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Vesicular Stomatitis Virus Transcription Is Inhibited by TRIM69 in the Interferon-Induced Antiviral State.

Kueck T, Bloyet LM, Cassella E, Zang T, Schmidt F, Brusic V, Tekes G, Pornillos O, Whelan SPJ, Bieniasz PD.

J Virol. 2019 Nov 26;93(24). pii: e01372-19. doi: 10.1128/JVI.01372-19. Print 2019 Dec 15.


New approach to investigate Common Variable Immunodeficiency patients using spectrochemical analysis of blood.

Callery EL, Morais CLM, Paraskevaidi M, Brusic V, Vijayadurai P, Anantharachagan A, Martin FL, Rowbottom AW.

Sci Rep. 2019 May 10;9(1):7239. doi: 10.1038/s41598-019-43196-5.


Analysis of viral diversity for vaccine target discovery.

Khan AM, Hu Y, Miotto O, Thevasagayam NM, Sukumaran R, Abd Raman HS, Brusic V, Tan TW, Thomas August J.

BMC Med Genomics. 2017 Dec 21;10(Suppl 4):78. doi: 10.1186/s12920-017-0301-2.


Game meat authentication through rare earth elements fingerprinting.

Danezis GP, Pappas AC, Zoidis E, Papadomichelakis G, Hadjigeorgiou I, Zhang P, Brusic V, Georgiou CA.

Anal Chim Acta. 2017 Oct 23;991:46-57. doi: 10.1016/j.aca.2017.09.013. Epub 2017 Sep 13.


PO and ID BCG vaccination in humans induce distinct mucosal and systemic immune responses and CD4+ T cell transcriptomal molecular signatures.

Hoft DF, Xia M, Zhang GL, Blazevic A, Tennant J, Kaplan C, Matuschak G, Dube TJ, Hill H, Schlesinger LS, Andersen PL, Brusic V.

Mucosal Immunol. 2018 Mar;11(2):486-495. doi: 10.1038/mi.2017.67. Epub 2017 Aug 30.


TANTIGEN: a comprehensive database of tumor T cell antigens.

Olsen LR, Tongchusak S, Lin H, Reinherz EL, Brusic V, Zhang GL.

Cancer Immunol Immunother. 2017 Jun;66(6):731-735. doi: 10.1007/s00262-017-1978-y. Epub 2017 Mar 9.


Elemental metabolomics.

Zhang P, Georgiou CA, Brusic V.

Brief Bioinform. 2018 May 1;19(3):524-536. doi: 10.1093/bib/bbw131.


Phenotypic lentivirus screens to identify functional single domain antibodies.

Schmidt FI, Hanke L, Morin B, Brewer R, Brusic V, Whelan SP, Ploegh HL.

Nat Microbiol. 2016 Jun 20;1(8):16080. doi: 10.1038/nmicrobiol.2016.80.


Repeatable Population Dynamics among Vesicular Stomatitis Virus Lineages Evolved under High Co-infection.

Williams ES, Morales NM, Wasik BR, Brusic V, Whelan SP, Turner PE.

Front Microbiol. 2016 Mar 31;7:370. doi: 10.3389/fmicb.2016.00370. eCollection 2016.


Advances in Computational Immunology.

Pappalardo F, Brusic V, Pennisi M, Zhang G.

J Immunol Res. 2015;2015:170920. doi: 10.1155/2015/170920. Epub 2015 Dec 30. No abstract available.


An adaptive genetic algorithm for selection of blood-based biomarkers for prediction of Alzheimer's disease progression.

Vandewater L, Brusic V, Wilson W, Macaulay L, Zhang P.

BMC Bioinformatics. 2015;16 Suppl 18:S1. doi: 10.1186/1471-2105-16-S18-S1. Epub 2015 Dec 9.


A computational method for identification of vaccine targets from protein regions of conserved human leukocyte antigen binding.

Olsen LR, Simon C, Kudahl UJ, Bagger FO, Winther O, Reinherz EL, Zhang GL, Brusic V.

BMC Med Genomics. 2015;8 Suppl 4:S1. doi: 10.1186/1755-8794-8-S4-S1. Epub 2015 Dec 9.


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 Nov;33(11):1152-8.


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.


InCoB2012 Conference: from biological data to knowledge to technological breakthroughs.

Schönbach C, Tongsima S, Chan J, Brusic V, Tan TW, Ranganathan S.

BMC Bioinformatics. 2012;13 Suppl 17:S1. doi: 10.1186/1471-2105-13-S17-S1. Epub 2012 Dec 13.


Mutated BCR-ABL generates immunogenic T-cell epitopes in CML patients.

Cai A, Keskin DB, DeLuca DS, Alonso A, Zhang W, Zhang GL, Hammond NN, Nardi V, Stone RM, Neuberg D, Sidney J, Brusic V, Wu CJ.

Clin Cancer Res. 2012 Oct 15;18(20):5761-72. doi: 10.1158/1078-0432.CCR-12-1182. Epub 2012 Aug 21.


Critical phosphoprotein elements that regulate polymerase architecture and function in vesicular stomatitis virus.

Rahmeh AA, Morin B, Schenk AD, Liang B, Heinrich BS, Brusic V, Walz T, Whelan SP.

Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14628-33. doi: 10.1073/pnas.1209147109. Epub 2012 Aug 20.


Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing.

Lank SM, Golbach BA, Creager HM, Wiseman RW, Keskin DB, Reinherz EL, Brusic V, O'Connor DH.

BMC Genomics. 2012 Aug 6;13:378. doi: 10.1186/1471-2164-13-378.


West Nile virus T-cell ligand sequences shared with other flaviviruses: a multitude of variant sequences as potential altered peptide ligands.

Jung KO, Khan AM, Tan BY, Hu Y, Simon GG, Nascimento EJ, Lemonnier F, Brusic V, Miotto O, Tan TW, Marques ET, Dhalia R, Salmon J, August JT.

J Virol. 2012 Jul;86(14):7616-24. doi: 10.1128/JVI.00166-12. Epub 2012 May 9.


PB1-F2 Finder: scanning influenza sequences for PB1-F2 encoding RNA segments.

DeLuca DS, Keskin DB, Zhang GL, Reinherz EL, Brusic V.

BMC Bioinformatics. 2011;12 Suppl 13:S6. doi: 10.1186/1471-2105-12-S13-S6. Epub 2011 Nov 30.


Novel myeloma-associated antigens revealed in the context of syngeneic hematopoietic stem cell transplantation.

Biernacki MA, Tai YT, Zhang GL, Alonso A, Zhang W, Prabhala R, Zhang L, Munshi N, Neuberg D, Soiffer RJ, Ritz J, Alyea EP, Brusic V, Anderson KC, Wu CJ.

Blood. 2012 Mar 29;119(13):3142-50. doi: 10.1182/blood-2011-11-388926. Epub 2012 Jan 20.


Combining cellular automata and Lattice Boltzmann method to model multiscale avascular tumor growth coupled with nutrient diffusion and immune competition.

Alemani D, Pappalardo F, Pennisi M, Motta S, Brusic V.

J Immunol Methods. 2012 Feb 28;376(1-2):55-68. doi: 10.1016/j.jim.2011.11.009. Epub 2011 Dec 2.


Machine learning competition in immunology - Prediction of HLA class I binding peptides.

Zhang GL, Ansari HR, Bradley P, Cawley GC, Hertz T, Hu X, Jojic N, Kim Y, Kohlbacher O, Lund O, Lundegaard C, Magaret CA, Nielsen M, Papadopoulos H, Raghava GP, Tal VS, Xue LC, Yanover C, Zhu S, Rock MT, Crowe JE, Panayiotou C, Polycarpou MM, Duch W, Brusic V.

J Immunol Methods. 2011 Nov 30;374(1-2):1-4. doi: 10.1016/j.jim.2011.09.010. Epub 2011 Sep 29. No abstract available.


Dana-Farber repository for machine learning in immunology.

Zhang GL, Lin HH, Keskin DB, Reinherz EL, Brusic V.

J Immunol Methods. 2011 Nov 30;374(1-2):18-25. doi: 10.1016/j.jim.2011.07.007. Epub 2011 Jul 18.


Efficacy of HLA-DRB1∗03:01 and H2E transgenic mouse strains to correlate pathogenic thyroglobulin epitopes for autoimmune thyroiditis.

Kong YC, Brown NK, Flynn JC, McCormick DJ, Brusic V, Morris GP, David CS.

J Autoimmun. 2011 Sep;37(2):63-70. doi: 10.1016/j.jaut.2011.05.010. Epub 2011 Jun 17.


Optimizing vaccine development.

Hoft DF, Brusic V, Sakala IG.

Cell Microbiol. 2011 Jul;13(7):934-42. doi: 10.1111/j.1462-5822.2011.01609.x. Epub 2011 Jun 2. Review.


Impaired tumor antigen processing by immunoproteasome-expressing CD40-activated B cells and dendritic cells.

Anderson KS, Zeng W, Sasada T, Choi J, Riemer AB, Su M, Drakoulakos D, Kang YJ, Brusic V, Wu C, Reinherz EL.

Cancer Immunol Immunother. 2011 Jun;60(6):857-67. doi: 10.1007/s00262-011-0995-5. Epub 2011 Mar 13.


Database resources for proteomics-based analysis of cancer.

Zhang GL, DeLuca DS, Brusic V.

Methods Mol Biol. 2011;723:349-64. doi: 10.1007/978-1-61779-043-0_22. Review.


Data processing and analysis for protein microarrays.

DeLuca DS, Marina O, Ray S, Zhang GL, Wu CJ, Brusic V.

Methods Mol Biol. 2011;723:337-47. doi: 10.1007/978-1-61779-043-0_21.


Transcriptionally abundant major histocompatibility complex class I alleles are fundamental to nonhuman primate simian immunodeficiency virus-specific CD8+ T cell responses.

Budde ML, Lhost JJ, Burwitz BJ, Becker EA, Burns CM, O'Connor SL, Karl JA, Wiseman RW, Bimber BN, Zhang GL, Hildebrand W, Brusic V, O'Connor DH.

J Virol. 2011 Apr;85(7):3250-61. doi: 10.1128/JVI.02355-10. Epub 2011 Jan 26.


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