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Author Details

Jie Zheng
University of Pennsylvania Perelman School of Medicine
2010
29
12
PMIDPaper TitleJournal TitlePublished Year
37180100VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data.Front Immunol2023
33947809Correction for Vangay et al., "Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities".mSystems2021
33622857Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities.mSystems2021
33777032VaximmutorDB: A Web-Based Vaccine Immune Factor Database and Its Application for Understanding Vaccine-Induced Immune Mechanisms.Front Immunol2021
34697637OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.Database (Oxford)2021
34454610CIDO ontology updates and secondary analysis of host responses to COVID-19 infection based on ImmPort reports and literature.J Biomed Semantics2021
34244718Standardization of assay representation in the Ontology for Biomedical Investigations.Database (Oxford)2021
31272389OSCI: standardized stem cell ontology representation and use cases for stem cell investigation.BMC Bioinformatics2019
31865910VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions.BMC Bioinformatics2019
31888755OHMI: the ontology of host-microbiome interactions.J Biomed Semantics2019
29329592The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.J Biomed Semantics2018
29106667MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments.Nucleic Acids Res2018
27733503Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.Nucleic Acids Res2017
30034908The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines.Quant Biol2017
27903906EuPathDB: the eukaryotic pathogen genomics database resource.Nucleic Acids Res2017
27099700VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms.J Biomed Semantics2016
27627881The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis.J Biomed Semantics2016
27148435OBIB-a novel ontology for biobanking.J Biomed Semantics2016
27128319The Ontology for Biomedical Investigations.PLoS One2016
25785185Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns.J Biomed Semantics2015
26259944A Framework for Global Collaborative Data Management for Malaria Research.Am J Trop Med Hyg2015
25632945Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach.Database (Oxford)2015
24413522Ontodog: a web-based ontology community view generation tool.Bioinformatics2014
25852852CLO: The cell line ontology.J Biomed Semantics2014
24936976Standardized metadata for human pathogen/vector genomic sequences.PLoS One2014
22621763The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms.J Biomed Semantics2012
22190598AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments.Database (Oxford)2011
20200009Modeling sample variables with an Experimental Factor Ontology.Bioinformatics2010
20626927Modeling biomedical experimental processes with OBI.J Biomed Semantics2010
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Collaborators

Yongqun He
University of Michigan Medical School ann arbor
Co-authored papers 17
Christian J Stoeckert
Perelman School of Medicine, University of Pennsylvania
Co-authored papers 13
Yu Lin
School of Pharmaceutical Sciences, Sun Yat-sen University
Co-authored papers 7
Anna Maria Masci
Duke University School of Medicine
Co-authored papers 6
Zuoshuang Xiang
College of Literature, University of Michigan ann arbor
Co-authored papers 6
Bjoern Peters
University of Washington School of Medicine
Co-authored papers 5
Edison Ong
University of Michigan Medical School ann arbor
Co-authored papers 5
Christopher J Mungall
International Society for Biocuration, Lawrence Berkeley National Laboratory, University of Edinburgh, University of Edinburgh School of Biological Sciences
Co-authored papers 5
Lynn M Schriml
University of Maryland School of Medicine, Institute for Genome Sciences
Co-authored papers 4
James Malone
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 4
William D Duncan
University of Florida
Co-authored papers 4
M??lanie Courtot
Ontario Institute for Cancer Research
Co-authored papers 4
Alan Ruttenberg
University at Buffalo
Co-authored papers 4
Helen Parkinson
European Bioinformatics Institute
Co-authored papers 4
James A Overton
Knocean Inc.
Co-authored papers 4
Barry Smith
University at Buffalo
Co-authored papers 4
Nasim Sanati
Oregon Health & Science University
Co-authored papers 3
Jessica C Kissinger
University of Georgia
Co-authored papers 3
Daniel C Berrios
NASA Ames Research Center
Co-authored papers 3
Matthew H Brush
University of Colorado Anschutz Medical Campus
Co-authored papers 3
Randi Vita
Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology
Co-authored papers 3
David S Roos
University of Pennsylvania
Co-authored papers 3
Guanming Wu
Oregon Health and Science University
Co-authored papers 3
Melissa A Haendel
Co-authored papers 3
Philippe Rocca-Serra
University of Oxford
Co-authored papers 3
Susanna-Assunta Sansone
Oxford e-Research Centre, University of Oxford
Co-authored papers 3
Alexander D Diehl
Jacobs School of Medicine and Biomedical Sciences, University at Buffalo
Co-authored papers 3
Mathias Brochhausen
College of Medicine, University of Arkansas for Medical Sciences
Co-authored papers 3
Richard H Scheuermann
J. Craig Venter Institute
Co-authored papers 3
Melissa A Haendel
American Medical Informatics Association, Oregon Health and Science University, Oregon State University, University of Colorado Anschutz Medical Campus, University of North Carolina at Chapel Hill, University of Wisconsin-Madison
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