A Multi-Omics-Empowered Framework for Precision Diagnosis and Treatment of Lysosomal Diseases

Journal of Pharmaceutical Analysis, Год журнала: 2025, Номер unknown, С. 101274 - 101274

Опубликована: Март 1, 2025

Язык: Английский

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Genotype–phenotype correlations in inherited cardiomyopathies, their role in clinical decision-making, and implications in personalized cardiac medicine in multi-omics as well as disease modeling eras

Saudi Journal for Health Sciences, Год журнала: 2025, Номер 14(1), С. 30 - 41

Опубликована: Янв. 1, 2025

Inherited cardiomyopathies are a diverse group of heart muscle diseases caused by genetic mutations that result in structural and functional abnormalities the myocardium. Understanding genotype–phenotype correlations these conditions is vital for personalized cardiac medicine, enabling targeted therapeutic strategies predictive diagnostics. This review explores major types inherited cardiomyopathies–hypertrophic cardiomyopathy, dilated arrhythmogenic restrictive cardiomyopathy–and provides detailed insights into how different manifest as clinical features. The integration multi-omics approaches advanced disease modeling techniques has enhanced our ability to dissect correlations. also discusses implications findings including tailored strategies, diagnostics, future research directions. JOURNAL/sjfhs/04.03/01772839-202501000-00004/figure1/v/2025-04-19T121403Z/r/image-tiff

Язык: Английский

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Study of tree shrew biology and models: A booming and prosperous field for biomedical research

动物学研究, Год журнала: 2024, Номер 45(4), С. 877 - 909

Опубликована: Янв. 1, 2024

The tree shrew (Tupaia belangeri) has long been proposed as a suitable alternative to non-human primates (NHPs) in biomedical and laboratory research due its close evolutionary relationship with primates. In recent years, significant advances have facilitated studies, including the determination of genome, genetic manipulation using spermatogonial stem cells, viral vector-mediated gene delivery, mapping brain atlas. However, limited availability shrews globally remains substantial challenge field. Additionally, determining key questions best answered constitutes another difficulty. Tree models historically used study hepatitis B virus (HBV) C (HCV) infection, myopia, psychosocial stress-induced depression, more studies focusing on developing animal for infectious neurodegenerative diseases. Despite these efforts, impact not yet matched that rodent or NHP research. This review summarizes prominent advancements reflects biological addressed this model. We emphasize intensive dedication robust international collaboration are essential achieving breakthroughs studies. use unique resource is expected gain considerable attention application advanced techniques development viable models, meeting increasing demands life science

Язык: Английский

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Expanding our thought horizons in systems biology and medicine

Frontiers in Systems Biology, Год журнала: 2024, Номер 4

Опубликована: Март 6, 2024

SPECIALTY GRAND CHALLENGE article Front. Syst. Biol., 06 March 2024Sec. Systems Concepts, Theory and Policy in Biology Medicine Volume 4 - 2024 | https://doi.org/10.3389/fsysb.2024.1385458

Язык: Английский

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The 2024 Report on the Human Proteome from the HUPO Human Proteome Project

Journal of Proteome Research, Год журнала: 2024, Номер 23(12), С. 5296 - 5311

Опубликована: Ноя. 8, 2024

The Human Proteome Project (HPP), the flagship initiative of Organization (HUPO), has pursued two goals: (1) to credibly identify at least one isoform every protein-coding gene and (2) make proteomics an integral part multiomics studies human health disease. past year seen major transitions for HPP. neXtProt was retired as official HPP knowledge base, UniProtKB became reference proteome Ensembl-GENCODE provides protein target list. A function evidence FE1–5 scoring system been developed functional annotation proteins, parallel PE1–5 UniProtKB/neXtProt scheme expression. This report includes updates from (version 2023–09) release 2024_04, with expression detected (PE1) 18138 19411 GENCODE genes (93%). number non-PE1 proteins ("missing proteins") is now 1273. transition a net reduction 367 (19,411 instead 19,778 PE1–4 last in neXtProt). We include reports Biology Disease-driven HPP, Protein Atlas, Grand Challenge Project. expect new Functional Evidence energize throughout global community, including π-HuB China.

Язык: Английский

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Centralized and Federated Models for the Analysis of Clinical Data

Annual Review of Biomedical Data Science, Год журнала: 2024, Номер 7(1), С. 179 - 199

Опубликована: Май 9, 2024

The progress of precision medicine research hinges on the gathering and analysis extensive diverse clinical datasets. With continued expansion modalities, scales, sources datasets, it becomes imperative to devise methods for aggregating information from these varied achieve a comprehensive understanding diseases. In this review, we describe two important approaches namely centralized model federated model. We compare contrast strengths weaknesses inherent in each present recent methodologies their associated challenges. Finally, an outlook opportunities that both models hold future data.

