Yongqun He
Orcid: 0000-0001-9189-9661
According to our database1,
Yongqun He
authored at least 134 papers
between 2005 and 2024.
Collaborative distances:
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on orcid.org
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on github.com
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Bibliography
2024
J. Biomed. Semant., December, 2024
2023
BMC Medical Informatics Decis. Mak., December, 2023
An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C).
J. Am. Medical Informatics Assoc., November, 2023
Evaluation of GPT and BERT-based models on identifying protein-protein interactions in biomedical text.
CoRR, 2023
The Occupation Ontology (OccO): Building a Bridge between Global Occupational Standards.
Proceedings of the Joint Ontology Workshops 2023 Episode IX: The Quebec Summer of Ontology co-located with the 13th International Conference on Formal Ontology in Information Systems (FOIS 2023), 2023
Ontology-based Representation and Analysis of Conditional Vaccine Immune Responses Using Omics Data.
Proceedings of the International Conference on Biomedical Ontologies 2023 together with the Workshop on Ontologies for Infectious and Immune-Mediated Disease Data Science (OIIDDS 2023) and the FAIR Ontology Harmonization and TRUST Data Interoperability Workshop (FOHTI 2023), Brasília, Brazil, August 28, 2023
2022
Mass spectrometry-based immunopeptidomics and computational vaccinology strategies for the identification of universal <i>Shigella</i> immunogenic candidates.
Comput. Biol. Medicine, 2022
Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs.
J. Biomed. Semant., 2022
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.
J. Biomed. Semant., 2022
COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning.
Briefings Bioinform., 2022
Proceedings of the Joint Ontology Workshops 2022 Episode VIII: The Svear Sommar of Ontology, 2022
2021
Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning.
Nucleic Acids Res., 2021
J. Biomed. Informatics, 2021
An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C).
CoRR, 2021
Development of the International Classification of Diseases Ontology (ICDO) and its application for COVID-19 diagnostic data analysis.
BMC Bioinform., 2021
CIDO ontology updates and secondary analysis of host responses to COVID-19 infection based on ImmPort reports and literature.
J. Biomed. Semant., 2021
Standardization of assay representation in the Ontology for Biomedical Investigations.
Database J. Biol. Databases Curation, 2021
Ontology Modeling and Analysis of COVID-19-associated Acute Kidney Injury and Its Underlying Molecular Mechanisms.
Proceedings of the International Conference on Biomedical Ontologies 2021 co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021), 2021
Ontology-based Modeling, Representation, and Analysis of Biomarkers in Healthy and Disease Kidney Tissue.
Proceedings of the International Conference on Biomedical Ontologies 2021 co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021), 2021
Proceedings of the International Conference on Biomedical Ontologies 2021 co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021), 2021
Identification and Ontology Term Enrichment Analysis of Genes Associated with COVID-19 and Acute Kidney Disease.
Proceedings of the International Conference on Biomedical Ontologies 2021 co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021), 2021
2020
Proceedings of the Protein-Protein Interaction Networks, Methods and Protocols., 2020
OntoPlot: A Novel Visualisation for Non-hierarchical Associations in Large Ontologies.
IEEE Trans. Vis. Comput. Graph., 2020
Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events.
J. Am. Medical Informatics Assoc., 2020
Vaxign-ML: supervised machine learning reverse vaccinology model for improved prediction of bacterial protective antigens.
Bioinform., 2020
OGG-CoV: Ontology Representation and Analysis of Genes and Genomes of Coronaviruses (short paper).
Proceedings of the 11th International Conference on Biomedical Ontologies (ICBO) joint with the 10th Workshop on Ontologies and Data in Life Sciences (ODLS) and part of the Bolzano Summer of Knowledge (BoSK 2020), 2020
Proceedings of the 11th International Conference on Biomedical Ontologies (ICBO) joint with the 10th Workshop on Ontologies and Data in Life Sciences (ODLS) and part of the Bolzano Summer of Knowledge (BoSK 2020), 2020
2019
Victors: a web-based knowledge base of virulence factors in human and animal pathogens.
