogeneity; yet, the consequences on metabolic dynamics in a cell-type-specific manner and the underlying metabolite-sensor network basis remain unclear. Here, we show that neurons exhibit a s…
View article: Development and Characterization of Triazole-Based WDR5 Inhibitors for the Treatment of Glioblastoma
Development and Characterization of Triazole-Based WDR5 Inhibitors for the Treatment of Glioblastoma Open
Glioblastoma (GBM) cancer stem cells (CSCs) contribute to tumor recurrence, treatment resistance, and dismal clinical outcomes. Genetic and pharmacological evidence suggests that the nuclear scaffolding protein WD-repeat containing protein…
View article: Cell type-specific master metabolic regulators of Alzheimer’s disease
Cell type-specific master metabolic regulators of Alzheimer’s disease Open
Alzheimer’s disease (AD) exhibits metabolic heterogeneity; yet, the consequences on metabolic dynamics in a cell-type-specific manner and the underlying metabolite-sensor network basis remain unclear. Here, we show that neurons exhibit a s…
View article: DrugLM: A Unified Framework to Enhance Drug-Target Interaction Predictions by Incorporating Textual Embeddings via Language Models
DrugLM: A Unified Framework to Enhance Drug-Target Interaction Predictions by Incorporating Textual Embeddings via Language Models Open
Motivation Accurate prediction of drug–target interactions (DTIs) is central to computational drug discovery, offering the potential to reduce experimental costs and accelerate development timelines. While existing deep learning approaches…
View article: A Scalable Human Brain Cell Atlas Foundation Model Dissects the Cellular Immune Codes and Cognitive Resilience
A Scalable Human Brain Cell Atlas Foundation Model Dissects the Cellular Immune Codes and Cognitive Resilience Open
The biological basis of resilience to cognitive decline and Alzheimer’s disease (AD) remains unclear, hindering the development of effective interventions for brain health. Here, we present the largest human brain single-nucleus RNA-seq at…
View article: Prediction of Protein Three-dimensional Structures via a Hardware-Executable Quantum Computing Framework
Prediction of Protein Three-dimensional Structures via a Hardware-Executable Quantum Computing Framework Open
Accurate prediction of protein active site structures remains a central challenge in structural biology, particularly for short and flexible peptide fragments where conventional methods often fail. Here, we present a quantum computing fram…
View article: Globalization of Alzheimer’s disease clinical trials: Current characteristics and future goals
Globalization of Alzheimer’s disease clinical trials: Current characteristics and future goals Open
There are 182 active trials and 138 unique drugs in the current Alzheimer's disease drug development pipeline. Of these, 33 % of trials are global involving both North American and non-North American sites. Phase 3 clinical trials are more…
View article: Erratum to ‘Utilization of precision medicine digital twins for drug discovery in Alzheimer's disease’, Neurotherapeutics, 22(3), e00553
Erratum to ‘Utilization of precision medicine digital twins for drug discovery in Alzheimer's disease’, Neurotherapeutics, 22(3), e00553 Open
View article: SOAR elucidates biological insights and empowers drug discovery through spatial transcriptomics
SOAR elucidates biological insights and empowers drug discovery through spatial transcriptomics Open
Spatial transcriptomics enables multiplex profiling of gene cellular expression and location within the tissue context. Although large volumes of spatial transcriptomics data have been generated, the lack of systematic curation and analysi…
View article: Combining xQTL and genome-wide association studies from ethnically diverse populations improves druggable gene discovery
Combining xQTL and genome-wide association studies from ethnically diverse populations improves druggable gene discovery Open
View article: A Deep Subgrouping Framework for Precision Drug Repurposing via Emulating Clinical Trials on Real-world Patient Data
A Deep Subgrouping Framework for Precision Drug Repurposing via Emulating Clinical Trials on Real-world Patient Data Open
Drug repurposing identifies new therapeutic uses for existing drugs, reducing the time and costs compared to traditional de novo drug discovery. Most existing drug repurposing studies using real-world patient data often treat the en…
View article: Alzheimer's disease drug development pipeline: 2025
Alzheimer's disease drug development pipeline: 2025 Open
Clinical trials for Alzheimer's disease (AD) must be registered on clinicaltrials.gov. The registry presents a variety of types of information related to the planned clinical trial. We assess clinicaltrials.gov to document and compare aspe…
View article: Genomic and epigenomic insights into purkinje and granule neurons in Alzheimer’s disease and related dementia using single-nucleus multiome analysis
Genomic and epigenomic insights into purkinje and granule neurons in Alzheimer’s disease and related dementia using single-nucleus multiome analysis Open
View article: Efficacy and safety of passive immunotherapies targeting amyloid beta in Alzheimer’s disease: A systematic review and meta-analysis
Efficacy and safety of passive immunotherapies targeting amyloid beta in Alzheimer’s disease: A systematic review and meta-analysis Open
Background While recently U.S. FDA-approved anti-amyloid beta (anti-Aβ) monoclonal antibodies (mAbs) offer new treatment approaches for patients suffering from Alzheimer’s disease (AD), these medications also carry potential safety concern…
