 |
Professor, University of Michigan Medical School:
Dr. He is also an affiliated member in the Michigan Institute for Data Science (MIDAS).
|
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., Biomedical and Veterinary Sciences (Focus: Microbiology and Immunology), Virginia Tech, Blacksburg, VA, USA. 1996-2000.
- Postdoc (part-time), Molecular Immunology, Virginia Tech, Blacksburg, VA, USA. 2000-2001.
- M.S., Computer Science, Virginia Tech, Blacksburg, VA, USA. 2000-2002.
- Senior Research Associate, Bioinformatics, Virginia Bioinformatics Institute (now named Biocomplexity Institute in University of Virginia), 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.
- Professor (with tenure), University of Michigan Medical School, effective September 1, 2024.
- 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 can all be classified under artificial intelligence (AI).
Overall, we do biomedical AI research. Specifically, AI includes three complementary domains: knowledge representation and reasoning (KRR), natural language processing (NLP) and machine learning (ML). Ontology engineering is a major part of the KRR. We develop interoperable ontologies and ontology tools, and we apply them to NLP and ML, and use them all to further address interesting biomedical questions and challenges.
Our active research can be summarized in the following areas:
- Development of community-based ontologies and ontology tools, and applying them for NLP and ML.
- Vaccine informatics.
- Microbiology: Brucellosis, COVID-19, and host-pathogen interactions.
- Kidney precision medicine.
- Biological interaction network classification and analysis.
- 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.
Teaching:
- 2005 - Present: Mentored many PhD and MS graduate students; Mentored many visiting scholars; Also, mentored a large number of undergraduate students, most of whom were supported by the Undergraduate Research Opportunity Program (UROP) at the University of Michigan. Noted that Dr. He mentored 26 undergraduate students during the COVID-19 pandemic (2020-2023). See more information Here.
- 2012 - 2024 (in most years): Course facilitator for PIBS 503: Responsible Conduct of Research.
- Fall 2008, Winter 2011-2018 annually: Molecular Biology in Laboratory Animal Medicine (Lecturer for topic: Microarrays and Bioinformatics)
- 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)
Services:
Grant Review Services (selected):
- 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), etc.
- 2016 -2022: Standing member on USA NIH-NIAID Microbiology and Infectious Diseases B Subcommittee (MIDB) study section.
- 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.
Conferences and Workshops (selected):
- 2012-2024: Co-organizer of annual international Vaccine and Drug Ontology Studies (VDOS) workshops. The VDOS workshop series was originally named "Vaccine and Drug Ontology in the Study of Mechanism and Effect" (VDOSME 2012) in 2012.
- 2017-2024: Co-organizer of annual International Workshop on Cells in ExperimentaL Life Science (CELLS), for example, CELLS-2022 and CELLS-2024.
- 2022: Local host and head co-chair of the 2022 2022 International Conference on Biomedical Ontology (ICBO-2022) in September 2022 at the University of Michigan, Ann Arbor, MI, USA.
- 2020: Co-organizer of the WCO-2020: Workshop on COVID-19 Ontologies, i.e., the 8th Annual Workshop of the Clinical and Translational Science Ontology Group, Oct 29-30, 2020, Zoom.
- 2018: Hosted and co-organized the 2018 "Workshop on Ontologies for Stem Cells and Stem Cell Line Cells" on April 26-27, 2018, in the University of Michigan, Ann Arbor, MI, USA.
- 2017: Hosted and co-organized the 2017 annual "Clinical and Translational Science (CTS) Ontology Workshop" in the University of Michigan, Ann Arbor, MI, USA. The theme of the 2017 workshop is: "Microbiology for the CTSA: Ontological Approaches".
- 2014-2016: President of annual Immunology Summit conferences: Immunology Summit - 2014, and Immunology Summit - 2015.
- 10/27/2013: Co-chair of the 3rd ISV Pre-conference Computational Vaccinology Workshop (ICoVax 2013), a satellite workshop of the general Vaccine & ISV Annual Global Congress, held in Spain. Check the selected papers of ICoVax 2013 published in BMC Bioinformatics.
- 10/13/2012: Co-chair of the 2nd ISV Pre-conference Computational Vaccinology Workshop (ICoVax 2012), a satellite workshop of the general Vaccine & ISV Annual Global Congress, held in Shanghai, China. Check the selected papers of the workshop published in BMC Bioinformatics.
Journal Special Issues or Research Topics (selected):
Journal Editorial Board:
Services in the University of Michigan (selected):
- 10/2020 - 9/2021: Served as one of 16 faculty members on the President's COVID-19 Faculty Council in the University of Michigan.
International Advisory Board:
- 2020-2026: Chair of Board of Directors (2024-2026), President (2022-2024), President elect (2020-2022),Overseas Chinese Society for Microbiology (Sino-Micro).
- 2017-present: Co-founder and Advisory committee member of China Biomedical Ontology Consortium (i.e., “OntoChina”), Beijing, China.
He Group Members:
- He Group members and collaborators are listed in Here.
Publications:
|