Nucleic Acids Res., 2019
BMC Medical Informatics Decis. Mak., 2019
BMC Medical Informatics Decis. Mak., 2019
ODAE: Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions.
BMC Bioinform., 2019
Machine learning-based identification and rule-based normalization of adverse drug reactions in drug labels.
BMC Bioinform., 2019
Cells in ExperimentaL Life Sciences (CELLS-2018): capturing the knowledge of normal and diseased cells with ontologies.
BMC Bioinform., 2019
The cell line ontology-based representation, integration and analysis of cell lines used in China.
BMC Bioinform., 2019
VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions.
BMC Bioinform., 2019
OSCI: standardized stem cell ontology representation and use cases for stem cell investigation.
BMC Bioinform., 2019
ICDO: Ontological Representation of the International Classification of Diseases (ICD) and its Application in English and Chinese Healthy Data Standardization.
Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019), Buffalo, New York, USA, July 30, 2019
Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019), Buffalo, New York, USA, July 30, 2019
Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019), Buffalo, New York, USA, July 30, 2019
Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019), Buffalo, New York, USA, July 30, 2019
Alignment of the Ontology of Host-Microbiome Interactions (OHMI) High Level Terms with Existing OBO Ontologies.
Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019), Buffalo, New York, USA, July 30, 2019
OPMI: the Ontology of Precision Medicine and Investigation and its Support for Clinical Data and Metadata Representation and Analysis.
Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019), Buffalo, New York, USA, July 30, 2019
Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019), Buffalo, New York, USA, July 30, 2019
ICEO: a Biological Ontology for Representing and Analyzing the Bacterial Integrative and Conjugative Element.
Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019), Buffalo, New York, USA, July 30, 2019
2018
Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs.
J. Biomed. Semant., 2018
The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.
J. Biomed. Semant., 2018
VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria.
Briefings Bioinform., 2018
Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018
Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018
KTAO: A Kidney Tissue Atlas Ontology to Support Community-Based Kidney Knowledge Base Development and Data Integration.
Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018
2017
The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines.
Quant. Biol., 2017
Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.
Nucleic Acids Res., 2017
Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism.
BMC Syst. Biol., 2017
Cells in experimental life sciences - challenges and solution to the rapid evolution of knowledge.
BMC Bioinform., 2017
Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses.
BMC Bioinform., 2017
Comparison, alignment, and synchronization of cell line information between CLO and EFO.
BMC Bioinform., 2017
Ontology-based literature mining of E. coli vaccine-associated gene interaction networks.
J. Biomed. Semant., 2017
Large-scale adverse effects related to treatment evidence standardization (LAERTES): an open scalable system for linking pharmacovigilance evidence sources with clinical data.
J. Biomed. Semant., 2017
Extracting Adverse Drug Reactions using Deep Learning and Dictionary Based Approaches.
Proceedings of the 2017 Text Analysis Conference, 2017
OLOBO: A New Ontology for Linking and Integrating Open Biological and Biomedical Ontologies.
Proceedings of the 8th International Conference on Biomedical Ontology (ICBO 2017), Newcastle-upon-Tyne, United Kingdom, September 13th, 2017
Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs.
Proceedings of the AMIA 2017, 2017
From Scoping Review to Metadata: An Evidence-Based Approach to Identifying Informed Consent Metadata for Biorepositories.
Proceedings of the AMIA 2017, 2017
2016
The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis.
J. Biomed. Semant., 2016
VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms.
J. Biomed. Semant., 2016
The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology.
J. Biomed. Semant., 2016
Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events.
J. Biomed. Semant., 2016
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.
J. Biomed. Semant., 2016
The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature.
BioData Min., 2016
Ignet: A Centrality and INO-based Web System for Analyzing and Visualizing Literature-mined Networks.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016
Ontobull and BFOConvert: Web-based Programs to Support Automatic Ontology Conversion.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016
The Cell Line Ontology Integration and Analysis of the Knowledge of LINCS Cell Lines.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016
Proceedings of the AMIA 2016, 2016
Ontology-Based Analysis of Adverse Drug Reactions Associated with Anti-infection Drugs in China.
