Bioinformatics and AI/ML approaches using multi-omics data to accelerate diagnosis and delivery of precision care for patients with rare diseases

Methods in cell biology, Год журнала: 2025, Номер unknown

Опубликована: Янв. 1, 2025

Язык: Английский

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A Multi-omics approach to identify and validate shared genetic architecture in rheumatoid arthritis, multiple sclerosis, and type 1 diabetes: integrating GWAS, GEO, MSigDB, and scRNA-seq data

Functional & Integrative Genomics, Год журнала: 2025, Номер 25(1)

Опубликована: Апрель 21, 2025

Язык: Английский

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The Use of Biomarkers in Precision Health Symptom Science—Opportunities and Challenges

Seminars in Oncology Nursing, Год журнала: 2025, Номер unknown, С. 151886 - 151886

Опубликована: Апрель 1, 2025

Язык: Английский

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TCMD: A High‐Throughput and Rapid Method for Screening Antimicrobial Ingredients from Renewable Bio‐Based Resources

Advanced Science, Год журнала: 2025, Номер unknown

Опубликована: Апрель 28, 2025

Abstract Antibiotic resistance and pathogenic infections underscore the importance urgency of novel control agent development. Bio‐based products represent a rich reservoir antimicrobial agents. However, traditional strategies for screening new active compounds are time‐consuming, costly, limited by accessible resources. Here, transcriptomic combinatorial molecular docking (TCMD), method enabling fast identification components in complex mixtures without requiring prior knowledge is proposed. Results show that, eukaryotic microorganism systems, TCMD demonstrates superior performances antifungal within hydrothermal liquefaction aqueous. The high accuracy confirmed dynamics simulation, experiments, RT‐qPCR (reverse transcription real‐time quantitative polymerase chain reaction) analysis. Furthermore, exhibits cross‐system applicability, as evidenced successful antibacterial substances prokaryotic systems using plant essential oil Chinese medicine from previous studies. Compared to conventional approaches, estimated be 3–20 times faster ≈10 more cost‐effective, while maintaining high‐throughput capacity analyzing thousands simultaneously. These demonstrate that rapid, precise, flexible compound discovery, significantly accelerating development

Язык: Английский

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Protein interactions, network pharmacology, and machine learning work together to predict genes linked to mitochondrial dysfunction in hypertrophic cardiomyopathy

Scientific Reports, Год журнала: 2025, Номер 15(1)

Опубликована: Апрель 29, 2025

Язык: Английский

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Impact of <i>RANGAP1 </i>SUMOylation on Smad4 nuclear export by bioinformatic analysis and cell assays

Biomolecules and Biomedicine, Год журнала: 2024, Номер 24(6), С. 1620 - 1636

Опубликована: Май 24, 2024

Small Ubiquitin-like Modifier (SUMOylation) regulates a variety of cellular activities, and its dysregulation has been associated with glioma etiology. The aim this research was to clarify the function SUMOylation-related genes in determine relevant prognostic markers. Cancer Genome Atlas (TCGA) Glioma GSE16011 datasets were analyzed through bioinformatics identify Ran GTPase activating protein 1 (RANGAP1) as hub gene for further study. Experimental validation consisted quantitative real-time polymerase chain reaction (qRT-PCR), western blotting (WB), immunoprecipitation (IP) evaluate RANGAP1 expression, function, interaction SUMO1. To assess role knockdown SUMOylation cells, various assays conducted, including cell proliferation, migration, invasion, apoptosis. In addition, cycle analysis immunofluorescence performed. Through bioinformatics, identified crucial glioma. studies confirmed downregulation cells verified that repair impedes tumor growth. When it comes silencing, enhanced invasion migration. Additionally, SUMO1 specific SUMO molecule coupled RANGAP1, affecting location Sma Mad related 4 (Smad4) nucleocytoplasm transforming growth factor (TGF)-β/Smad signaling pathway. functional impact on proliferation migration experiments using SUMOylation-impairing mutation (K524R). Our findings suggest may be potential marker gliomas could play regulating invasion. is responsible TGF-β/Smad pathway, which progression tumors. Further investigations are necessary confirm these results.

