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JMIR Bioinformatics and Biotechnology
Scopus
ISSN 2563-3570 · JMIR Publications · 46 articles in the index
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Journal Article
Deep Generative and Graph-Based Representation Learning for Multiomics Survival Stratification in Ovarian Cancer: Secondary Analysis
Abstract BackgroundOvarian cancer remains one of the most lethal gynecologic malignancies, largely due to pronounced molecular heterogeneity, nonspecific clinical presentation, and frequent diagnosis at advanced stages. Multiomics profiling—including genomics, transcriptomics, and…
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Journal Article
Application of aiAtlas Version 1.2 to Simulate Variant Gene Function Restoration and Rescue Thresholds in Rare Diseases: Validation Case Study
Abstract BackgroundXeroderma pigmentosum group D (XPD), caused by ERCC2 gene dysfunction, leads to defective nucleotide excision repair and hypersensitivity to UV radiation. Robust experimental models for variant-level functional assessment remain limited. ObjectiveThis study aimed to use aiAtlas…
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Journal Article
A Strategic Partnership to Advance AI Applications in Genomics and Bioinformatics for Health Innovation
AbstractJMIR Bioinformatics and Biotechnology
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Journal Article
Prevalence and Associated Risk Factors of Bovine Fasciolosis in Bahir Dar, Ethiopia: Cross-Sectional Study
Abstract BackgroundCattle are among the most important livestock resources in Ethiopia, contributing significantly to the agricultural economy and rural livelihoods. They provide meat, milk, hides, draft power for crop production, and serve as a major source of income for farmers. Despite their…
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Journal Article
Random Survival Forest Versus Elastic-Net Regularized Cox Regression for Survival Prediction in Acute Myeloid Leukemia at Distinct Treatment Time Points: Model Performance Comparison Study
Abstract BackgroundRisk group stratification based on the prediction of survival of patients with acute myeloid leukemia (AML) is complex. Despite common risk group categorization guidelines, the overall prognosis remains poor. Machine learning techniques have been shown to provide more accurate…
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Journal Article
Temporal Reproducibility of a Genetic Algorithm–Derived Health Risk Score: Standardized Out-of-Fold Validation Framework (2021-2023)
Abstract BackgroundGenetic algorithm (GA)–based scoring has been proposed as a data-driven approach for health risk stratification . However, performance estimates may be inflated when preprocessing, optimization, and evaluation are not strictly separated within a prespecified validation framework…
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Journal Article
The AudioGene Translational Dashboard for Diagnosing Autosomal Dominant Nonsyndromic Hearing Loss: Phenotypic Data Visualization and Analysis Study
Abstract BackgroundAutosomal dominant nonsyndromic hearing loss (ADNSHL) is highly heterogeneous, with more than 64 genes implicated in its etiology. This complexity limits the diagnostic power of clinical examinations and audiometry alone, while existing computational approaches have achieved only…
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Journal Article
Readability of AI-Generated Patient Information on Glucagon-Like Peptide-1 Receptor Agonists
AbstractArtificial intelligence (AI)–generated content on glucagon-like peptide-1 receptor agonists (GLP-1RAs) gave informationally detailed responses, but its readability remains suboptimal for many patients. Incorporating literacy-sensitive design principles into AI health communication is…
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Journal Article
Systematic Mining of Bioactive Compounds for Wound Healing From Cayratia Japonica Exosome-Like Nanovesicles: A Workflow Combining LC-MS and DeepSeek Models
Abstract BackgroundPlant-derived exosome-like nanovesicles (P-ELNs) effectively deliver bioactive compounds due to their high biocompatibility and low immunogenicity. While liquid chromatography-mass spectrometry (LC-MS) profiles compounds in complex samples, its analysis of large datasets remains…
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Journal Article
Development and Validation of a Generative Artificial Intelligence-Based Pipeline for Automated Clinical Data Extraction From Electronic Health Records: Technical Implementation Study
Abstract BackgroundThe manual abstraction of unstructured clinical data is often necessary for granular clinical outcomes research but is time consuming and can be of variable quality. Large language models (LLMs) show promise in medical data extraction yet integrating them into research workflows…
