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Yongqun "Oliver" He, D.V.M., Ph.D.

Associate Professor
    Unit for Laboratory Animal Medicine (Dr. He's Biopage)
    Department of Microbiology and immunology (Dr. He's Biopage)
    Center for Comput. Med. & Bioinformatics (Dr. He's Biopage), and
    Comprehensive Cancer Center (Dr. He's membership)
 University of Michigan Medical School, Ann Arbor, Michigan, USA.


  • B.S. in Veterinary Med. (equivalent to DVM in US), Jiangxi Agricultural Univ, Nanchang, China. 1986-1991
  • Assistant Veterinarian (licensed), Beijing Xijiao Livestock & Poultry Company, Beijing, China. 1991-1993
  • M.S., Infect. Dis. & Veterinary Preventive Med., China Agricultural University, Beijing, China. 1993-1996
  • Ph.D., Molecular Immunology, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA. 1996-2000
  • Postdoc, Molecular Immunology, Virginia Tech, Blacksburg, VA, USA. 2000-2001
  • M.S., Computer Science, Virginia Tech, Blacksburg, VA, USA. 2000-2002
  • Senior Research Associate, Bioinformatics & Molecular Immunology, Virginia Bioinformatics Institute, Blacksburg, VA, USA. 2002-2005
  • Assistant Professor, University of Michigan Medical School. 2005-2011
  • Associate Professor (with tenure), University of Michigan Medical School, effective September 1, 2011


Dr. Yongqun "Oliver" He (何勇群)'s laboratory research has two major thrusts: (1) Dry-lab bioinformatics research; and (2) Wet-lab Brucella microbiology and immunology research. Our primary research theme is to study scientific questions using integrated systems biology approaches.

Dr. He's primary bioinformatics research focuses on the development of ontologies, ontology tools, databases, and analysis systems to address various biomedical questions. Dr. He has initiated and led the developed of many ontologies, including the community-based Vaccine Ontology (VO) and Ontology of Adverse Events (OAE). These ontologies are being used in different areas, for example, in ontology-based genome-wide literature mining. He group has also developed many ontology-oriented tools (such as OntoFox and Ontobee) to support ontology development and applications. He group is also interested in high throughput gene expression data analysis, especially using Bayesian network (BN) approaches. Our BN analysis methods can be used to identify novel gene interactions and networks for advanced study of different biological networks and pathways. We are also interested in comparative genomics, esp. microbial comparative genomics.

We have focused our bioinformatics research efforts on the study of host-pathogen interactions (HPI) and vaccines against infectious diseases. For the vaccine informatics, we developed VIOLIN, a web-based vaccine database and analysis system. A key program of VIOLIN is Vaxign, the first web-based publically available vaccine target design tool based on bioinformatics analysis of genome sequences using the strategy of reverse vaccinology. For the host-pathogen interaction (HPI) data analysis, we developed PHIDIAS, a web-based comprehensive HPI database and analysis system. In our bioinformatics projects, we often use Brucella as our case study.

Brucella spp. are Gram-negative, facultative intracellular bacteria that cause chronic brucellosis in various animals and humans. Human brucellosis remains one of the commonest zoonotic diseases worldwide with more than 500,000 new cases annually. Treatment of brucellosis is very difficult. Presently there is still no safe and effective Brucella vaccine available for human use. Dr. He's wet-lab Brucella research focuses on understanding of Brucella pathogenesis and vaccine-induced protective immunity in host against virulent Brucella. He laboratory is also developing effective and safe Brucella vaccines with an aim for eventual human use. Systems biology and bioinformatics approaches are also being applied to study Brucella pathogenesis and predict Brucella vaccine candidates.

