~ 2010 ~

He Y, Xiang Z. Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN. Immunome Research. Accepted.

Hodges AP, Woolf P, He Y. BN+1 Bayesian network expansion for identifying molecular pathway elements. Communicative & Integrative Biology. In press. (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. A chapter in a book under the working title "Bayesian Network". Publisher: Sciyo.com. In press.

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]

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, accepted.

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, accepted.

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]

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]

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]

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]

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]

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]

~ 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]

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 (4 pages).

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].

~ 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.

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.

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.

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.

~ 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.

~ 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.

~ 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.

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.

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.

~ 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.