PubMed HealthSearch

SEARCH · PubMed Health

Results for “Machine learning integration”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 145 records · Page 8Linked to original sources

Q RadFusion: Hybrid Quantum Classical Radiogenomic Framework for Breast Cancer Diagnosis.

BACKGROUND AND PURPOSE: Breast cancer remains the most common cancer in women worldwide, with early and accurate diagnosis critical for patient survival. Radiogenomics integrates imaging phenotypes with genomic profiles, offering a pathway to precision diagnostics. However, existing classical machine learning models often struggle with the high dimensionality and heterogeneity of multimodal data, leading to issues in calibration and reproducibility. This study presents Q RadFusion, a hybrid quantum-classical framework designed to enhance breast cancer diagnosis by fusing mammography and genomics data. METHODS: Q RadFusion was implemented on two publicly available datasets: CBIS-DDSM (2,600 curated mammography cases, TCIA) and TCGA-BRCA (1,000 genomic profiles, GDC). Imaging preprocessing included bias-field correction, segmentation, and harmonization, while genomic data underwent normalization and imputation. Feature selection was performed using the Quantum Approximate Optimization Algorithm (QAOA), and features were mapped into a quantum Hilbert space using Variational Quantum Circuits (VQC). For multimodal fusion, ResNet encoded mammography features, and a Transformer encoded genomic features. Patient-level and site-held-out splits were used for evaluation. RESULTS: Q RadFusion achieved an AUC of 0.96 and accuracy of 94%, outperforming baselines including CNN-LSTM, ResNet + XGBoost, and multimodal Transformers. Ablation studies confirmed the contribution of quantum components, with optimal performance observed at circuit depth, qubits, and QAOA layers. The model also demonstrated improved calibration and ~ 80% fewer parameters compared to deep fusion networks. CONCLUSION: Q RadFusion demonstrates that hybrid quantum-classical radiogenomic integration can deliver accurate, reproducible, and clinically meaningful diagnostic support for breast cancer, with strong potential for future clinical translation.

Breast Cancer

Engineering Bacillus Subtilis for Efficient Biosynthesis of Riboflavin: Current Knowledge and Future Perspectives.

Riboflavin is an essential water-soluble vitamin that serves as a precursor for the biosynthesis of the flavin cofactors FMN and FAD, which play pivotal roles in numerous redox and energy metabolism reactions. With the growing global demand for sustainable vitamin production, microbial fermentation has become an attractive alternative to chemical synthesis due to its environmental and economic advantages. Among microbial hosts, Bacillus subtilis has emerged as a leading cell factory for riboflavin production owing to its GRAS status, well-characterized genetics, and efficient protein secretion system. This review provides a comprehensive overview of recent advances in metabolic engineering strategies to enhance riboflavin biosynthesis in B. subtilis. Key topics include strengthening biosynthetic and precursor pathways, relieving feedback inhibition, balancing metabolic flux and cell growth, employing adaptive laboratory evolution, and utilizing omics-guided optimization and 13C metabolic flux analysis. Moreover, the integration of synthetic biology tools such as riboswitch engineering, regulatory element design, and high-throughput screening has significantly accelerated strain improvement. Despite remarkable progress, challenges remain in achieving precise regulatory control, optimizing multi-gene expression, and enhancing genome integration efficiency. Future research combining multi-omics data, synthetic regulatory design, and machine learning-driven predictive modeling is expected to further advance the development of intelligent B. subtilis cell factories. However, the practical implementation of these systems remains constrained by the metabolic burden of overproduction and the lack of universal regulatory models that can predict strain performance across varying industrial scales.

Bacillus subtilis

Integrated multi-omics analyses identify an RAS-SLC11A2-associated molecular framework linking iron metabolism with PCOS-related cardiometabolic risk.

