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Selected Publications

~ 2017 ~

***Journal papers:

Ni Z, Chen Y, Ong E, He Y. Antibiotic resistance determinants-focused Acinetobacter baumannii vaccine design using reverse vaccinology. International Journal of Molecular Sciences. 2017, 18(2), 458.

The Knowledge Base workgroup of the Observational Health Data Sciences and Informatics (OHDSI) collaborative. LAERTES: An open scalable system for linking pharmacovigilance evidence sources with clinical data. J Biomed Semantics. In press.

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. Safety and immunogenicity of mammalian cell derived and modified-vaccinia Ankara vectored African swine fever subunit antigens in swine. Veterinary Immunology and Immunopathology. 2017. DOI: 10.1016/j.vetimm.2017.01.004.

Li J, Tai C, Deng Z, Zhong W, He Y, Ou H. VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria. Briefings in Bioinformatics. 2017, 1-9. PMID: 28077405.

Ong E, Xiang Z, Zhao B, Liu Y, Lin Y, Zheng J, Mungall C, Courtot M, Ruttenberg A, He Y. Ontobee: A linked ontology data server to support ontology term
dereferencing, linkage, query, and integration
. Nucleic Acid Research. 2017 Jan 4;45(D1):D347-D352. PMID: 27733503. PMCID: PMC5210626.

~ 2016 ~

***Journal papers:

Hur J, Özgür A, He Y. The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature. BioData Mining. 2016 Dec 19;9:41. PMID: 28031747. PMCID: PMC5168857

Huang J, Eilbeck K, Smith B, Blake JA, Dou D, Huang W, Natale DA, Ruttenberg A, Huan J, Zimmermann MT, Jiang G, Lin Y, Wu B, Strachan HJ, de Silva N, Kasukurthi MV, Jha VK, He Y, Zhang S, Wang X, Liu Z, Borchert GM, Tan M. The development of non-coding RNA ontology. Int J Data Min Bioinform. 2016; 15(3):214-232. PMID: 27990175. PMCID: PMC5156483.

Xie J, Codd C, Mo K, He Y. Differential adverse event profiles associated with BCG as a preventive tuberculosis vaccine or therapeutic bladder cancer vaccine identified by comparative ontology-based VAERS and literature meta-analysis. PLoS ONE. 2016 Oct 17;11(10):e0164792. PMID: 27749923. PMCID: PMC5066964.

Malachowski AN, Yosri M, Park G, Bahn YS, He Y, Olszewski MA. Systemic approach to virulence gene network analysis for gaining new insight into cryptococcal virulence. Frontiers in Microbiology. 2016. 7:1652. PMID: 27833589. PMCID: PMC5081415.

Xie J, Zhao L, Zhou S, He Y. Statistical and ontological analysis of adverse events associated with monovalent and combination vaccines against hepatitis A and B diseases. Scientific Reports. 2016. 6:3418. PMID: 27694888. PMCID: PMC5046117

Zheng J, Harris MR, Masci AM, Lin Y, Hero A, Smith B, He Y. The Ontology of Biological and Clinical Statistics (OBCS) for Standardized and Reproducible Statistical Analysis. J Biomed Semantics. 2016. Sep 14;7(1):53. PMID: 27627881. PMCID: PMC5024438.  

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.

Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, He Y, Osumi-Sutherland D, Ruttenberg A, Sarntivijai S, Van Slyke CE, Vasilevsky NA, Haendel MA, Blake JA, Mungall CJ. The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. J Biomed Semantics. 2016 Jul 4;7(1):44. PMID: 27377652. PMCID: PMC4932724.

He Y, Ong E, Xie J. Integrative representations and analyses of vaccine-induced intended protective immunity and unintended adverse events using ontology-based and theory-guided approaches. Global Vaccines and Immunology. 2016. 1 (2): 37-39. DOI: 10.15761/GVI.1000110. [PDF] PMID: 27868103. PMCID: PMC5111632.

Guo A*, Racz R*, Hur J, Lin Y, Xiang Z, Zhao L, Rinder J, Jiang G, Zhu Q, He Y. Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events. Journal of Biomedical Semantics. 2016. 7:29. PMID: 27213033. PMCID: PMC4875649.

Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone S, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert Jr. CJ, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J. The Ontology for Biomedical Investigations. PLoS ONE. 11(4): e0154556. PMID: 27128319. PMCID: PMC4851331.

Huang J, Eilbeck K, Smith B, Blake JA, Dou, D, Huang W, Natale DA, Ruttenberg A, Huan J, Zimmermann MT, Jiang G, Lin Y, Wu B, Strachan HJ, He Y, Zhang S, Wang X, Liu Z, Borchert G, Tan M. The Non-Coding RNA Ontology (NCRO): A comprehensive resource for the unification of non-coding RNA biology. Journal of Biomedical Semantics. 2016. 7:24. DOI: 10.1186/s13326-016-0066-0. PMID: 27152146. PMCID: PMC4857245.

Lin Y, Zheng J, He Y. VICO: Ontology-based representation and integrative analysis of vaccination informed consent forms. J Biomed Semantics. 2016 Apr 19;7:20. doi: 10.1186/s13326-016-0062-4. PMID: 27099700. PMCID: PMC4837519.