One major finding from our wet-lab Brucella research is that we for the first time identified a novel caspase-2-mediated proinflammatory cell death (see our references He et al, 2006, Chen and He, 2009, Chen et al, 2011, Li and He, 2012, and Bronner, O'Riordan, and He, 2013). This cell death is induced by many rough attenuated Brucella strains, including Brucella cattle vaccine strain RB51, B. abortus wboA mutant VTRA1, and B. suis wboA mutant VTRS1.This cell death is prevented by wild type virulent Brucella in infected macrophages, but not in dendritic cells. The caspase-2 mediated cell death differs from apoptosis because apoptosis is not proinflammatory. It also differs from classic caspase-1-mediated pyroptosis because caspase-1 does not play a role in the cell death induction. 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. We are dissecting the detailed caspase-2-mediated pyroptosis pathway and its biological effect on microbial pathogenesis, and protective immunity against brucellosis and many other diseases.

More specific research projects are described Here.

Special Feature Report on Dr. He and He group by International Innovation:
Yongqun He: 'Analysing multidisciplinary vaccine mechanisms'. In research topic: The Mechanics of Health, International Innovation, July 2013, pp 41-43. Publisher: Research Media Ltd. ISSN 2041-4552.
(Note: International Innovation is the leading global dissemination resource for the wider scientific, technology and research communities, dedicated to disseminating the latest science, research and technological innovations on a global level. More information and a complimentary subscription offer to the publication can be found at: www.researchmedia.eu).

Services (selected):

Conferences and Workshops:

Journal Special issues:

  • 2013-2014: Topic co-editor of the Frontier Microbiology Research Topic "Microbial Modulation of Host Apoptosis and Pyroptosis". All papers are published in the journal Frontiers in Cellular and Infection Microbiology.
  • 2010: Lead guest editor for the Special Issue on Vaccine Informatics in the Journal of Biomedicine and Biotechnology. Note: The journal title has been changed to "BioMed Research International" in 2012.
  • Note: The workshops listed above, including VDOSME-2012, VDOS 2013-2016, and ICoVax 2012/2013, all have corresponding special issues published.

Journal Editorial Board:

Grant Review Service:

  • 2016 -2022: USA NIH-NIAID Microbiology and Infectious Diseases B Subcommittee (MIDB) member (permanent).
  • 2005-present: Ad hoc grant reviewer for: U.S. NIH study sections; the Life Sciences Division of the Army Research Office in USA; Defense Threat Reduction Agency (DTRA); U.S. Department of Agriculture (USDA); US - Israel Binational Agricultural Research and Development Fund; South Africa Medical Research Council, the Wellcome Trust at UK; Wellcome Trust/DBT India Alliance; and National Natural Science Foundation of China (NSFC).
  • 2012-2014: Eligible for continuous US NIH grant submissions from August 16, 2013 to September 30, 2014 based on my having participated in NIH peer reviews for at least six times in the 18 months ending June 30, 2013.

Teaching (selected):

  • Fall 2008, Winter 2011-2016 annually: Molecular Biology in Laboratory Animal Medicine (Lecturer for topic: Microarrays and Bioinformatics)
  • Fall 2012-2015 annually: Course facilitator for PIBS 503 (Research Responsibility and Ethics), for discussion sessions: (1) Fraud, Fabrication and Plagiarism (representing ULAM), and (4) Animal Use and Care (representing Bioinformatics Program).
  • Winter 2011, 2012, and 2013: Bacteriology (Module 1 of undergraduate course: Medical Microbiology - Micro 301 001, Instructor)
  • Winter 2009-2012 annually and 2016: Vaccines in Public Health (EPID 609) (Invited Speaker: Reverse vaccinology and ontology-based information network to support vaccine research)
  • Fall 2008: Bioinformatics and Computational Biology (Bioinfo 527) (Teacher: Genomics/comparative genomics)
  • Winter 2008: Bioinformatics on the Web (Bioinfo 800.006, Instructor)
  • Fall 2006: Microbial Genomics (Micro 619, Co-instructor)

He Group Members:

  • He Group members and collaborators are listed in Here.


  • Selected publications are listed in Here.

ORCID ID: http://orcid.org/0000-0001-9189-9661

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