INTRODUCTION: PCOS is a common endocrine disorder with elevated cardiometabolic risk, yet the role of the renin-angiotensin system (RAS)-iron metabolism axis in this comorbidity remains unclear. We explored its underlying mechanisms and evaluated the therapeutic potential of gentiopicroside. METHODS: Integrated multi-omics analyses combining transcriptomics, single-cell RNA sequencing, Mendelian randomization, machine learning, molecular docking, and in vitro functional assays were performed to identify shared molecular pathways and therapeutic targets across PCOS, hypertension, NAFLD, and T2DM. RESULTS: SLC11A2 was consistently dysregulated in PCOS transcriptomic datasets, and associated with iron metabolism, inflammatory response and oxidative stress pathways. Genetic analyses validated RAS-related regulation in hypertension susceptibility and revealed shared genetic architecture between PCOS and cardiometabolic traits. Network and single-cell analyses characterized SLC11A2-associated molecular patterns in disease-relevant cell types; machine learning identified disease-classifying molecular signatures. Gentiopicroside alleviated inflammatory and oxidative stress phenotypes, including reduced IL-6 expression and reactive oxygen species accumulation. CONCLUSION: This study defines an RAS-SLC11A2 molecular framework linking iron metabolism dysregulation to PCOS-related cardiometabolic risk, elucidating the mechanisms connecting ovarian dysfunction, inflammation, oxidative stress and hypertension, and supports gentiopicroside as a promising therapeutic candidate.

Humans

Predicting host tropism in influenza a viruses: insights from multi-segment nucleotide signatures.

BACKGROUND: Influenza A virus (IAV) poses a significant public health threat due to its cross-species transmission and complex host adaptation mechanisms. This study integrated whole-genome data from avian, human, swine, and bovine IAV strains, using machine learning to predict viral host tropism based on nucleotide site features and to identify key sites driving host adaptation along with their synergistic effects. METHODS: A total of 64,000 IAV sequences from avian, human, swine, and bovine hosts were analyzed to build host-prediction models. A four-class classification framework (avian, human, swine, bovine) was constructed using nucleotide site features from all eight genomic segments (PB2, PB1, PA, HA, NP, NA, MP, NS). Eight machine learning algorithms (logistic regression, decision tree, random forest, SVM, KNN, gradient boosting, XGBoost, LightGBM) were benchmarked via 10-fold stratified cross-validation. Model performance was evaluated using accuracy, precision, recall, F1-score, AUPRC, and AUC. SHAP (SHapley Additive exPlanations) analysis prioritized critical nucleotide sites, while bivariate association tests identified synergistic/antagonistic interactions between sites. Nucleotide composition profiles were compared across host groups using hierarchical clustering and heatmap visualization. RESULTS: The XGBoost algorithm demonstrated the best and most stable performance, achieving an AUC value of over 0.95 in distinguishing human-derived sequences from non-human ones. SHAP analysis identified the top 20 critical nucleotide sites for each gene segment, such as sites 46 and 698 in the NS segment. Nucleotide composition analysis revealed high similarity between human and swine sequences in the HA and PB2 segments, and between avian and bovine sequences. The HA segment was particularly challenging in differentiating human from swine strains. Bivariate site association analysis uncovered significant synergistic or antagonistic effects between key sites within gene segments, forming complex networks. For instance, in the NS segment, a positive prediction contribution was observed when sites 371, 698, and 419 were all G. CONCLUSIONS: This study advances our mechanistic understanding of IAV host adaptation, identifies molecular determinants for zoonotic risk stratification, and establishes a scalable machine learning framework for predicting viral host tropism through nucleotide signature analysis, thereby enhancing surveillance strategies and informing preventive measures against emerging viral threats.

Influenza A virus

Machine Learning-Based Identification of Survival-Associated CpG Biomarkers in Pancreatic Ductal Adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is an exceptionally aggressive cancer with a 5-year survival rate of less than 10%, driven by late-stage diagnosis, limited treatment options, and a lack of reliable biomarkers for early detection and prognosis. In this study, we integrated DNA methylation data from TCGA and ICGC cohorts, categorizing samples based on survival time, and identified 688 differentially methylated CpG sites, along with 224 CpG biomarkers significantly associated with patient survival through statistical and machine learning-based analyses. We developed a random forest model to predict patient survival, achieving 85.2% accuracy for short-survival patients and 70.0% for long-survival patients in the validation set. External dataset validation further confirmed the model's robustness and accuracy. De novo motif analysis of genomic regions surrounding the 224 CpG biomarkers identified TWIST1 and FOXA2 as key transcriptional regulators enriched in survival-associated CpG sites, linking their activity to patient survival outcomes. Collectively, our findings highlight valuable epigenetic biomarkers and provide a predictive model to assess PDAC risk levels post-surgery, offering the potential for improved patient stratification and personalized therapeutic strategies.

