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.
- 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.
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. More insights about this pathway was identified by our collaborative research as shown in Bronner et al, 2015. 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.
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.
More specific research projects are described Here.
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:
- 2018: Co-organize and host 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 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".
- 2017: Co-organized "the 1st International Workshop on Cells in ExperimentaL Life Science" （CELLS-2017）, held on September 13, 2017, in Newcastle, UK.
- 2013-2018: Co-chair of annual international Vaccine and Drug Ontology Studies (VDOS) workshops: VDOS 2013, VDOS 2014, VDOS 2015, and VDOS 2016, 2017, and 2018. All these workshops are held together with the annual International Conference on Biomedical Ontology (ICBO) meetings. Note: The VDOSME 2012 workshop was the first of the workshop series. Since 2013 the name of the workshop has been changed to VDOS.
- 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.
- 7/21/2012: Co-chair of the ICBO 2012 workshop entitled "Vaccine and Drug Ontology in the Study of Mechanism and Effect" (VDOSME 2012), in the Medical University of Graz, Austria. See the VDOSME thematic series in the Journal of Biomedical Semantics (JBMS), and VDOSME 2012 Editorial article.
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:
- 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.