Racz R, He Y. The web-based DNA vaccine database DNAVaxDB and Its usage for rational DNA vaccine design. Methods Mol Biol. 2016;1404:741-52. doi: 10.1007/978-1-4939-3389-1_48. PMID: 27076334.

Sarntivijai S, Zhang S, Jagannathan DG, Zaman S, Burkhart KK, Omenn GS, He Y, Athey BD, Abernethy DR. Linking MedDRA-coded clinical phenotypes to biological mechanisms by the Ontology of Adverse Events: A pilot study on Tyrosine Kinase Inhibitors (TKIs). Drug Safety. 2016. pp 1-11. First online: 22 March 2016. DOI: 10.1007/s40264-016-0414-0. PMID: 27003817. PMCID: PMC4933310 [Available on 2017-07-01]

He Y. Ontology-based vaccine and drug adverse event representation and theory-guided systematic causal network analysis toward integrative pharmacovigilance research. Current Pharmacology Reports. 2016, Volume 2, Issue 3, pp 113-128. DOI: 10.1007/s40495-016-0055-0. PMID: 27458549. PMCID: PMC4957564 [Available on 2017-06-01]

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. PMCID: PMC4825961.

Tao C, He Y, Arabandi S. Vaccine and Drug Ontology Studies (VDOS 2014). Journal of Biomedical Semantics..2016, 7:6. DOI: 10.1186/s13326-015-0039-8. PMID: 26918107. PMCID: PMC4766598.

***Peer-reviewed proceeding papers:

Edison Ong, Jiangan Xie, Zhaohui Ni, Qingping Liu, Yu Lin, Vasileios Stathias, Caty Chung, Stephan Schurer, Yongqun He. The Cell Line Ontology Integration and Analysis of the Knowledge of LINCS Cell Lines. International Conference on Biomedical Ontologies (ICBO-2016), August 1-4, 2016, Oregon State University, Corvallis, OR, USA. 2-page proceeding paper.

He Y, Zheng J, Qin Z. EGO: a biomedical ontology for integrative epigenome representation and analysis. International Conference on Biomedical Ontologies (ICBO-2016), August 1-4, 2016, Oregon State University, Corvallis, OR, USA. 2-page proceeding paper.

Ozgur A, Hur J, Xiang Z, Ong E, Radev D, He Y. Ignet: A centrality and INO-based web system for analyzing and visualizing literature-mined networks. August 1-2, 2016, joint session ICBO+BioCreative, at the International Conference on Biomedical Ontologies (ICBO-2016) and BioCreative 2016, August 1-4, 2016, Oregon State University, Corvallis, OR, USA. 2-page proceeding paper.

Edison Ong, Zuoshuang Xiang, Jie Zheng, Barry Smith, Yongqun He. Ontobull and BFOConvert: Web-based Programs to Support Automatic Ontology Conversion. August 1-2, 2016, joint session ICBO+BioCreative, at the International Conference on Biomedical Ontologies (ICBO-2016) and BioCreative 2016, August 1-4, 2016, Oregon State University, Corvallis, OR, USA. 2-page proceeding paper (SOftware Demo).

Hur J, Ozgur A, Ong E, He Y. Ontology-based literature mining of E. coli vaccine-associated gene interaction networks. Vaccines and Drug Ontology Studies workshop (VDOS-2016), August 1, 2016, in connection with International Conference on Biomedical Ontologies (ICBO-2016), August 1-4, 2016, Oregon State University, Corvallis, OR, USA. 6-page full-length proceeding paper.

Boyce RD, Voss E, Huser V, Evans L, Reich C, Duke J, Tatonetti N, Dumontier M, Hauben M, Wallberg M, Peng L, Dempster S, He Y, Sena A, Ryan P. LAERTES : An open scalable architecture for linking pharmacovigilance evidence sources with clinical data. Vaccines and Drug Ontology Studies workshop (VDOS-2016), August 1, 2016, in connection with International Conference on Biomedical Ontologies (ICBO-2016), August 1-4, 2016, Oregon State University, Corvallis, OR, USA. 6-page full-length proceeding paper.

Ong E, He Y. Community-based Ontology Development, Annotation and Discussion with MediaWiki extension Ontokiwi and Ontokiwi-based Ontobedia. 2016 Joint Summits on Translational Science, American Medical Informatics Association (AMIA), March 21-24, San Francisco, CA, USA. Full-length 10-page paper, accepted for oral presentation (Conference presentation link).

***Book chapters:

Bhattacharyya A, He Y. Genome Sequence Databases: Annotation. Reference Module in Biomedical Sciences. Elsevier. 11-Jan-2016. doi: 10.1016/B978-0-12-801238-3.98823-8.

~ 2015 ~

***Journal papers:


Karadeniz İ, Hur J*, He Y*, Ozgur A*. Literature mining and ontology based analysis of host-Brucella gene-gene interaction network. Front. Microbiol. 2015 Dec 9; 6:1386. PMID: 26696993. PMCID: PMC4673313.