DNA methylation

Machine Learning-Based Identification of Survival-Associated CpG Biomarkers in Pancreatic Ductal Adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is an exceptionally aggressive cancer with a 5-year survival rate of less than 10%, driven by late-stage diagnosis, limited treatment options, and a lack of reliable biomarkers for early detection and prognosis. In this study, we integrated DNA methylation data from TCGA and ICGC cohorts, categorizing samples based on survival time, and identified 684 differentially methylated CpG sites, along with 224 CpG biomarkers significantly associated with patient survival through statistical and machine learning-based analyses. We developed a random forest model to predict patient survival, achieving 85.2% accuracy for short-survival patients and 70.0% for long-survival patients in the validation set. External dataset validation further confirmed the model's robustness and accuracy. De novo motif analysis of genomic regions surrounding the 224 CpG biomarkers identified TWIST1 and FOXA2 as key transcriptional regulators enriched in survival-associated CpG sites, linking their activity to patient survival outcomes. Collectively, our findings highlight valuable epigenetic biomarkers and provide a predictive model to assess PDAC risk levels post-surgery, offering the potential for improved patient stratification and personalized therapeutic strategies.

Journal Article

Integrative multi-omics analysis unravels the metabolic landscape and reveals serum biomarkers for early diagnosis of hyperuricemia.

BACKGROUND: Hyperuricemia (HUA) is a major risk factor for gout and multiple metabolic disorders. Although serum uric acid (UA) is the gold standard for HUA diagnosis, it fails to reflect early metabolic disturbances and shows limited predictive value for asymptomatic HUA. This study sought to elucidate the pathological mechanisms underlying HUA and identify novel diagnostic biomarkers beyond UA. METHODS: This study enrolled 195 patients with HUA and 98 healthy controls. Global metabolomics and proteomics profiling were performed to characterize molecular alterations underlying HUA. Based on the biological relevance of the shared dysregulated pathways, a pathway correlation network was constructed to elucidate the pathological mechanisms driving HUA initiation and progression. Furthermore, diagnostic biomarkers for HUA were identified using machine learning algorithms, and were validated with an external cohort. RESULTS: HUA patients exhibited distinct metabolic and proteomic profiles compared with healthy controls. Integrated multi-omics pathway analysis revealed that peroxisome proliferators-activated receptor signaling pathway, arachidonic acid metabolism, purine metabolism, pyrimidine metabolism and sphingolipid signaling pathway were significantly dysregulated in HUA. Among them, arachidonic acid metabolism was identified as a hub pathway involved in HUA progression. Furthermore, a metabolite panel consisting of cysteine-S-sulfate, glycerophosphocholine and 4-hydroxyphenylpyruvic acid was screened by machine learning and validated in an independent cohort, which showed slightly higher diagnostic performance for HUA than UA. CONCLUSIONS: This study reveals the core metabolic and protein regulatory networks of HUA, and identifies a novel serum metabolite panel for the diagnosis of HUA. These findings provide new insights for improved clinical diagnosis and management.

Humans

Social disconnection integrates genetic and proteomic risks in suicidal ideation and depression.

