Programs

Program affiliation
Neurosciences
Computational and Systems Biology
Biomedical Informatics and Data Science

Research summary
Elucidating the biological pathways underlying cognition, emotion, and behavior, determining developmental deviations and degenerative processes in these pathways

Key words

Program affiliation
Molecular Microbiology and Microbial Pathogenesis
Biochemistry Biophysics and Structural Biology
Immunology
Molecular Cell Biology

Research summary
The Whelan laboratory studies the biology of negative-strand (NS) RNA viruses, divided between two major areas of focus: viral gene expression and viral-host cell interactions.

Key words

Program affiliation
Molecular Genetics and Genomics
Computational and Systems Biology
Molecular Cell Biology
Biomedical Informatics and Data Science
Biochemistry Biophysics and Structural Biology

Research summary
My lab seeks to understand how DNA sequence determines its regulatory function. We combine functional genomic technologies with deep learning models to answer this question.

Key words
computational biology, gene regulation, genomics, deep learning, technology development

Program affiliation
Biomedical Informatics and Data Science

Research summary

Key words

Program affiliation
Biomedical Informatics and Data Science

Research summary
Our lab develops and applies informatics methods to support clinical research and learning health systems across a range of neurological and chronic disease domains. Core research areas include **computational phenotyping**, where we focus on developing, evaluating, and critically appraising algorithms that identify patient populations from large-scale EHR data; **real-world evidence generation**, where we build automated pipelines and predictive models that translate clinical data into actionable insights for care and research; and **research infrastructure for learning health systems**, where we design and evaluate the data harmonization pipelines, classification tools, and integration methods that make large-scale clinical research possible. Across all of these areas, we maintain a strong emphasis on algorithmic equity, examining how methods perform across demographic subgroups and surfacing structural disparities in access and care. These methods are applied to a broad set of clinically significant conditions—including diabetes, stroke, Alzheimer's disease, ALS, movement disorders, and epilepsy—that share common informatics challenges such as diagnostic uncertainty, heterogeneous data, and underrepresented populations. Trainees gain hands-on experience in EHR-based cohort construction, multimodal data integration, algorithm development and validation, and the translation of informatics tools into practice, with opportunities to collaborate with clinical experts across these domains.

Key words
precision medicine, ehr, data science, phenotyping, informatics

Program affiliation
Neurosciences
Developmental Regenerative and Stem Cell Biology

Research summary
Strategies to improve outcomes of nervous system injury and disease, regeneration and preservation

Key words

Program affiliation
Developmental Regenerative and Stem Cell Biology
Biochemistry Biophysics and Structural Biology

Research summary
Role of transcription factors in differentiation and development

Key words
embryonic development, lung development, mouse models, transcriptional regulation

Program affiliation
Neurosciences

Research summary
Mechanisms of epileptogenesis and seizure-induced brain injury

Key words
epilepsy, glia, imaging, multi-photon microscopy, neurophysiology

Program affiliation
Molecular Cell Biology
Neurosciences

Research summary
Repair and regeneration following nerve injury and soft tissue injury

Key words
Plastic Surgery, Peripheral nerve, Regeneration, Tissue Engineering, Biomaterials

Program affiliation
Immunology
Neurosciences

Research summary
Inflammation and autoimmunity of the central nervous system

Key words
antigen presentation, dendritic cells, B cells, immunology, intravital microscopy, multiple sclerosis, neurobiology