Research

Our research focuses on developing and applying computational methods to understand complex biological systems and human diseases.

Literature Mining and Ontology-Based Knowledge Systems

• SciMiner: Bio-NLP (natural language processing) web application for finding molecular targets (genes/proteins) in biomedical literature and functional enrichment analyses (Gene, GO, MeSH, Pathway, and PPI).
• SciMiner-VO: Expansion of SciMiner to include the functionality of identifying Vaccine Ontology (VO) terms and indexing PubMed documents with VOs.
• VIOLIN 2.0 (NIH/NIAID U24; MPI): Vaccine ontology and knowledgebase development integrating AI-based literature mining and ontology-driven annotation.
• Development of interoperable ontologies and AI-driven frameworks for data standardization, integration, and literature mining (e.g., VIOLIN, OLAS, MILAM).

Artificial Intelligence and Machine Learning

Application of deep learning and natural language processing to biomedical data, focusing on biological age prediction, disease modeling, and knowledge extraction.

Systems Pharmacology

• Computational modeling of drug treatment-associated adverse events by integrating literature mining, cheminformatics, and network-level transcriptomic analyses.
• Development of a drug-repurposing prioritization system based on high-throughput gene expression/drug perturbation data.

Bioinformatics Approaches to Human Diseases

Integration and analysis of multi-omics data (transcriptomics, epigenomics, metabolomics, lipidomics, proteomics) to identify molecular mechanisms underlying human diseases.

• Diabetic Peripheral Neuropathy (DPN): identification of conserved/unique genetic/transcriptomic signatures and the underlying mechanisms of DPN.
• Epileptogenesis: identification of potential therapeutic targets and conserved/unique genetic/transcriptomic signatures of epileptogenesis.
• Neurological disorders: identification of pathogenic mechanisms of multiple neurological disorders (such as ALS, Alzheimer's disease, and Parkinson's disease) using systems biology approaches combining multiple omics spaces, in collaboration with Drs. Eva Feldman and Stephen Goutman (University of Michigan).
• Metabolic Syndrome and Cognitive Impairment: multi-omics studies to understand how metabolic dysfunction and neuroinflammation impair neuronal and glial communication.

Host-Pathogen Interactions

Ontology-based modeling of infectious diseases and immune responses, in collaboration with Dr. Yongqun He (University of Michigan).

Current external supports

• NIAID U24 1U24AI171008 (MPIs: Tao, He, Hur)
  Role: MPI (7/1/2022-5/31/2027)
  Title: VIOLIN 2.0: Vaccine Information and Ontology LInked kNowledgebase
• NIAID U24 Administrative Supplement
  Role: MPI (7/1/2026-5/31/2027)
  Title: Administrative Supplement: VIOLIN 2.0: Vaccine Information and Ontology LInked kNowledgebase
• NIDDK R01
  Role: MPI (9/1/2026-5/31/2031)
  Title: Schwann Cell Senescence and the Secretome Provide a Unifying Mechanism for the Onset and Progression of Diabetic Neuropathy
• ARPA-H (PI: Tavakolian)
  Role: Co-Investigator (8/22/2025-8/21/2028)
  Title: Decentralized Diabetes Data Platform for Senior Health Management
• NIDDK R01
  Role: Co-Investigator (Site PI) (7/1/2026-6/30/2028)
  Title: Lipids and inflammation in peripheral neuropathy and metabolic syndrome
• NIGMS P30
  Role: Core Director (7/1/2026-6/30/2031)
  Title: Center for Excellence in Host Pathogen Interactions (HPI COBRE) Phase 3
• NIH/NIGMS 5P20GM155890 CTR (PI: Schwartz)
  Role: Core Lead (7/1/2024-6/30/2029)
  Title: Translational Science Engaging North Dakota (TRANSCEND)
  Note: Research Design, Compliance & Data Management Core (RDCDC)