Suicidal ideation (SI) and major depressive disorder (MDD) are complex psychiatric conditions arising from the interplay of genetic liability, molecular processes, and psychosocial factors. While these dimensions have been extensively studied in isolation, their joint contribution to SI and MDD remains unclear. This study integrates multi-modal data to elucidate these synergistic effects and develop robust models for individual-level risk stratification. Leveraging longitudinal multi-modal data from 13,085 UK Biobank participants, we integrated genomic, proteomic, and social connection profiles. We developed interpretable risk scores using a rigorous supervised machine learning framework encompassing diverse linear and ensemble classifiers. Permutation importance was employed to quantify feature contributions and derive transparent, weighted risk metrics across diverse classifiers. These scores were validated through association, interaction, and mediation analyses. Social connection-based risk scores significantly differentiated cases and controls across the two suicidal ideation phenotypes at 2017 and 2023 with cross-sectional analyses (AUCs: 0.70 - 0.73), outperforming proteomic-only models. Functional dimensions of social connection emerged as the most informative predictors. Longitudinal analyses revealed that social risk scores at baseline predicted suicidal ideation onset six years later, independent of demographic covariates. Interaction analyses demonstrated that polygenic risk for suicide attempt significantly interacted with both social and proteomic risk features in relation to depression. Structural equation models further confirmed that social disconnection acts as a key mediator linking genetic predisposition to MDD and SI. Social disconnection is a critical risk factor mediating the impact of genetic vulnerability on psychiatric outcomes. Integrating social, genetic, and molecular data supports a multilevel framework for risk stratification and highlights the potential of socially oriented interventions to mitigate biological risk.

Humans

Integrative multi-omics analysis proposes a metabolic classification of gliomas: distinct metabolic states, immune infiltration, and prognosis.

BACKGROUND: The tumor microenvironment (TME) of glioma harbors diverse cell types; however, cell metabolic heterogeneity remains to be explored. This study aims to characterize the metabolic features of different cell types in the TME by integrating multiple datasets, including genomics, bulk and single-cell transcriptomics, and metabolomics. METHODS: Unsupervised machine learning was used to construct an energy metabolic classifier based on the metabolic pathways identified from bulk RNA-seq of gliomas in the TCGA dataset. The classifier was externally validated using multiple datasets, including genomics, bulk RNA-seq, snRNA-seq, and the metabolomics data. Furthermore, metabolic heterogeneity associated with the classifier was further characterized at single-cell resolution. RESULTS: The energy metabolism-based classifier stratified patients into two prognostic clusters: patients in cluster 1 were characterized by high pathway activity of glycolysis, the pentose phosphate pathway (PPP), and fatty acid oxidation (FAO), whereas patients in cluster 2 exhibited higher activity in glutaminolysis. This metabolic classifier revealed both intratumoral and intertumoral metabolic heterogeneity, and the complexity was further validated by the metabolomics profiling and snRNA-seq data from the CPTAC dataset. Notably, OSMR, highly expressed in cluster 1, showed significant co-expression with key glycolytic enzyme genes. The OSM/OSMR/JAK1/STAT3 axis potently drives malignant progression of glioma cells, specially enhancing their invasive and migratory capabilities. Single-cell resolution analyses demonstrated that tumor metabolic heterogeneity is primarily driven by malignant cells rather than non-malignant components, while tumor microenvironment (TME) factors were also found to modulate malignant cell metabolism. Significantly, glycolytic activity in glioma cells increased during the phenotypic transition from PN (proneural) to MES (mesenchymal), with cluster 1 metabolic phenotypes predominating in the tumor core. Compared to cluster 2, cluster 1 patients exhibited higher mRNA expression of immunosuppressive checkpoint genes, which correlated with pronounced immunosuppression in the TME. Furthermore, various immune cells demonstrated distinct metabolic preferences at single-cell resolution. CONCLUSIONS: This study developed an energy metabolic-based classifier for gliomas with prognostic and therapeutic potential. Metabolic reprogramming was linked with the PN-to-MES transition of glioma cells and immunosuppression in the tumor microenvironment. Multi-omics data, especially snRNA-seq, offered insights into metabolism heterogeneity at single-cell resolution, enabling personalized treatment strategies.

Humans

Development and validation of a serum peptidomic signature for early detection of asymptomatic ovarian cancer: A multi-center prospective study.

