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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),
    in the Medical School of the University of Michigan , Ann Arbor, Michigan, USA.

Background:

  • 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 (now named Biocomplexity 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
  • See more information: Dr. He's expert profile in the University of Michigan.

Research:

Dr. Yongqun "Oliver" He (何勇群)'s laboratory research has been briefly summarized in the Cover page of our website, and detailed in our Projects website.

Briefly, our group has now focused on computational medicine and bioinformatics research, with primary research interests in the areas of microbiology, vaccinology, nephrology, ontology, literature mining, and machine learning. Our primary scientific research domains are microbiology, vaccinology, and nephrology. Our primary technical research domains are ontology, semantic web, literature mining, and mechine learning. These technical domains are all closely related to artificial intelligence (AI), so we do AI research! We are also interested in applying our technologies to other interesting areas as well.

Our research can be summarized in the following five areas:

  • Development and applications of community-based ontologies.
  • Development of Ontoanimal tools to support interoperable ontology development and applications.
  • Vaccine informatics, host-pathogen interactions, and vaccine/drug safety.
  • Systematic ontology and bioinformatics analysis of biological interaction networks.
  • Wet-lab (not active now): Host-Brucella interaction and protective vaccine immune mechanisms.

Dr. He has recently proposed a OneNet Theory of Life to systematically and comprehensively study the complex interaction networks of the life of organism. To study such a theory, he also proposes the development and applications of ontologies. He is also constructing a intergrative computational and mathematical model for better study of the OneNet life system.

 

Services (selected):

Grant Review Service:

  • 2016 -2022: USA NIH-NIAID Microbiology and Infectious Diseases B Subcommittee (MIDB) member (permanent).
  • 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.
  • 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).

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:

International Advisory Board:

Teaching (selected):

  • Fall 2008, Winter 2011-2018 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 2016-2018: 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.

Publications:


Ontobee|Ontofox|OAE|VO|Genomesh|Ignet|miniTUBA|PHIDIAS|VIOLIN
He Group
University of Michigan Medical School
Ann Arbor, MI 48109
U of M NIAIDNIAID