 Vladimir Brusic, PH.D.
| Title | Principal Associate in Medicine |
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| Institution | Dana-Farber Cancer Institute |
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| Department | Medicine |
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| Address | Dana Farber Cancer Institute
Med Onc /HIM 401
44 Binney St
Boston MA 02115
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| Phone | 617/632-3824 |
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| Fax | 617/632-3351 |
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 Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications.
Faculty can login to make corrections and additions.
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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.
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Pappalardo F, Brusic V, Fröhlich H. Immune system modeling and related pathologies. Comput Math Methods Med. 2012; 2012:274702.
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Schönbach C, Tongsima S, Chan J, Brusic V, Tan TW, Ranganathan S. InCoB2012 Conference: from biological data to knowledge to technological breakthroughs. BMC Bioinformatics. 2012; 13 Suppl 17:S1.
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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. Mutated BCR-ABL Generates Immunogenic T-cell Epitopes in CML Patients. Clin Cancer Res. 2012 Oct 15; 18(20):5761-72.
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Lank SM, Golbach BA, Creager HM, Wiseman RW, Keskin DB, Reinherz EL, Brusic V, O'Connor DH. Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing. BMC Genomics. 2012; 13:378.
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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. West Nile virus T-cell ligand sequences shared with other flaviviruses: a multitude of variant sequences as potential altered peptide ligands. J Virol. 2012 Jul; 86(14):7616-24.
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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. Novel myeloma-associated antigens revealed in the context of syngeneic hematopoietic stem cell transplantation. Blood. 2012 Mar 29; 119(13):3142-50.
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Olsen LR, Zhang GL, Keskin DB, Reinherz EL, Brusic V. Conservation analysis of dengue virus T-cell epitope-based vaccine candidates using Peptide block entropy. Front Immunol. 2011; 2:69.
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Keskin DB, Reinhold B, Lee SY, Zhang G, Lank S, O'Connor DH, Berkowitz RS, Brusic V, Kim SJ, Reinherz EL. Direct identification of an HPV-16 tumor antigen from cervical cancer biopsy specimens. Front Immunol. 2011; 2:75.
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Alemani D, Pappalardo F, Pennisi M, Motta S, Brusic V. Combining cellular automata and Lattice Boltzmann method to model multiscale avascular tumor growth coupled with nutrient diffusion and immune competition. J Immunol Methods. 2012 Feb 28; 376(1-2):55-68.
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Olsen LR, Zhang GL, Reinherz EL, Brusic V. FLAVIdB: A data mining system for knowledge discovery in flaviviruses with direct applications in immunology and vaccinology. Immunome Res. 2011; 7(3):1-9.
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Deluca DS, Keskin DB, Zhang GL, Reinherz EL, Brusic V. PB1-F2 Finder: scanning influenza sequences for PB1-F2 encoding RNA segments. BMC Bioinformatics. 2011 Nov 30; 12 Suppl 13:S6.
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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. Machine learning competition in immunology - Prediction of HLA class I binding peptides. J Immunol Methods. 2011 Nov 30; 374(1-2):1-4.
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Zhang GL, Lin HH, Keskin DB, Reinherz EL, Brusic V. Dana-Farber repository for machine learning in immunology. J Immunol Methods. 2011 Nov 30; 374(1-2):18-25.
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Kong YC, Brown NK, Flynn JC, McCormick DJ, Brusic V, Morris GP, David CS. Efficacy of HLA-DRB1*03:01 and H2E transgenic mouse strains to correlate pathogenic thyroglobulin epitopes for autoimmune thyroiditis. J Autoimmun. 2011 Sep; 37(2):63-70.
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Hoft DF, Brusic V, Sakala IG. Optimizing vaccine development. Cell Microbiol. 2011 Jul; 13(7):934-42.
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Anderson KS, Zeng W, Sasada T, Choi J, Riemer AB, Su M, Drakoulakos D, Kang YJ, Brusic V, Wu C, Reinherz EL. Impaired tumor antigen processing by immunoproteasome-expressing CD40-activated B cells and dendritic cells. Cancer Immunol Immunother. 2011 Jun; 60(6):857-67.