Early detection of asymptomatic ovarian cancer (asym-OC) remains a critical challenge, the failure of which underlies its high mortality. Performing serum peptidomic profiling of 843 participants in the cohort SOCFCP, we distill 1,081 initial features into a 7-marker panel for asym-OC detection via a biology-informed machine-learning (ML)-based feature selection strategy. Three markers significantly revert toward non-OC levels after surgery. Integrating the panel with age, CA125, and HE4, we develop and externally validate (n = 159) a LightGBM model, ProMS+. For early-stage OC detection, ProMS+ shows a specificity of 92.6% at 95.0% sensitivity, outperforming CA125 (44.7%), HE4 (11.2%), and Risk of Ovarian Malignancy Algorithm (ROMA) (24.0%), with an area under the curve (AUC) of 0.993. In a simulated high-risk population (n = 100,000; OC prevalence = 1%), ProMS+ yields a high AUC (0.983) and a higher positive predictive value than CA125, HE4, and Age + CA125 + HE4 combined model (0.201 vs. 0.027, 0.090, and 0.064). ProMS+ offers a promising, non-invasive, and interpretable approach for the early detection of asym-OC.

Humans

Application of Omics Technologies for Cowpea Improvement.

Cowpea (Vigna unguiculata) is a vital crop for food security, nutrition, and climate resilience in sub-Saharan African and other semi-arid regions. However, its improvement is constrained by the complexity of polygenic traits such as drought tolerance, pest resistance, and seed quality. Conventional breeding, while foundational, remains insufficient to address these challenges at the required pace. Recent advances in multi-omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, provide new opportunities to dissect complex traits, identify candidate genes, and accelerate the development of resilient, high-yielding cultivars. This review presents a critical synthesis of current applications of omics technologies in cowpea improvement, highlighting their contributions to stress adaptation, nutritional enhancement, and precision breeding. The review also examines key technical and institutional constraints limiting the adoption of omics-assisted breeding in cowpea, including inadequate research infrastructure, challenges in multi-omics data integration, and limited technical capacity across breeding programs in sub-Saharan Africa. It discusses strategies to address these barriers through regional collaboration, investment in bioinformatics capacity, and the integration of computational approaches into breeding pipelines. Overall, the review concludes that combining multi-omics technologies with artificial intelligence and machine learning has strong potential to improve genotype-phenotype prediction, accelerate breeding decisions, and support the development of climate-resilient and nutritionally enhanced cowpea cultivars.

cowpea

Tree Killer, Qu'est-ce Que C'est? Insights From Forest Pathogen Genomes.

Forests are central to planetary health but are increasingly challenged by emerging diseases driven by climate change, global trade, and anthropogenic disturbance. Despite the apparent resilience of long-lived, genetically diverse tree hosts, forest ecosystems have repeatedly experienced landscape-level pathogen-driven transformations. Advances in genomics, transcriptomics, and functional biology have transformed our understanding of how fungal and oomycete pathogens interact with their hosts across a continuum of lifestyles, from saprotrophy and necrotrophy to biotrophy. Here, we synthesize insights from comparative and population genomics and functional studies across diverse forest pathosystems to examine the traits that characterize successful tree pathogens. We highlight how lifestyle plasticity, adaptations to woody tissues, vector-mediated transmission, and biotrophic stealth enable pathogens to colonize perennial hosts and persist over long temporal scales. We further examine how genome plasticity, hybridization, and horizontal gene transfer generate adaptive potential that often outpaces host evolutionary responses under current environmental change. Finally, we discuss emerging genomic tools, including biosurveillance, machine learning-based classification, and genome editing, that are beginning to link genotype to phenotype and inform assessments of disease risk. By integrating genomic, ecological, and evolutionary perspectives, this review outlines general principles governing forest pathogen success and identifies priorities for future research aimed at improving understanding, early detection, and management of forest diseases in a changing world.

Trees

Stage-specific ROMO1 in rheumatoid arthritis: predictive immune insights into the MIF pathway and HLA-DR/IL2RA axis via integrated GWAS, transcriptomic, single-cell, and spatial profiling.

