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Frequently Asked Questions

1. Who is He Group?

He Group is the research group in Dr. Yongqun "Oliver" He's laboratory located in the University of Michigan Medical School. He Group includes integrated wet-lab group and bioinformatics group. Our primary research interests are pathogen-host interactions (PHI) and vaccine research and development (R&D). Please look our Projects website for detailed project description. Our goal is to integrate wet-lab and dry-lab research methods into the better understanding of fundamental principles of microbial pathogenesis and host immunity that further leads to rationale vaccine design and development.

2. What software programs developed in He Group can be used to study infectious diseases?

All databases and tools developed in He Group can be used to study infectious diseases, specially pathogen-host interactions (PHI, or called host-pathogen interactions or HPI) and vaccine R&D. BBP is focused on Brucella genomics data integration and literature annotation, and study of Brucella pathogenesis is a BBP focus. PHIDIAS is a pathogen-host interaction data integration and analysis system. BBP is a model system for our PHIDIAS development. VIOLIN is targeted for research and development of vaccines against infectious diseases. As a critical part of further VIOLIN development, we have initiated the Vaccine Ontology project by collaborating with the National Center for Biomedical Ontology (NCBO) and the Infectious Disease Ontology (IDO) Consortium.

We have also developed several web-based methods to address various biological questions. CRCView is a web-based microarray data clustering and GO enrichment system. GenoMesh is a genome-wide literature mining algorithm and data analysis system. MARIMBA and miniTUBA are two web-based Bayesian network modeling systems particularly useful to study biological pathways/networks. These computation systems are general tools and have also been applied to study infectious diseases.

3. What types of vaccine research is He Group doing?

One ultimate goal in infectious disease research is to develop effective and safe vaccines against contagious infectious diseases. Understanding of fundamental pathogen-host interaction mechanisms allows rational vaccine design. Besides our basical PHI study with an aim leading to rationale vaccine design, we have also undergone wet-lab and dry-lab projects for translational vaccine research and development. Our wet-lab vaccine research is aimed to develop a subunit Brucella vaccine for human use. Our bioinformatics vaccine research is to continuously develop VIOLIN. One recent focus is to develop the Vaccine Ontology through a community-based collaboration, and futher apply the ontology for vaccine-oriented literature mining.

4. Are your bioinformatics systems publicly available?

Yes. All our bioinformatics systems are publicly available for free use. Your suggestions and comments are also welcome and appreciated.

5. How can I get help on how to use your software?

Each software we developed includes its own documentations and/or tutorial, brief or detailed depending on how difficult to use. In most cases, they are very easy to use, which is one of our goals. You are also welcome to ask us questions by email or phone call.

6. How can we collaborate with He Group?

We welcome collaborations from various groups inside and outside University of Michigan. Please contact Dr. He for possible collaborations.

7. How can I join He Research Group?

We welcome your interest and application for a research  position in Dr. He's laboratory. See Here for possible opportunities.

 

He Lab |Ontobee|OntoFox|OAE|VO|Genomesh|Ignet|miniTUBA|PHIDIAS|VIOLIN
He Group
University of Michigan Medical School
Ann Arbor, MI 48109
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