Computational and Systems Biology

Program affiliation
Computational and Systems Biology
Molecular Genetics and Genomics
Ecology and Evolutionary Biology
Human and Statistical Genetics

Research summary
Epigenome evolution and epigenetic determinants of cell fate

Key words
DNA methylation, transposable elements, epigenomics, evolution, genomics, systems biology

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 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
Molecular Microbiology and Microbial Pathogenesis
Immunology
Computational and Systems Biology
Molecular Genetics and Genomics

Research summary
We investigate the interplay among the microbiota, stromal cells, and the immune system through the integration of microbiology and immunology with systems biology.

Key words
Microbiota, Microbiome, Immune system, Stromal cells, Vaccines, Germinal Centers

Program affiliation
Molecular Microbiology and Microbial Pathogenesis
Immunology
Computational and Systems Biology
Molecular Genetics and Genomics

Research summary
Host-microbe dynamics during pregnancy

Key words
virome, microbiome, pregnancy, papillomavirus, herpesvirus

Program affiliation
Computational and Systems Biology
Biomedical Informatics and Data Science
Developmental Regenerative and Stem Cell Biology

Research summary

Key words
Bioinformatics, epigenetics

Program affiliation
Plant and Microbial Biosciences
Molecular Microbiology and Microbial Pathogenesis
Computational and Systems Biology
Biochemistry Biophysics and Structural Biology

Research summary
Synthetic biology for advanced biofuels, biomaterials, and chemicals.

Key words
Synthetic biology, Metabolic engineering, regulatory systems, biomaterials

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

Research summary
Deep learning; AI; Multi-omics; Translational cancer research; Cancer; Genomics; Imaging

Key words
RNA-seq, WGS, genomics, sequencing, deep learning, machine learning, artificial intelligence, AI, bioinformatics, computational biology, algorithm, multi-omics, cancer, HPV, radiation, PET, MRI, image

Program affiliation
Biomedical Informatics and Data Science
Computational and Systems Biology

Research summary
My research integrates causal modeling and machine learning to improve the reliability of real-world evidence generation and to improve the trustworthiness of AI-based clinical algorithms.

Key words
causal inference, machine learning, artificial intelligence, electronic health records, clinical informatics

Program affiliation
Molecular Genetics and Genomics
Computational and Systems Biology
Biomedical Informatics and Data Science
Neurosciences

Research summary
Understand the molecular mechanisms of neurodegeneration through integrated genomic and network inference approaches.

Key words
computational biology, neurogenomics, transcription regulation, neurodegeneration, Alzheimer’s disease, Parkinson disease