VIOLIN Logo
VIOLIN Banner
Search: for Help
About
Introduction
Statistics
VIOLIN News
Your VIOLIN
Register or Login
Submission
Tutorial
Vaccine & Components
Vaxquery
Vaxgen
VBLAST
Protegen
VirmugenDB
DNAVaxDB
CanVaxKB
Vaxjo
Vaxvec
Vevax
Huvax
Vaccine Mechanisms
Vaximmutordb
Vaxism
Vaxar
Vaccine Literature
VO-SciMiner
Litesearch
Vaxmesh
Vaxlert
Vaccine Design
Vaxign2
Vaxign
Community Efforts
Vaccine Ontology
ICoVax 2012
ICoVax 2013
Advisory Committee
Vaccine Society
Vaxperts
VaxPub
VaxCom
VaxLaw
VaxMedia
VaxMeet
VaxFund
VaxCareer
Data Exchange
V-Utilities
VIOLINML
Help & Documents
Publications
Documents
FAQs
Links
Acknowledgements
Disclaimer
Contact Us
UMMS Logo

Publications

Search for PubMed for Dr. Yongqun "Oliver" He's vaccine or ontology related publications between 2008 and 2020:

Search online for hits citing the grant 1R01AI081062 that supports this VIOLIN and Vaccine Ontology (VO) project:

The following is a list of papers based on different categories (Note: one paper may appears in more than one category; Also, this list may not always updated):


The VIOLIN system in general:

  • He Y, Racz R, Sayers S, Lin Y, Todd T, Hur J, Li X, Patel M, Zhao B, Chung M, Ostrow J, Sylora A, Dungarani P, Ulysse G, Kochhar K, Vidri B, Strait K, Jourdian GW, Xiang Z. Updates on the web-based VIOLIN vaccine database and analysis system. Nucleic Acids Research. 2014. 42 (D1): D1124-D1132. doi: 10.1093/nar/gkt1133. [NAR] [PubMed PMID: 24259431] [PDF]
  • Xiang Z, Todd T, Ku KP, Kovacic BL, Larson CB, Chen F, Hodges AP, Tian Y, Olenzek EA, Zhao B, Colby LA, Rush HG, Gilsdorf JR, Jourdian GW, He Y. VIOLIN: Vaccine Investigation and Online Information Network. Nucleic Acids Res. 2008 Jan;36(Database issue):D923-8. [NAR] [PubMed: PMID: 1802504] [PDF].

 


Vaccine design tool Vaxign and newly developed Vaxign-ML:

Papers introducting Vaxign:

Vaxign Machine Learning (new in 2020):

  • Ong E, Wang H, Wong MU, Seetharaman M, Valdez N, He Y. Vaxign-ML: supervised machine learning reverse vaccinology model for improved prediction of bacterial protective antigens. Bioinformatics. Feb 25. pii: btaa119. doi: 10.1093/bioinformatics/btaa119. [Epub ahead of print] (Acceptance date: 2020-02-18). PMID: 32096826.

Selected papers citing Vaxign:

Based on Google Scholars search, Vaxign has been cited for over 260 times as of March 14, 2020, and 346 times as of February 18, 2021.

Below is a list of papers that reported the applications of Vaxign with our own participation:

 


Vaccine Components:

Protegen: Protective Antigens:

  • Yang B, Sayers S, Xiang Z, He Y. Protegen: a web-based protective antigen database and analysis system. Nucleic Acids Research. 2010. 2010 Oct 19. [Epub ahead of print]. [PMID: 20959289]

Protegen data analysis:

Vaxjo: Vaccine Adjuvants:

Virmugen: Virulence factors whose mutants are live attenuated vaccines:

DNAVaxDB: DNA Vaccine database:

Vaxvec: Recombinant Vaccine Vector database:

  • Deng S, Martin C, Patil R, Zhu F, Zhao B, Xiang Z, He Y. Vaxvec: The first web-based recombinant vaccine vector database and its data analysis. Vaccine. 2015 Sep 21. pii: S0264-410X(15)01284-0. doi: 10.1016/j.vaccine.2015.07.113. [Epub ahead of print] PMID: 26403370.

 


Vaccine immune responses:

VaximmutorDB: Vaccine immune factor (which is coined as "vaximmutor") database:

Vaxar: Vaccine Animal Responses:

  • Todd T*, Dunn N*, Xiang Z, He Y. Vaxar: A web-based database of laboratory animal responses to vaccinations and its application in the meta-analysis of different animal responses to tuberculosis vaccinations. Comparative Medicine. 2016. 66(2):119-28. PMID: 27053566.

