Bioinformatics Insights and Analytics
type: channel
description: Bioinformatics Insights and Analytics is an international peer-reviewed journal dedicated to advancing interdisciplinary research at the intersection of bioinformatics, computational biology, artificial intelligence, and data-driven biomedical analytics. The journal publishes high-quality original research, review articles, and applied studies covering areas such as genomic data analysis, machine learning in healthcare, systems biology, precision medicine, biomedical signal processing, and AI-assisted clinical decision systems. The journal aims to provide a global platform for researchers, academics, engineers, and healthcare professionals to share innovative methodologies, computational frameworks, and analytical techniques that support modern biological and medical research. Emphasis is placed on scientifically rigorous, reproducible, and impactful studies that contribute to the advancement of intelligent biomedical technologies and translational healthcare applications. Bioinformatics Insights and Analytics operates under a double-blind peer review process and is committed to maintaining high academic and ethical publishing standards through transparent editorial practices and international scholarly collaboration.
language: en-US
publication name: Bioinformatics Insights and Analytics
issn: 3135-6567
items: AI-Driven Spatiotemporal Modeling of Environmental Radiation Exposure and Respiratory Health Risk in Vulnerable Populations
items: Artificial Intelligence-Driven Prioritization of Combination Therapies for Multigenic Diseases
items: https://www.bioinfia.org/index.php/home/article/view/157
items: AI-Driven Indoor Air Quality Prediction and Health Risk Assessment of Volatile Organic Compounds
items: Dietary Polysaccharides and Host–Microbiota Interactions: Emerging Strategies for Precision Nutrition in Metabolic Disorders
items: Federated Deep Learning for Privacy-Preserving Prostate Cancer Diagnosis from Multicenter Multiparametric MRI Data
items: Personalized Healthcare Recommendation Systems Based on Patient Narratives and Large Language Model-Based Self-Representation Learning
items: Computational Systems Biology for Decoding Synergistic Therapeutic Mechanisms in Complex Biological Systems
items: An Explainable AI Framework Integrating Traditional Chinese Medicine Knowledge Graphs and Digital Biomarkers for Personalized Edible Herbal Formula Recommendations in Chronic Disease Management
items: Building Energy Efficiency, Ventilation Strategies, and Indoor VOC Accumulation: A Data-Driven Assessment
items: Graph Neural Networks for Predicting Drug–Target Interactions and Synergistic Therapeutic Combinations
items: Knowledge Graph Construction for Systematic Discovery of Bioactive Compounds and Therapeutic Targets in Natural Products
items: Network-Based Discovery of Multi-Target Therapeutic Strategies for Complex Inflammatory Diseases
items: Computational Systems Biology for Revealing Multi-Target Mechanisms of Traditional Herbal Medicines in Immune Regulation
items: Multi-Omics Network Analysis for Mechanism-Based Discovery of Natural Product Therapeutics
items: Integrative Bioinformatics Analysis of Herbal Compound–Target Interactions in Precision Medicine
items: Explainable Artificial Intelligence for Mechanism-Based Discovery of Multi-Component Herbal Therapies
items: Network Pharmacology and Molecular Docking-Based Investigation of Herbal Compounds Against Cancer-Related Signaling Pathways
items: Integrating Explainable Machine Learning and Environmental Epidemiology to Predict Acute Pulmonary Function Decline Associated with Ambient Particle Gamma Radiation Exposure
items: Multimodal Explainable AI for Healthcare Resource Allocation and Patient Risk Stratification: Integrating Graph Representation Learning with Clinical Decision Support
items: Green Building Materials, Residential VOC Emissions, and Carbon-Neutral Healthy Housing: A Sustainability-Oriented Assessment
items: Multi-Modal Large Language Model-Guided Discovery of Gut Microbiota-Targeting Plant Polysaccharides for Precision Intervention in Metabolic Dysfunction-Associated Steatotic Liver Disease
items: Multi-Omics Analysis of Plant Bioactive Compounds in the Regulation of Insulin Resistance and Intestinal Microbial Ecology

AI-Driven Spatiotemporal Modeling of Environmental Radiation Exposure and Respiratory Health Risk in Vulnerable Populations
type: item
description: Environmental radiation originating from both natural and anthropogenic sources constitutes a persistent and inequitably distributed health threat. Vulnerable populations, including children, the elderly, and those with pre-existing respiratory conditions, often experience disproportionately high exposure due to residential proximity to contamination, substandard housing, or limited access to protective infrastructures. The complex interplay between spatiotemporal radiation dispersion, meteorological factors, and population mobility requires computational frameworks that surpass conventional exposure assessment methods. This paper presents an interdisciplinary system-level analysis of artificial intelligence-driven spatiotemporal modeling for environmental radiation exposure and respiratory health risk, with a particular emphasis on structural architecture, data integration, and deployment governance. We examine how deep learning architectures, including convolutional long short-term memory networks, graph neural networks, and spatiotemporal transformers, can be orchestrated within a hybrid cloud-edge infrastructure to produce high-resolution exposure maps and health risk projections. The discussion extends to the challenges posed by multisource data heterogeneity, privacy constraints associated with health records, and the necessity of fairness-aware modeling to prevent algorithmic magnification of existing disparities. We articulate trade-offs between centralized and federated learning paradigms, real-time inference capabilities, and model interpretability in public health contexts. Robustness against environmental data drift, missing sensor readings, and adversarial reporting conditions is analyzed alongside sustainability considerations encompassing institutional capacity, funding models, and open-source ecosystems. Policy implications are evaluated through the lens of environmental justice frameworks, highlighting how AI-driven exposure surveillance can inform …
creator: Mark A. Rao
creator: Guangqin Qian
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-07-03
publication date: 2026-07-03
volume: 1
number: 2