Lin Y, Xiang Z, and He Y. Ontology-based representation and analysis of host-Brucella interactions. J Biomed Semantics. 2015, 6:37. DOI: 10.1186/s13326-015-0036-y. PMID: 26445639. PMCID: PMC4594885.

Nemzek JA, Hodges AP, He Y. Bayesian network analysis of multi-compartmentalized immune responses in a murine model of sepsis and direct lung injury. BMC Research Notes. 2015 Sep 30;8(1):516. PMID: 26423575. PMCID: PMC4589912.

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 Nov 27;33(48):6938-6946. Epub 2015 Sep 25. PMID: 26403370. PMCID: PMC4679550 [Available on 2016-11-27]

Bronner DN, Abuaita BH, Chen X, Fitzgerald KA, Nunez G, He Y, Yin XM, O’Riordan MXD. ER stress activates the inflammasome via NLRP3-caspase-2 driven mitochondrial damage. Immunity. 2015 Sep 15;43(3):451-62. PMID: 26341399. PMCID: PMC4582788.

Liu W, Dong H, Li J, Ou Q, Lv Y, Wang X, Xiang Z, He Y*, Wu Q*. RNA-seq reveals the critical role of OtpR in regulating Brucella melitensis metabolism and virulence under acidic stress. Scientific Reports. 2015 Aug 5;5:10864. doi: 10.1038/srep10864. PMID: 26242322. PMCID: PMC4542472.

Zhang B, Xiao R, Ronan EA, He Y, Hsu AL, Liu J, Xu XZ. Environmental temperature differentially modulates C. elegans longevity through a thermosensitive TRP channel. Cell Rep. 2015 Jun 9;11(9):1414-24. doi: 10.1016/j.celrep.2015.04.066. PMID: 26027928. PMCID: PMC4758836

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

Hur J, Özgür A, Xiang Z, He Y. Development and application of an Interaction Network Ontology for literature mining of vaccine-associated gene-gene interactions. Journal of Biomedical Semantics. 2015, 6:2. doi:10.1186/2041-1480-6-2. PMID: 25785184. PMCID: PMC4362819.

Dean AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csõsz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendle M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lapp H, Lawrence CJ, Le Novère N, Lecointre G, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Voget L, Wall CE, Walls RL, Westerfield M, Wharton RA, Wirkner CS, Wooley JB, Yoder MJ, Zorn AM, Mabee PM. Finding our way through phenotypes. PLOS Biology. 13(1): e1002033. PMID: 25562316. PMCID: PMC4285398.

***Peer-reviewed proceeding papers:

Jingshan Huang, Karen Eilbeck, Judith Blake, Dejing Dou, Darren Natale, Alan Ruttenberg, Barry Smith, Michael Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Yongqun He, Shaojie Zhang, Xiaowei Wang, He Zhang, David Schmitt, and Ming Tan. Non-Coding RNA Ontology: A comprehensive resource for unification of non-coding RNA biology. The 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM'15), Washington D.C., Nov 9-12, 2015. 4-page short paper accepted.

Ozgur A, Hur J, He Y. Extension of the Interaction Network Ontology for literature mining of gene-gene interaction networks from sentences with multiple interaction keywords. The 2015 International Workshop on Biomedical Data Mining, Modeling, and Semantic Integration (BDM2I 2015) workshop, The International Semantic Web Conference (ISWC 2015), October 11-15, 2015, Bethlehem, PA, USA. 12 pages full-length proceeding paper. Full time oral presentation.

Guo A, Racz R, Hur J, Lin Y, Xiang Z, Zhao L, Jiang G, Zhu Q, Bai J, He Y. Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events. Vaccines and Drug Ontology Studies workshop (VDOS-2015), in connection with International Conference on Biomedical Ontologies (ICBO 2015), Lisbon, Portugal, July 27-30, 2015. Full-length proceeding paper. Full time oral presentation.

Lin Y, Zheng J, He Y. Ontology-based representation and analysis of vaccination informed consent. Vaccines and Drug Ontology Studies workshop (VDOS-2015), in connection with International Conference on Biomedical Ontologies (ICBO), Lisbon, Portugal, July 27-30, 2015. Full-length proceeding paper. Full time oral presentation.

He Y, Zheng J, Lin Y. Onto-animal tools for reusing ontologies, generating and editing ontology terms, and dereferencing ontology terms.International Conference on Biomedical Ontologies (ICBO-2015). Lisbon, Portugal, July 27-30, 2015. 2-page short paper for poster presentation and flask talk. URL: http://ceur-ws.org/Vol-1515/poster3.pdf.

He Y, Jiang G. Bridging Vaccine Ontology and NCIt vaccine domain for cancer vaccine data integration and analysis. International Conference on Biomedical Ontologies (ICBO-2015). Lisbon, Portugal, July 27-30, 2015. 2-page short paper for poster presentation and flask talk. URL: http://ceur-ws.org/Vol-1515/poster4.pdf.

Ong E, He Y. GOfox: Semantics-based simplified hierarchical classification and interactive visualization to support GO enrichment analysis. International Conference on Biomedical Ontologies (ICBO-2015). Lisbon, Portugal, July 27-30, 2015. 2-page short paper for software demonstration. URL: http://ceur-ws.org/Vol-1515/demo1.pdf.