 


Ontology development:

VO: Vaccine Ontology:

OAE: Ontology of Adverse Events

  • Yongqun He Y, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao and Barry Smith. OAE: The Ontology of Adverse Events. Journal of Biomedical Semantics. 2014, 5:29  doi:10.1186/2041-1480-5-29. PMID: 25093068.PMCID: PMC4120740.

OVAE: Ontology of Vaccien Adverse Events

VICO: Vaccination Informed Consent Ontology:

VIO: Vaccine Investigation Ontology:

  • Ong E, Sun P, Berke K, Zheng J, Wu G, He Y. VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions. BMC Bioinformatics. 2019, 20(Suppl 21): 704. PMID: 31865910. PMCID: PMC6927110.

OGSF: Ontology of Genetic Susceptibility Factors, and its use in vaccine adverse event domain:

  • Lin Y, He Y. The Ontology of Genetic Susceptibility Factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events. Journal of Biomedical Semantics. 2014, 5:19. doi:10.1186/2041-1480-5-19. PMID: 24963371. PMCID: PMC4068904.

INO: Interaction Network Ontology

OBCS: Ontology of Biological and Clinical Statistics

 


Ontology-based Literature Mining:

 


Ontology-based modeling:

 


Ontoanimal ontology tool development based on the VIOLIN R01 grant support:

Ontobee: http://www.ontobee.org:

Ontofox: http://ontofox.hegroup.org:

Ontodog: http://ontodog.hegroup.org:

Ontorat: http://ontorat.hegroup.org:

  1. Xiang Z, Zheng J, Lin Y, He Y. Ontorat: Automatic generation of new ontology terms, annotations, and axioms based on ontology design patternsJournal of Biomedical Semantics. 2015, 6:4  doi:10.1186/2041-1480-6-4. PMID: 25785185. PMCID: PMC4362828.

Ontobull: http://ontobull.hegroup.org, and BFOConvert:

Ontokiwi and Ontokiwi-based Ontobedia:

  • Ong E, He Y. Community-based ontology development, annotation and discussion with MediaWiki extension Ontokiwi and Ontokiwi-based Ontobedia. AMIA Jt Summits Transl Sci Proc. 2016 Jul 20;2016:65-74. eCollection 2016. PMID: 27570653. PMCID: PMC5001762.

 

Proposed eXtensible ontology development (XOD) principles:

  • He Y, Xiang Z, Zheng J, Lin Y, Overton JA, Ong E. The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability. J Biomed Semantics. 2018 Jan 12;9(1):3. PMID: 29329592. PMCID: PMC5765662.

 


VO-based Annotation and Curation:

  • He Y, Xiang Z. Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN. Immunome Res. 2010 Sep 27;6 Suppl 1:S5. [NAR] [PubMed] [PDF].
    (Note: use VO to study Brucella vaccines)
  • Yang B, Sayers S, Xiang Z, He Y. Protegen: a web-based protective antigen database and analysis system. Nucleic Acids Research. 2010. 2010 Oct 19. [Epub ahead of print]. [PMID: 20959289]
    (Note: all protective antigens in Protegen are annotated in VO)
  • Sayers S, Ulysse G, Xiang Z, and He Y. Vaxjo: a web-based vaccine adjuvant database and its application for analysis of vaccine adjuvants and their uses in vaccine development. Journal of Biomedicine and Biotechnology. In press.
    (Note: all vaccine adjuvants in Vaxjo are annotated in VO)

 


Vaccine adverse events:

 


Pathogen use case studies using VIOLIN or supported by the VIOLIN R01 funding:

COVID-19 vaccine use case:

Brucella use case:

Other use cases:

 


Papers related to Community Participation:

 


The OneNet Theory of Life and vaccine research:

 


Reviews and book chapters:

 


Special Feature Report on Dr. He and He group's vaccine informatics research by International Innovation:

  • Yongqun He: 'Analysing multidisciplinary vaccine mechanisms'. In research topic: The Mechanics of Health, International Innovation, July 2013, (Research Media, pp 41-43) ISSN 2041-4552.
    (Note: International Innovation is the leading global dissemination resource for the wider scientific, technology and research communities, dedicated to disseminating the latest science, research and technological innovations on a global level. More information and a complimentary subscription offer to the publication can be found at: www.researchmedia.eu).

 

Notes: This website is not routinely updated and may miss some papers. More Hegroup publications can be found here: http://www.hegroup.org/publications.html (all areas).