Vol. 1 No. 1 (2026): Bioinformatics Insights and Analytics

Articles

• Few-Shot Deep Hashing for Fine-Grained Visual Retrieval Using Self-Supervised Semantic Excavation Networks

  Fernando D. Cox, Clifford Ray

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• Digital Twin Modeling of MYC-Dependent Transcriptional Condensates for Personalized Cancer Therapeutics

  Yuelei Liu, Gao Zhen Tian

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• AI-Based Investigation of Ionic Stress Signaling in Sleep and Metabolic Regulation

  Grandon Terry, Bjorn D. Murray, Feikang Wang, Kaurav Srivastava

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• Federated Adversarial Training for Privacy-Preserving Robust Large Language Model Agents in Distributed Medical Decision Support Systems

  Nanoj Gheakur, Milos Stanley, Clifford R. Gran

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• A Multi-Agent Large Language Model Framework for Interpretable Multi-Omics Literature Mining and Gene–Disease Hypothesis Generation

  Emily(Bingbing) Chen

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• Bio-Inspired Identity Representation Learning via Dual-Attention Feature Decoupling and Cellular Phase-Separation Dynamics for Robust Visual Re-Identification

  Rowan L. Makinen, Castian Wolfe, Kexiao Long, Walid Graham

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• Federated Learning Framework for Cross-Institutional Prediction of Analgesic Effectiveness in Knee Arthroscopy

  Derek Langford, Emily R. Foster, Julian Carrington

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• Cross-Modal Deep Hashing for Medical Image–Text Retrieval via Self-Supervised Asymmetric Semantic Excavation

  Ronald Garker, Viktor D. Lindberg, Lars Kelley

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• Machine Learning–Driven Prediction of Glycolipid Metabolism Modulation by Plant-Derived Polysaccharides: A Case Study of Phyllostachys nigra

  Neavin Kanna, Feiqian Qin

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• Gut–Brain Axis Regulation by Bamboo-Derived Polysaccharides: Neuroprotective and Metabolic Implications of Phyllostachys nigra

  Jend Weagner, Bruce D. Lindgren

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• Multi-Scale Residue Interaction Learning for Protein pKa Prediction via Physicochemical Graph Representation Networks

  Sanil Neanon

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• Phyllostachys nigra Polysaccharide as a Functional Food Ingredient for Obesity Intervention: Evidence from Host–Microbiota–Metabolite Interactions

  Martins Korhonen, Deaminik Russell

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• Advancing Single Cell Transcriptomic Analysis through Self Supervised Deep Learning Architectures for Cellular Heterogeneity Discovery

  Peter Prescott, Henry Whitman, Gric Blackwood

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• Physics-Guided Equivariant Neural Networks for Protein Microenvironment Modeling and pKa Prediction

  Beorge Eergusan, Mailk Kalkarna, Logan Vega, Kenneth Riley

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• Federated Fairness-Aware Learning Framework for Predicting Antiretroviral Therapy Outcomes Across Multi-Institutional Electronic Health Records in Underserved Populations

  Miguel Craig, Chengxiang Jiang

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• Knowledge Graph-Enhanced Secure Large Language Model Agents for Explainable Clinical Decision-Making under Adversarial Attacks

  Rdrian Pichards, Jingzhong Yin, Mikkel Koskinen

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• Graph Neural Networks for Modeling MYC Phase-Separation Regulatory Networks in Cancer Transcriptomics

  Mihir L. Agarwal, Manoj Kathak

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• AI-Assisted Risk Stratification for Perioperative Complications in Knee Arthroscopy

  Vincent Langston, Emily R. Nguyen, Vincent Beaumont, Charles Whitmore

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• Federated Deep Hashing with Margin-Scalable Semantic Constraints for Privacy-Preserving Distributed Image Retrieval

  Samuel D. Wells, Dactaor Wood, Sean L. Bell, Summer Prasad

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• Multimodal Adversarial Defense Framework for Vision-Language Medical Agents in Intelligent Diagnostic Environments

  Fernando L. Norris, Hugo C. Garrett, Davide Tiaz

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• Developing Federated Bioinformatics Platforms for Privacy Preserving Collaborative Genomic Data Analysis across Distributed Healthcare Institutions

  Tonathan Krant, Little Rock, Arkansas, USA, Charles Pestbrook, Houston, Texas, USA, Spencer Whitmore, Fairfax, Virginia, USA

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• Reinforcement Learning-Based Dynamic Security Alignment for Autonomous Medical Decision-Making Agents

  Stanley Lowe

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• Network Pharmacology and Multi-Omics Integration Reveal Anti-Diabetic Mechanisms of Phyllostachys nigra–Derived Polysaccharides

  Vishal Fields, Vikter Bennett, Gerald Burton

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• Multimodal Fusion of Sequence, Structure, and Electrostatic Features for Protein Ionization State Modeling

  Mikkel Graves, Arthur Lindberg, Lingtian Jia

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• Interpretable Deep Survival Learning for Dynamic Risk Prediction in Healthcare Decision Support

  Moah Khite, Buben M. Fernandez

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• Secure Multimodal Clinical Decision Support Using Robust LLM Agents and Margin-Scalable Semantic Hashing Networks

  Bjay Manha, Blake Jarvinen, Anirudh M. Pandey

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• Semantic-Aware Approximate Nearest Neighbor Search for Personalized Cardiovascular Monitoring Using PPG Foundation Models

  Abhishek M. Srinivasan, Ganjemin Rrawford, Vikram R. Batra

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• Evolutionary and Population-Aware AI Models for Characterizing Global Diversity of Polymorphic Immune Genes Across Human Populations