He Y, Zheng J, Lin Y. Ontorat: Automatic generation and editing of ontology terms. International Conference on Biomedical Ontologies (ICBO-2015). Lisbon, Portugal, July 27-30, 2015. 2-page short paper for software demonstration. URL: http://ceur-ws.org/Vol-1515/demo2.pdf.

***Book chapter:

Racz R, He Y. The web-based DNA vaccine database DNAVaxDB and its usage for rational DNA vaccine design. In book: Vaccine Design, Methods in Molecular Biology Series. Editor: Sunil Thomas. Springer. 2015. ISBN 978-1-4939-3387-7.

~ 2014 ~

***Journal papers:

Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer TC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y. CLO: The Cell Line Ontology. Journal of Biomedical Semantics. 2014, 5:37. doi:10.1186/2041-1480-5-37. PMID: 25852852. PMCID: PMC4387853.

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.

He Y, Amer AO. Microbial modulation of host apoptosis and pyroptosis. Front. Cell. Infect. Microbiol. doi: 10.3389/fcimb.2014.00083. Accepted on June 3, 2014. PMID: 24995165. PMCID: PMC4062964.

He Y. Ontology-supported research on vaccine efficacy, safety, and integrative biological networks. Expert Reviews in Vaccines. 2014 Jul;13(7):825-41. doi: 10.1586/14760584.2014.923762. Epub 2014 Jun 7. PMID: 24909153. PMCID: PMC4815432. (Note: In this paper, the One Network (OneNet) Theory of Life” was introduced for the first time.)

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.

Tao C, He Y, Arabandi S. A 2013 Workshop: Vaccine and Drug Ontology Studies (VDOS 2013). Journal of Biomedical Semantics. 2014 Mar 20;5(1):16. doi: 10.1186/2041-1480-5-16. PMID: 24650607. PMCID: PMC3994568.

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. PMID: 25104313.

De Groot AS, De Groot P, He Y. ICoVax 2013: The 3rd ISV Pre-conference Computational Vaccinology Workshop. BMC Bioinformatics. 2014, 15(Suppl 4):I1. PMID: 25104130. PMCID: PMC4094997.

He Y. Vaccine adjuvant informatics: from data integration and analysis to rational vaccine adjuvant design. Front. Immunol. 2014. doi: 10.3389/fimmu.2014.00032. PMID: 24550916. PMCID: PMC3909948.

Zheng J, Xiang Z, Stoeckert Jr. CJ, He Y. Ontodog: a web-based ontology community view generation tool. Bioinformatics. 2014, 30(9):1340-2. doi: 10.1093/bioinformatics/btu008. [PDF] PMID: 24413522. PMCID: PMC3998133.

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. [PDF]. PMID: 24259431. PMCID: PMC3964998.

***Peer-reviewed proceeding papers:

He Y, Liu Y, Zhao B. OGG: a biological ontology for representing genes and genomes in specific organisms. Proceedings of the 5th International Conference on Biomedical Ontologies (ICBO), Houston, Texas, USA. October 8-9, 2014. Pages 13-20. [http://ceur-ws.org/Vol-1327/icbo2014_paper_23.pdf, or: http://www.hegroup.org/docs/OGG-ICBO2014.pdf, whcih has correctly formatted Figure 3]

Zheng J, Harris MR, Masci AM, Lin Y, Hero A, Smith B, He Y. OBCS: The Ontology of Biological and Clinical Statistics.Proceedings of the 5th International Conference on Biomedical Ontologies (ICBO), Houston, Texas, USA. October 8-9, 2014. Page 65. [http://ceur-ws.org/Vol-1327/icbo2014_paper_21.pdf]

Lin Y, Harris MR, Manion FJ, Eisenhauer E, Zhao B, Shi W, Karnovsky, He Y. Development of a BFO-based Informed Consent Ontology (ICO). Proceedings of the 5th International Conference on Biomedical Ontologies (ICBO), Houston, Texas, USA. October 8-9, 2014. Page 84-86. [http://ceur-ws.org/Vol-1327/icbo2014_paper_54.pdf]

Xiang Z, Lin Y, He Y. Ontobat: An Ontology-based semantic web approach for linked data processing and analysis. Proceedings of the 5th International Conference on Biomedical Ontologies (ICBO), Houston, Texas, USA. October 8-9, 2014. Page 93-95. [http://ceur-ws.org/Vol-1327/icbo2014_paper_58.pdf]

Hur J, Özgür A, Xiang Z, He Y. Development and application of an Interaction Network Ontology (INO) for literature mining of vaccine-associated gene-gene interactions. Vaccines and Drug Ontology Studies workshop (VDOS-2014), in connection with International Conference on Biomedical Ontologies (ICBO), Houston, Texas, USA. October 7, 2014. Full-length proceeding paper (Note: this paper was later extended and published in 2015 in the Journal of Biomedical Semantics. 2015, 6:4  doi:10.1186/2041-1480-6-2. See above.)

