~ 2013 ~

Ma J, He Y, Hu B, Luo Z. Genome sequence of an environmental isolate of the bacterial pathogen Legionella pneumophila. Genome Announcement. In press.

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.

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.

~ 2012 ~

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.

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

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.

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.

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.

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. 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.

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.

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

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.

~ 2011 ~

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.

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.

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.

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. International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Full length paper. Pages 25 - 32.

Lin Y, Xiang Z, He Y. Towards a Semantic Web application: Ontology-driven ortholog clustering analysis. International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Full length paper. Page 33 - 40.

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.

~ 2010 ~

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)

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-.

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.

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.

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.

~ 2009 ~

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.

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.

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.

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.

~ 1998 ~

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