Research Topics
| Yongqun HeSummaryAffiliation: University of Michigan Country: USA Publications
Research Grants
| Collaborators
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Detail Information
Publications
Analyses of Brucella pathogenesis, host immunity, and vaccine targets using systems biology and bioinformaticsYongqun He
Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, University of Michigan Medical School Ann Arbor, MI, USA
Front Cell Infect Microbiol 2:2. 2012..The recent development of community-based Vaccine Ontology and Brucellosis Ontology provides an efficient way for Brucella data integration, exchange, and computer-assisted automated reasoning...
Identification of fever and vaccine-associated gene interaction networks using ontology-based literature miningJunguk Hur
Unit for Laboratory Animal Medicine, University of Michigan, 48109, Ann Arbor, MI, USA
J Biomed Semantics 3:18. 2012....- A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012)Yongqun He
Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, and Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
J Biomed Semantics 3:12. 2012.... - Modeling biomedical experimental processes with OBIRyan R Brinkman
British Columbia Cancer Agency, Vancouver, Canada
J Biomed Semantics 1:S7. 2010..AVAILABILITY : OBI is available at http://purl.obolibrary.org/obo/obi/2009-11-02/obi.owl... - Vaxign: the first web-based vaccine design program for reverse vaccinology and applications for vaccine developmentYongqun He
Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
J Biomed Biotechnol 2010:297505. 2010..Our results indicate that Vaxign is an accurate and efficient vaccine design program... - Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine OntologyArzucan Ozgür
Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
J Biomed Semantics 2:S8. 2011..The Vaccine Ontology (VO) contains a hierarchy of vaccine names. It is hypothesized that the application of VO will enhance the prediction of IFN-γ and vaccine-mediated gene interaction network... - Emerging vaccine informaticsYongqun He
Department of Microbiology and Immunology, Unit for Laboratory Animal Medicine, Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, 48109, USA
J Biomed Biotechnol 2010:218590. 2010..Computational literature mining and databases effectively process, mine, and store large amounts of vaccine literature and data. Vaccine Ontology (VO) has been initiated to integrate various vaccine data and support automated reasoning... - Proinflammatory caspase-2-mediated macrophage cell death induced by a rough attenuated Brucella suis strainFang Chen
Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
Infect Immun 79:2460-9. 2011..This unique cell death differs from apoptosis, which is not proinflammatory. It is also different from classical pyroptosis, which is caspase-1 mediated... - Bayesian network expansion identifies new ROS and biofilm regulatorsAndrew P Hodges
Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
PLoS ONE 5:e9513. 2010..The presently reported BN+1 expansion method is a generalized approach applicable to the characterization and expansion of other biological pathways and living systems... - Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association networkJunguk Hur
Bioinformatics Program, University of Michigan, Ann Arbor, MI 48109, USA
BMC Immunol 12:49. 2011..As a test case, we have examined vaccines for Brucella, the causative agent of brucellosis in humans and animals... 
CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clusteringZuoshuang Xiang
Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, USA
Bioinformatics 23:1843-5. 2007..It allows flexible input data format, rich graphical illustration as well as integrated GO term based annotation/interpretation of clustering results. Availability: http://helab.bioinformatics.med.umich.edu/crcview/...- Caspase-2-dependent dendritic cell death, maturation, and priming of T cells in response to Brucella abortus infectionXinna Li
Unit for Laboratory Animal Medicine and Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
PLoS ONE 7:e43512. 2012.... - VIOLIN: vaccine investigation and online information networkZuoshuang Xiang
Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, USA
Nucleic Acids Res 36:D923-8. 2008..VIOLIN is publicly available at http://www.violinet.org... - Vaxjo: a web-based vaccine adjuvant database and its application for analysis of vaccine adjuvants and their uses in vaccine developmentSamantha Sayers
Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
J Biomed Biotechnol 2012:831486. 2012..To support data exchange, the information of vaccine adjuvants is stored in the Vaccine Ontology (VO) in the Web Ontology Language (OWL) format... - Literature-based discovery of IFN-gamma and vaccine-mediated gene interaction networksArzucan Ozgür
Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA
J Biomed Biotechnol 2010:426479. 2010..Literature evidence was manually curated for the IFN-gamma relatedness of 56 genes and vaccine development relatedness for 52 genes. This study also generated many new hypotheses worth further experimental studies... - Protegen: a web-based protective antigen database and analysis systemBrian Yang
Unit for Laboratory Animal Medicine, University of Michigan Medical School, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
Nucleic Acids Res 39:D1073-8. 2011..Protegen is publically available at http://www.violinet.org/protegen... - miniTUBA: medical inference by network integration of temporal data using Bayesian analysisZuoshuang Xiang
Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, USA
Bioinformatics 23:2423-32. 2007..No software pipeline currently exists for interpretation and inference of dynamic Bayesian networks learned from biomedical and clinical data... - Presence of putative repeat-in-toxin gene tosA in Escherichia coli predicts successful colonization of the urinary tractPatrick D Vigil
Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
MBio 2:e00066-11. 2011..coli isolates regardless of source. Rapid identification of uropathogenic strains of E. coli may aid in the development of therapeutic and preventive therapies... - Group XV phospholipase A₂, a lysosomal phospholipase A₂James A Shayman
Nephrology Division, Department of Internal Medicine, University of Michigan, USA
