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FluKB: A Knowledge-Based System for Influenza Vaccine Target Discovery and Analysis of the Immunological Properties of Influenza Viruses.

Simon C, Kudahl UJ, Sun J, Olsen LR, Zhang GL, Reinherz EL, Brusic V.

J Immunol Res. 2015;2015:380975. doi: 10.1155/2015/380975. Epub 2015 Oct 4.


Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes.

Shukla SA, Rooney MS, Rajasagi M, Tiao G, Dixon PM, Lawrence MS, Stevens J, Lane WJ, Dellagatta JL, Steelman S, Sougnez C, Cibulskis K, Kiezun A, Hacohen N, Brusic V, Wu CJ, Getz G.

Nat Biotechnol. 2015 Sep 15;33(11):1152-1158. doi: 10.1038/nbt.3344. [Epub ahead of print]


Computational and bioinformatics techniques for immunology.

Pappalardo F, Brusic V, Castiglione F, Schönbach C.

Biomed Res Int. 2014;2014:263189. doi: 10.1155/2014/263189. Epub 2014 Dec 31. No abstract available.


Tumor antigens as proteogenomic biomarkers in invasive ductal carcinomas.

Olsen L, Campos B, Winther O, Sgroi DC, Karger BL, Brusic V.

BMC Med Genomics. 2014;7 Suppl 3:S2. doi: 10.1186/1755-8794-7-S3-S2. Epub 2014 Dec 8.


Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells--a benchmarking study.

Sun J, Zhang GL, Li S, Ivanov AR, Fenyo D, Lisacek F, Murthy SK, Karger BL, Brusic V.

BMC Genomics. 2014;15 Suppl 9:S1. doi: 10.1186/1471-2164-15-S9-S1. Epub 2014 Dec 8.


Human leukocyte antigen typing using a knowledge base coupled with a high-throughput oligonucleotide probe array analysis.

Zhang GL, Keskin DB, Lin HN, Lin HH, DeLuca DS, Leppanen S, Milford EL, Reinherz EL, Brusic V.

Front Immunol. 2014 Nov 27;5:597. doi: 10.3389/fimmu.2014.00597. eCollection 2014.


Bioinformatics for cancer immunotherapy target discovery.

Olsen LR, Campos B, Barnkob MS, Winther O, Brusic V, Andersen MH.

Cancer Immunol Immunother. 2014 Dec;63(12):1235-49. doi: 10.1007/s00262-014-1627-7. Epub 2014 Oct 26. Review.


Mathematical modeling for novel cancer drug discovery and development.

Zhang P, Brusic V.

Expert Opin Drug Discov. 2014 Oct;9(10):1133-50. doi: 10.1517/17460441.2014.941351. Epub 2014 Jul 25. Review.


Big data analytics in immunology: a knowledge-based approach.

Zhang GL, Sun J, Chitkushev L, Brusic V.

Biomed Res Int. 2014;2014:437987. doi: 10.1155/2014/437987. Epub 2014 Jun 22.


HLA-binding properties of tumor neoepitopes in humans.

Fritsch EF, Rajasagi M, Ott PA, Brusic V, Hacohen N, Wu CJ.

Cancer Immunol Res. 2014 Jun;2(6):522-9. doi: 10.1158/2326-6066.CIR-13-0227. Epub 2014 Mar 3. Review.


Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia.

Rajasagi M, Shukla SA, Fritsch EF, Keskin DB, DeLuca D, Carmona E, Zhang W, Sougnez C, Cibulskis K, Sidney J, Stevenson K, Ritz J, Neuberg D, Brusic V, Gabriel S, Lander ES, Getz G, Hacohen N, Wu CJ.

Blood. 2014 Jul 17;124(3):453-62. doi: 10.1182/blood-2014-04-567933. Epub 2014 Jun 2.


HPVdb: a data mining system for knowledge discovery in human papillomavirus with applications in T cell immunology and vaccinology.

Zhang GL, Riemer AB, Keskin DB, Chitkushev L, Reinherz EL, Brusic V.

Database (Oxford). 2014 Apr 4;2014:bau031. doi: 10.1093/database/bau031. Print 2014.


Large-scale analysis of B-cell epitopes on influenza virus hemagglutinin - implications for cross-reactivity of neutralizing antibodies.

Sun J, Kudahl UJ, Simon C, Cao Z, Reinherz EL, Brusic V.

Front Immunol. 2014 Feb 7;5:38. doi: 10.3389/fimmu.2014.00038. eCollection 2014.


Literature classification for semi-automated updating of biological knowledgebases.

Olsen L, Johan Kudahl U, Winther O, Brusic V.

BMC Genomics. 2013;14 Suppl 5:S14. doi: 10.1186/1471-2164-14-S5-S14. Epub 2013 Oct 16.


Computational resources for high-dimensional immune analysis from the Human Immunology Project Consortium.

Brusic V, Gottardo R, Kleinstein SH, Davis MM; HIPC steering committee.

Nat Biotechnol. 2014 Feb;32(2):146-8. doi: 10.1038/nbt.2777. Epub 2014 Jan 19. No abstract available.


Disruption of helix-capping residues 671 and 674 reveals a role in HIV-1 entry for a specialized hinge segment of the membrane proximal external region of gp41.

Sun ZY, Cheng Y, Kim M, Song L, Choi J, Kudahl UJ, Brusic V, Chowdhury B, Yu L, Seaman MS, Bellot G, Shih WM, Wagner G, Reinherz EL.

J Mol Biol. 2014 Mar 6;426(5):1095-108. doi: 10.1016/j.jmb.2013.09.030. Epub 2013 Sep 26.


Identification of human leucocyte antigen (HLA)-A*0201-restricted cytotoxic T lymphocyte epitopes derived from HLA-DOβ as a novel target for multiple myeloma.

Kang YJ, Zeng W, Song W, Reinhold B, Choi J, Brusic V, Yamashita T, Munshi A, Li C, Minvielle S, Anderson KC, Munshi N, Reinherz EL, Sasada T.

Br J Haematol. 2013 Nov;163(3):343-51. doi: 10.1111/bjh.12544. Epub 2013 Aug 30.


BlockLogo: visualization of peptide and sequence motif conservation.

Olsen LR, Kudahl UJ, Simon C, Sun J, Schönbach C, Reinherz EL, Zhang GL, Brusic V.

J Immunol Methods. 2013 Dec 31;400-401:37-44. doi: 10.1016/j.jim.2013.08.014. Epub 2013 Aug 31.


Computational vaccinology and the ICoVax 2012 workshop.

He Y, Cao Z, De Groot AS, Brusic V, Schönbach C, Petrovsky N.

BMC Bioinformatics. 2013;14 Suppl 4:I1. doi: 10.1186/1471-2105-14-S4-I1. Epub 2013 Mar 8.


Immune system modeling and related pathologies.

Pappalardo F, Brusic V, Fröhlich H.

Comput Math Methods Med. 2012;2012:274702. doi: 10.1155/2012/274702. Epub 2012 Dec 17. No abstract available.

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