Proceedings of the AMIA 2016, 2016
2015
Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns.
J. Biomed. Semant., 2015
J. Biomed. Semant., 2015
Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions.
J. Biomed. Semant., 2015
Extension of the Interaction Network Ontology for Literature Mining of Gene-gene Interaction Networks from Sentences with Multiple Interaction Keywords.
Proceedings of International Workshop on Biomedical Data Mining, 2015
GOfox: Semantics-based simplified hierarchical classification and interactive visualization to support GO enrichment analysis.
Proceedings of the International Conference on Biomedical Ontology, 2015
Proceedings of the International Conference on Biomedical Ontology, 2015
Ontoanimal tools for reusing ontologies, generating and editing ontology terms, and dereferencing ontology terms.
Proceedings of the International Conference on Biomedical Ontology, 2015
Bridging Vaccine Ontology and NCIt vaccine domain for cancer vaccine data integration and analysis.
Proceedings of the International Conference on Biomedical Ontology, 2015
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015
2014
Nucleic Acids Res., 2014
BMC Bioinform., 2014
ICoVax 2013: The 3<sup>rd </sup>ISV Pre-conference Computational Vaccinology Workshop.
BMC Bioinform., 2014
J. Biomed. Semant., 2014
The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events.
J. Biomed. Semant., 2014
Proceedings of the 5th International Conference on Biomedical Ontology, 2014
Ontobat: An Ontology-based Semantic Web Approach for Linked Data Processing and Analysis.
Proceedings of the 5th International Conference on Biomedical Ontology, 2014
Proceedings of the 5th International Conference on Biomedical Ontology, 2014
Proceedings of the 5th International Conference on Biomedical Ontology, 2014
Proceedings of the AMIA 2014, 2014
2013
CoRR, 2013
A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks.
BMC Syst. Biol., 2013
Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology.
BMC Bioinform., 2013
Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates.
BMC Bioinform., 2013
Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology.
J. Biomed. Semant., 2013
The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines.
J. Biomed. Semant., 2013
Analysis of Vaccine-related Networks using Semantic MEDLINE and the Vaccine Ontology.
Proceedings of the ICBO2013 Workshops: International Workshop on Vaccine and Drug Ontology Studies (VDOS 2013), International Workshop on Definitions in Ontologies (DO 2013), part of the Semantic Trilogy 2013 , Montreal, Quebec, Canada, July 6th, 2013
HINO: BFO-aligned ontology representation of human molecular interactions and pathways.
Proceedings of the 4th International Conference on Biomedical Ontology, 2013
The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing vaccine adverse events.
Proceedings of the ICBO2013 Workshops: International Workshop on Vaccine and Drug Ontology Studies (VDOS 2013), International Workshop on Definitions in Ontologies (DO 2013), part of the Semantic Trilogy 2013 , Montreal, Quebec, Canada, July 6th, 2013
Proceedings of the ICBO2013 Workshops: International Workshop on Vaccine and Drug Ontology Studies (VDOS 2013), International Workshop on Definitions in Ontologies (DO 2013), part of the Semantic Trilogy 2013 , Montreal, Quebec, Canada, July 6th, 2013
Alignment of Cultured Cell Modeling Across OBO Foundry Ontologies: Key Outcomes, Insights.
Proceedings of the 4th International Conference on Biomedical Ontology, 2013
2012
Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis.
J. Biomed. Semant., 2012
Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses.
J. Biomed. Semant., 2012
Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining.
J. Biomed. Semant., 2012
A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012).
J. Biomed. Semant., 2012
Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012
Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012
2011
Nucleic Acids Res., 2011
Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology.
J. Biomed. Semant., 2011
J. Biomed. Semant., 2011
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011
Cell Line Ontology: Redesigning the Cell Line Knowledgebase to Aid Integrative Translational Informatics.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011
2010
2008
Nucleic Acids Res., 2008
2007
CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering.
Bioinform., 2007
miniTUBA: medical inference by network integration of temporal data using Bayesian analysis.
Bioinform., 2007
2006
BMC Bioinform., 2006
2005