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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. Transcriptionally abundant major histocompatibility complex class I alleles are fundamental to nonhuman primate simian immunodeficiency virus-specific CD8+ T cell responses. J Virol. 2011 Apr; 85(7):3250-61.
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Zhang GL, DeLuca DS, Brusic V. Database resources for proteomics-based analysis of cancer. Methods Mol Biol. 2011; 723:349-64.
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DeLuca DS, Marina O, Ray S, Zhang GL, Wu CJ, Brusic V. Data processing and analysis for protein microarrays. Methods Mol Biol. 2011; 723:337-47.
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Zhang GL, DeLuca DS, Keskin DB, Chitkushev L, Zlateva T, Lund O, Reinherz EL, Brusic V. MULTIPRED2: a computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles. J Immunol Methods. 2011 Nov 30; 374(1-2):53-61.
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You L, Brusic V, Gallagher M, Bodén M. Using Gaussian process with test rejection to detect T-cell epitopes in pathogen genomes. IEEE/ACM Trans Comput Biol Bioinform. 2010 Oct-Dec; 7(4):741-51.
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Riemer AB, Keskin DB, Zhang G, Handley M, Anderson KS, Brusic V, Reinhold B, Reinherz EL. A conserved E7-derived cytotoxic T lymphocyte epitope expressed on human papillomavirus 16-transformed HLA-A2+ epithelial cancers. J Biol Chem. 2010 Sep 17; 285(38):29608-22.
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Halling-Brown M, Pappalardo F, Rapin N, Zhang P, Alemani D, Emerson A, Castiglione F, Duroux P, Pennisi M, Miotto O, Churchill D, Rossi E, Moss DS, Sansom CE, Bernaschi M, Lefranc MP, Brunak S, Lund O, Motta S, Lollini PL, Murgo A, Palladini A, Basford KE, Brusic V, Shepherd AJ. ImmunoGrid: towards agent-based simulations of the human immune system at a natural scale. Philos Transact A Math Phys Eng Sci. 2010 Jun 13; 368(1920):2799-815.
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Zhang W, Choi J, Zeng W, Rogers SA, Alyea EP, Rheinwald JG, Canning CM, Brusic V, Sasada T, Reinherz EL, Ritz J, Soiffer RJ, Wu CJ. Graft-versus-leukemia antigen CML66 elicits coordinated B-cell and T-cell immunity after donor lymphocyte infusion. Clin Cancer Res. 2010 May 15; 16(10):2729-39.
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Ofran Y, Kim HT, Brusic V, Blake L, Mandrell M, Wu CJ, Sarantopoulos S, Bellucci R, Keskin DB, Soiffer RJ, Antin JH, Ritz J. Diverse patterns of T-cell response against multiple newly identified human Y chromosome-encoded minor histocompatibility epitopes. Clin Cancer Res. 2010 Mar 1; 16(5):1642-51.
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Miotto O, Heiny AT, Albrecht R, García-Sastre A, Tan TW, August JT, Brusic V. Complete-proteome mapping of human influenza A adaptive mutations: implications for human transmissibility of zoonotic strains. PLoS One. 2010; 5(2):e9025.
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Marina O, Hainz U, Biernacki MA, Zhang W, Cai A, Duke-Cohan JS, Liu F, Brusic V, Neuberg D, Kutok JL, Alyea EP, Canning CM, Soiffer RJ, Ritz J, Wu CJ. Serologic markers of effective tumor immunity against chronic lymphocytic leukemia include nonmutated B-cell antigens. Cancer Res. 2010 Feb 15; 70(4):1344-55.
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Biernacki MA, Marina O, Zhang W, Liu F, Bruns I, Cai A, Neuberg D, Canning CM, Alyea EP, Soiffer RJ, Brusic V, Ritz J, Wu CJ. Efficacious immune therapy in chronic myelogenous leukemia (CML) recognizes antigens that are expressed on CML progenitor cells. Cancer Res. 2010 Feb 1; 70(3):906-15.