Язык: Английский

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Advancements in Gene Structure Prediction: Innovation and Prospects of Deep Learning Models Apply in Multi-species

Опубликована: Янв. 25, 2025

In recent years, advancements in gene structure prediction have been significantly driven by the integration of deep learning technologies into bioinformatics. Transitioning from traditional thermodynamics and comparative genomics methods to modern learning-based models such as CDSBERT, DNABERT, RNA-FM, PlantRNA-FM accuracy generalization seen remarkable improvements. These models, leveraging genome sequence data along with secondary tertiary information, facilitated diverse applications studying functions across animals, plants, humans. They also hold substantial potential for multi-application early disease diagnosis, personalized treatment, genomic evolution research. This review combines learning, showcasing functional region annotation, protein-RNA interactions, cross-species analysis. It highlights their contributions animal, plant, human research while exploring future opportunities cancer mutation prediction, RNA vaccine design, CRISPR editing optimization. The emphasizes directions, model refinement, multimodal integration, global collaboration. By offering a concise overview forward-looking insights, this article aims provide foundational resource practical guidance advancing nucleic acid

Язык: Английский

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Anti-fibrotic effects of thrombin inhibition in systemic sclerosis-associated interstitial lung disease: Proof of concept

Journal of Scleroderma and Related Disorders, Год журнала: 2025, Номер unknown

Опубликована: Фев. 24, 2025

Introduction: Activation of the coagulation cascade leading to generation thrombin is well documented in various forms lung injury including systemic sclerosis-associated interstitial disease (SSc-ILD). We previously demonstrated that direct inhibitor dabigatran inhibits thrombin-induced profibrotic signaling fibroblasts isolated from scleroderma patients. The objective this study was characterize and compare an SSc-ILD patient at baseline after treatment ascertain therapy’s differential effects on fibrogenic gene expression. Materials methods: Lung by bronchoalveolar lavage (BAL) a before receiving (Pradaxa ® ) 75 mg twice daily for 6 months (ClinicalTrials.gov Identifier NCT02426229) were analyzed RNA sequencing, real-time quantitative reverse transcription polymerase chain reaction (qRT)-PCR, immunofluorescent staining. Results: Thrombin inhibition six-months oral resulted significantly decreased expression 708 fibroblast genes as compared basal levels treatment. Using Kyoto Encyclopedia Genes Genomes pathway enrichment analysis, we determined thrombin-inhibition primarily affected extracellular matrix (ECM) ECM-related genes. Fibrosis-associated genes, smooth muscle alpha-actin (SMA, ACTA2), tenascin C, collagen 1 alpha (COL1A1), 3 alpha1 (COL3A1), 8 2 (COL8A2), 10 (COL10A1), 5 (COL5A1), fibronectin 1, connective tissue growth factor (CTGF), procollagen-lysine-2-oxoglutarate-5-dioxygenase-2 (PLOD2) all down regulated following Real-time qRT-PCR staining confirmed significant downregulation selected mRNA protein levels. Conclusion: Inhibition treated with low-dose etexilate downregulated proteins fibroblasts, providing further support use inhibitors therapeutic approach patients SSc-ILD.

Язык: Английский

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Multi-omics data tools and integration approaches

Elsevier eBooks, Год журнала: 2025, Номер unknown, С. 13 - 47

Опубликована: Янв. 1, 2025

Язык: Английский

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Interaction between post-tumor inflammation and vascular smooth muscle cell dysfunction in sepsis-induced cardiomyopathy

Frontiers in Immunology, Год журнала: 2025, Номер 16

Опубликована: Апрель 10, 2025

Sepsis-induced cardiomyopathy (SIC) presents a critical complication in cancer patients, contributing notably to heart failure and elevated mortality rates. While its clinical relevance is well-documented, the intricate molecular mechanisms that link sepsis, tumor-driven inflammation, cardiac dysfunction remain inadequately explored. This study aims elucidate interaction between post-tumor intratumor heterogeneity, of VSMC SIC, as well evaluate therapeutic potential exercise training specific pharmacological interventions. Transcriptomic data from NCBI GEO databases were analyzed identify differentially expressed genes (DEGs) associated with SIC. Weighted gene co-expression network analysis (WGCNA), ontology (GO), KEGG pathway enrichment analyses utilized biological significance these genes. Molecular docking dynamics simulations used investigate drug-target interactions, immune infiltration mutation carried out by means platforms like TIMER 2.0 DepMap comprehend influence DVL1 on responsiveness. Through utilization datasets, we discovered core exhibited remarkable up-regulated expression both SIC diverse kinds cancers, which poor prognosis inflammatory responses. revealed Digoxin could bind reduce oxidative stress The module related was identified WGCNA, demonstrated distinctive cell patterns impact immunotherapeutic resistance. regulator other cancers and, therefore, can serve target. present suggests targeted therapies enhance response regimens may be novel tool during particularly patients. drugs, Digoxin, require further vivo studies confirm their effects efforts improve outcomes immunotherapy-resistant

Язык: Английский

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