Artificial Intelligence-Driven Prioritization of Combination Therapies for Multigenic Diseases
type: item
description: Artificial intelligence is increasingly positioned as a decision-support layer for prioritizing combination therapies in multigenic diseases, where single-target interventions often fail. This paper examines the systems-level architecture required to translate molecular, pharmacological, and clinical data into actionable combination therapy rankings. The central argument is that the primary challenge is not only predictive accuracy but also the construction of robust socio-technical infrastructure capable of integrating heterogeneous evidence, network-level disease models, and adaptive learning loops. The discussion addresses structural trade-offs in centralized and federated architectures, data harmonization across omics and real-world health records, network-based reasoning, and deployment constraints in clinical environments. Special attention is given to fairness, transparency, regulatory alignment, and long-term sustainability. The prioritization of combination therapies requires balancing polypharmacology, patient heterogeneity, and uncertainty in mechanistic evidence. The paper explores how graph-based representations and community detection can reveal candidate synergies while cautioning against overreliance on black-box predictors. It concludes with policy recommendations for auditing, documentation, and continuous monitoring of AI-driven therapeutic prioritization systems.
creator: Nils Mills
creator: Hego Chambers
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-07-30
publication date: 2026-07-30
volume: 1
number: 2

https://www.bioinfia.org/index.php/home/article/view/157
type: item
title: AI-Guided Multi-Omics Risk Prediction of Foodborne Pathogen–Induced Metabolic Dysregulation: Integrating Gut Microbiome Signatures, Natural Polysaccharide Intervention, and Rapid Microbial Detection Frameworks
description: The rising incidence of foodborne infections, coupled with their long-term metabolic sequelae, demands integrated surveillance and intervention systems that transcend conventional food safety paradigms. This paper presents a system-level architecture for AI-guided multi-omics risk prediction of metabolic dysregulation induced by foodborne pathogens. The proposed framework synthesizes high-resolution gut microbiome signatures, metabolomic and proteomic profiles, natural polysaccharide intervention modeling, and rapid microbial detection networks into an interoperable, data-driven decision infrastructure. Core to the design is a federated learning backbone that ingests heterogeneous multi-omics data from clinical cohorts, environmental sampling, and food supply chain sensors, training ensemble deep learning models to predict individualized risk trajectories for insulin resistance, non-alcoholic fatty liver disease, and dyslipidemia following enteric infection. By embedding rapid detection frameworks capable of single-cell sensitivity for pathogens such as Salmonella, the system enables near-real-time alert generation and targeted polysaccharide-based dietary countermeasures, informed by mechanistic insights into glycolipid metabolism regulation. The paper foregrounds structural trade-offs between model accuracy, latency, and interpretability, and analyzes the socio-technical demands of deploying such a system across fragmented regulatory jurisdictions. Governance challenges, including data sovereignty, algorithmic fairness across demographic and nutritional strata, and the sustainability of multi-omics data pipelines, are examined in depth. A comparative analysis of centralized versus edge-based AI architectures demonstrates that hybrid deployments best balance computational load, privacy preservation, and responsiveness in field settings. The discussion extends to policy frameworks needed to ensure equitable access to predictive risk tools and to prevent algorithmic …
creator: Aape Kerhonan
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-07-31
publication date: 2026-07-31
volume: 1
number: 2

AI-Driven Indoor Air Quality Prediction and Health Risk Assessment of Volatile Organic Compounds
type: item
description: Indoor air quality is a persistent public health challenge because volatile organic compounds emitted from building materials, furnishings, cleaning products, and occupant activities can produce chronic and acute health effects that are not well captured by episodic monitoring. The increasing availability of low-cost sensors, building management data, and machine learning methods has created new opportunities for continuous indoor air quality prediction. However, the translation of predicted volatile organic compound concentrations into meaningful health risk information requires more than model accuracy. It demands careful attention to system architecture, exposure science, data governance, uncertainty communication, robustness, fairness, and deployment context. This paper presents a system-level analysis of AI-driven indoor air quality prediction and health risk assessment for volatile organic compounds. It examines the structural design of sensing and modeling pipelines, the integration of toxicological and exposure considerations, the governance of occupant-related data, and the policy trade-offs that arise when predictive systems are deployed in heterogeneous buildings. The discussion emphasizes that AI-based prediction should be understood as part of a larger socio-technical infrastructure rather than as an isolated computational task. A well-designed system must balance predictive performance with interpretability, privacy protection, equity, and operational sustainability. The paper concludes by identifying directions for interdisciplinary research and policy development to ensure that AI-enhanced indoor air quality management improves health outcomes without exacerbating existing environmental disparities.
creator: Danqing Duan
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-07-26
publication date: 2026-07-26
volume: 1
number: 2