***Book chapter:

He Y. Bacterial whole genome determination and applications (Chapter 20). 2014. In book: Molecular Medical Microbiology, Second Edition, Editors: Yi-Wei Tang, Max Sussman, Dongyou Liu, Ian R. Poxton, and Joseph D. Schwartzman. Elsevier Ltd. Pages 357-368. ISBN: 9780123971692. [Elsevier link] [Amazon link] [Google Books]

***E-Book:

Editors: He Y, Amer AO. Microbial modulation of host apoptosis and pyroptosis, by Front. Cell. Infect. Microbiol. 2014. [Download E-Book PDF]

~ 2013 ~

***Journal papers:

Bronner DN, O'Riordan MXD, He Y. Caspase-2 mediates a Brucella abortus RB51-induced hybrid cell death having features of apoptosis and pyroptosis. Frontiers in Cellular and Infection Microbiology. 2013. 3:83. PMID: 24350060. PMCID: PMC3842122.

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.

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.

Xiang Z, Qin T, Qin Z, He Y. A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks. BMC Systems Biology. 2013, 7(Suppl 3):S9. doi:10.1186/1752-0509-7-S3-S9. (note: this paper was also presented in InCoB2013 and collected in F1000Posters; see the presentation slides) PMID: 24555475. PMCID: PMC3852244.

Ma J, He Y, Hu B, Luo Z. Genome sequence of an environmental isolate of the bacterial pathogen Legionella pneumophila. Genome Announcement. 2013 vol. 1 no. 3 e00320-13. PMID: 23792742. PMCID: PMC3675512.

Todd TE, Tibi O, Lin Y, Sayers S, Bronner DN, Xiang Z, He Y. Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics. 2013, 14(Suppl 6):S3. PMID: 23735014. PMCID: PMC3633026.

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.]

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, 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.

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. 2013 Jan 21;31(5):797-805. Epub Dec. DOI: 10.1016/j.vaccine.2012.11.066. PMID: 23219434. PMCID: PMC3556277.

***Peer-reviewed proceeding papers:

Racz R, Li X, Patel M, Xiang Z, and He Y. DNAVaxDB: the first web-based DNA vaccine database and its data analysis. The 3rd Pre-ISV Computational Vaccinology workshop (ICoVax 2013), October 26 , 2013, Sitges, Barcelona, Spain. Full length article.

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]

Lin Y, He Y. Ontology modeling of genetic susceptibility to adverse events following vaccination. 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/Paper3_vdos2013.pdf]

Zhang Y, Tao C, He Y, Kanjamala P, Liu H. Analysis of Vaccine-related Networks using Semantic MEDLINE and the Vaccine Ontology. 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/Paper6_vdos2013.pdf]

***Book chapter:

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.

***Electronic preprint full-length paper:

He Y, Xiang Z. HINO: a BFO-aligned ontology representing human molecular interactions and pathways. arXiv. 2013. arXiv:1311.3355.

***Special Feature Report on Dr. He and He group 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).

~ 2012 ~

***Journal papers:

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.

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.

Tao C, He Y, Yang H, Gregory PA, Chute CG. Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis. Journal of Biomedical Semantics. 2012, 3:13. PMID: 23256916. PMCID: PMC3554604.

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.

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. PMID: 23209624. PMCID: PMC3509157.

Liu W, Jing Z, Ou Q, Cui B, He Y*, Wu Q*. Complete genome sequence of Brucella melitensis biovar 3 strain NI, isolated from an aborted bovine fetus. Journal of Bacteriology. 2012, 194(22):6321. PMID: 23105063. PMCID: PMC3486367.

Li X, He Y. Caspase-2-dependent dendritic cell death, maturation, and priming of T cells in response to Brucella abortus infection. PLoS ONE, 2012, 7(8): e43512. doi:10.1371/journal.pone.0043512. PMID: 22927979. PMCID: PMC3425542.

Lin Y, He Y. New era of developing and using ontologies for microbiology research and diagnosis. Journal of Microbiology and Diagnosis. 2012. 1:e107. doi:10.4172/2161- 0703.1000e107.

Banai M, He Y. Systems biology and bioinformatics help decipher Brucella antigens involved in clinical manifestation of the disease. Frontiers in Cellular and Infection Microbiology. 2012. 2:34. Epub 2012 Mar 21. PMID: 22919626. PMCID: PMC3417652.

Akhtar R, He Y, Larson CB, Chaudhary ZI, ud-Din Ahmad M. Differential stimulatory activities of smooth and rough Brucella abortus lipopolysaccharide in murine macrophages. Pak Vet J. 2012. 32(3): 339-344.

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. PMID: 22919594. PMCID: PMC3417401.

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. PMCID: PMC3312338.

***Peer-reviewed proceeding papers:

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

Lin Y, He Y. Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses. Workshop “Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME-2012)”, International Conference on Biomedical Ontologies (ICBO), University of Graz, Austria, July 2012. URL: http://kr-med.org/icbofois2012/vdosme/index.htm. Full-length proceeding paper.