Prog Lipid Res 50:1-13. 2011..In addition, older LPLA₂(-/-) mice develop a phenotype similar to human autoimmune disease. These observations indicate that LPLA₂ may play a primary role in phospholipid homeostasis, drug toxicity, and host defense... - BBP: Brucella genome annotation with literature mining and curationZuoshuang Xiang
Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
BMC Bioinformatics 7:347. 2006..It is further hypothesized that literature-based Brucella gene annotation would increase understanding of complicated Brucella pathogenesis mechanisms... - PHIDIAS: a pathogen-host interaction data integration and analysis systemZuoshuang Xiang
Unit for Laboratory Animal Medicine, University of Michigan, 1150 W Medical Dr, Ann Arbor, MI 48109, USA
Genome Biol 8:R150. 2007..In addition, PHIDIAS allows submission, search and analysis of PHI genes and molecular networks curated from peer-reviewed literature. PHIDIAS is publicly available at http://www.phidias.us... - Caspase-2 mediated apoptotic and necrotic murine macrophage cell death induced by rough Brucella abortusFang Chen
Unit for Laboratory Animal Medicine and Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
PLoS ONE 4:e6830. 2009..The biological relevance of Brucella O antigen and caspase-2-mediated macrophage cell death in Brucella pathogenesis and protective Brucella immunity is discussed... - Characterization of recombinant B. abortus strain RB51SOD toward understanding the uncorrelated innate and adaptive immune responses induced by RB51SOD compared to its parent vaccine strain RB51Jianguo Zhu
Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, University of Michigan Medical School Ann Arbor, MI, USA
Front Cell Infect Microbiol 1:10. 2011..This unique and apparently contradictory profile is likely associated with the differences in outer membrane integrity and Cu/Zn SOD release... - Databases and in silico tools for vaccine designYongqun He
Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
Methods Mol Biol 993:115-27. 2013..Vaccine information and resources can be integrated with Vaccine Ontology (VO). This chapter introduces databases and in silico tools that facilitate vaccine design, especially those in the VIOLIN system... - Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinologyZuoshuang Xiang
Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
BMC Bioinformatics 14:S2. 2013..Overall, our Vaxign computational prediction provides many promising candidates for rational HSV vaccine development. The method is generic and can also be used to predict other viral vaccine targets... - Computational vaccinology and the ICoVax 2012 workshopYongqun He
Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, and Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
BMC Bioinformatics 14:I1. 2013..This Editorial provides a list of major challenges for the future of computational vaccinology and identifies developing themes that will expand and evolve over the next few years... - Systematic annotation and analysis of "virmugens"-virulence factors whose mutants can be used as live attenuated vaccinesRebecca Racz
College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA
Vaccine 31:797-805. 2013..The bioinformatics annotation and analysis of virmugens helps to elucidate enriched virmugen profiles and the mechanisms of protective immunity, and further supports rational vaccine design... - Ontology-based combinatorial comparative analysis of adverse events associated with killed and live influenza vaccinesSirarat Sarntivijai
National Center for Integrative Biomedical Informatics, University of Michigan, Ann Arbor, MI, USA
PLoS ONE 7:e49941. 2012..In addition, our meta-analysis found that all previously reported positive correlation between GBS and influenza vaccine immunization were based on trivalent influenza vaccines instead of monovalent influenza vaccines... - Using epitope predictions to evaluate efficacy and population coverage of the Mtb72f vaccine for tuberculosisLucy A McNamara
Department of Epidemiology University of Michigan, Ann Arbor, MI 48109, USA
BMC Immunol 11:18. 2010..The present study assesses Mtb72f's predicted efficacy in people with different DRB1 genotypes to predict whether the vaccine will protect against diverse clinical strains of M. tuberculosis in a diverse host population... - Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLINYongqun He
Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, and Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
Immunome Res 6:S5. 2010..The use of VIOLIN provides a general approach that can be applied for analyses of vaccines against other pathogens and infection diseases... - Pathobiology and management of laboratory rodents administered CDC category A agentsYongqun He
Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, USA
Comp Med 57:18-32. 2007.... - Brucella melitensis triggers time-dependent modulation of apoptosis and down-regulation of mitochondrion-associated gene expression in mouse macrophagesYongqun He
Unit for Laboratory Animal Medicine, University of Michigan Medical School, 018 Animal Research Facility, 1150 W Medical Center Drive, Ann Arbor, MI 48109, USA
Infect Immun 74:5035-46. 2006..melitensis 16M appears to inhibit apoptosis of macrophages by blocking release of cytochrome c and production of reactive oxygen species in the mitochondria, thus preventing activation of caspase cascades... - OntoFox: web-based support for ontology reuseZuoshuang Xiang
Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
BMC Res Notes 3:175. 2010..abstract:.. - Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease OntologyYu Lin
Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
J Biomed Semantics 2:9. 2011..abstract:..
Research Grants
- Ontology-based Information Network to Support Vaccine ResearchYongqun He; Fiscal Year: 2009..and E. coli will lay a strong foundation for further advanced informatics research on vaccines against infectious diseases in the post-genomics and information era. ..
- Ontology-based Information Network to Support Vaccine ResearchYongqun He; Fiscal Year: 2010..and E. coli will lay a strong foundation for further advanced informatics research on vaccines against infectious diseases in the post-genomics and information era. ..