Dietary Polysaccharides and Host–Microbiota Interactions: Emerging Strategies for Precision Nutrition in Metabolic Disorders
type: item
description: The escalating global burden of metabolic disorders demands a fundamental rethinking of nutritional intervention design, moving beyond population-level guidelines toward precision frameworks that account for inter-individual variability in host–microbiota ecosystems. Dietary polysaccharides, as primary substrates for gut microbial fermentation, represent a class of inputs with profound but incompletely leveraged potential to modulate metabolic health. This paper reframes the challenge of polysaccharide-based precision nutrition as a large-scale, multiscale systems problem, where the gut microbiome functions as a distributed biological processor transforming complex carbohydrate structures into systemically active metabolites. We examine the structural trade-offs inherent in designing polysaccharide interventions, from molecular diversity and fermentation kinetics to host metabolic responses, and propose a layered architecture for precision nutrition platforms that integrates multi-omics data ingestion, machine-learning-driven personalization engines, and continuous monitoring loops. Governance challenges, including data sovereignty, algorithmic fairness across diverse populations, and the robustness of microbial ecosystem interventions to perturbation, are dissected in the context of socio-technical infrastructure. Further, we explore the sustainability implications of scaling novel polysaccharide sourcing, from underutilized plant biomass to precision-fermented oligosaccharides, and discuss the policy frameworks needed to translate emerging science into equitable, resilient food systems. By treating the host–microbiota–polysaccharide nexus as an engineerable, governed system, this work provides a blueprint for deploying precision nutrition at scale while safeguarding against unintended systemic failures.
creator: Abhishek Hegde
creator: Enzo A. Gonzalez
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-07-19
publication date: 2026-07-19
volume: 1
number: 2

Federated Deep Learning for Privacy-Preserving Prostate Cancer Diagnosis from Multicenter Multiparametric MRI Data
type: item
description: Multiparametric magnetic resonance imaging has become a cornerstone in the diagnostic pathway for prostate cancer, yet the development of robust deep learning models for its interpretation is hampered by the fragmentation of sensitive imaging datasets across medical institutions. Federated learning offers a paradigm in which collaborative model training can occur without centralized data aggregation, preserving patient privacy while harnessing multicenter data diversity. This paper presents a comprehensive systems-level examination of federated deep learning architectures for privacy-preserving prostate cancer diagnosis using multiparametric MRI. We dissect the structural trade-offs inherent in designing federated topologies, aggregation strategies, and communication protocols that must contend with the high dimensionality and multimodal nature of prostate imaging. The analysis extends beyond algorithmic design to encompass privacy-enhancing technologies including differential privacy and secure aggregation, threat modeling against gradient leakage and inference attacks, and the intricate balance between utility and confidentiality. A substantial portion of the discussion is devoted to robustness and fairness across heterogeneous clinical sites, where variations in scanner vendors, imaging protocols, and patient demographics challenge the generalization guarantees of the global model. We further scrutinize the infrastructure demands for real-world multicenter deployment, addressing computational resource orchestration, longitudinal model maintenance, and integration with radiology workflows. Governance, regulatory compliance under GDPR and HIPAA, ethical accountability, and sustainable lifecycle management are framed as equally critical components of the federated ecosystem. By weaving together these technical and socio-technical dimensions, the paper articulates a systemic perspective that positions federated deep learning not merely as a distributed optimization t…
creator: Xuanxinyu Peng
creator: Kegang Zhao
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-08-14
publication date: 2026-08-14
volume: 1
number: 2

Personalized Healthcare Recommendation Systems Based on Patient Narratives and Large Language Model-Based Self-Representation Learning
type: item
description: The increasing availability of unstructured patient-generated health narratives, ranging from symptom diaries to psychosocial reflections, presents a transformative opportunity for precision medicine. This paper investigates the design, infrastructure, and governance of personalized healthcare recommendation systems that integrate patient narratives with large language model (LLM)-based self-representation learning. Rather than focusing narrowly on model accuracy, we offer a system-level analysis of the architectural trade-offs, deployment challenges, and regulatory implications inherent in such platforms. We conceptualize self-representation as a dynamic, linguistically encoded construct that LLMs can extract and refine through iterative narrative processing, enabling recommendations that align not only with clinical histories but also with an individual’s evolving self-concept, values, and experiential context. The paper examines the complete pipeline from narrative ingestion and semantic segmentation to the construction of a personal knowledge graph fused with a continuously updated latent self-representation. Key system dimensions are dissected: the tension between centralized and federated architectures for data governance, the robustness of self-representation against distributional shifts and adversarial noise, fairness considerations when modeling subjective identity constructs, and the sustainability of deploying compute-intensive LLMs in health systems. We further address policy implications surrounding data ownership, the right to explanation in algorithmically derived self-models, and the need for auditability. By integrating perspectives from human-computer interaction, clinical informatics, and responsible AI, this work provides a comprehensive framework for building narrative-driven recommendation systems that are clinically safe, ethically grounded, and structurally resilient. The analysis highlights how the fusion of patient narratives and self-repr…
creator: Arjun Kerhra
creator: Dustin Page
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-08-01
publication date: 2026-08-01
volume: 1
number: 2