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Halling-Brown M, Shaban R, Frampton D, Sansom CE, Davies M, Flower D, Duffield M, Titball RW, Brusic V, Moss DS. Proteins accessible to immune surveillance show significant T-cell epitope depletion: Implications for vaccine design. Mol Immunol. 2009 Aug; 46(13):2699-705.
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Pappalardo F, Halling-Brown MD, Rapin N, Zhang P, Alemani D, Emerson A, Paci P, Duroux P, Pennisi M, Palladini A, Miotto O, Churchill D, Rossi E, Shepherd AJ, Moss DS, Castiglione F, Bernaschi M, Lefranc MP, Brunak S, Motta S, Lollini PL, Basford KE, Brusic V. ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization. Brief Bioinform. 2009 May; 10(3):330-40.
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Koo QY, Khan AM, Jung KO, Ramdas S, Miotto O, Tan TW, Brusic V, Salmon J, August JT. Conservation and variability of West Nile virus proteins. PLoS One. 2009; 4(4):e5352.
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Cao X, Maloney KB, Brusic V. Data mining of cancer vaccine trials: a bird's-eye view. Immunome Res. 2008; 4:7.
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Lin HH, Zhang GL, Tongchusak S, Reinherz EL, Brusic V. Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research. BMC Bioinformatics. 2008; 9 Suppl 12:S22.
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Khan AM, Miotto O, Nascimento EJ, Srinivasan KN, Heiny AT, Zhang GL, Marques ET, Tan TW, Brusic V, Salmon J, August JT. Conservation and variability of dengue virus proteins: implications for vaccine design. PLoS Negl Trop Dis. 2008; 2(8):e272.
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Brusic V, Ranganathan S. Critical technologies for bioinformatics. Brief Bioinform. 2008 Jul; 9(4):261-2.
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Brown NK, McCormick DJ, Brusic V, David CS, Kong YC. A novel H2A-E+ transgenic model susceptible to human but not mouse thyroglobulin-induced autoimmune thyroiditis: identification of mouse pathogenic epitopes. Cell Immunol. 2008 Jan; 251(1):1-7.
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Marina O, Biernacki MA, Brusic V, Wu CJ. A concentration-dependent analysis method for high density protein microarrays. J Proteome Res. 2008 May; 7(5):2059-68.
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Tongchusak S, Leelayuwat C, Brusic V, Chaiyaroj SC. In silico prediction and immunological validation of common HLA-DRB1-restricted T cell epitopes of Candida albicans secretory aspartyl proteinase 2. Microbiol Immunol. 2008 Apr; 52(4):231-42.
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Lin HH, Ray S, Tongchusak S, Reinherz EL, Brusic V. Evaluation of MHC class I peptide binding prediction servers: applications for vaccine research. BMC Immunol. 2008; 9:8.
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Zhang GL, Khan AM, Srinivasan KN, Heiny A, Lee K, Kwoh CK, August JT, Brusic V. Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes. BMC Bioinformatics. 2008; 9 Suppl 1:S19.
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Miotto O, Heiny A, Tan TW, August JT, Brusic V. Identification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis. BMC Bioinformatics. 2008; 9 Suppl 1:S18.
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Sun ZY, Oh KJ, Kim M, Yu J, Brusic V, Song L, Qiao Z, Wang JH, Wagner G, Reinherz EL. HIV-1 broadly neutralizing antibody extracts its epitope from a kinked gp41 ectodomain region on the viral membrane. Immunity. 2008 Jan; 28(1):52-63.
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Miotto O, Tan TW, Brusic V. Rule-based knowledge aggregation for large-scale protein sequence analysis of influenza A viruses. BMC Bioinformatics. 2008; 9 Suppl 1:S7.
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Rajapakse M, Schmidt B, Feng L, Brusic V. Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms. BMC Bioinformatics. 2007; 8:459.
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Heiny AT, Miotto O, Srinivasan KN, Khan AM, Zhang GL, Brusic V, Tan TW, August JT. Evolutionarily conserved protein sequences of influenza a viruses, avian and human, as vaccine targets. PLoS One. 2007; 2(11):e1190.
