Yongqun He

Summary

Affiliation: University of Michigan
Country: USA

Publications

  1. pmc Vaxjo: a web-based vaccine adjuvant database and its application for analysis of vaccine adjuvants and their uses in vaccine development
    Samantha Sayers
    Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    J Biomed Biotechnol 2012:831486. 2012
  2. pmc Literature-based discovery of IFN-gamma and vaccine-mediated gene interaction networks
    Arzucan Ozgür
    Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA
    J Biomed Biotechnol 2010:426479. 2010
  3. pmc Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis
    Cui Tao
    Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
    J Biomed Semantics 3:13. 2012
  4. pmc Analyses of Brucella pathogenesis, host immunity, and vaccine targets using systems biology and bioinformatics
    Yongqun 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
  5. pmc Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining
    Junguk Hur
    Unit for Laboratory Animal Medicine, University of Michigan, 48109, Ann Arbor, MI, USA
    J Biomed Semantics 3:18. 2012
  6. pmc 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
  7. pmc Modeling biomedical experimental processes with OBI
    Ryan R Brinkman
    British Columbia Cancer Agency, Vancouver, Canada
    J Biomed Semantics 1:S7. 2010
  8. pmc Vaxign: the first web-based vaccine design program for reverse vaccinology and applications for vaccine development
    Yongqun He
    Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    J Biomed Biotechnol 2010:297505. 2010
  9. pmc Emerging vaccine informatics
    Yongqun 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
  10. pmc Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology
    Arzucan Ozgür
    Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
    J Biomed Semantics 2:S8. 2011

Collaborators

Detail Information

Publications41

  1. pmc Vaxjo: a web-based vaccine adjuvant database and its application for analysis of vaccine adjuvants and their uses in vaccine development
    Samantha 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...
  2. pmc Literature-based discovery of IFN-gamma and vaccine-mediated gene interaction networks
    Arzucan 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...
  3. pmc Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis
    Cui Tao
    Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
    J Biomed Semantics 3:13. 2012
    ..abstract:..
  4. pmc Analyses of Brucella pathogenesis, host immunity, and vaccine targets using systems biology and bioinformatics
    Yongqun 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...
  5. pmc Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining
    Junguk Hur
    Unit for Laboratory Animal Medicine, University of Michigan, 48109, Ann Arbor, MI, USA
    J Biomed Semantics 3:18. 2012
    ....
  6. pmc 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
    ....
  7. pmc Modeling biomedical experimental processes with OBI
    Ryan 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...
  8. pmc Vaxign: the first web-based vaccine design program for reverse vaccinology and applications for vaccine development
    Yongqun 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...
  9. pmc Emerging vaccine informatics
    Yongqun 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...
  10. pmc Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology
    Arzucan 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...
  11. pmc Updates on the web-based VIOLIN vaccine database and analysis system
    Yongqun He
    Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA, Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA, Center for Computational Medicine and Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA, Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA, Division of Comparative Medicine, University of South Florida, Tampa, FL 33612, USA, Department of Neurology, University of Michigan, 48109, Ann Arbor, MI, USA, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA, Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Nucleic Acids Res 42:D1124-32. 2014
    ..The Vaccine Ontology is applied to standardize and integrate various data in VIOLIN. VIOLIN also hosts the Ontology of Vaccine Adverse Events (OVAE) that logically represents adverse events associated with licensed human vaccines. ..
  12. pmc Proinflammatory caspase-2-mediated macrophage cell death induced by a rough attenuated Brucella suis strain
    Fang 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...
  13. pmc Bayesian network expansion identifies new ROS and biofilm regulators
    Andrew 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...
  14. pmc Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates
    Thomas E Todd
    Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    BMC Bioinformatics 14:S3. 2013
    ..Using Brucella vaccines and vaccine candidates as study models, this hypothesis was tested by meta-analysis of Brucella vaccine studies reported in the literature...
  15. pmc Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network
    Junguk 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...
  16. ncbi request reprint CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering
    Zuoshuang 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/...
  17. pmc Protegen: a web-based protective antigen database and analysis system
    Brian 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...
  18. pmc Caspase-2 mediates a Brucella abortus RB51-induced hybrid cell death having features of apoptosis and pyroptosis
    Denise N Bronner
    Department of Microbiology and Immunology, University of Michigan Medical School Ann Arbor, MI, USA
    Front Cell Infect Microbiol 3:83. 2013
    ..Taken together, our data has demonstrated that caspase-2 can play an important role in mediating a proinflammatory response and a hybrid cell death that demonstrates features of both apoptosis and pyroptosis. ..
  19. pmc Presence of putative repeat-in-toxin gene tosA in Escherichia coli predicts successful colonization of the urinary tract
    Patrick D Vigil
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
    MBio 2:e00066-11. 2011
    ..The presence of tosA was predictive of successful colonization of a murine model of infection, even among fecal isolates, and can be used as a marker of pathogenic strains of UPEC within a distinct subset of the B2 lineage...
  20. pmc BBP: Brucella genome annotation with literature mining and curation
    Zuoshuang 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...
  21. pmc Caspase-2-dependent dendritic cell death, maturation, and priming of T cells in response to Brucella abortus infection
    Xinna 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
    ....
  22. pmc VIOLIN: vaccine investigation and online information network
    Zuoshuang 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...
  23. doi request reprint Databases and in silico tools for vaccine design
    Yongqun He
    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...
  24. pmc Computational vaccinology and the ICoVax 2012 workshop
    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 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...
  25. ncbi request reprint miniTUBA: medical inference by network integration of temporal data using Bayesian analysis
    Zuoshuang 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...
  26. pmc Group XV phospholipase A₂, a lysosomal phospholipase A₂
    James 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...
  27. pmc Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology
    Zuoshuang 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...
  28. pmc Systematic annotation and analysis of "virmugens"-virulence factors whose mutants can be used as live attenuated vaccines
    Rebecca 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...
  29. pmc PHIDIAS: a pathogen-host interaction data integration and analysis system
    Zuoshuang 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...
  30. pmc Caspase-2 mediated apoptotic and necrotic murine macrophage cell death induced by rough Brucella abortus
    Fang 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...
  31. pmc 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 RB51
    Jianguo 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...
  32. pmc Ontodog: a web-based ontology community view generation tool
    Jie Zheng
    Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 and Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 30:1340-2. 2014
    ..We demonstrate the application of Ontodog for the generation of community views using the Ontology for Biomedical Investigations as the source ontology...
  33. pmc Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses
    Yu Lin
    Unit of Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    J Biomed Semantics 3:17. 2012
    ..Vaccine formulation and administration methods may affect vaccine safety and efficacy significantly...
  34. pmc Ontology-based combinatorial comparative analysis of adverse events associated with killed and live influenza vaccines
    Sirarat 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...
  35. pmc Using epitope predictions to evaluate efficacy and population coverage of the Mtb72f vaccine for tuberculosis
    Lucy 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...
  36. pmc OntoFox: web-based support for ontology reuse
    Zuoshuang Xiang
    Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    BMC Res Notes 3:175. 2010
    ..abstract:..
  37. pmc Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN
    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 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...
  38. ncbi request reprint Pathobiology and management of laboratory rodents administered CDC category A agents
    Yongqun He
    Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, USA
    Comp Med 57:18-32. 2007
    ....
  39. pmc Brucella melitensis triggers time-dependent modulation of apoptosis and down-regulation of mitochondrion-associated gene expression in mouse macrophages
    Yongqun 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...
  40. pmc Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology
    Yu Lin
    Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    J Biomed Semantics 2:9. 2011
    ..abstract:..

Research Grants2

  1. Ontology-based Information Network to Support Vaccine Research
    Yongqun 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. ..
  2. Ontology-based Information Network to Support Vaccine Research
    Yongqun 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. ..