Computational Systems Biology for Decoding Synergistic Therapeutic Mechanisms in Complex Biological Systems
type: item
description: The identification of synergistic therapeutic mechanisms in complex biological systems increasingly depends on computational systems biology. Single-target paradigms are insufficient for diseases governed by distributed molecular networks, where combinations of interventions can produce non-additive effects that arise from compensatory pathways, feedback loops, and cross-scale interactions. This paper examines how integrative computational architectures decode these mechanisms. It discusses network-based representations of molecular interactions, multi-omics data integration, machine learning models, and simulation frameworks as complementary components of a systems-level research infrastructure. Emphasis is placed on structural trade-offs among predictive accuracy, interpretability, scalability, and biological realism. The analysis further addresses robustness, fairness, generalizability, data governance, and the translational deployment of synergy prediction models. By connecting computational methods to the organizational properties of complex biological systems, the paper argues that reliable therapeutic synergy discovery requires not only algorithmic advancement but also coherent data infrastructure, model validation standards, and policy frameworks that support transparent and equitable translation. Future directions include tighter coupling between causal inference, dynamic network modeling, and clinically representative validation cohorts, as well as sustainable governance mechanisms for reusable predictive models and multimodal biomedical data.
creator: Mason Little
creator: Nils J. Wagner
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-08-03
publication date: 2026-08-03
volume: 1
number: 2

An Explainable AI Framework Integrating Traditional Chinese Medicine Knowledge Graphs and Digital Biomarkers for Personalized Edible Herbal Formula Recommendations in Chronic Disease Management
type: item
description: Chronic diseases remain the leading cause of mortality and disability worldwide, demanding a shift from standardized treatment toward precision health strategies that account for inter-individual variability. Traditional Chinese Medicine (TCM) offers a holistic paradigm of syndrome differentiation and personalized herbal formulations that has been refined over millennia, yet its integration into modern clinical workflows is hindered by a lack of quantitative evidence, methodological standardization, and computational tools that can reconcile its conceptual depth with contemporary biomedical data. This paper presents a system-level framework for an explainable artificial intelligence (XAI) engine that combines structured TCM knowledge graphs with longitudinally acquired digital biomarkers to generate personalized edible herbal formula recommendations. We critically examine the architectural design choices, data governance models, interoperability requirements, fairness considerations, and sustainability challenges associated with deploying such a system at scale. The proposed framework adopts a layered architecture in which a dynamically curated TCM knowledge graph, populated with herb-compound-target relationships, syndrome associations, and safety constraints, interacts with a multi-modal biomarker ingestion pipeline that processes data from wearable sensors, continuous metabolic monitors, and self-reported outcomes. Explainability is achieved not through post-hoc approximation alone but through an inherently interpretable inference backbone that traces evidential paths across the knowledge graph and communicates therapeutic rationales aligned with TCM diagnostic principles. The discussion extends to regulatory alignment, the mitigation of cultural and demographic biases, and the long-term institutional and environmental costs of maintaining a living knowledge ecosystem. By articulating these cross-cutting concerns, the paper offers a blueprint for future translati…
creator: Isaac D. Sanders
creator: Manav Gendhe
creator: Cesar A. Fox
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-08-01
publication date: 2026-08-01
volume: 1
number: 2

Building Energy Efficiency, Ventilation Strategies, and Indoor VOC Accumulation: A Data-Driven Assessment
type: item
description: The pursuit of energy efficiency in buildings has transformed envelope design, mechanical systems, and operational control strategies. However, the same interventions that reduce heating, cooling, and ventilation energy can also alter indoor pollutant dynamics, particularly for volatile organic compounds emitted by building materials, furnishings, finishes, and consumer products. This paper presents a data-driven assessment of the coupled relationships among building energy efficiency, ventilation strategies, and indoor VOC accumulation. It examines buildings as socio-technical systems in which energy codes, ventilation standards, occupant behavior, sensor infrastructure, and indoor chemistry interact in ways that are not captured by conventional single-domain performance metrics. The analysis addresses emission source behavior, air exchange variability, sensor deployment, machine learning integration, and governance challenges. It further considers structural trade-offs between envelope tightening and pollutant dilution, robustness of automated ventilation, fairness in exposure distribution, and policy instruments needed to avoid unintended health consequences in low-energy buildings. The paper argues that indoor air quality should be treated as a coequal performance dimension with energy efficiency, supported by interoperable data infrastructure, transparent modeling practices, and institutional routines that protect occupants across diverse building types. The assessment highlights opportunities for digital twins, urban-scale building modeling, and dynamic ventilation standards while cautioning against excessive reliance on algorithmic control without independent commissioning and audit structures.
creator: Miguel Burton
creator: Brooks D. Hughes
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-08-22
publication date: 2026-08-22
volume: 1
number: 2

Graph Neural Networks for Predicting Drug–Target Interactions and Synergistic Therapeutic Combinations
type: item
description: The identification of drug-target interactions and synergistic therapeutic combinations remains a central challenge in modern drug discovery, particularly as the complexity of biological systems and the cost of experimental screening continue to grow. Graph neural networks have emerged as a powerful framework for representing relational structure in molecular, genomic, and pharmacological data. Unlike traditional machine learning approaches that rely on independent feature vectors, graph-based methods explicitly model interactions among drugs, proteins, pathways, and diseases. This paper provides a system-level analysis of graph neural network architectures for drug-target interaction prediction and synergistic combination discovery. It examines the structural and architectural trade-offs associated with molecular graph encoding, heterogeneous biomedical networks, message passing, and multi-relational learning. The discussion further addresses data infrastructure, standardization, validation, and integration with experimental platforms. Emphasis is placed on deployment in clinical and pharmaceutical settings, including regulatory considerations, explainability, robustness, fairness, and environmental sustainability. The paper also considers policy implications for open data sharing, model governance, and equitable access. By synthesizing technical advances with socio-technical infrastructure concerns, the article offers a comprehensive perspective on the opportunities and systemic constraints that shape the translation of graph neural network models into reliable tools for precision medicine and combination therapy development.
creator: Ishaan C. Prasad
creator: Jean Meraleis
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-08-14
publication date: 2026-08-14
volume: 1
number: 2