View article: Author Correction: The lactate receptor HCAR1 drives the recruitment of immunosuppressive PMN-MDSCs in colorectal cancer
Author Correction: The lactate receptor HCAR1 drives the recruitment of immunosuppressive PMN-MDSCs in colorectal cancer Open
View article: Deep learning-based cell-specific gene regulatory networks inferred from single-cell multiome data
Deep learning-based cell-specific gene regulatory networks inferred from single-cell multiome data Open
Gene regulatory networks (GRNs) provide a global representation of how genetic/genomic information is transferred in living systems and are a key component in understanding genome regulation. Single-cell multiome data provide unprecedented…
View article: Drug repurposing for Alzheimer’s disease and other neurodegenerative disorders
Drug repurposing for Alzheimer’s disease and other neurodegenerative disorders Open
Repurposed drugs provide a rich source of potential therapies for Alzheimer's disease (AD) and other neurodegenerative disorders (NDD). Repurposed drugs have information from non-clinical studies, phase 1 dosing, and safety and tolerabilit…
View article: Discovery of plasma proteins and metabolites associated with left ventricular cardiac dysfunction in pan-cancer patients
Discovery of plasma proteins and metabolites associated with left ventricular cardiac dysfunction in pan-cancer patients Open
Background Cancer-therapy related cardiac dysfunction (CTRCD) remains a significant cause of morbidity and mortality in cancer survivors. In this study, we aimed to identify differential plasma proteins and metabolites associated with left…
View article: Elucidating the pharmacological foundations and mechanisms of the Sihai Shuyu formula in treating Graves’ disease through integrated serum metabolomics and network pharmacology with molecular docking techniques
Elucidating the pharmacological foundations and mechanisms of the Sihai Shuyu formula in treating Graves’ disease through integrated serum metabolomics and network pharmacology with molecular docking techniques Open
Ethnopharmacological relevance The Sihai Shuyu Formula (SHSY) shows promising potential for treating Graves’ disease (GD), although the therapeutic mechanisms and pharmacological basis of SHSY have not been thoroughly evaluated. Objective …
View article: A network-based systems genetics framework identifies pathobiology and drug repurposing in Parkinson’s disease
A network-based systems genetics framework identifies pathobiology and drug repurposing in Parkinson’s disease Open
Parkinson's disease (PD) is the second most prevalent neurodegenerative disorder. However, current treatments only manage symptoms and lack the ability to slow or prevent disease progression. We utilized a systems genetics approach to iden…
View article: Single-cell digital twins identify drug targets and repurposable medicine in Alzheimer’s disease
Single-cell digital twins identify drug targets and repurposable medicine in Alzheimer’s disease Open
Alzheimer’s disease (AD) is a complex and poorly understood neurodegenerative disorder without sufficiently effective treatments. Novel approaches to identify FDA-approved drugs that may hold potential for mitigating symptoms of AD hold pr…
View article: Combining genetics with real-world patient data enables ancestry-specific target identification and drug discovery in Alzheimer’s disease
Combining genetics with real-world patient data enables ancestry-specific target identification and drug discovery in Alzheimer’s disease Open
Although high-throughput DNA/RNA sequencing technologies have generated massive genetic and genomic data in human disease, these findings have not been translated into new patient treatments. To address this problem, we utilized Mendelian …
View article: Combining xQTL and Genome-Wide Association Studies from Ethnically Diverse Populations Improves Druggable Gene Discovery
Combining xQTL and Genome-Wide Association Studies from Ethnically Diverse Populations Improves Druggable Gene Discovery Open
View article: Critical Evaluation of Real-World Evidence for Repurposable Medicines in the Alzheimer's Disease Drug Development Pipeline Using a Target Trial Emulation
Critical Evaluation of Real-World Evidence for Repurposable Medicines in the Alzheimer's Disease Drug Development Pipeline Using a Target Trial Emulation Open
View article: Single‐microglia transcriptomic transition network‐based prediction and real‐world patient data validation identifies ketorolac as a repurposable drug for Alzheimer's disease
Single‐microglia transcriptomic transition network‐based prediction and real‐world patient data validation identifies ketorolac as a repurposable drug for Alzheimer's disease Open
INTRODUCTION High microglial heterogeneities hinder the development of microglia‐targeted treatment for Alzheimer's disease (AD). METHODS We integrated 0.7 million single‐nuclei RNA‐sequencing transcriptomes from human brains using a varia…
View article: Single‐Microglia Transcriptomic Transition Network‐based Prediction and Real‐world Patient Data Validation Identifies Ketorolac as a Repurposable Drug for Alzheimer’s Disease
Single‐Microglia Transcriptomic Transition Network‐based Prediction and Real‐world Patient Data Validation Identifies Ketorolac as a Repurposable Drug for Alzheimer’s Disease Open
Background Microglia have been implicated as a key aspect of the pathology of Alzheimer’s disease (AD). However, high microglial heterogeneities, including disease‐associated microglia (DAM), tau microglia (tau‐pathology related), and neur…