Hur J, Özgür A, Xiang Z, He Y. Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining. Workshop “Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME-2012)”, International Conference on Biomedical Ontologies (ICBO), University of Graz, Austria, July 2012. Full-length proceeding paper.

Tao C, He Y, Poland G, Chute C. Time Modeling of Vaccine Adverse Events in VAERS for Temporal Analysis. Workshop “Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME-2012)”, International Conference on Biomedical Ontologies (ICBO), University of Graz, Austria, July 2012. Full-length proceeding paper.

***Book chapter:

He Y. Omics-based systems vaccinology for vaccine target identification. Drug Development Research. In: Special Issue: Impact of Omics on Drug Discovery and Development. Part II. Volume 73, Issue 8, pages 559–568, December 2012. DOI: 10.1002/ddr.21049.

***Interviewd for peer-reviewed article:

Jones D. Reverse vaccinology on the cusp. Nat Rev Drug Discov. 2012 Feb 10;11(3):175-6. PMID: 22322255. doi: 10.1038/nrd3679.

~ 2011 ~

***Journal papers:

Zhu J*, Larson CB*, Ramaker MA, Quandt K, Wendte J, Ku K, Chen F, Jourdian G, Vemulapalli R, Schurig GG, He Y. Characterization of recombinant B. abortus strain RB51SOD towards understanding the uncorrelated innate and adaptive immune responses induced by RB51SOD compared to its parent vaccine strain RB51. Front. Cell. Inf. Microbio. 1:10. doi: 10.3389/fcimb.2011.00010. (*: co-first authors). PMID: 22919576. PMCID: PMC3417361.

Lin Y, Xiang Z, He Y. Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology. Journal of Biomedical Semantics. 2011 Oct 31;2(1):9. [Epub ahead of print] PMID: 22041276. PMCID: PMC3217896.

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. PMCID: PMC3180695.

Akhtar R, Chaudhary ZI, He Y, Ahmad MU, Younus M. (2011). Murine macrophages are more brucellicidal than bovine macrophages. Pakistan Journal of Zoology. In press.

He Y, Rappuoli R, De Groot A, Chen RT. Vaccine informatics. Journal of Biomedicine and Biotechnology. 2010;2010:765762. Epub 2011 Jun 22. PMID: 21772788. PMCID: PMC3134834.

He Y, Rappuoli R, De Groot A, Chen RT. Emerging vaccine informatics. Journal of Biomedicine and Biotechnology. 2010 (2010), Article ID 218590, 26 pages. 2010;2010:218590. Epub 2011 Jun 15. (Note: This is a comprehensive 26-page review article in the Special Issue on Vaccine Informatics.) PMID: 21772787. PMCID: PMC3134832.

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.

Vigil1 PD, Stapleton AE, Johnson JR, Hooton TM, Hodges AP, He Y, Mobley HLT. Putative Repeat-in-Toxin (RTX) gene tosA of Escherichia coli predicts successful colonization of the urinary tract. MBio. 2011 May 3;2(3). pii: e00066-11. doi: 10.1128/mBio.00066-11. PMID: 21540363. PMCID: PMC3088117.

Chen F, Ding X, Ding Y, Xiang Z, Li X, Ghosh D, Schurig GG, Sriranganathan N, Boyle SM, He Y. Proinflammatory caspase-2 mediated macrophage cell death induced by rough attenuated Brucella suis. Infection and Immunity. 2011 Jun;79(6):2460-9. PMID: 21464087. PMCID: PMC3125819.

Yang B*, Sayers S*, Xiang Z, He Y. Protegen: a web-based protective antigen database and analysis system. Nucleic Acids Research. 2011 Jan;39(Database issue):D1073-8. Epub 2010 Oct 19. PMID: 20959289. PMCID: PMC3013795. (*: co-first authors)

Shayman JA, Kelly R, Kollmeyer J, He Y, Abe A. Group XV phospholipase A2, a lysosomal phospholipase A2. Prog Lipid Res. 2011 Jan;50(1):1-13. Epub 2010 Nov 11. PMID: 21074554. PMCID: PMC3039127.

***Peer-reviewed proceeding papers:

He Y, Xiang Z, Sarntivijai S, Toldo L, Ceusters W. AEO: a realism-based biomedical ontology for the representation of adverse events. Adverse Event Representation Workshop, International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Full length paper. Pages 309 - 315. [http://ceur-ws.org/Vol-833/paper59.pdf]

Sarntivijai S, Xiang Z, Meehan TF, Diehl AD,Vempati U, Schurer S, Pang C, Malone J, Parkinson H, Athey BD, He Y. Cell Line Ontology: Redesigning Cell Line Knowledgebase to Aid Integrative Translational Informatics. Proceedings of the 2nd International Conference on Biomedical Ontologies (ICBO-2011), Buffalo, NY, USA, July 28-30, 2011. Pages 25 - 32. [http://ceur-ws.org/Vol-833/paper4.pdf]

Lin Y, Xiang Z, He Y. Towards a Semantic Web application: Ontology-driven ortholog clustering analysis. Proceedings of the 2nd International Conference on Biomedical Ontologies (ICBO-2011), Buffalo, NY, USA, July 28-30, 2011. Page 33 - 40. [http://ceur-ws.org/Vol-833/paper5.pdf]

Xiang Z, Mungall C, Ruttenberg A, He Y. Ontobee: A Linked Data Server and Browser for Ontology Terms. Proceedings of the 2nd International Conference on Biomedical Ontologies (ICBO), Buffalo, NY, USA, July 28-30, 2011. Pages 279-281. [http://ceur-ws.org/Vol-833/paper48.pdf]

***Book chapter:

Hodges AP, Woolf P, He Y. Prediction of novel pathway elements and interactions using Bayesian networks. A chapter in book: "Bioinformatics - Experimental Biology Systems". ISBN 978-953-307-280-7. Editor: Ning-Sun Yang. InTech - Open Access Publisher. Page 185-204.