Emerging evidence links reactive oxygen species modulator 1 (ROMO1), a key mitochondrial ROS regulator, to rheumatoid arthritis (RA) pathogenesis. However, its exact mechanism remains elusive given the conflicting evidence about its specific function. We used a four-level integrative framework combining multi-omics data and literature‑supported mechanistic inference. At the genetic level, Mendelian randomization (MR) was performed to explore potential causal relationships between ROMO1, IL2RA, HLA-DR, MIF, and RA risk, followed by differential expression analysis and machine learning-based feature selection to identify key mROS genes. The temporal expression dynamics of ROMO1 were assessed in RA progression. At the cellular and tissue levels, we integrated single-cell RNA sequencing and spatial transcriptomics to map cell-type-specific expression and synovial localization of ROMO1-related immune cells and pathways. Finally, our multi-omics findings were contextualized with literature-supported mechanistic inference. (1) MR results were consistent with a potential protective effect of ROMO1 on RA (OR = 0.52) and its potential regulation of risk factors IL2RA (OR = 0.46) and HLA-DR (OR = 0.40). Conversely, IL2RA (OR = 1.42), HLA-DR (OR = 1.88), and MIF (OR = 1.17) were positively associated with RA risk. Additionally, ROMO1 was identified as a top candidate diagnostic predictor with stage-specific dynamics: downregulated in the early but upregulated in the late/remission stages. (2) Single-cell RNA sequencing showed ROMO1's cell-specific expression in CD14+ HLA-DR+ CD74+ monocytes and CD4+ IL2RA+ T cells. Cell communication analysis further suggested that these cells may participate in MIF pathway regulation. Spatial transcriptomics subsequently identified that ROMO1-related cells localized to synovial pathological regions, with MIF pathway changes correlated with RA progression. (3) Finally, literature-supported mechanistic inference suggests that ROMO1 may modulate mROS levels to promote anti-inflammatory M2 macrophage polarization, which could theoretically contribute to reduced systemic inflammation and the alleviation of multi-organ decline in RA. This integrated multi-omics investigation, supported by literature-based mechanistic inference, suggests ROMO1 as a stage-dependent biomarker candidate and potential immune regulator in RA.

Humans

GRNContext: an interactive web platform for contextualized gene regulatory networks visualization across human cancers.

SUMMARY: While current Gene Regulatory Network (GRN) databases provide comprehensive reference maps of potential interactions between transcription factors and target genes, they do not specify which regulatory interactions are active within specific biological contexts. This limitation is particularly critical in cancer, where transcriptional programs are inherently tissue-specific. To address this gap, we developed GRNContext, an interactive web platform designed for the visualization, exploration, and comparative analysis of gene regulatory networks contextualized across 33 cancer types from The Cancer Genome Atlas (TCGA). Our approach uses the TFLink human reference GRN as a starting point and integrates TCGA transcriptomic profiles to infer cancer-specific regulatory activity. Regulatory relevance was assessed using complementary machine learning and statistical methods, which were unified into a consensus score to prioritize and filter the most relevant candidate regulators for each target gene. By providing both curated context-specific GRNs and a user-friendly platform, GRNContext constitutes a comprehensive and accessible resource that supports mechanistic investigations, hypothesis generation, and translational research focused on transcriptional regulation in cancer. AVAILABILITY AND IMPLEMENTATION: GRNContext is supported by all major browsers and freely available on the web at https://apps.cienciavida.org/grncontext. It is implemented as a client-server web application featuring a FastAPI backend and a React frontend utilizing Cytoscape.js for interactive network visualization, all containerized via Docker for cross-platform compatibility.

Humans

Cancer of unknown primary: the evolution of tissue of origin identification in the artificial intelligence era.

Cancer of Unknown Primary (CUP) presents substantial diagnostic and therapeutic challenges owing to its heterogeneous nature and the absence of an identifiable primary tumor site. This review provides a structured search of the pathogenesis, epidemiological characteristics, and limitations of traditional diagnostic and therapeutic approaches for CUP, with an emphasis on the evolution of Tissue of Origin (TOO) identification techniques. Recent advances in precision medicine have accelerated the development of machine learning-based TOO identification tools, representing a paradigm shift in CUP diagnostics. Deep learning (DL) algorithms that integrate multi-omics data (such as genomics and transcriptomics) with clinical features have markedly enhanced the accuracy of tracing tumor origin, and artificial intelligence (AI) driven TOO models are increasingly being incorporated into clinical practice, offering new insights for pathological diagnosis, treatment selection, and prognostic evaluation. Nevertheless, several challenges remain, including issues of data standardization, model generalizability, and interpretability. Ethical considerations related to data privacy, algorithmic fairness, and clinical implementation also warrant careful attention. Future research should focus on establishing standardized multi-center databases, developing more interpretable AI models, and fostering multidisciplinary collaborative strategies for CUP management. Through continued refinement of technical solutions and regulatory guidelines, TOO identification is anticipated to progress from research to routine clinical application, ultimately supporting precise and personalized care for patients with CUP.