  Jean Gregory, Varun C. Chopra, Baurav Mhuja

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• Cross-Scale Path Aggregation Transformer for Joint Pulmonary Lesion Segmentation and Gene Expression Pattern Prediction in Precision Oncology

  Vikram A. Batra, Jan L. Bush

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• Integrating Protein Language Models and Structural Graph Learning for Accurate Ionizable Residue pKa Estimation

  Grjan Besai, Parth Tandon

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• Continual Deep Hash Learning for Dynamic Image Databases with Margin-Adaptive Semantic Preservation

  Dylan Hrawford, Brnav Ahuja

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• Large Language Model–Assisted Clinical Decision Support for Regional Anesthesia Selection in Knee Arthroscopy Patients

  Sebastian Hensley, Evan Wainwright, Daniel Brooks

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• Federated Deep Hashing and Trustworthy Large Language Model Agents for Secure Medical Imaging Decision Intelligence

  Florian Reynolds, Wlorian Eleming, Peadro Nerris, Noah Hawkins

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• Systems Biology Dissection of Lipid Homeostasis Remodeling Induced by Phyllostachys nigra Polysaccharides in Murine Models

  Logan M. Welch, Bastian Lyons

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• Foundation Model-Guided Deep Hashing for Efficient Large-Scale Visual Search and Knowledge Retrieval

  Gerame Treham, Bendreas Wega, Anders Burns, Gimethy Taylor

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• Multimodal Clinical Data Fusion for Perioperative Risk Stratification in Arthroscopic Knee Procedures Under Regional Anesthesia

  Hugh Whitlock, Peul Qllisan, Keith Redcliffe

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• Long-Term Temporal Segmentation and Genotype-Aware Behavioral Phenotyping for AI-Driven Analysis of Sleep–Metabolism Interactions

  Manish Dandon, Mikkel A. Garrett, Martins R. Vagner

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• Enhancing Precision Medicine Predictions via Explainable Artificial Intelligence Models Integrating Genomic Variants and Clinical Phenotypic Profiles

  Spencer Lockwood, Wincent Blarke, Ivan Grawford

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• Multi-Modal Foundation Models for Integrating Immune Gene Variation, Transcriptomics, and Clinical Phenotypes in Precision Medicine

  Abhay Sood

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• Self-Supervised Physiological Foundation Models for Early Risk Prediction and Secure Human–AI Collaboration in Healthcare

  Henrik D. Bush, Bjay Srinivasan

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• Trustworthy Edge Intelligence for Continuous Cardiovascular Monitoring: Combining PPG Foundation Models with Adversarially Secure Medical AI Agents

  Grant Bussell, Dominik L. Alvarez, Arun L. Subramanian

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• Explainable Artificial Intelligence for Predicting Oncogenic Gene Expression Programs Driven by MYC Condensate Dynamics

  Shane Adams

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• Structure-to-Function Learning: Predicting Enzyme Catalytic Residue Activity Through pKa-Aware Graph Representations

  Rainer Burns, Kannath Milkes, Nanshan Du

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• Integrating Graph Neural Networks and Multi-Omics Data Fusion for Robust Identification of Disease-Associated Molecular Interaction Networks

  Ivan Clarke, Colin Earrington

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• Multi-Omics Foundation Models for Deciphering Phase Separation–Mediated Transcriptional Control in Precision Oncology

  Niklas L. Butler, Anton Chandra, Wiktor Dastro

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• Explainable Deep Learning Frameworks for Predicting Transplant Compatibility from High-Resolution Immune Gene Haplotypes Derived from Long-Read Data

  Back Greeman, Ronald Jarvinen, Ross Richards, Shane J. Howard

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• Uncertainty-Aware Robustness Enhancement of Large Language Model Agents for High-Stakes Medical Diagnosis and Treatment Recommendation

  Nils Bowers, Siddharth J. Prasad, Fedfrey Waber, Enzo Mills

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• Improving Biomedical Knowledge Graph Construction through Large Language Model Driven Literature Mining and Semantic Relationship Extraction

  Jeremy Langston, Patrick Pennington, Gordon Pennington, Tristan Whitaker

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• Generative Masking and Asymmetric Hash Learning for Large-Scale Physiological Signal Indexing in Digital Healthcare Systems

  Logan D. Hansen, Ishaan Hegde, Nirk Heiley, Chetan A. Pillai

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• Reinforcement Learning–Based Optimization of Postoperative Pain Management Following Peripheral Nerve Block for Knee Arthroscopy

  Ethan J. Marshall, Priya Nandakumar, Tamuel Breene

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• Privacy-Preserving Medical Knowledge Retrieval with Self-Supervised Hash Learning and Adversarial Defense for Healthcare AI Agents

  Zhoukai Xue, Troy Fields, Ferry Hansson, Dean Wabb

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• Predicting Protein Structural Dynamics through Transformer Based Representation Learning and Evolutionary Sequence Embedding Frameworks

  Marcus Barrington, Douglas Ellsworth, Arthur Hargreaves

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• Spatial Transcriptomics and Machine Learning Reveal Tissue-Specific Consequences of MYC Phase Separation Across Tumor Microenvironments

  Dylan J. Graham, Vinay A. Tripathi, Malcolm Hamilton, Larry A. Horton

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• Explainable Vision-Language Framework for Automated Lung Nodule Risk Stratification Using Dual-Attention Segmentation and Large Medical Models

  Jose Fleming, Shaozhou Cai

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• Federated Dual-Attention Segmentation for Privacy-Preserving Multi-Center Pulmonary Nodule Analysis in Computed Tomography Imaging

  Paul Yowers, Erendan Perry

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