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Tongchusak S, Brusic V, Chaiyaroj SC. Promiscuous T cell epitope prediction of Candida albicans secretory aspartyl protienase family of proteins. Infect Genet Evol. 2008 Jul; 8(4):467-73.
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Tong JC, Zhang ZH, August JT, Brusic V, Tan TW, Ranganathan S. In silico characterization of immunogenic epitopes presented by HLA-Cw*0401. Immunome Res. 2007; 3:7.
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Ostrout ND, McHugh MM, Tisch DJ, Moormann AM, Brusic V, Kazura JW. Long-term T cell memory to human leucocyte antigen-A2 supertype epitopes in humans vaccinated against smallpox. Clin Exp Immunol. 2007 Aug; 149(2):265-73.
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Falus A, Brusic V. Highlights of international conference of immunogenomics and immunomics, October 8-12, 2006 Budapest, Hungary. Cell Immunol. 2006 Dec; 244(2):65-76.
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Zhang ZH, Tan SC, Koh JL, Falus A, Brusic V. ALLERDB database and integrated bioinformatic tools for assessment of allergenicity and allergic cross-reactivity. Cell Immunol. 2006 Dec; 244(2):90-6.
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Khan AM, Miotto O, Heiny AT, Salmon J, Srinivasan KN, Nascimento EJ, Marques ET, Brusic V, Tan TW, August JT. A systematic bioinformatics approach for selection of epitope-based vaccine targets. Cell Immunol. 2006 Dec; 244(2):141-7.
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Brusic V. The growth of bioinformatics. Brief Bioinform. 2007 Mar; 8(2):69-70.
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Brusic V, Marina O, Wu CJ, Reinherz EL. Proteome informatics for cancer research: from molecules to clinic. Proteomics. 2007 Mar; 7(6):976-91.
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Zhang GL, Bozic I, Kwoh CK, August JT, Brusic V. Prediction of supertype-specific HLA class I binding peptides using support vector machines. J Immunol Methods. 2007 Mar 30; 320(1-2):143-54.
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Khan AM, Heiny AT, Lee KX, Srinivasan KN, Tan TW, August JT, Brusic V. Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus. BMC Bioinformatics. 2006; 7 Suppl 5:S4.
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Rajapakse M, Zhang GL, Srinivasan KN, Schmidt B, Petrovsky N, Brusic V. PREDNOD, a prediction server for peptide binding to the H-2g7 haplotype of the non-obese diabetic mouse. Autoimmunity. 2006 Dec; 39(8):645-50.
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Petrovsky N, Brusic V. Bioinformatics for study of autoimmunity. Autoimmunity. 2006 Dec; 39(8):635-43.
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Tan PT, Ranganathan S, Brusic V. Deduction of functional peptide motifs in scorpion toxins. J Pept Sci. 2006 Jun; 12(6):420-7.
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Zhang GL, Petrovsky N, Kwoh CK, August JT, Brusic V. PRED(TAP): a system for prediction of peptide binding to the human transporter associated with antigen processing. Immunome Res. 2006; 2:3.
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Tong JC, Zhang GL, Tan TW, August JT, Brusic V, Ranganathan S. Prediction of HLA-DQ3.2beta ligands: evidence of multiple registers in class II binding peptides. Bioinformatics. 2006 May 15; 22(10):1232-8.
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Tan PT, Veeramani A, Srinivasan KN, Ranganathan S, Brusic V. SCORPION2: a database for structure-function analysis of scorpion toxins. Toxicon. 2006 Mar; 47(3):356-63.
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Gupta V, Tabiin TM, Sun K, Chandrasekaran A, Anwar A, Yang K, Chikhlikar P, Salmon J, Brusic V, Marques ET, Kellathur SN, August TJ. SARS coronavirus nucleocapsid immunodominant T-cell epitope cluster is common to both exogenous recombinant and endogenous DNA-encoded immunogens. Virology. 2006 Mar 30; 347(1):127-39.