~ 2010 ~

***Journal papers:

Akhtar R, Chaudhary ZI, He Y. Modified method for isolation of peripheral blood neutrophils from bovines and humans. International Journal of Agro Veterinary Medicine. 2010. 4: 8-14.

He Y, Xiang Z. Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN. Immunome Research. 2010 Sep 27;6 Suppl 1:S5. PMID: 20875156. PMCID: PMC2946783.

Hodges AP, Woolf P, He Y. BN+1 Bayesian network expansion for identifying molecular pathway elements. Communicative & Integrative Biology. 2010. Volume 3, Issue 6, Page 1-6. PMID: 21331236. PMCID: PMC3038060. (NOTE: this is an invited Addendum Article to our recent PloS ONE paper with PMID: 20209085)

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. PMCID: PMC2911465.

He Y, Xiang Z, Mobley HLT. Vaxign: the first web-based vaccine design program for reverse vaccinology and an application for vaccine development. Journal of Biomedicine and Biotechnology. Volume 2010 (2010), Article ID 297505, 15 pages. [PMID: 20671958]. PMCID: PMC2910479.

Ozgur A, Xiang Z, Radev D, He Y. Literature-based discovery of IFN-γ and vaccine-mediated gene interaction networks. Journal of Biomedicine and Biotechnology. Volume 2010 (2010), Article ID 426479, 13 pages. PMID: 20625487. PMCID: PMC2896678.

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. PMCID: PMC2903726.

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. PMCID: PMC2862017.

Hodges AP, Dai D, Xiang Z, Woolf P, Xi C, He Y. Bayesian network expansion identifies new ROS and biofilm regulators. PLoS ONE. 2010 Mar 3;5(3):e9513. PMID: 20209085. PMCID: PMC2831072.

Sloat BR, Sandoval MA, Hau AM, He Y, Cui Z. Strong antibody responses induced by protein antigens conjugated onto the surface of lecithin-based nanoparticles. J Control Release. 2010 Jan 4;141(1):93-100. PMID: 19729045. PMCID: PMC2789915.

***Peer-reviewed proceeding papers:

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.

He Y, Xiang Z, Todd T, Courtot M, Brinkman R, Zheng J, Stoeckert CJ, Malone J, Rocca-Serra P, Sansone S, Fostel J, Soldatova LN, Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper.

***Book chapter:

He Y, Xiang Z. miniTUBA: a web-based dynamic Bayesian network analysis system and an application in host-pathogen interaction analysis. Bayesian Network, Ahmed Rebai (Ed.), ISBN: 978-953-307-124-4, Sciyo, Available from: http://www.intechopen.com/articles/show/title/minituba-a-web-based-dynamic-bayesian-network-analysis-system-.

~ 2009 ~

***Journal paper:

Chen F, He Y. Caspase-2 mediated apoptotic and necrotic murine macrophage cell death induced by rough Brucella abortus. PLoS ONE. 2009 Aug 28;4(8):e6830. PMID: 19714247. PMCID: PMC2729395.

***peer-reviewed proceeding papers:

In alphabetic order: Brinkman RR, Courtot M, Derom D, Foste JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone S, Soldatova LN, Stoeckert Jr. CJ, Jessica Turner J, Zheng J, and the OBI consortium. 2009. The modeling of biomedical experimental processes with OBI. Bio-Ontolgies Workshop (at ISMB 2009). Full length paper.

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

***Book chapter:

Boyle SM, He Y, Tsolis RM. 2009. Genome mapping and microarray contributions to understanding Brucella pathobiology and host responses to Brucella infections (Brucella subchapter 9). In: V. Nene, and C. Cole, editors. Genome Mapping and Genomics in Animal-Associated Microbes (ISBN: 978-3-540-74040-7). Springer, New York, NY. p. 44-50.

~ 2008 ~

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 Research. 2008, Vol. 36, Database issue D923-D928. [NAR link] [PMID: 18025042]. PMCID: PMC2238972.

~ 2007 ~

Xiang Z, Minter RM, Bi X, Woolf PJ, He Y. miniTUBA: medical inference by network integration of temporal data using Bayesian analysis. Bioinformatics. 2007 Sep 15;23(18):2423-32. PMID: 17644819.

Xiang Z, Tian Y, He Y. PHIDIAS: a pathogen-host interaction data integration and analysis system. Genome Biology. 2007 Jul 30;8(7):R150. PMID: 17663773. PMCID: PMC2323235.

