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28 articles for “Multi-omics integration”
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STRUCTURAL–EPIGENOMIC ATLAS: CNV/SV- DRIVEN PROGNOSTIC REFINEMENT ACROSS CANCERS
Abstract: Structural genomic alterations, including copy number variations (CNVs) and structural variants (SVs), play a central role in cancer initiation and progression. These alterations extend beyond gene dosage effects and interact dynamically with epigenomic mechanisms such as DNA methylation, histone modifications, and three-dimensional chromatin organization. Recent pan-cancer studies have demonstrated that CNV burden and SV signatures reflect key oncogenic processes including chromothripsis, homologous recombination deficiency, enhancer hijacking, and extrachromosomal DNA (ecDNA) …
Published in International Journal of Cell Biology and Cellular Functions · Vol. 4, Issue 1, 2026 Read article
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Pathophysiology Reimagined: Integrating Systems Biology and AI for Disease Understanding
Abstract: Pathophysiology, the study of disease mechanisms at molecular, cellular, and systemic levels, has traditionally relied on reductionist approaches that often fail to capture the complex, dynamic, and interconnected nature of biological systems. Diseases such as cancer, neurodegenerative disorders, and infectious diseases arise from intricate interactions among genetic, epigenetic, metabolic, and environmental factors, necessitating integrative, data-driven methodologies for a deeper understanding. Systems biology has emerged as a powerful approach by leveraging …
Published in Research and Reviews: A Journal of Pharmaceutical Science · Vol. 16, Issue 2, 2025 · pp. 63–71 Read article
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Mass Spectrometry–Based Phosphoproteomic Markers to Predict Kinase Inhibitor Response in Solid Tumors
Abstract: Mass spectrometry-based phosphoproteomics has emerged as a powerful tool for predicting kinase inhibitor responses in solid tumors, offering direct functional insights into signaling pathways that surpass traditional genomic profiling by capturing dynamic kinase activities and adaptive resistance mechanisms. Technological breakthroughs, including data- independent acquisition (DIA), trapped ion mobility spectrometry (timsTOF), and efficient enrichment methods like TiO2 or IMAC, now enable comprehensive profiling of over 40,000 phosphorylation sites from limited clinical …
Published in International Journal of Cell Biology and Cellular Functions · Vol. 4, Issue 2, 2026 Read article
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Data Integration and Visualization in Bioinformatics: Techniques and Challenges
Abstract: Data integration and visualization play essential roles in bioinformatics, facilitating the thorough analysis, and interpretation of intricate biological datasets. In the field of bioinformatics, vast amounts of data are generated from various experimental platforms, such as genomic sequencing, proteomics, transcriptomics, and metabolomics. However, the heterogeneity of these datasets, coupled with their large scale and complexity, presents significant challenges in terms of integration, analysis, and visualization. Data integration techniques aim to …
Published in Research and Reviews : Journal of Computational Biology · Vol. 13, Issue 3, 2024 · pp. 1–8 Read article
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Nutrient Sensing and Microbiota Crosstalk: Driving Determinants Shaping Metabolic Stability and Adaptive Physiology for Animal Health
Abstract: Nutrient sensing is a fundamental cellular process that enables animals to adapt to fluctuating dietary inputs while maintaining metabolic homeostasis and health. Recent advances reveal that the gut microbiota functions as an active metabolic partner, producing bioactive metabolites that directly influence host nutrient-sensing pathways and downstream cellular responses. This review synthesizes current knowledge on the integration of key signalling networks, including adenosine monophosphate activated protein kinase (AMPK), mechanistic target of …
Published in International Journal of Molecular Biotechnological Research · Vol. 4, Issue 2, 2026 Read article
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AI-Driven Pharmacogenomics and Precision Medicine: Future of Personalized Therapy
Abstract: Pharmacogenomics and artificial intelligence (AI) are emerging as important drivers of precision medicine, enabling healthcare systems to adopt individualized therapeutic approaches. Pharmacogenomics examines how genetic variations influence drug response, efficacy, metabolism, and toxicity, while AI provides advanced computational tools for analyzing complex genomic and clinical data. This review highlights the integration of AI-driven pharmacogenomics in personalized therapy and its potential to improve treatment outcomes. Machine learning, deep learning, natural language …
Published in Emerging Trends in Personalized Medicines · Vol. 3, Issue 2, 2026 · pp. 1–12 Read article
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The Intersection of Bioinformatics and Cellular Function in Disease Modeling
Abstract: The integration of bioinformatics and cellular biology has revolutionized our understanding of disease mechanisms, offering unprecedented opportunities to model complex biological systems. Bioinformatics is an interdisciplinary field that merges biology, computer science, and statistics, offering advanced tools to analyze vast biological datasets. Cellular functions, including gene expression, protein interactions, and metabolic pathways, form the foundation of physiological and pathological states. Disruptions in these processes can result in diseases like cancer, …
Published in International Journal of Cell Biology and Cellular Functions · Vol. 2, Issue 2, 2024 · pp. 1–7 Read article
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A Comprehensive Review of Metabolite
Abstract: Metabolites, tiny chemicals, are essential to physiology, signalling, and biological function. This extensive review classifies metabolites into primary and secondary categories by biological relevance. Alkaloids, flavonoids, and terpenoids contribute to ecological interactions and defence systems, while amino acids, nucleotides, and carbohydrates directly affect development and cellular function. The article examines metabolic pathways, mass spectrometry, NMR, and metabolomics, a growing field. Metabolites play a crucial role in various scientific and practical …
Published in Emerging Trends in Metabolites · Vol. 2, Issue 2, 2025 Read article
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Gut Microbial Metabolites in Inflammatory, Metabolic, and Neurologic Disorders.