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Brusic V. Information management for the study of allergies. Inflamm Allergy Drug Targets. 2006 Jan; 5(1):35-42.
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Zhang GL, Khan AM, Srinivasan KN, August JT, Brusic V. Neural models for predicting viral vaccine targets. J Bioinform Comput Biol. 2005 Oct; 3(5):1207-25.
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Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schönbach C, Sekiguchi K, Semple CA, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y. The transcriptional landscape of the mammalian genome. Science. 2005 Sep 2; 309(5740):1559-63.
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Tan PT, Srinivasan KN, Seah SH, Koh JL, Tan TW, Ranganathan S, Brusic V. Accurate prediction of scorpion toxin functional properties from primary structures. J Mol Graph Model. 2005 Sep; 24(1):17-24.
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Zhang GL, Srinivasan KN, Veeramani A, August JT, Brusic V. PREDBALB/c: a system for the prediction of peptide binding to H2d molecules, a haplotype of the BALB/c mouse. Nucleic Acids Res. 2005 Jul 1; 33(Web Server issue):W180-3.
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Zhang GL, Khan AM, Srinivasan KN, August JT, Brusic V. MULTIPRED: a computational system for prediction of promiscuous HLA binding peptides. Nucleic Acids Res. 2005 Jul 1; 33(Web Server issue):W172-9.
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Brusic V, August JT, Petrovsky N. Information technologies for vaccine research. Expert Rev Vaccines. 2005 Jun; 4(3):407-17.
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Brusic V, Petrovsky N. Immunoinformatics and its relevance to understanding human immune disease. Expert Rev Clin Immunol. 2005 May; 1(1):145-57.
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Mandic M, Castelli F, Janjic B, Almunia C, Andrade P, Gillet D, Brusic V, Kirkwood JM, Maillere B, Zarour HM. One NY-ESO-1-derived epitope that promiscuously binds to multiple HLA-DR and HLA-DP4 molecules and stimulates autologous CD4+ T cells from patients with NY-ESO-1-expressing melanoma. J Immunol. 2005 Feb 1; 174(3):1751-9.
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Miotto O, Tan TW, Brusic V. Supporting the curation of biological databases with reusable text mining. Genome Inform. 2005; 16(2):32-44.
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Schönbach C, Koh JL, Flower DR, Brusic V. An update on the functional molecular immunology (FIMM) database. Appl Bioinformatics. 2005; 4(1):25-31.
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Petrovsky N, Brusic V. Virtual models of the HLA class I antigen processing pathway. Methods. 2004 Dec; 34(4):429-35.
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Brusic V, Bajic VB, Petrovsky N. Computational methods for prediction of T-cell epitopes--a framework for modelling, testing, and applications. Methods. 2004 Dec; 34(4):436-43.
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Brusic V, August JT. The changing field of vaccine development in the genomics era. Pharmacogenomics. 2004 Sep; 5(6):597-600.
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Srinivasan KN, Zhang GL, Khan AM, August JT, Brusic V. Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens. Bioinformatics. 2004 Aug 4; 20 Suppl 1:i297-302.
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Siew JP, Khan AM, Tan PT, Koh JL, Seah SH, Koo CY, Chai SC, Armugam A, Brusic V, Jeyaseelan K. Systematic analysis of snake neurotoxins' functional classification using a data warehousing approach. Bioinformatics. 2004 Dec 12; 20(18):3466-80.
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Lenffer J, Lai P, El Mejaber W, Khan AM, Koh JL, Tan PT, Seah SH, Brusic V. CysView: protein classification based on cysteine pairing patterns. Nucleic Acids Res. 2004 Jul 1; 32(Web Server issue):W350-5.
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Flynn JC, McCormick DJ, Brusic V, Wan Q, Panos JC, Giraldo AA, David CS, Kong YC. Pathogenic human thyroglobulin peptides in HLA-DR3 transgenic mouse model of autoimmune thyroiditis. Cell Immunol. 2004 Jun; 229(2):79-85.