Artificial intelligence

A Risk Score for Polycystic Ovary Syndrome Based on Meta-Analysis and Machine Learning of Gut Microbiota Signatures.

Polycystic Ovary Syndrome (PCOS) is a prevalent endocrine and metabolic disorder among reproductive-age women, in which emerging evidence suggests a substantial role played by the gut microbiota. To comprehensively evaluate gut microbiota alterations in PCOS and identify microbial biomarkers through integrated analysis, a systematic search of PubMed, Web of Science, and Embase was conducted for studies employing 16S rRNA gene sequencing of fecal samples from PCOS cohorts. Ten eligible PCOS cohorts, comprising 858 individuals, were included in the study, from which a risk score was derived using a 20-gene gut microbial signature associated with PCOS. Meta-analysis at the genus level identified that Subdoligranulum, NK4A214_group, and Collinsella significantly decreased, and Bacteroides increased in PCOS across multiple cohorts. Machine learning analysis identified a 20-genus microbial signature using the least absolute shrinkage and selection operator (LASSO) method, which was used to construct a risk score with an AUC of 0.835 in diagnosis prediction. Network analysis further identified Negativibacillus and Lachnospiraceae_UCG_010 as potential driver microbes in PCOS. The analysis in this study highlights key alterations in the gut microbiota across PCOS cohorts. The identified gut microbial signature and derived LASSO-based risk model offer novel insights and a potential tool for PCOS diagnosis.

Polycystic Ovary Syndrome

Proteo-metabolomic integration identifies stage-specific candidate biomarkers for Parkinson's disease.

Parkinson's disease (PD) is a progressive neurodegenerative disorder with a prolonged prodromal phase and complex motor symptoms. Despite improved clinical criteria, early diagnosis and longitudinal monitoring remain challenging. While cerebrospinal fluid (CSF) and plasma metabolites and proteins show biomarker potential, their utility in predictive models is insufficiently characterized. We employed a secondary computational approach to integrate proteometabolomic profiles from CSF and plasma samples of >1100 Parkinson's Progression Markers Initiative (PPMI) participants. Using multi-omics machine learning, we identified biofluid-specific signatures and evaluated predictive performance. Twenty-one biomarker candidates were validated across three models (SVM, GLMNET, RF); SVM and GLMNET achieved the highest recall (83-86%) and AUCs of 0.84-0.89. Longitudinal mixed-effects modeling revealed eight candidates associated with progression across diagnostic stages. We identified a three-part molecular framework characterizing neurodegeneration: a diagnostic subpanel reflecting early microbiome dysregulation (secretory granins and metabolites) and synaptic breakdown; a second subpanel monitoring phenoconversion via neurogenesis precursors and extracellular matrix proteins; and a third subpanel tracking progression through chronic neuroinflammation and immune activation. This integrated multi-omics approach provides a robust framework for stage-specific PD monitoring and potential clinical deployment.

Journal Article

Knowledge-driven interpretable neural networks provide mechanistic insight.

Analyzing omics data in the context of pathway knowledge is critical for understanding the molecular mechanisms underlying pathological changes. However, current pathway analysis methods do not model the detailed mechanistic nature of biological interactions, limiting the understanding of pathway behavior to a relatively shallow level. To address this issue, we present a knowledge-driven machine learning framework that embeds features into pathway graphs and models reactions analytically, producing interpretable feature hierarchies and subnetworks in which functional associations are estimated to model biological interactions. The approach is agnostic to feature selection, enabling the use of full omics data sets without discarding weak signals. Applications to breast cancer microRNA-gene regulation data and COVID-19 metabolomic data highlight immune and metabolic pathways relevant to disease progression. This framework bridges predictive modeling with mechanistic interpretation and offers a foundation for integrative pathway analysis.

Humans