Abstract: The human gut microbiota transforms dietary and hostderived substrates into a diverse array of metabolites—including shortchain fatty acids (SCFAs), hydrogen sulfide (H₂S), bile acid derivatives, indoles, trimethylamine Noxide (TMAO), branchedchain amino acid (BCAA) derivatives, and lipopolysaccharide (LPS)—that act as key signaling mediators along epithelial, immune, endocrine, and neural axes. These metabolites regulate barrier integrity, energy homeostasis, inflammation, and gut–brain communication and are increasingly implicated in the pathogenesis of inflammatory bowel …
Published in Emerging Trends in Metabolites · Vol. 3, Issue 1, 2026 · pp. 58–64 Read article
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Antimicrobial Resistance and AI-Based Strategies for Rapid Pathogen Detection
Abstract: Antimicrobial resistance (AMR) has become a major global health threat, significantly reducing the effectiveness of antimicrobial therapies and increasing the burden of infectious diseases worldwide. The rapid emergence of multidrug-resistant pathogens has created an urgent need for faster, more accurate, and scalable diagnostic approaches to support timely treatment and effective infection control. Artificial intelligence (AI) has emerged as a promising technology capable of transforming pathogen detection and AMR surveillance through …
Published in Recent Trends in Infectious Diseases · Vol. 3, Issue 2, 2026 · pp. 26–36 Read article
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Genetic Variability and Statistical Methods: Key Insights for Computational Genetics Research
Abstract: Genetic variability, defined as the differences in DNA sequences among individuals, serves as the foundation of evolutionary biology and plays a pivotal role in species’ adaptability, resilience, and overall survival. Advances in genomic technologies, particularly high-throughput sequencing, have enabled unprecedented exploration of genetic diversity, fostering the growth of computational genetics. This interdisciplinary field combines statistical methods and computational tools to analyze genetic data, identify patterns, and link phenotypes to genotypes. …
Published in Research and Reviews : Journal of Computational Biology · Vol. 13, Issue 3, 2024 · pp. 19–23 Read article
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Statistical Models for Predicting Genetic Variability and Disease Susceptibility
Abstract: Differences in genetics are key to understanding why some individuals are more prone to certain diseases than others. Recent advancements in genomic research, combined with statistical modeling techniques, have made significant strides in predicting disease risk based on genetic factors. This review explores the application of statistical models for predicting genetic variability and their role in disease susceptibility. We discuss traditional methods like linear regression and genome-wide association studies (GWAS), …
Published in Research and Reviews : Journal of Computational Biology · Vol. 14, Issue 1, 2025 · pp. 30–34 Read article
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Progression of Health and Wellness: Artificial Intelligence (AI) and Deep Learning (DL) for Precision Medicines
Abstract: Deep learning and artificial intelligence in the field of precision medicine is revolutionizing healthcare to make personalized therapeutic approaches desirable based on the unique characteristics of the patient. AI technologies improve diagnostic accuracy by analyzing medical data, spotting patterns and anomalies that human experts may miss. AI-driven models are instrumental in precision medicine, where they can predict patient response to therapies to tailor treatment plans, enhancing outcomes and reducing adverse …
Published in Emerging Trends in Personalized Medicines · Vol. 2, Issue 2, 2025 · pp. 1–5 Read article
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Innovations in Targeted Drug Discovery for Personalized Medicine
Abstract: Personalized medicine is revolutionizing modern healthcare by custoizing treatment plans to match an individual’s genetic makeup, protein expression, and metabomlic characteristics. Also referred to as precision medicine, this approach seeks to improve therapeutic outcomes, reduce adverse effects, and make efficient use of healthcare resources. The incorporation of various omics technologies—including genomics, proteomics, transcriptomics, metabolomics, and epigenomics—has greatly advanced our ability to understand disease biology and molecular variations specific to each …
Published in Research & Reviews: A Journal of Drug Design & Discovery · Vol. 12, Issue 3, 2025 · pp. 19–41 Read article
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Gene Edited Livestock for Enhanced Feed Efficiency and Metabolic Adaptation Through Precision Genomic Interventions