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Silva DG, Schönbach C, Brusic V, Socha LA, Nagashima T, Petrovsky N. Identification of "pathologs" (disease-related genes) from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system. BMC Genomics. 2004 Apr 29; 5(1):28.
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Brusic V, Takagi Y, Nakamura H. [Bioinformatics in Asia]. Tanpakushitsu Kakusan Koso. 2004 Jan; 49(1):74-83.
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Brahmachary M, Krishnan SP, Koh JL, Khan AM, Seah SH, Tan TW, Brusic V, Bajic VB. ANTIMIC: a database of antimicrobial sequences. Nucleic Acids Res. 2004 Jan 1; 32(Database issue):D586-9.
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Brusic V, Millot M, Petrovsky N, Gendel SM, Gigonzac O, Stelman SJ. Allergen databases. Allergy. 2003 Nov; 58(11):1093-100.
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Brusic V, Petrovsky N, Gendel SM, Millot M, Gigonzac O, Stelman SJ. Computational tools for the study of allergens. Allergy. 2003 Nov; 58(11):1083-92.
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Fry BG, Wüster W, Kini RM, Brusic V, Khan A, Venkataraman D, Rooney AP. Molecular evolution and phylogeny of elapid snake venom three-finger toxins. J Mol Evol. 2003 Jul; 57(1):110-29.
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Brusic V, Pillai RS, Silva DG, Petrovsky N, Schönbach C. Cytokine-related genes identified from the RIKEN full-length mouse cDNA data set. Genome Res. 2003 Jun; 13(6B):1307-17.
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Brusic V, Petrovsky N. Bioinformatics for characterisation of allergens, allergenicity and allergic crossreactivity. Trends Immunol. 2003 May; 24(5):225-8.
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Brusic V. From immunoinformatics to immunomics. J Bioinform Comput Biol. 2003 Apr; 1(1):179-81.
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Bajic VB, Seah SH, Chong A, Krishnan SP, Koh JL, Brusic V. Computer model for recognition of functional transcription start sites in RNA polymerase II promoters of vertebrates. J Mol Graph Model. 2003 Mar; 21(5):323-32.
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Tatsumi T, Kierstead LS, Ranieri E, Gesualdo L, Schena FP, Finke JH, Bukowski RM, Brusic V, Sidney J, Sette A, Logan TF, Kasamon YL, Slingluff CL, Kirkwood JM, Storkus WJ. MAGE-6 encodes HLA-DRbeta1*0401-presented epitopes recognized by CD4+ T cells from patients with melanoma or renal cell carcinoma. Clin Cancer Res. 2003 Mar; 9(3):947-54.
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Tan PT, Khan AM, Brusic V. Bioinformatics for venom and toxin sciences. Brief Bioinform. 2003 Mar; 4(1):53-62.
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Bajic VB, Brusic V. Computational detection of vertebrate RNA polymerase II promoters. Methods Enzymol. 2003; 370:237-50.
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Petrovsky N, Schönbach C, Brusic V. Bioinformatic strategies for better understanding of immune function. In Silico Biol. 2003; 3(4):411-6.
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Brusic V, Petrovsky N. Immunoinformatics--the new kid in town. Novartis Found Symp. 2003; 254:3-13; discussion 13-22, 98-101, 250-2.
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Petrovsky N, Silva D, Brusic V. The future for computational modelling and prediction systems in clinical immunology. Novartis Found Symp. 2003; 254:23-32; discussion 33-42, 98-101, 250-2.
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Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schönbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002 Dec 5; 420(6915):563-73.
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Petrovsky N, Brusic V. Computational immunology: The coming of age. Immunol Cell Biol. 2002 Jun; 80(3):248-54.
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Schönbach C, Kun Y, Brusic V. Large-scale computational identification of HIV T-cell epitopes. Immunol Cell Biol. 2002 Jun; 80(3):300-6.
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Brusic V, Petrovsky N, Zhang G, Bajic VB. Prediction of promiscuous peptides that bind HLA class I molecules. Immunol Cell Biol. 2002 Jun; 80(3):280-5.
