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Publications

General VIOLIN (Note: please cite the following paper if you want to cite the VIOLIN system. Thanks!):

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. First published online: November 19, 2013. [NAR] [PubMed PMID: 24259431] [PDF]

You can also cite the previous VIOLIN publication:

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].

 


VIOLIN use case studies:

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].

He Y. Analyses of Brucella pathogenesis, host immunity, and vaccine targets using systems biology and bioinformatics. Frontiers in Cellular and Infection Microbiology. 2012. 2:2. doi: 10.3389/fcimb.2012.00002.

 


Vaccine design tool Vaxign:

He Y. Genome-based computational vaccine discovery by reverse vaccinology (Chapter 5); in book: Immunomic Discovery of Adjuvants and Candidate Subunit Vaccines, edited by Darren R. Flower, Yvonne Perrie. Publisher: Springer, New York, 2013. ISBN-13: 978-1461450696. ISBN 978-1-4614-5070-2 (eBook). Links in: Google eBook, and Amazon book.

Xiang Z, He Y. Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology. BMC Bioinformatics. 2013, 14(Suppl 4):S2 (8 March 2013). PMID: 23514126; PMCID: PMC3599071.

He Y, Xiang Z, Mobley HLT. Vaxign: the first web-based vaccine design program for reverse vaccinology and an application for vaccine development.J Biomed Biotechnol. 2010;2010:297505. Epub 2010 Jul 4. [PMID:20671958] [Journal Link]

Xiang Z, He Y. 2009. Vaxign: a web-based vaccine target design program for reverse vaccinology. Procedia in Vaccinology. Volume 1, Issue 1, Pages 23-29.

McNamara L, He Y, Yang Z. Using epitope predictions to evaluate efficacy and population coverage of the Mtb72f vaccine for tuberculosis. BMC Immunology. 2010 Mar 30;11(1):18. [PMID: 20353587] [Journal Link]

 


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]

He Y, Xiang Z. Bioinformatics analysis of bacterial protective antigens in manually curated Protegen database. Procedia in Vaccinology. 2012. Volume 6. Pages 3 – 9.

 

Vaxjo: Vaccine Adjuvants:

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. 2012;2012:831486. Epub 2012 Mar 13. PMID: 22505817.

 

Virmugen: Virulence factors whose mutants are live attenuated vaccines:

Racz R, Chung M, Xiang Z, and He Y. Systematic annotation and analysis of “virmugens” - virulence factors whose mutants can be used as live attenuated vaccines. Vaccine. Available online December 6, 2012. DOI: 10.1016/j.vaccine.2012.11.066.

DNAVaxDB: DNA vaccine database:

Racz R, Li X, Patel M, Xiang Z, and He Y. DNAVaxDB: the first web-based DNA vaccine database and its data analysis. BMC Bioinformatics. 2014, 15(Suppl 4):S2 (19 March 2014).  doi:10.1186/1471-2105-15-S4-S2.

 


Ontology research papers:

The following document has been frequently cited for the Vaccine Ontology:

He Y, Cowell L, Diehl AD, Mobley HL, Peters B, Ruttenberg A, Scheuermann RH, Brinkman RR, Courtot M, Mungall C, Xiang Z, Chen F, Todd T, Colby LA, Rush H, Whetzel T, Musen MA, Athey BD, Omenn GS, Smith B. Proceedings of the 1st International Conference on Biomedical Ontology (ICBO 2009), Buffalo, NY, USA. VO: Vaccine Ontology. The 1st International Conference on Biomedical Ontology (ICBO 2009), Buffalo, NY, USA. Nature Precedings. 2009. http://precedings.nature.com/documents/3553/version/1.

Lin Y, He Y. Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses. Journal of Biomedical Semantics. 2012, 3:17. PMID: 23256535. PMCID: PMC3639077. (NOTE: This paper can be used for citing VO. We are currently preparing a journal article fully describing VO)

 

VO-based Literature Mining:

Hur J, Xiang Z, Feldman EL, He Y. Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network. BMC Immunology. 12(1):49 2011 Aug 26. PMID: 21871085.

Ozgur A, Xiang Z, Radev D, He Y. Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology. Journal of Biomedical Semantics. 2011, 2(Suppl 2):S8. PMID: 21624163. PMCID: PMC3102897. (Note: This paper may also be used for citing VO)

Ozgur A, Xiang Z, Radev D, He Y. Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper.

