Welcome to hegroup.org!
Welcome to the home page of Dr. Yongqun "Oliver" He's laboratory research group at the University of Michigan! We do both dry-lab (bioinformatics lab) and wet-lab (microbiology and immunology lab) biomedical research.
Our primary bioinformatics research has many topics: (1) Ontology development. Dr. He has initiated and led the development of the community-based Vaccine Ontology (VO) and Ontology of Adverse Events (OAE). VO and OAE can be used in many applications such as data integration and literature mining. We are also leading or involving the development of several other ontologies. (2) Ontology tool development. We have developed many ontology tools that are used for ontology reuse, ontology development, and ontology applications. (3) Literature mining, with a focus on ontology-based literature mining approaches. (4) Bayesian network (BN) modeling. BNs can model linear, nonlinear, combinatorial, and stochastic relationships among variables across multiple levels of biological organizations. We have developed new BN algorithms and tools for analysis of gene interaction networks using high throughput gene expression data.
The above and existing bioinformatics approaches have been used primarily in the following research areas: (1) Vaccine Informatics. We have developed the VIOLIN vaccine database and analysis system. As a part of VIOLIN, we have developed Vaxign, the first web-based publically available vaccine target design tool based on bioinformatics analysis of genome sequences using the strategy of reverse vaccinology. logy. (2) Bioinformatics analysis of host-microbe interactions. We are interested in developing and applying bioinformatics methods to study the intricate interactions between host (e.g., human and mouse) and microbes (pathogens or bacterial microbiota).
(3) Analysis of vaccine and drug adverse event mechanisms. We are interested in applying the Ontology of Adverse Events to study the mechanisms of vaccine and drug-induced adverse events.
Our wet-lab research is focused on the study of Brucella, a facultative intracellular bacterium that causes brucellosis, one of the most common zoonotic diseases in the world in humans and a variety of animal species. Our Brucella research has two focuses: (1) Analysis of the caspase-2 cell death pathway and its role in Brucella pathogenesis and immunity. Virulent Brucella survives inside macrophages and prevents macrophage cell death, while attenuated rough Brucella strains (e.g., B. abortus cattle vaccine RB51 and B. suis vaccine candidate VTRS1) cannot survive inside macrophages and induce a novel caspase-2-mediated proinflammatory cell death that is different from classical apoptosis or pyroptosis. We coined such a cell death as "caspase-2-mediated pyroptosis". Caspase-2 is critical in regulating cell death, DNA damage, stress, cancer, and microbial infections. Our research aims to elucidate the caspase-2-mediated proinflammatory cell death pathway and its biological effect on microbial pathogenesis, and protective immunity against brucellosis and other diseases.
(2) Development of effective and safe Brucella vaccines potentially for human use. We are interested in applying reverse vaccinology and more effective adjuvant strategies for Brucella subunit vaccine research and development (R & D).
Your suggestions and comments are welcome. Thank you.