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Journal Article
Unpacking Genomic Biomarkers for Programmed Cell Death Receptor-1 Immunotherapy Success in Non–Small Cell Lung Cancer Using Deep Neural Networks: Quantitative Study
Abstract BackgroundNon–small cell lung cancer (NSCLC) is one of the leading causes of cancer-related mortality. Programmed cell death receptor-1 (PD-1) immunotherapy has shown results in the treatment of NSCLC; however, not all patients respond effectively to it. Identifying predictive biomarkers…
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Journal Article
Systemic Anticancer Therapy Timelines Extraction From Electronic Medical Records Text: Algorithm Development and Validation
Abstract BackgroundThe systemic treatment of cancer typically requires the use of multiple anticancer agents in combination or sequentially. Clinical narrative texts often contain extensive descriptions of the temporal sequencing of systemic anticancer therapy (SACT), setting up an important task…
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Journal Article
Lung Cancer Diagnosis From Computed Tomography Images Using Deep Learning Algorithms With Random Pixel Swap Data Augmentation: Algorithm Development and Validation Study
Abstract BackgroundDeep learning (DL) shows promise for automated lung cancer diagnosis, but limited clinical data can restrict performance. While data augmentation (DA) helps, existing methods struggle with chest computed tomography (CT) scans across diverse DL architectures. ObjectiveThis study…
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Journal Article
In Silico Analysis and Validation of A Disintegrin and Metalloprotease (ADAM) 17 Gene Missense Variants: Structural Bioinformatics Study
Abstract BackgroundThe protein A disintegrin and metalloprotease (ADAM) domain containing 17, also called tumor necrosis factor alpha–converting enzyme, is mainly responsible for cleaving a specific sequence Pro-Leu-Ala-Gln-Ala-/-Val-Arg-Ser-Ser-Ser in the membrane-bound precursor of tumor necrosis…
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Journal Article
Conversational Artificial Intelligence for Integrating Social Determinants, Genomics, and Clinical Data in Precision Medicine: Development and Implementation Study of the AI-HOPE-PM System
Abstract BackgroundIntegrating clinical, genomic, and social determinants of health (SDOH) data is essential for advancing precision medicine and addressing cancer health disparities. However, existing bioinformatics tools often lack the flexibility to perform equity-driven analyses or require…
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Journal Article
Estimating Antigen Test Sensitivity via Target Distribution Balancing: Development and Validation Study
Abstract BackgroundSensitivity—expressed as percent positive agreement (PPA) with a reference assay—is a primary metric for evaluating lateral-flow antigen tests (ATs), typically benchmarked against a quantitative reverse transcription polymerase chain reaction (qRT-PCR). In SARS-CoV-2 diagnostics…
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Journal Article
Paired-Sample and Pathway-Anchored MLOps Framework for Robust Transcriptomic Machine Learning in Small Cohorts: Model Classification Study
Abstract BackgroundApproximately 90% of the 65,000 human diseases are infrequent, collectively affecting ~400 million people, substantially limiting cohort accrual. This low prevalence constrains the development of robust transcriptome-based machine learning (ML) classifiers. Standard data-driven…
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Journal Article
Genetic Diversity and Mutation Frequency Databases in Ethnic Populations: Systematic Review
Abstract BackgroundNational and ethnic mutation frequency databases (NEMDBs) play a crucial role in documenting gene variations across populations, offering invaluable insights for gene mutation research and the advancement of precision medicine. These databases provide an essential resource for…
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Journal Article
Stacked Deep Learning Ensemble for Multiomics Cancer Type Classification: Development and Validation Study
Abstract BackgroundCancer is one of the leading causes of disease burden globally, and early and accurate diagnosis is crucial for effective treatment. This study presents a deep learning–based model designed to classify 5 common types of cancer in Saudi Arabia: breast, colorectal, thyroid…
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Journal Article
Harnessing AI and Quantum Computing for Revolutionizing Drug Discovery and Approval Processes: Case Example for Collagen Toxicity
AbstractArtificial intelligence (AI) and quantum computing will change the course of new drug discovery and approval. By generating computational data, predicting the efficacy of pharmaceuticals, and assessing their safety, AI and quantum computing can accelerate and optimize the process of…