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Yu K, Petrovsky N, Schönbach C, Koh JY, Brusic V. Methods for prediction of peptide binding to MHC molecules: a comparative study. Mol Med. 2002 Mar; 8(3):137-48.
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Schönbach C, Koh JL, Flower DR, Wong L, Brusic V. FIMM, a database of functional molecular immunology: update 2002. Nucleic Acids Res. 2002 Jan 1; 30(1):226-9.
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Bajic VB, Seah SH, Chong A, Zhang G, Koh JL, Brusic V. Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters. Bioinformatics. 2002 Jan; 18(1):198-9.
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Zarour HM, Maillere B, Brusic V, Coval K, Williams E, Pouvelle-Moratille S, Castelli F, Land S, Bennouna J, Logan T, Kirkwood JM. NY-ESO-1 119-143 is a promiscuous major histocompatibility complex class II T-helper epitope recognized by Th1- and Th2-type tumor-reactive CD4+ T cells. Cancer Res. 2002 Jan 1; 62(1):213-8.
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Noguchi H, Kato R, Hanai T, Matsubara Y, Honda H, Brusic V, Kobayashi T. Hidden Markov model-based prediction of antigenic peptides that interact with MHC class II molecules. J Biosci Bioeng. 2002; 94(3):264-70.
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Srinivasan KN, Gopalakrishnakone P, Tan PT, Chew KC, Cheng B, Kini RM, Koh JL, Seah SH, Brusic V. SCORPION, a molecular database of scorpion toxins. Toxicon. 2002 Jan; 40(1):23-31.
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Kierstead LS, Ranieri E, Olson W, Brusic V, Sidney J, Sette A, Kasamon YL, Slingluff CL, Kirkwood JM, Storkus WJ. gp100/pmel17 and tyrosinase encode multiple epitopes recognized by Th1-type CD4+T cells. Br J Cancer. 2001 Nov 30; 85(11):1738-45.
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Yan Y, Panos JC, McCormick DJ, Wan Q, Giraldo AA, Brusic V, David CS, Kong YC. Characterization of a novel H2A(-)E+ transgenic model susceptible to heterologous but not self thyroglobulin in autoimmune thyroiditis: thyroiditis transfer with Vbeta8+ T cells. Cell Immunol. 2001 Aug 25; 212(1):63-70.
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Brusic V, Bucci K, Schönbach C, Petrovsky N, Zeleznikow J, Kazura JW. Efficient discovery of immune response targets by cyclical refinement of QSAR models of peptide binding. J Mol Graph Model. 2001; 19(5):405-11, 467.
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Zarour HM, Storkus WJ, Brusic V, Williams E, Kirkwood JM. NY-ESO-1 encodes DRB1*0401-restricted epitopes recognized by melanoma-reactive CD4+ T cells. Cancer Res. 2000 Sep 1; 60(17):4946-52.
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Schönbach C, Kowalski-Saunders P, Brusic V. Data warehousing in molecular biology. Brief Bioinform. 2000 May; 1(2):190-8.
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Brusic V, Zeleznikow J, Petrovsky N. Molecular immunology databases and data repositories. J Immunol Methods. 2000 Apr 21; 238(1-2):17-28.
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Zarour HM, Kirkwood JM, Kierstead LS, Herr W, Brusic V, Slingluff CL, Sidney J, Sette A, Storkus WJ. Melan-A/MART-1(51-73) represents an immunogenic HLA-DR4-restricted epitope recognized by melanoma-reactive CD4(+) T cells. Proc Natl Acad Sci U S A. 2000 Jan 4; 97(1):400-5.
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Schönbach C, Koh JL, Sheng X, Wong L, Brusic V. FIMM, a database of functional molecular immunology. Nucleic Acids Res. 2000 Jan 1; 28(1):222-4.
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Brusic V, Zeleznikow J. Knowledge Engineering Review. Knowledge discovery and data mining in biological databases. 1999; 14(3):257-277.
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Brusic V, van Endert P, Zeleznikow J, Daniel S, Hammer J, Petrovsky N. A neural network model approach to the study of human TAP transporter. In Silico Biol. 1999; 1(2):109-21.