Knowledge Graph Construction for Systematic Discovery of Bioactive Compounds and Therapeutic Targets in Natural Products
type: item
description: The discovery of bioactive compounds and therapeutic targets from natural products remains a central challenge in biomedical research because the relevant evidence is scattered across heterogeneous chemical, genomic, pharmacological, and clinical data sources. This paper examines the construction and use of knowledge graphs as an integrative systems infrastructure for systematic discovery in natural product research. Rather than proposing a single algorithm, the paper develops a system-level account of how knowledge graph architectures can reconcile chemical structure, species provenance, bioactivity, protein interactions, pathway membership, disease associations, and phenotypic outcomes within one queryable semantic fabric. We analyze the structural trade-offs among schema-centric, property-graph, and linked-data designs, and we discuss entity resolution, relation extraction, provenance modeling, and quality assurance as governance challenges rather than purely technical tasks. The paper further addresses scalability, updating, deployment, fairness, and regulatory implications when such graphs support target prioritization and compound repurposing. Throughout, we emphasize that the value of a knowledge graph lies not only in inference accuracy but also in its capacity to make evidence transparent, contestable, and maintainable across research communities. We argue that sustainable knowledge graph infrastructures for natural products require a balance between automated extraction and expert curation, between open interoperability and local control, and between exploratory discovery and rigorous validation. The discussion offers forward-looking perspectives on how these systems can support more reproducible, equitable, and policy-aware natural product drug discovery.
creator: Akash A. Melhetria
creator: Jeramy J. Beiley
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-08-01
publication date: 2026-08-01
volume: 1
number: 2

Network-Based Discovery of Multi-Target Therapeutic Strategies for Complex Inflammatory Diseases
type: item
description: Complex inflammatory diseases such as rheumatoid arthritis, inflammatory bowel disease, asthma, and systemic lupus erythematosus arise from persistent maladaptive interactions among immune, stromal, microbial, metabolic, and neural components. Single-target interventions frequently fail because compensatory pathways, feedback loops, and patient heterogeneity sustain disease activity. Network-based discovery offers a systems-level framework for identifying multi-target therapeutic strategies by representing disease mechanisms as interacting molecular and phenotypic networks. This paper examines the conceptual foundations, computational architectures, data integration strategies, and governance challenges of network-based multi-target discovery. It argues that successful platforms require not only algorithmic sophistication but also modular infrastructure, robust validation workflows, transparent uncertainty quantification, and mechanisms for addressing bias and equity. The paper discusses structural trade-offs between network completeness and interpretability, between model generality and disease specificity, and between innovation speed and regulatory accountability. It situates multi-target network analysis within broader trends in precision medicine, polypharmacology, machine learning, and real-world data. The analysis highlights community detection, graph representation learning, causal inference, and federated data governance as central to future systems. The conclusion emphasizes that network-based discovery is not merely a computational technique but an institutional and epistemic strategy for managing the complexity of inflammatory disease. It requires sustained investment in data infrastructure, interdisciplinary governance, and clinical translation to deliver safe, equitable, and effective multi-target therapies.
creator: Gareld Breen
creator: Hristephir Glark
creator: Rehit Nekherjee
creator: Aarav Natarajan
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-08-22
publication date: 2026-08-22
volume: 1
number: 2

Computational Systems Biology for Revealing Multi-Target Mechanisms of Traditional Herbal Medicines in Immune Regulation
type: item
description: Traditional herbal medicines regulate immune function through multiple chemical constituents, multiple molecular targets, and multi-scale physiological feedback mechanisms. Single-target experimental frameworks are poorly suited to capture these combinatorial and context-dependent effects. Computational systems biology provides a conceptual and technical foundation for integrating heterogeneous molecular, pharmacological, and clinical data to reveal such multi-target mechanisms. This article examines the structural trade-offs and architectural choices that arise when systems biology approaches are applied to herbal immune regulation. It discusses network pharmacology, multi-scale data integration, mechanism inference, validation, and translational deployment as interdependent components of a larger computational research infrastructure. The analysis emphasizes that computational models are not neutral technical artifacts but are embedded in governance structures, data quality regimes, and policy environments. The paper compares herbal systems pharmacology with polypharmacology in conventional drug discovery and with other complex infrastructure domains, illustrating how network-based representations can expose both robustness and fragility in immune regulatory systems. It argues that the long-term value of computational systems biology for herbal medicine depends not only on predictive accuracy but also on reproducibility, fairness, interpretability, institutional sustainability, and equitable access to data and computational resources. By connecting systems-level modeling with governance and policy concerns, the article offers a forward-looking perspective for researchers, regulators, and platform designers seeking to integrate traditional knowledge with modern computational evidence.
creator: Keyao Bai
creator: Maxime R. Lehtonen
creator: Fengjing Yang
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-07-03
publication date: 2026-07-03
volume: 1
number: 2