Abstract: Advances in gene editing technologies have transformed the landscape of livestock production by enabling precise manipulation of genetic material associated with productivity, health, and environmental adaptability. Tools such as CRISPR Cas9 and emerging next generation editors allow targeted modifications that improve feed efficiency, growth performance, nutrient utilization, and stress tolerance in farm animals. This review highlights the genetic basis of feed efficiency and metabolic regulation, focusing on key genes and …
Published in Research and Reviews : A Journal of Biotechnology · Vol. 16, Issue 2, 2026 Read article
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The Parasitic Fingerprint: Tracing Infection to Host Illness
Abstract: Parasitic infections remain a major global health burden, causing significant morbidity and mortality, particularly in tropical and subtropical regions. A critical aspect of disease pathogenesis is the unique molecular and cellular imprint left by parasites in their hosts, termed the “parasitic fingerprint.” These fingerprints encompass parasite-derived proteins, nucleic acids, metabolites, extracellular vesicles, and host responses, including gene expression changes, cytokine profiles, and metabolic adaptations. Advances in multi-omics technologies, which integrate …
Published in Recent Trends in Infectious Diseases · Vol. 3, Issue 1, 2026 · pp. 29–50 Read article
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Immune Dysregulation and Cytokine Circuitry in Genital Endometriosis: Mechanistic Insights and Next-Generation Immunotherapeutic Strategies
Abstract: Genital endometriosis is increasingly recognized as an immune-mediated inflammatory disorder driven by complex interactions between dysregulated immune cells, cytokine hubs, and microbiome-derived modulators. This review introduces a novel “immune–cytokine circuitry” framework that unifies innate and adaptive immune abnormalities with key cytokine loops sustaining chronic inflammation, angiogenesis, neuroinflammation, and immune tolerance. Within this circuitry, macrophage polarization, dendritic cell immaturity, NK-cell anergy, Treg expansion, Th17 amplification, and B-cell–mediated autoimmunity converge to establish …
Published in Research and Reviews: A Journal of Pharmacology · Vol. 16, Issue 1, 2026 · pp. 06–16 Read article
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Extracellular Vesicle-Based Liquid Biopsies: Decoding the Tumor Microenvironment for Precision Oncology
Abstract: The tumor microenvironment (TME) plays a pivotal role in cancer initiation, progression, and therapeutic response. Decoding the TME is, therefore, essential for advancing precision oncology. Extracellular vesicles (EVs), including exosomes and microvesicles, are nanoscale lipid bilayer particles secreted by tumor and stromal cells. They transport a wide range of bioactive molecules, such as DNA, RNA, proteins, lipids, and metabolites, which reflect the dynamic state of the TME. Recent advances in …
Published in Research and Reviews: Journal of Oncology and Hematology · Vol. 15, Issue 1, 2026 · pp. 43–62 Read article
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REVIEW OF PHARMACOEPIGENETICS: BRIDGING EPIGENETICS AND PERSONALIZED MEDICINE
Abstract: Pharmacoepigenetics is an emerging field that explores how alterations in gene expression, independent of DNA sequence changes, influence individual responses to drugs. Unlike pharmacogenetics, which focuses primarily on genetic variation, pharmacoepigenetics integrates genetic, environmental, and lifestyle factors to explain interindividual differences in drug efficacy, toxicity, and resistance. Key epigenetic mechanisms including DNA methylation, histone modifications, non-coding RNAs, and RNA methylation play critical roles in regulating drug metabolism and therapeutic outcomes. …
Published in International Journal of Molecular Biotechnological Research · Vol. 4, Issue 1, 2026 Read article
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Neuro-Symbolic Agentic AI for Autonomous Scientific Discovery: Integrating Deep Reinforcement Learning, Quantum Simulation, and XAI-Audited LLM Hypothesis Generation in Drug Target Identification
Abstract: The exponential growth of multi-omics data and the increasing complexity of disease-associated protein interactomes have rendered conventional drug target identification pipelines computationally and epistemologically inadequate. This paper presents the Neuro-Symbolic Agentic AI for Scientific Discovery (NS-AASD) framework, a unified architecture that cohesively integrates deep reinforcement learning (DRL) exploration strategies, variational quantum simulation (VQS) of protein conformational dynamics, and XAI-audited large language model (LLM) hypothesis generation within an autonomous scientific discovery …
Published in Research and Reviews : Journal of Computational Biology · Vol. 15, Issue 2, 2026 Read article