Xiang Z, Qin ZS, He Y. CRCView: A web server for analyzing and visualizing microarray gene expression data using model-based clustering. Bioinformatics. 2007 Jul 15;23(14):1843-5. PMID: 17485426.

He Y, Rush HG, Liepman RS, Xiang Z, Colby LA. Pathobiology and management of laboratory rodents administered CDC Category A agents. Comparative Medicine. 2007. Feb;57(1):18-32. PMID: 17348288.

~ 2006 ~

He Y, Reichow S, Ramamoorthy S, Ding X, Lathigra R, Craig JC, Sobral BW, Schurig GG, Sriranganathan N, Boyle SM. Brucella melitensis triggers time-dependent modulation of apoptosis and down-regulation of mitochondria-associated gene expression in mouse macrophages. Infection and Immunity. 2006 Sep;74(9):5035-46. PMID: 16926395. PMCID: PMC1594834.

Xiang Z, Zheng W, He Y. BBP: Brucella genome annotation with literature mining and curation. BMC Bioinformatics. 2006 Jul 16;7(1):347. (Highly accessed). PMID: 16842628. PMCID: PMC1539029.

Ratushna VG, Sturgill DM, Ramamoorthy S, Reichow SA, He Y, Lathigra R, Sriranganathan N, Halling SM, Boyle SM, Gibas CJ. Molecular targets for rapid identification of Brucella spp. BMC Microbiol. 2006 Feb 22;6:13. PMID: 16504063. PMCID: PMC1413539.

~ 2005 ~

He Y, Vines RR, Wattam AR, Abramochkin GV, Dickerman AW, Eckart JD, Sobral BW. PIML: The Pathogen Information Markup Language. Bioinformatics. 2005;21(1):116-21. PMID: 15297293.

***Book chapter:

Lathigra R, He Y, Vines RR, Nordberg EK, Sobral BWS. 2005. A biologist's view of systems integration for system biology - the Pathogen Portal Project (Chapter 13). In: J. Perry Gustafson, Randy Shoemaker and John W. Snape, editors. Genome Exploitation: Data Mining the Genome (ISBN: 0-387-24123-X). Springer, New York, NY. p 183-196.

~ 2002 ~

Vemulapalli R, He Y, Sriranganathan N, Boyle SM, Schurig GG. Brucella abortus RB51: Enhancing vaccine efficacy and developing multivalent vaccines. Veterinary Microbiology, 2002, 2406: 1-12. PMID: 12414168.

He Y, Vemulapalli R, Schurig GG. Recombinant Ochrobactrum anthropi expressing Brucella Cu/Zn-superoxide dismutase protects mice against B. abortus infection only after switching immune responses to Th1 type. Infection and Immunity, 2002, 70(5): 2535-2543. PMID: 11953393. PMCID: PMC127893.

~ 2001 ~

He Y, Vemulapalli R, Zeytun A, Schurig GG. Induction of specific cytotoxic lymphocytes in mice vaccinated with Brucella abortus RB51. Infection and Immunity. 2001, 69(9): 5502-5508. PMID: 11500423. PMCID: PMC98663.

~ 2000 ~

Vemulapalli R, He Y, Buccolo LS, Boyle SM, Sriranganathan N, Schurig GG. Complementation of Brucella abortus RB51 with a functional wboA gene results in O-antigen synthesis and enhanced vaccine efficacy but no change in its rough phenotype and attenuation. Infection and Immunity. 2000. 68(7): 3927-3932. PMID: 10858205. PMCID: PMC101669.

Vemulapalli R, He Y, Boyle SM, Sriranganathan N, Schurig GG. Brucella abortus RB51 as a vector for heterologous protein expression and induction of specific Th-1 type immune responses in mice. Infection and Immunity. 2000. 68(6): 3290-3296. PMID: 10816476. PMCID: PMC97584.

Vemulapalli R, He Y, Cravero S, Sriranganathan N, Boyle SM, Schurig GG. Overexpression of protective antigen as a novel approach to enhance vaccine efficacy of Brucella abortus strain RB51. Infection and Immunity. 2000. 68(6): 3286-3289. PMID: 10816475. PMCID: PMC97582.

~ Before 2000 ~

Yongqun He, Zhongzhi Zhang, Hanchun Yang. A serological survey of the reticuloendotheliosis virus infection in Beijing chicken flocks. Chinese Journal of Animal and Veterinary Sciences (i.e., Acta Veterinaria et Zootechnica Sinica). 1998. 29 (1): 71-78.

Haiquan Gui, Jianming Zhang, Yongqun He, Shuling Xie. A diagnosis report of a duck NewCastle Disease. Contemporary Animal Husbandry. 1993. 1: 23-24.

 

Note: See more about Yongqun He (Oliver)'s and He group's publications from other repositories, you can check:

He Lab |Ontobee|OntoFox|OAE|VO|Genomesh|Ignet|miniTUBA|PHIDIAS|VIOLIN
He Group
University of Michigan Medical School
Ann Arbor, MI 48109
U of M NIAIDNIAID