Completed grants

External

• NIDDK R01 R01DK130913 (MPIs: Feldman, Hur)
  Role: MPI (8/23/2022-9/30/2026)
  Title: Metabolic coupling between Schwann cells and axons is functionally distinct from myelination and is disrupted in obesity, prediabetes, and diabetes
• NIGMS P20 5P20GM113123 COBRE (MPI: Bradley, Brissette)
  Role: Core Director (7/1/2021-6/30/2026)
  Title: Center for Excellence in Host Pathogen Interactions (HPI COBRE) - Phase 2
• NIAID R01 1R01AI143741 (PI: Khan)
  Role: Co-investigator (12/2019-12/2021)
  Title: Pathogenic role of IL-17 response in Streptococcus pneumoniae nasopharyngeal pathogenesis during an influenza virus co-infection
• NINDS R01 5R01NS065957 (MPIs: Boison, Geiger, Masino)
  Role: Co-investigator (6/2018-6/2024)
  Title: Ketogenic diet and adenosine: epigenetics and antiepileptogenesis
• NIDDK 1R24DK082841 (MPIs: Feldman, Abcouwer, Brosius, Kretzler, Pennathur, Sharma)
  Role: Co-investigator (4/2017-7/2021)
  Title: Integrated systems biology approach to diabetic microvascular complications
• Diabetic Complication Consortium Pilot & Feasibility Grant
  Role: Project PI (10/2015-1/2017)
  Title: Comparative Transcriptomics to Identify Key Gene Networks of Diabetic Neuropathy
• Juvenile Diabetes Research Foundation Postdoctoral Research Fellowship Grant
  Role: Project PI (3/1/2011-6/30/2014)
  Title: Cross-tissue transcriptomics predict diabetic complications
• NINDS R01 5R01NS120926 (MPIs: Goutman, Murdock)
  Role: Co-investigator
  Title: Creating a foundation for personalized age- and sex-based immune-targeted therapies from an ALS longitudinal cohort by identifying peripheral and central immune signatures

Internal

• UND SMHS Pilot Grant
  Role: Co-Investigator (8/1/2024-7/31/2025)
  Title: Deciphering transcriptional and epigenetic priming mechanisms contributing to refractory Lyme disease
• UND Epigenomics COBRE Pilot
  Role: MPI (contact) (7/1/2023-6/30/2025)
  Title: Spatial pattern of microglial transcriptomic response to α-Synuclein overexpression in Thy1-αSynuclein mice
• UND COBRE Epigenetics Pilot Grant
  Role: Co-PI (10/2021-5/2022)
  Title: Correlated Epigenetic and Behavioral Modifications in α-Synucleinopathy Disorders
• UND COBRE Host-Pathogen Interaction Pilot Grant
  Role: PI (7/2019-4/2020)
  Title: Development of ontology-based literature mining system for host-pathogen interactions
• UND Epigenetics COBRE Pilot
  Role: Co-PI (12/2019-5/2020)
  Title: Epigenetic modifications of microglial phenotypes in α-synucleinopathy disorders
• UND Post-doctoral Pilot Funding Program
  Role: Co-PI (1/2019-12/2021)
  Title: Alpha-Synuclein-mediated epigenomic modification of microglial neuroinflammatory profiles during the Progression of Parkinson's Disease from Early to Advanced Stages
• UND Post-doctoral Pilot Funding Program
  Role: Co-PI (7/2018-6/2020)
  Title: Exploring epithelial-to-mesenchymal transitions in Lyme arthritis through a systems approach
• UND COBRE Epigenomics and Development and Disease Pilot Grant
  Role: Co-PI (10/2017-5/2019)
  Title: Epigenetic modification of microglial phenotype in Parkinson's Disease
• UND Health Challenge Seed Program
  Role: Co-PI (10/2017-5/2018)
  Title: Transcription proteins and mRNA splicing: a novel molecular mechanism influencing cancer progression
• UND Neuroscience COBRE Pilot Grant
  Role: Project PI (9/2016-5/2017)
  Title: Cross-center validation study for epigenetic changes associated with epileptogenesis
• UND Post-doctoral Pilot Funding Program
  Role: PI (7/2016-6/2018)
  Title: Epigenetics for anti-epileptogenic therapy
• UND COBRE Epigenomics and Development and Disease Pilot Grant
  Role: Project PI (10/2015-5/2016)
  Title: RNA-Seq and Comparative Transcriptomics to Identify Key Gene Networks of Diabetic Neuropathy