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Honeyman MC, Brusic V, Stone NL, Harrison LC. Neural network-based prediction of candidate T-cell epitopes. Nat Biotechnol. 1998 Oct; 16(10):966-9.
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Daniel S, Brusic V, Caillat-Zucman S, Petrovsky N, Harrison L, Riganelli D, Sinigaglia F, Gallazzi F, Hammer J, van Endert PM. Relationship between peptide selectivities of human transporters associated with antigen processing and HLA class I molecules. J Immunol. 1998 Jul 15; 161(2):617-24.
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Brusic V, Rudy G, Honeyman G, Hammer J, Harrison L. Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network. Bioinformatics. 1998; 14(2):121-30.
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Brusic V, Rudy G, Harrison LC. MHCPEP, a database of MHC-binding peptides: update 1997. Nucleic Acids Res. 1998 Jan 1; 26(1):368-71.
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Hon L, Abernethy NF, Brusic V, Chai J, Altman RB. MHCWeb: converting a WWW database into a knowledge-based collaborative environment. Proc AMIA Symp. 1998; 947-51.
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Honeyman MC, Brusic V, Harrison LC. Strategies for identifying and predicting islet autoantigen T-cell epitopes in insulin-dependent diabetes mellitus. Ann Med. 1997 Oct; 29(5):401-4.
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Ramakrishna V, Negri DR, Brusic V, Fontanelli R, Canevari S, Bolis G, Castelli C, Parmiani G. Generation and phenotypic characterization of new human ovarian cancer cell lines with the identification of antigens potentially recognizable by HLA-restricted cytotoxic T cells. Int J Cancer. 1997 Sep 26; 73(1):143-50.
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Nakagawa K, Brusic V, McColl G, Harrison LC. Direct evidence for the expression of multiple endogenous retroviruses in the synovial compartment in rheumatoid arthritis. Arthritis Rheum. 1997 Apr; 40(4):627-38.
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Harrison LC, Honeyman MC, Trembleau S, Gregori S, Gallazzi F, Augstein P, Brusic V, Hammer J, Adorini L. A peptide-binding motif for I-A(g7), the class II major histocompatibility complex (MHC) molecule of NOD and Biozzi AB/H mice. J Exp Med. 1997 Mar 17; 185(6):1013-21.
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Brusic V, Rudy G, Harrison LC. Molecular mimicry-from hypothesis towards evidence. Immunol Today. 1997 Feb; 18(2):95-6.
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Brusic V, Rudy G, Kyne AP, Harrison LC. MHCPEP, a database of MHC-binding peptides: update 1996. Nucleic Acids Res. 1997 Jan 1; 25(1):269-71.
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Brusic V, Schönbach C, Takiguchi M, Ciesielski V, Harrison LC. Application of genetic search in derivation of matrix models of peptide binding to MHC molecules. Proc Int Conf Intell Syst Mol Biol. 1997; 5:75-83.
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Brusic V, Rudy G, Kyne AP, Harrison LC. MHCPEP--a database of MHC-binding peptides: update 1995. Nucleic Acids Res. 1996 Jan 1; 24(1):242-4.
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Rudy G, Stone N, Harrison LC, Colman PG, McNair P, Brusic V, French MB, Honeyman MC, Tait B, Lew AM. Similar peptides from two beta cell autoantigens, proinsulin and glutamic acid decarboxylase, stimulate T cells of individuals at risk for insulin-dependent diabetes. Mol Med. 1995 Sep; 1(6):625-33.
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Rudy G, Brusic V, Harrison LC, Lew AM. Sequence similarity between beta-cell autoantigens. Immunol Today. 1995 Aug; 16(8):406-7.
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Baum H, Brusic V, Choudhuri K, Cunningham P, Vergani D, Peakman M. MHC molecular mimicry in diabetes. Nat Med. 1995 May; 1(5):388.
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Brusic V, Rudy G, Harrison LC. MHCPEP: a database of MHC-binding peptides. Nucleic Acids Res. 1994 Sep; 22(17):3663-5.
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