Integrating multiple molecular data types provides a systems-level view of disease biology, enabling the identification of molecular processes and biomarkers that would be missed by studying individual data types.
AuGER: Clinical-phenotype guided transcriptomic modeling (Batra*†, Stark*, Lauffer*, Jargosch* et al., 2021);
PathEval: Systematic benchmarking of module detection methods (Batra† et al., 2017);
KeyPathwayMiner: Connected subnetwork extraction across omics layers (Alcaraz N*, Pauling J*, Batra R*, et al., 2014)
Identifying biologically meaningful disease subgroups helps distinguish different disease mechanisms and trajectories, enabling more precise prediction of disease progression and treatment response.
AutoSGI: Automated feature selection for clinical subgroup identification (Dharani et al., under revision 2026);
Longmixr: Robust mixture modeling for longitudinal mixed-type clinical data (Haggenberg et al., 2024);
Pathclass: De novo pathway-based classification of disease subtypes (List, Alcaraz, Batra 2020; method: Alcaraz et al., 2017).
Linking molecular signatures to disease pathology helps identify mechanisms, reveal clinically relevant variation, and uncover targets for intervention.
Neurodegenerative Diseases
Alzheimer's Disease: Large-scale untargeted metabolomics of 500 postmortem brain samples demonstrated that tau pathology (rather than beta-amyloid) is the dominant driver of metabolic dysfunction (Batra*, Arnold* et al., 2022).
Progressive Supranuclear Palsy: Comparative analyses across tauopathies further revealed convergent metabolic signatures across AD and PSP (Batra*, Krumsiek*, Wang* et al., 2024).
Dietary Intervention: A randomized dietary intervention study demonstrated that Alzheimer’s-associated metabolic states are modifiable, with coordinated serum–CSF remodeling under a ketogenic regimen (Schweickart*, Batra* et al., 2024).
Pulmonary Diseases
COVID-19: In acute respiratory distress syndrome (ARDS), integrated multi-omic profiling distinguished molecular subtypes across COVID-19 and bacterial sepsis etiologies, identifying signatures of vascular injury and mortality-associated signatures (Price*, Benedetti*, et al., 2022; Buyukozkan*, Alvarez-Mulett*, et al., 2022; Batra*, Whalen*, et al., 2022; Batra*, Uni*, et al., 2023).
Pediatric Asthma: Obesity reshapes inflammatory fatty-acid pathways in pediatric severe asthma (Orozco et al., submitted 2026).