Research Topics
| Yongqun HeSummaryAffiliation: University of Michigan Country: USA Publications
Research Grants
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Detail Information
Publications
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...- Molecular targets for rapid identification of Brucella sppVladyslava G Ratushna
Department of Computer Science, College of Information Technology, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
BMC Microbiol 6:13. 2006..We then screened a set of differentiating genes against classical Brucella biovars and showed the applicability of these regions in the design of diagnostic tests... - 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... - 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:.. - 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... - 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:.. - 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... - 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... - 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... - 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... - 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/... - 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... - 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... - 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... - Group XV phospholipase A?, a lysosomal phospholipase A?James A Shayman
Nephrology Division, Department of Internal Medicine, University of Michigan, USA
Prog Lipid Res 50:1-13. 2011..In addition, older LPLA?(-/-) mice develop a phenotype similar to human autoimmune disease. These observations indicate that LPLA? 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... - Mining of vaccine-associated IFN-? 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-? and vaccine-mediated gene interaction network... - 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... - 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... - 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... - PIML: the Pathogen Information Markup LanguageYongqun He
Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, 1880 Pratt Drive, Blacksburg, VA 24061 0477, USA
Bioinformatics 21:116-21. 2005.... - Recombinant Ochrobactrum anthropi expressing Brucella abortus Cu,Zn superoxide dismutase protects mice against B. abortus infection only after switching of immune responses to Th1 typeYongqun He
Center for Molecular Medicine and Infectious Diseases, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0342, USA
Infect Immun 70:2535-43. 2002..anthropi strain 49237 and the recombinant O. anthropi strain 49237SOD induced protection in mice. However, the protection conferred by strain 49237SOD was significantly better than that induced by the parental strain, 49237...
Research Grants
- GENE EXPRESSION IN BRUCELLA-INFECTED MACROPHAGESYongqun He; Fiscal Year: 2005..abstract_text> ..