Язык: Английский

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Lifestyle factors in the biomedical literature: An ontology and comprehensive resources for named entity recognition

Bioinformatics, Год журнала: 2024, Номер 40(11)

Опубликована: Окт. 16, 2024

Abstract Motivation Despite lifestyle factors (LSFs) being increasingly acknowledged in shaping individual health trajectories, particularly chronic diseases, they have still not been systematically described the biomedical literature. This is part because no named entity recognition (NER) system exists, which can comprehensively detect all types of LSFs text. The task challenging due to their inherent diversity, lack a comprehensive LSF classification for dictionary-based NER, and corpus deep learning-based NER. Results We present novel factor ontology (LSFO), we used develop normalization LSFs. Additionally, introduce manually annotated (LSF200) suitable training evaluation NER systems, use it train transformer-based system. Evaluating performance both systems on revealed an F-score 64% 76% Large-scale application these PubMed abstracts PMC Open Access articles identified over 300 million mentions Availability implementation LSFO, LSF200 corpus, detected PMC-OA using are available under open licenses via following GitHub repository: https://github.com/EsmaeilNourani/LSFO-expansion. repository contains links two associated repositories Zenodo project related study. LSFO also at BioPortal: https://bioportal.bioontology.org/ontologies/LSFO.

Язык: Английский

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Pheno-Ranker: a toolkit for comparison of phenotypic data stored in GA4GH standards and beyond

BMC Bioinformatics, Год журнала: 2024, Номер 25(1)

Опубликована: Дек. 4, 2024

Abstract Background Phenotypic data comparison is essential for disease association studies, patient stratification, and genotype–phenotype correlation analysis. To support these efforts, the Global Alliance Genomics Health (GA4GH) established Phenopackets v2 Beacon standards storing, sharing, discovering genomic phenotypic data. These provide a consistent framework organizing biological data, simplifying their transformation into computer-friendly formats. However, matching participants using GA4GH-based formats remains challenging, as current methods are not fully compatible, limiting effectiveness. Results Here, we introduce Pheno-Ranker, an open-source software toolkit individual-level of As input, it accepts JSON/YAML exchange from models, well any structure encoded in JSON, YAML, or CSV Internally, hierarchical flattened to one dimension then transformed through one-hot encoding. This allows efficient pairwise (all-to-all) comparisons within cohorts patient’s profile cohorts. Users have flexibility refine by including excluding terms, applying weights variables, obtaining statistical significance Z-scores p -values. The output consists text files, which can be further analyzed unsupervised learning techniques, such clustering multidimensional scaling (MDS), with graph analytics. Pheno-Ranker’s performance has been validated simulated synthetic showing its accuracy, robustness, efficiency across various health scenarios. A real use case PRECISESADS study highlights practical utility clinical research. Conclusions Pheno-Ranker user-friendly, lightweight semantic similarity analysis formats, extendable other types. It enables wide range variables beyond HPO OMIM terms while preserving full context. designed command-line tool additional utilities import, simulation, summary statistics plotting, QR code generation. For interactive analysis, also includes web-based user interface built R Shiny. Links online documentation, Google Colab tutorial, tool’s source available on project home page: https://github.com/CNAG-Biomedical-Informatics/pheno-ranker .

Язык: Английский

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A data-driven approach to improve wellness and reduce recurrence in cancer survivors

Frontiers in Oncology, Год журнала: 2024, Номер 14

Опубликована: Апрель 11, 2024

For many cancer survivors, toxic side effects of treatment, lingering the aftermath disease and recurrence adversely affect quality life (QoL) reduce healthspan. Data−driven approaches for quantifying improving wellness in healthy individuals hold great promise lives survivors. The data-driven strategy will also guide personalized nutrition exercise recommendations that may help prevent secondary malignancies

Язык: Английский

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A Influência dos Traços de Personalidade na Prevenção e Tratamento das Doenças Cardiovasculares

Brazilian Journal of Implantology and Health Sciences, Год журнала: 2024, Номер 6(8), С. 1299 - 1322

Опубликована: Авг. 9, 2024

A evidência atual indica que os traços de personalidade influenciam significativamente a saúde cardiovascular, contribuindo para prevenção e manejo das doenças cardiovasculares (DCV). Este estudo integra elementos psicologia, medicina ciências comportamentais oferecer uma compreensão holística dos fatores afetam as DCV. O artigo revisa literatura sobre diferentes tipos personalidade, com foco nas personalidades Tipo D, além Cinco Grandes, como eles cardiovascular por meio diversos mecanismos complexos. Traços neuroticismo hostilidade estão associados um maior risco enquanto conscienciosidade atua fator protetor significativo. Esses do coração reatividade ao estresse, comportamentos saúde, suporte social inflamação sistêmica. exacerbada estresse em indivíduos alto pode levar ativação crônica eixo hipotálamo-pituitária-adrenal aumento níveis cortisol, promovendo condições favorecem aterosclerose outros processos patológicos cardiovasculares. integração avaliações no atendimento clínico ajudar identificar intervenções direcionadas. controle terapia cognitivo-comportamental atenção plena são recomendados D. Mais pesquisas necessárias compreender interações entre psicossociais cardiovascular.

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