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Vaxign-ML: Supervised Machine Learning Reverse Vaccinology Model for Improved Prediction of Bacterial Protective Antigens.

Ong E, Wang H, Wong MU, Seetharaman M, Valdez N, He Y.

Bioinformatics. 2020 Feb 25. pii: btaa119. doi: 10.1093/bioinformatics/btaa119. [Epub ahead of print]


Epitope promiscuity and population coverage of Mycobacterium tuberculosis protein antigens in current subunit vaccines under development.

Ong E, He Y, Yang Z.

Infect Genet Evol. 2020 Jun;80:104186. doi: 10.1016/j.meegid.2020.104186. Epub 2020 Jan 8.


VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions.

Ong E, Sun P, Berke K, Zheng J, Wu G, He Y.

BMC Bioinformatics. 2019 Dec 23;20(Suppl 21):704. doi: 10.1186/s12859-019-3194-6.


A 2018 workshop: vaccine and drug ontology studies (VDOS 2018).

Hur J, Tao C, He Y.

BMC Bioinformatics. 2019 Dec 23;20(Suppl 21):705. doi: 10.1186/s12859-019-3191-9.


A statistical analysis of vaccine-adverse event data.

Ren JJ, Sun T, He Y, Zhang Y.

BMC Med Inform Decis Mak. 2019 May 28;19(1):101. doi: 10.1186/s12911-019-0818-8.


Victors: a web-based knowledge base of virulence factors in human and animal pathogens.

Sayers S, Li L, Ong E, Deng S, Fu G, Lin Y, Yang B, Zhang S, Fa Z, Zhao B, Xiang Z, Li Y, Zhao XM, Olszewski MA, Chen L, He Y.

Nucleic Acids Res. 2019 Jan 8;47(D1):D693-D700. doi: 10.1093/nar/gky999.


Novel Immunoprotective Proteins of Streptococcus pneumoniae Identified by Opsonophagocytosis Killing Screen.

Wang Y, Wen Z, Pan X, Briles DE, He Y, Zhang JR.

Infect Immun. 2018 Aug 22;86(9). pii: e00423-18. doi: 10.1128/IAI.00423-18. Print 2018 Sep.


Ontology-Based Meta-Analysis of Animal and Human Adverse Events Associated With Licensed Brucellosis Vaccines.

Xie J, Wang J, Li Z, Wang W, Pang Y, He Y.

Front Pharmacol. 2018 May 15;9:503. doi: 10.3389/fphar.2018.00503. eCollection 2018.


Identification of New Features from Known Bacterial Protective Vaccine Antigens Enhances Rational Vaccine Design.

Ong E, Wong MU, He Y.

Front Immunol. 2017 Oct 26;8:1382. doi: 10.3389/fimmu.2017.01382. eCollection 2017.


Ontology-Based Vaccine Adverse Event Representation and Analysis.

Xie J, He Y.

Adv Exp Med Biol. 2017;1028:89-103. doi: 10.1007/978-981-10-6041-0_6. Review.


Conservation in gene encoding Mycobacterium tuberculosis antigen Rv2660 and a high predicted population coverage of H56 multistage vaccine in South Africa.

Perez-Martinez AP, Ong E, Zhang L, Marrs CF, He Y, Yang Z.

Infect Genet Evol. 2017 Nov;55:244-250. doi: 10.1016/j.meegid.2017.09.023. Epub 2017 Sep 21.


Analysis of Individual Differences in Vaccine Pharmacovigilance Using VAERS Data and MedDRA System Organ Classes: A Use Case Study With Trivalent Influenza Vaccine.

Du J, Cai Y, Chen Y, He Y, Tao C.

Biomed Inform Insights. 2017 Apr 11;9:1178222617700627. doi: 10.1177/1178222617700627. eCollection 2017.


Ontology-based literature mining of E. coli vaccine-associated gene interaction networks.

Hur J, Özgür A, He Y.

J Biomed Semantics. 2017 Mar 14;8(1):12. doi: 10.1186/s13326-017-0122-4.


Safety and immunogenicity of mammalian cell derived and Modified Vaccinia Ankara vectored African swine fever subunit antigens in swine.

Lopera-Madrid J, Osorio JE, He Y, Xiang Z, Adams LG, Laughlin RC, Mwangi W, Subramanya S, Neilan J, Brake D, Burrage TG, Brown WC, Clavijo A, Bounpheng MA.

Vet Immunol Immunopathol. 2017 Mar;185:20-33. doi: 10.1016/j.vetimm.2017.01.004. Epub 2017 Jan 24.


Antibiotic Resistance Determinant-Focused Acinetobacter baumannii Vaccine Designed Using Reverse Vaccinology.

Ni Z, Chen Y, Ong E, He Y.

Int J Mol Sci. 2017 Feb 21;18(2). pii: E458. doi: 10.3390/ijms18020458.


Integrative representations and analyses of vaccine-induced intended protective immunity and unintended adverse events using ontology-based and theory-guided approaches.

He Y, Ong E, Xie J.

Glob Vaccines Immunol. 2016 Jun;1(2):37-39. doi: 10.15761/GVI.1000110. Epub 2016 May 23. No abstract available.


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