Multi-Omics Network Analysis for Mechanism-Based Discovery of Natural Product Therapeutics
type: item
description: The integration of multi-omics data with network-based analytical frameworks has become a central strategy for understanding the mechanisms of action of natural product therapeutics. Natural products frequently exhibit polypharmacological behavior that cannot be adequately captured by single-target models. Multi-omics network analysis provides a systems-level representation in which genomic, transcriptomic, proteomic, metabolomic, and phenotypic layers are jointly modeled to reveal how natural product interventions perturb molecular interaction networks and disease modules. This paper presents a systemic examination of the conceptual foundations, integration architectures, network construction methods, and mechanism-based discovery workflows that support the study of natural products. It addresses structural trade-offs among data integration paradigms, the interpretive challenges of network community detection, and the importance of robustness and fairness in computational predictions. The discussion extends beyond algorithmic performance to consider data governance, reproducibility, sustainability, deployment infrastructure, and policy implications. The analysis emphasizes that mechanism-based discovery of natural product therapeutics is not solely a technical problem but a socio-technical challenge requiring coherent institutional coordination, transparent validation standards, and equitable data-sharing practices. The paper situates multi-omics network analysis within broader efforts to modernize natural product pharmacology while preserving the complexity and contextual richness of traditional therapeutic knowledge. It concludes by outlining forward-looking perspectives on federated data ecosystems, explainable network models, and regulatory frameworks that can support sustainable translation of natural product candidates into clinically relevant interventions.
creator: Shansiyuan Wu
creator: Pradeep M. Anand
creator: Andres M. Beck
creator: Anirudh L. Basu
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-07-30
publication date: 2026-07-30
volume: 1
number: 2

Integrative Bioinformatics Analysis of Herbal Compound–Target Interactions in Precision Medicine
type: item
description: The shift toward precision medicine has created both opportunities and challenges for integrating herbal pharmacopeias into modern therapeutic reasoning. Herbal medicines are intrinsically multi-component and multi-target, which makes them poorly suited to reductionist single-target discovery models. Integrative bioinformatics now offers a systems-level pathway for analyzing compound-target interactions across heterogeneous molecular, pharmacological, and clinical data. This paper examines the conceptual foundations, architectural strategies, network-based inference methods, and clinical translation pathways that connect herbal compound interaction data to precision medicine. It argues that the value of integrative analysis lies not merely in predicting isolated interactions, but in structurally encoding uncertainty, polypharmacology, synergy, and patient variability within interpretable systems. The discussion addresses data integration architectures, network medicine representations, machine learning deployment, governance, fairness, reproducibility, and policy implications. Rather than treating herbal network pharmacology as a supplement to conventional drug discovery, the paper positions it as a distinct socio-technical infrastructure requiring careful management of provenance, semantic heterogeneity, and clinical accountability. Structural trade-offs between model expressiveness, interpretability, and scalability are analyzed through cross-domain comparisons with genomic and pharmacovigilance systems. The conclusion emphasizes that sustainable precision medicine will require governance models that protect against algorithmic bias while preserving the therapeutic pluralism represented by herbal medicines.
creator: Pierre Erickson
creator: Cesar Doez
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-07-26
publication date: 2026-07-26
volume: 1
number: 2

Explainable Artificial Intelligence for Mechanism-Based Discovery of Multi-Component Herbal Therapies
type: item
description: Multi-component herbal therapies present a distinctive challenge for computational discovery because their therapeutic effects are rarely reducible to single molecular targets. Instead, they emerge from complex interactions among phytochemicals, biological pathways, disease states, and patient-specific contexts. Explainable artificial intelligence offers a promising route toward mechanism-based discovery in this domain, yet its application requires careful integration of network pharmacology, systems biology, causal reasoning, and regulatory knowledge. This paper provides a systems-level analysis of explainable artificial intelligence for multi-component herbal therapy discovery. It examines the structural trade-offs between predictive performance and interpretability, the role of network-based representations, the epistemic demands of mechanism-based explanation, and the deployment constraints imposed by clinical and regulatory environments. The discussion emphasizes that explanation in this setting cannot be reduced to feature attribution alone. It must connect model outputs to modular biological mechanisms that can be interrogated, replicated, and evaluated within a governance framework. The paper further considers robustness, fairness, and reproducibility as properties of the broader socio-technical infrastructure rather than as after-the-fact checks. By framing explainable artificial intelligence as part of an integrated discovery system, the analysis clarifies how computational models can support, rather than displace, the interpretive practices of pharmacologists, clinicians, and herbal medicine researchers. The paper concludes with forward-looking observations on the institutional and technical conditions needed for credible translation of multi-component herbal therapies into clinical settings.
creator: Ananya Parekh
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-07-19
publication date: 2026-07-19
volume: 1
number: 2

Network Pharmacology and Molecular Docking-Based Investigation of Herbal Compounds Against Cancer-Related Signaling Pathways
type: item
description: Cancer is a heterogeneous family of diseases characterized by the progressive dysregulation of intracellular and intercellular signaling networks. The limitations of single-target therapeutic strategies, including acquired resistance and systemic toxicity, have motivated the search for multicomponent interventions that can modulate multiple nodes within cancer-related pathways. Herbal medicines represent a rich source of structurally diverse compounds with potential polypharmacological activity, yet their mechanistic complexity poses substantial challenges for evidence-based investigation. This paper examines the integration of network pharmacology and molecular docking as a systems-level computational framework for investigating herbal compounds against cancer-related signaling pathways. The discussion is oriented toward architectural design, data integration, computational trade-offs, validation robustness, reproducibility, governance, and translational sustainability. Network pharmacology provides a high-level topological representation of compound-target-disease relationships, while molecular docking contributes structural filters for evaluating binding plausibility. The combined pipeline enables prioritization of herbal constituents for experimental and clinical follow-up, but it also introduces systemic vulnerabilities related to data bias, pathway incompleteness, scoring function uncertainty, and regulatory ambiguity. This paper argues that the utility of such platforms depends not only on algorithmic accuracy but also on transparent data provenance, interoperable infrastructure, rigorous external validation, and ethically aligned deployment. Future developments should emphasize adaptive learning architectures, federated data governance, cross-domain knowledge graphs, and robust frameworks for translating computational predictions into sustainable and equitable cancer therapeutic research.
creator: Bnaind Maliek
creator: Parth Kapoor
creator: Krish Trivedi
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-07-19
publication date: 2026-07-19
volume: 1
number: 2

Integrating Explainable Machine Learning and Environmental Epidemiology to Predict Acute Pulmonary Function Decline Associated with Ambient Particle Gamma Radiation Exposure
type: item
description: Ambient particulate matter serves as a vector for a range of hazardous constituents, including radon decay progeny that emit ionizing gamma radiation. Short-term elevations in particle-bound gamma activity have been associated with acute decrements in lung function, particularly among individuals with pre-existing respiratory disease. While environmental epidemiology has identified these associations, the translation of such evidence into operational early warning and clinical decision support systems remains nascent. This paper presents a systems-level framework that integrates explainable machine learning with environmental epidemiology to predict acute pulmonary function decline attributable to ambient particle gamma radiation exposure. We examine the architecture of a distributed monitoring and modeling infrastructure, emphasizing trade-offs between sensor fidelity, data granularity, and computational scalability. The design of interpretable predictive models is discussed, focusing on the tension between complex deep learning architectures and inherently transparent models, and on post hoc explanation techniques such as SHAP and LIME that can bridge the gap for clinical and regulatory acceptability. Governance challenges are analyzed with regard to fairness across heterogeneous populations, privacy-preserving health data linkage, and accountability in automated public health alerts. The paper further addresses deployment robustness in the face of concept drift, sensor attrition, and evolving emission profiles, along with sustainability considerations in model training and inference. Policy implications for air quality standards for particulate radioactivity, integration into clinical guidelines for chronic obstructive pulmonary disease management, and the institutional arrangements required to sustain such a system are explored. By synthesizing perspectives from exposure science, machine learning, and socio-technical governance, we delineate a pathway toward a t…
creator: Banjemin J. Lepozai
creator: Botianyi Xiong
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-08-14
publication date: 2026-08-14
volume: 1
number: 2

Multimodal Explainable AI for Healthcare Resource Allocation and Patient Risk Stratification: Integrating Graph Representation Learning with Clinical Decision Support
type: item
description: Healthcare systems worldwide confront the formidable challenge of optimally allocating finite resources while maintaining rigorous patient risk stratification, a task made more complex by the exponential growth of heterogeneous clinical data and the imperative for transparent decision-making. This paper presents a comprehensive systems-level analysis of a novel paradigm that combines multimodal data fusion with graph representation learning and post hoc explainable artificial intelligence to enhance clinical decision support for resource allocation. We delineate an architectural framework that ingests electronic health records, medical imaging, genomic profiles, and social determinants, transforming them into a unified patient-centric graph. Graph neural networks capture high-dimensional relational and temporal dependencies, yielding patient embeddings that encode risk trajectories and phenotypic similarities. Explainability mechanisms, including attention-based saliency and counterfactual reasoning, translate opaque model inferences into clinically interpretable narratives, thereby fostering trust and actionable insight. The paper further examines the integration of this framework into operational decision support systems for triage, intensive care unit bed assignment, and dynamic resource distribution, emphasizing structural trade-offs between sensitivity and specificity, over-triaging and under-triaging, and computational latency. Deep analytical attention is devoted to fairness under distributional shifts, adversarial robustness, and the ethical governance required to prevent embedding societal biases into allocation algorithms. Infrastructure considerations, ranging from federated learning for privacy preservation to continuous model monitoring in deployment, are examined alongside regulatory compliance and policy implications. Through this interdisciplinary lens, the paper argues that a tightly coupled system of multimodal graph learning and explainability can…
creator: Matthias R. Bryant
creator: Jossae Parker
creator: Neeraj Natarajan
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-08-01
publication date: 2026-08-01
volume: 1
number: 2

Green Building Materials, Residential VOC Emissions, and Carbon-Neutral Healthy Housing: A Sustainability-Oriented Assessment
type: item
description: The global built environment confronts a dual challenge: decarbonizing housing stocks to meet climate targets while safeguarding indoor environmental quality, particularly concerning volatile organic compound (VOC) exposures from building materials. This paper presents a sustainability-oriented assessment that systematically examines the interconnections among green building material selection, residential VOC emissions, and the emergence of carbon-neutral healthy housing. Adopting a systems-level perspective, the analysis exposes structural trade-offs between embodied carbon reduction, energy efficiency, and chemical safety that are inadequately captured by prevailing certification frameworks and life cycle assessment boundaries. It argues that the architecture of performance standards, material databases, and building information modeling systems must be re-engineered to incorporate dynamic indoor exposure pathways and health impact metrics. The discussion spans material chemistry, ventilation infrastructure, occupant exposure patterns, and multi-criteria decision-support tools, with attention to uncertainty, environmental justice, and robustness of assessments. Governance mechanisms, including building codes, product labeling, and smart monitoring networks, are evaluated for their capacity to align carbon-neutral trajectories with health-protective outcomes. The paper further integrates insights from digital twinning and adaptive ventilation control as enablers of responsive healthy housing. By synthesizing literature across building physics, exposure science, life cycle assessment, and policy studies, the study advances an integrated framework in which carbon neutrality and residential health are co-optimized rather than traded off. The conclusion highlights research needs for transdisciplinary data architectures, dynamic exposure models, and policy mixes that can bridge the current fragmentation between green material innovation and indoor air quality regulatio…
creator: Reid Freanklan
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-07-03
publication date: 2026-07-03
volume: 1
number: 2

Multi-Modal Large Language Model-Guided Discovery of Gut Microbiota-Targeting Plant Polysaccharides for Precision Intervention in Metabolic Dysfunction-Associated Steatotic Liver Disease
type: item
description: The rising global prevalence of metabolic dysfunction-associated steatotic liver disease (MASLD) demands innovative interventions that target its gut–liver pathophysiological axis. Plant polysaccharides have emerged as potent modulators of the gut microbiota, yet the vast chemical space and the complex multi-omics interactions render traditional discovery pipelines inefficient. This paper presents a system-level vision for multi-modal large language model (LLM)-guided discovery of gut microbiota-targeting plant polysaccharides as precision therapies for MASLD. We articulate a comprehensive architecture that integrates heterogeneous data streams—genomic, metabolomic, glycomic, clinical, and imaging data—into a unified multi-modal reasoning framework anchored by a generalist LLM. The system leverages cross-modal representation learning, knowledge graphs linking botanical sources to host–microbe metabolic networks, and in silico screening cascades to prioritize candidate polysaccharides. Beyond the computational engine, we examine the structural trade-offs between centralized and federated data governance models, the biases embedded in multi-modal training corpora that risk perpetuating inequitable interventions, and the sustainability costs of large-scale LLM training and inference. We discuss deployment pathways that span from cloud-based high-performance computing to edge inference within clinical and research settings, and we evaluate the robustness of such systems under data distribution shifts and adversarial perturbations. Policy dimensions are given sustained attention, particularly with respect to intellectual property of natural product sequences, regulatory approval of AI-discovered compounds, and international frameworks for equitable benefit sharing. The paper contends that responsible, system-scale design of multi-modal LLM architectures can not only accelerate the discovery of microbiota-directed polysaccharides but also recalibrate how AI is embedded in…
creator: Andries Heffman
creator: Aarav Mathur
creator: Shandan He
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-07-03
publication date: 2026-07-03
volume: 1
number: 2

Multi-Omics Analysis of Plant Bioactive Compounds in the Regulation of Insulin Resistance and Intestinal Microbial Ecology
type: item
description: The intersection of plant-derived bioactive compounds, host insulin signaling, and gut microbial ecology represents one of the most complex multi-scale challenges in contemporary biomedical and computational research. Understanding how polyphenols, terpenoids, alkaloids, and non-starch polysaccharides simultaneously modulate hepatic glucose output, adipose tissue inflammation, and the composition and function of the intestinal microbiome demands analytical frameworks capable of integrating heterogeneous data streams across genomic, transcriptomic, proteomic, metabolomic, and metagenomic layers. This paper presents a systems-level analysis of the multi-omics architectures required to decode these interactions, centering not on a single molecular mechanism but on the structural trade-offs, computational governance, and infrastructural sustainability that underpin reproducible, large-scale integrative studies. We examine the evolution of multi-omics fusion strategies from early concatenation-based approaches to contemporary graph neural networks and latent factor models, highlighting the architectural tensions between model interpretability and predictive performance. The role of public data commons, federated learning infrastructure, and standardized metadata schemas is discussed as a governance pillar for equitable and robust discovery. We further assess how plant bioactive compound research serves as a compelling use case for designing fairness-aware algorithms that account for population variability in both host genetics and gut microbial enterotypes. Policy implications concerning intellectual property, biospecimen sovereignty, and the environmental sustainability of large-scale computational phenotyping are critically evaluated. By reframing the study of plant bioactives and insulin resistance as a multi-omics system-of-systems problem, the paper articulates a roadmap for next-generation infrastructure that balances biological resolution with computational tracta…
creator: Dean Gutierrez
creator: Roy Ramirez
creator: Gduard Ramos
creator: Seagear Khanna
rights: Copyright (c) 2026 Bioinformatics Insights and Analytics https://creativecommons.org/licenses/by/4.0
license: https://creativecommons.org/licenses/by/4.0
date: 2026-07-03
publication date: 2026-07-03
volume: 1
number: 2