Oliver He's primary appointment is with the Unit for Laboratory Animal Medicine (ULAM) with a joint appointment in the Department of Microbiology and Immunology. He is also an affiliated member of the Center for Computational Medicine and Biology (CCMB) and a member of the (Comprehensive Cancer Center) in the University of Michigan (UM) Medical School.
MS, Virginia Tech, Bioinformatics, 2002
PhD, Virginia Tech, 2000
M.S., China Agricultural University in China, in Infectious Diseases and Veterinary Preventive Medicine
D.V.M. Jiangxi Agricultural University, China
Dr. He's laboratory performs both dry-lab (bioinformatics lab) and wet-lab (microbiology and immunology lab) biomedical research.
Our primary bioinformatics research has many topics: (1) Ontology development. Dr. He has initiated and led the development of the community-based Vaccine Ontology (VO) and Ontology of Adverse Events (OAE). VO and OAE can be used in many applications such as data integration and literature mining. We are also leading or collaborating the development of several other ontologies. (2) Ontology tool development. We have developed many ontology tools that are used for ontology reuse, ontology development, and ontology applications. (3) Literature mining, with a focus on ontology-based literature mining approaches. (4) Bayesian network (BN) modeling. BNs can model linear, nonlinear, combinatorial, and stochastic relationships among variables across multiple levels of biological organizations. We have developed new BN algorithms and tools for analysis of gene interaction networks using high throughput gene expression data.
The above and existing bioinformatics approaches have been used primarily in the following research areas: (1) Vaccine Informatics. We have developed the VIOLIN vaccine database and analysis system. As a part of VIOLIN, we have developed Vaxign, the first web-based publically available vaccine target design tool based on bioinformatics analysis of genome sequences using the strategy of reverse vaccinology. logy. (2) Comparative genomics. Various genome sequences can be compared to address many biomedical questions. (3) Bioinformatics analysis of host-microbe interactions. We are interested in developing and applying bioinformatics methods to study the intricate interactions between host (e.g., human and mouse) and microbes (pathogens or bacterial microbiota). (4) Analysis of vaccine and drug adverse event mechanisms. We are interested in applying the Ontology of Adverse Events to study the mechanisms of vaccine and drug-induced adverse events.
Our wet-lab research is focused on the study of Brucella, a facultative intracellular bacterium that causes brucellosis, one of the most common zoonotic diseases in the world in humans and a variety of animal species. Our Brucella research has two focuses: (1) Analysis of the caspase-2 cell death pathway and its role in Brucella pathogenesis and immunity. Virulent Brucella survives inside macrophages and prevents macrophage cell death, while attenated rough Brucella strains (e.g., B. abortus cattle vaccine RB51 and B. suis vaccine candidate VTRS1) cannot survive inside macrophages and induce a novel caspase-2-mediated proinflammatory cell death that is different from classical apoptosis or pyroptosis. 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. Our research aims to elucidate the caspase-2-mediated proinflammatory cell death pathway and its biological effect on microbial pathogenesis, and protective immunity against brucellosis and other diseases. (2) Development of effective and safe Brucella vaccines potentially for human use. We are interested in applying reverse vaccinology and more effective adjuvant strategies for Brucella subunit vaccine research and development (R & D).
More information can be found at: http://www.hegroup.org/
Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer TC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y. CLO: The Cell Line Ontology. Journal of Biomedical Semantics. 2014, 5:37. doi:10.1186/2041-1480-5-37.
Yongqun He Y, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao and Barry Smith. OAE: The Ontology of Adverse Events. Journal of Biomedical Semantics. 2014, 5:29 doi:10.1186/2041-1480-5-29. PMID: 25093068.PMCID: PMC4120740.
He Y, Amer AO. Microbial modulation of host apoptosis and pyroptosis. Front. Cell. Infect. Microbiol. doi: 10.3389/fcimb.2014.00083. Accepted on June 3, 2014. PMID: 24995165. PMCID: PMC4062964.
He Y. Ontology-supported research on vaccine efficacy, safety, and integrative biological networks. Expert Reviews in Vaccines. 2014 Jul;13(7):825-41. doi: 10.1586/14760584.2014.923762. Epub 2014 Jun 7. PMID: 24909153. (Note: In this paper, the “One Network (OneNet) Theory of Life” was introduced for the first time.)
Lin Y, He Y. The Ontology of Genetic Susceptibility Factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events. Journal of Biomedical Semantics. 2014, 5:19. doi:10.1186/2041-1480-5-19. PMID: 24963371. PMCID: PMC4068904.
Tao C, He Y, Arabandi S. A 2013 Workshop: Vaccine and Drug Ontology Studies (VDOS 2013). Journal of Biomedical Semantics. 2014 Mar 20;5(1):16. doi: 10.1186/2041-1480-5-16. PMID: 24650607. PMCID: PMC3994568.
Racz R, Li X, Patel M, Xiang Z, and He Y. DNAVaxDB: the first web-based DNA vaccine database and its data analysis. BMC Bioinformatics. 2014, 15(Suppl 4):S2. PMID: 25104313.
De Groot AS, De Groot P, He Y. ICoVax 2013: The 3rd ISV Pre-conference Computational Vaccinology Workshop. BMC Bioinformatics. 2014, 15(Suppl 4):I1. PMID: 25104130.
He Y. Vaccine adjuvant informatics: from data integration and analysis to rational vaccine adjuvant design. Front. Immunol. 2014. doi: 10.3389/fimmu.2014.00032. PMID: 24550916. PMCID: PMC3909948.
Zheng J, Xiang Z, Stoeckert Jr. CJ, He Y. Ontodog: a web-based ontology community view generation tool. Bioinformatics. 2014, 30(9):1340-2. doi: 10.1093/bioinformatics/btu008. [PDF] PMID: 24413522. PMCID: PMC3998133.
He Y, Racz R, Sayers S, Lin Y, Todd T, Hur J, Li X, Patel M, Zhao B, Chung M, Ostrow J, Sylora A, Dungarani P, Ulysse G, Kochhar K, Vidri B, Strait K, Jourdian GW, Xiang Z. Updates on the web-based VIOLIN vaccine database and analysis system. Nucleic Acids Research. 2014. 42 (D1): D1124-D1132. doi: 10.1093/nar/gkt1133. First published online: November 19, 2013. [PDF]. PMID: 24259431. PMCID: PMC3964998.
He Y. Bacterial whole genome determination and applications (Chapter 31). In book: Molecular Medical Microbiology, Second Edition, Editors: Yi-Wei Tang, Max Sussman, Dongyou Liu, Ian R. Poxton, and Joseph D. Schwartzman. Elsevier Ltd. ISBN: 9780123971692. [Elsevier link] [Amazon link]
*****More can be found at: http://www.hegroup.org/publications.html