Computational and Systems Biology

Program affiliation
Developmental Regenerative and Stem Cell Biology
Molecular Genetics and Genomics
Computational and Systems Biology
Molecular Cell Biology

Research summary
Our lab investigates how non-coding genetic variation controls developmental programs and contributes to human disease and evolutionary change. We focus on congenital structural anomalies, pregnancy complications, and bat wing development, combining mouse genetics, embryo genome engineering, and functional genomics approaches, including in vivo MPRAs, to functionally dissect regulatory elements.

Key words
Enhancers, non-coding regulatory variation, developmental genetics, evolution, GWAS, limb development, placental biology, craniofacial development, functional genomics, MPRA

Program affiliation
Molecular Microbiology and Microbial Pathogenesis
Immunology
Computational and Systems Biology
Plant and Microbial Biosciences

Research summary
Discovery and Characterization of Novel Viruses

Key words
microbial pathogenesis, functional genomics, virology, genome analysis, computational biology

Program affiliation
Computational and Systems Biology
Molecular Genetics and Genomics
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