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 wet-lab (microbiology and immunology lab) and dry-lab (bioinformatics lab) biomedical research. Our primary biomedical research interest is to understand pathogenesis and immunology of infectious diseases and develop vaccines against intracellular pathogens. In particular, we study Brucella, a facultative intracellular bacterium that causes brucellosis, the most common zoonotic disease in the world in humans and a variety of animal species.

Our wet-lab 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 attenated 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, tumors, 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 Brucella subunit 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). 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. Vaxign has been tested in many pathogens and is being used in our own Brucella wet-lab vaccine research.

Our primary bioinformatics research has many topics: (1) Ontology development and applications. 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 collaborating the development of several other ontologies and ontology tools. (2) Literature mining, with a focus on ontology-based literature mining approaches. (3) Bayesian network (BN) modeling. New BN algorithms and tools have been developed for analysis of gene interaction networks using high throughput gene expression data. These approaches have been used primarily in these two research areas: (1) Vaccine Informatics. We have developed the VIOLIN vaccine database and analysis system. (2) Bioinformatics analysis of host-pathogen interactions. We are interested in developing and applying bioinformatics methods to study the intricate interactions between host (e.g., human and mouse) and pathogen. Brucella has been used as a model pathogen organism in most of our bioinformatics studies.  

Annoucement: An ICBO 2012 workshop entitled "Vaccine and Drug Ontology in the Study of Mechanism and Effect" (VDOSME 2012) will be hold in the end of July, 2012, in the Medical University of Graz, Austria. The paper submission deadline is April 15, 2012. VDOSME 2012 will provide a platform for discussing problems and solutions in the development and application of biomedical ontologies to representing and analyzing vaccines/drugs, vaccine/drug administrations, vaccine/drug-induced immune responses, and similar topics. Please check the VDOSME 2012 website for more details.

Annoucement: Oliver and He lab ontology team will host a workshop of the Ontology of Biomedical Investigations (OBI) on May 30, May 31, and June 1. The detailed information is HERE.

Your suggestions and comments are welcome. Thank you.