Computational Genomics · Neurovascular Biology · Molecular Quality Control
Inner Architecture LLC applies discovery-first computational genomics to characterize gene co-expression networks, neurovascular architecture, and endogenous molecular quality control systems in human brain and body tissues.
About
An independent research organization conducting systematic computational analysis of gene expression networks across human tissues.
Inner Architecture LLC is an independent research organization headquartered in Canton, Ohio, conducting systematic computational genomics research across human tissues and disease states.
The company employs a discovery-first methodology — comprehensive correlation analysis across large-scale genomic datasets to identify previously uncharacterized biological relationships. This approach has identified ultra-high gene correlations (r > 0.90) between quality control-associated genes in healthy brain tissue, with systematic disruption in neurodegenerative and psychiatric conditions.
Our research program spans neurovascular biology, epigenetic regulation, neurodegeneration, and psychiatric genomics, unified by a focus on the sigma-1 receptor system and its associated gene networks as endogenous molecular quality control machinery.
Inner Architecture holds European Genome-Phenome Archive institutional access for controlled human genomic datasets and is registered as a federal contractor on SAM.gov, positioning the company for future NIH and DOD grant applications alongside established research universities.
Drake Harbert is a computational genomics researcher specializing in systematic co-expression analysis and gene network characterization. He adopted a discovery-first analytical methodology used across all Inner Architecture research programs and has built computational pipelines processing over 17,000 RNA-seq samples from the Genotype-Tissue Expression project, Human Protein Atlas, and Gene Expression Omnibus. His research has identified novel gene network relationships in neurovascular biology, neurodegenerative disease, and psychiatric genomics.
Institutional Access
Controlled human genomic dataset access granted to Inner Architecture LLC as a registered institution
Federal Registration
Federal contractor registration enabling NIH, NINDS, and DOD grant applications
Primary Data Sources
Systematic analysis across 17,382 RNA-seq samples from 54 tissues with cell-type deconvolution
Statistical Framework
Genome-wide Pearson correlation with Benjamini-Hochberg correction, cross-platform validation, and multi-species verification
Intellectual Property
Biosensor technology for real-time endogenous DMT detection leveraging SIGMAR1 binding characteristics
Research & Publications
Five independent manuscripts spanning neurovascular biology, epigenetic coordination, neurodegeneration, and psychiatric genomics.
PLoS ONE · Revision submitted
Systematic co-expression analysis across multiple brain regions reveals decoupling between SIGMAR1 and the stress-response gene FKBP5 in PTSD brain tissue, with preserved network structure in neurotypical controls. Identifies region-specific vulnerability patterns consistent with selective disruption of molecular quality control coordination under chronic stress.
Frontiers in Aging Neuroscience · Passed research integrity screening
Cross-dataset meta-analysis demonstrating systematic ALDH1A1 co-expression network disruption in Parkinson's disease substantia nigra. Fisher's z-transformation and random-effects modeling reveal coordinated loss of dopaminergic neuron gene relationships with heterogeneity analysis across independent cohorts.
Frontiers in Genetics · Passed research integrity screening
Systematic characterization of PCDH gene family methylation-expression relationships across human brain development, revealing coordinated epigenetic regulation patterns with implications for neurodevelopmental and psychiatric conditions.
Frontiers in Pharmacology · Passed research integrity screening
Theoretical framework supported by genome-wide co-expression evidence proposing the sigma-1 receptor operates as a unified quality control system bridging protein homeostasis with receptor-mediated signaling. The self-referential architecture generates specific predictions for neuroprotection and neurodegeneration research.
Target: Frontiers in Molecular Neuroscience
Cell-type deconvolution across 54 GTEx tissues demonstrates INMT co-expression with vascular smooth muscle and endothelial markers in brain (r = 0.4–0.87) with near-zero neuronal correlations, while SIGMAR1 shows the inverse pattern. Convergent validation from Human Protein Atlas single-cell annotation and genome-wide enrichment analysis identifies a paracrine architecture with tissue-specific compartmentalization.
Research Focus Areas
Neurovascular
Characterizing cell-type-specific expression and co-expression patterns of INMT across the neurovascular unit in human brain tissues
Neurodegeneration
Systematic mapping of gene co-expression breakdown in Alzheimer's, Parkinson's, and ALS
Epigenetics
Protocadherin family epigenetic coordination and methylation pathway interactions across brain development
Psychiatric Genomics
PTSD and trauma-induced decoupling of quality control gene networks from stress-response systems
Quality Control
Genome-wide characterization of sigma-1 receptor co-expression networks across neurological conditions
Methodology
Development of systematic co-expression analysis pipelines for hypothesis-generating research across large-scale datasets
Methodology
A systematic four-stage approach to discovering and validating novel gene expression relationships across human tissues and disease states.
Comprehensive Pearson correlation across all expressed gene pairs with FDR correction for multiple testing
Replication across independent datasets, platforms, and cohorts to distinguish biological signal from artifact
Integration with single-cell reference panels and HPA annotations to resolve cell-type-specific expression
Systematic network comparison using Fisher's z-test and random-effects meta-analytic models
Intellectual Property
Translating computational discoveries into diagnostic and research technologies.
Provisional Patent Filed · 2025
Real-time biosensor system for measuring endogenous N,N-dimethyltryptamine concentrations in biological fluids. Leverages sigma-1 receptor binding affinity characteristics for physiological DMT detection with applications in diagnostic monitoring, research instrumentation, and therapeutic guidance.
Non-invasive measurement of endogenous DMT levels as a biomarker for neurovascular function
Laboratory detection platform for quantifying DMT in tissue samples, blood, and cerebrospinal fluid
Real-time feedback during pharmacological interventions targeting sigma-1 receptor pathways
Miniaturizable sensor architecture for clinical deployment in neurology and psychiatry
Contact & Collaboration
Inner Architecture LLC actively seeks academic and industry collaborators with complementary expertise in experimental neuroscience, single-cell genomics, protein biophysics, and computational biology. We bring systematic computational analysis capabilities and novel gene network findings to collaborative research programs.
Wet-lab partners for immunohistochemistry, binding assays, and direct cell-type resolution of computational predictions
Access to brain single-cell RNA-seq datasets for direct validation of cell-type deconvolution findings
Neurology and psychiatry partners for sigma-1 receptor-based biomarker development
Academic institutions for co-PI arrangements on NIH R01/R21 applications