Welcome to MIRA

Discover the latest advancements in muscle biology and exercise physiology.

About Us

MIRA represents a collaborative research initiative focused on applying informatics and AI approaches to the study of skeletal muscle biology and related health conditions.

Vision

To bridge the gap between computational science and muscle biology, creating a future where comprehensive data integration and AI-driven analysis reveal previously hidden insights that advance human health and extend healthy muscle function throughout life.

Mission

MIRA's mission is to develop and implement advanced computational methods, multi-omics technologies, and AI-driven approaches that transform our understanding of muscle biology.

We accomplish this by:

  • Creating innovative data science solutions specifically tailored to muscle research challenges
  • Establishing robust infrastructure for the integration and analysis of complex biological datasets
  • Fostering interdisciplinary collaboration between computational scientists and muscle biologists
  • Developing novel sequencing and analytical methodologies that reveal molecular mechanisms of muscle function and aging
  • Translating computational insights into actionable knowledge that improves muscle health across the lifespan

Alliance

Our alliance focuses on muscle biology and exercise physiology in health and disease, utilizing bioinformatics and omics technologies to understand the molecular mechanisms underlying muscle function and adaptation.

MIRA Concept Figure
  • John McCarthy: Mechanisms of skeletal muscle plasticity.
  • Ahmed Ismaeel: Exercise on muscle and metabolic health in peripheral artery disease.
  • Tolulope Saliu: The role of muscle stem cell-derived vesicle communication in the muscle niche.
  • Jensen Goh: Contribution of muscle stem cell mitochondria to mature muscle cells.
  • Benjamin Burke: Exploring the impact of exercise on the microbiome and its implications for muscle aging.
  • Yuan Wen: Muscle-adipose communication through extracellular vesicles.
  • Bailey Peck: Investigating the role of specialized ribosomes in muscular dystrophy.
  • Laura Peterson Brown: Benefits of exercise in post-partum depression.
  • Nick Thomas: Mechanistic benefits of lifelong exercise on skeletal muscle healthspan
  • Kevin Murach: Epigenetic control of muscle healthspan.
  • Kirby Mayer: Mechanisms of ICU-acquired muscle weakness and mitochondrial dysfunction.
  • Brian Delisle: Circadian rhythms and genetic mutations affect cardiac ion channel function, arrhythmia susceptibility, and long QT syndrom.
  • Elizabeth Schroder Stumpf: Circadian rhythms regulate cardiac ion channel expression, influencing heart rhythm and health.

MIRA Capabilities

Cutting-Edge Sequencing Capabilities

MIRA is developing in-house sequencing capabilities that combine both short-read and long-read technologies:

  • Illumina MiSeq i100 Plus for high-throughput short-read applications, enabling rapid detection of mosaic copy number alterations (CNAs) across diverse aging populations
  • Oxford Nanopore PromethION for native DNA/RNA long-read sequencing, particularly valuable for detecting age-related splice variants, RNA modifications, complex structural variations, and somatic mosaicism patterns associated with aging

Multi-Omics Integration

MIRA utilizes a comprehensive suite of sequencing techniques that span different levels of biological regulation:

  • Genomics/Epigenomics: WGS/WES, WGBS/RRBS, ChIP-seq, ATAC-seq, and admixture mapping for identifying population-specific genetic variants related to aging
  • Transcriptomics/Epitranscriptomics: mRNA-seq, Ribo-seq, CLIP-seq, single-cell/nucleus RNA-seq, RNA modification detection (m6A, pseudouridine) in aged tissues
  • Microbiome Analysis: Metagenomics and 16S sequencing to study age-related microbiome changes
  • Aging Genomics: Specialized protocols for detecting age-related drivers through analysis of mosaic alterations in aging tissues

Advanced Sequencing Methodology Development

MIRA is actively developing and optimizing novel sequencing protocols:

  • Ribo-seq: Capturing ribosome-protected fragments to study age-related translation dynamics
  • SHARE-seq: Simultaneous profiling of chromatin accessibility and gene expression changes in aging
  • Native DNA/RNA sequencing: Direct detection of age-associated base modifications without chemical conversion
  • CNA-ancestry integration: Novel computational approaches combining copy number and haplotype-level ancestry data to investigate population-specific aging risks and longevity factors

Strategic Goals

  • Establish a Comprehensive Multi-Omics Platform
    • Fully integrate genomics, epigenomics, transcriptomics, and microbiome analysis capabilities
    • Develop standardized pipelines for processing and analyzing diverse data types
    • Create user-friendly interfaces for researchers to access and interpret multi-omics data
  • Advance Novel Sequencing Technologies
    • Optimize protocols for Ribo-seq and SHARE-seq specifically for muscle tissue analysis
    • Perfect native DNA/RNA sequencing techniques to detect age-associated modifications
    • Develop muscle-specific sequencing approaches that require minimal sample input
  • Build AI and Machine Learning Capabilities
    • Create specialized AI models trained on muscle biology datasets
    • Develop predictive algorithms for muscle aging and disease progression
    • Implement machine learning approaches that identify patterns across multi-omics datasets
  • Foster Interdisciplinary Collaboration
    • Establish partnerships between computational scientists and muscle biologists
    • Create training programs to build data science skills in muscle biology researchers
    • Host regular workshops and symposia bridging computational and biological disciplines
  • Translate Computational Insights to Clinical Applications
    • Identify biomarkers of muscle health and disease through computational analysis
    • Develop diagnostic tools based on multi-omics signatures
    • Create personalized intervention strategies informed by computational models
  • Build Sustainable Research Infrastructure
    • Develop open-source software tools specifically for muscle biology data analysis
    • Create accessible data repositories for sharing muscle research datasets
    • Establish cloud-based computing resources for complex data analysis
  • Advance Understanding of Muscle Aging
    • Map molecular signatures of healthy versus accelerated muscle aging
    • Identify population-specific factors influencing muscle longevity
    • Discover potential interventions to extend healthy muscle function throughout life

Contact Us

For more information, please reach out to us at ywen2@uky.edu.