Hur J, Özgür A, Xiang Z, He Y. Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining. Journal of Biomedical Semantics. 2012, 3:18. PMID: 23256563. PMCID: PMC3599673.

Y Zhang, C Tao, Y He, P Kanjamala, H Liu. Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology. Journal of Biomedical Semantics 2013, 4:33  doi:10.1186/2041-1480-4-33. PMID: 24209834.

 

Modeling of Vaccine Investigations by Collaborating with OBI:

Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone S, Soldatova LN, Stoeckert Jr. CJ, Turner J, Zheng J, the OBI consortium. Modeling biomedical experimental processes with OBI. Journal of Biomedical Semantics. 2010, 1(Suppl 1):S7. [PMID: 20626927]

 

Tool development using VO as use case study:

Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y. OntoFox: web-based support for ontology reuse. BMC Research Notes. 2010, 3:175. [PMID: 20569493]

 

VO-based Annotation and Curation (Note: these three papers have been listed above):

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)

 

Other related Ontology research:

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. In press.

 


Vaccine adverse events:

Sarntivijai S, Xiang Z, Shedden KA, Markel H, Omenn GS, Athey BD, and He Y. Ontology-based combinatorial comparative analysis of adverse events associated with killed and live influenza vaccines. PLoS ONE. 2012, 7(11): e49941. doi:10.1371/journal.pone.0049941.

Marcos E , He Y. The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing vaccine adverse events. Workshop “Vaccine and Drug Ontology Studies (VDOS 2013)". International Conference on Biomedical Ontologies (ICBO), Montreal, Qc, Canada. July 7, 2013 . Full-length proceeding paper. [http://ceur-ws.org/Vol-1061/Paper9_vdos2013.pdf]

Marcos E , Zhao B, He Y. The ontology of vaccine adverse events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines. Journal of Biomedical Semantics. 2013 Nov 26;4(1):40. PMID: 24279920.

 


Papers related to Community Participation:

Tao C, He Y, Arabandi S. A 2013 Workshop: Vaccine and Drug Ontology Studies (VDOS 2013). Journal of Biomedical Semantics. 2014. In press. (Note: check: http://www2.unb.ca/csas/data/ws/semantic-trilogy-workshops/proceedings.html)

De Groot AS, De Groot P, He Y. ICoVax 2013: The 3rd ISV Pre-conference Computational Vaccinology Workshop. BMC Bioinformatics. 2014. In press. (Note: check: http://www.violinet.org/icovax2013)

He Y, Cao Z, De Groot AS, Brusic V, Schönbach C, Petrovsky N. Computational vaccinology and the ICoVax 2012 workshop. BMC Bioinformatics. 2013, 14(Suppl 4):I1 (8 March 2013). PMID: 23514034; PMCID: PMC3599086. (Note: check: http://www.violinet.org/icovax2012)

He Y, Toldo L, Burns G, Tao C, Abernethy DR. A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012). Journal of Biomedical Semantics 2012, 3:12. PMID: 23249650. PMCID: PMC3554582. (Note: check: http://kr-med.org/icbofois2012/vdosme/)

 


Reviews and book chapters:

He Y. Genome-based computational vaccine discovery by reverse vaccinology (Chapter 5); in book: Immunomic Discovery of Adjuvants and Candidate Subunit Vaccines, edited by Darren R. Flower, Yvonne Perrie. Publisher: Springer, New York, 2013. ISBN-13: 978-1461450696. ISBN 978-1-4614-5070-2 (eBook). Links in: Google eBook, and Amazon book.

He Y, Xiang Z. Databases and in silico tools for vaccine design. Methods Mol Biol. 2013;993:115-27. doi: 10.1007/978-1-62703-342-8_8. PMID: 23568467. [Note: this is Chapter 8 in book: In Silico Models for Drug Discovery, Editor: Sandhya Kortagere.]

He Y. Analyses of Brucella pathogenesis, host immunity, and vaccine targets using systems biology and bioinformatics. Frontiers in Cellular and Infection Microbiology. 2012. 2:2. doi: 10.3389/fcimb.2012.00002.

 


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).

 

Note: More Hegroup publications can be found here: