Selected Publications


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Journal Articles

  1. Bae,J., Hideshima,T., Zhang,G.L., Zhou,J., Keskin,D., Munshi,N., Anderson,K. (2017) Identification and characterization of HLA-A24 specific XBP1, CD138 (Syndecan-1), and CS1 (SLAMF7) peptides inducing antigens-specific memory cytotoxic T lymphocytes targeting multiple myeloma. Leukemia (in press).
  2. Yoshizawa,A., Bi,K., Keskin,D., Zhang,G.L., Reinhold,B., Reinherz,E.L. (2017) TCR-pMHC encounter differentially regulates transcriptomes of- tissue-resident memory CD8 T cells, European Journal of Immunology (in press).
  3. Hoft,D.F., Xia,M., Zhang,G.L., Blazevic,A., Tennant,J., Kaplan,C., Matuschak,G., Dube,T.J., Hill,H., Schlesinger,L.S., Andersen,P.L., Brusic,V. (2017) PO and ID BCG vaccination in humans induce distinct mucosal and systemic immune responses and CD4+ T cell transcriptomal molecular signatures. Mucosal immunology.
  4. Olsen,L.R., Tongchusak,S., Lin,H., Reinherz,E.L., Brusic,V., Zhang,G.L. (2017) TANTIGEN: a comprehensive database of tumor T cell antigens. Cancer Immunology, Immunotherapy, 66(6), 731-735.
  5. Abelin,J.G., Keskin,D.B., Sarkizova,S., Hartigan,C.R., Zhang,W., Sidney,J., Stevens,J., Lane,W., Zhang,G.L., Eisenhaure,T.M. Clauser,K.R., Hacohen,N., Rooney,M.S., Carr,S.A., Wu,C.J. (2017) Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction. Immunity, 46, 315-326.
  6. Lian,H., Li,D., Zhou,Y., Landesman-Bollag,E., Zhang,G.L., Anderson,N.M., Tang,K.C., Roderick,J.E., Kelliher,M.A., Seldin,D.C., Fu,H., Feng,H. (2017) CK2 inhibitor CX-4945 destabilizes NOTCH1 and synergizes with JQ1 against human T-acute lymphoblastic leukemic cells. Haematologica. 02(1), e17-e21.
  7. Pappalardo,F., Brusic,V., Pennisi,M., Zhang,G.L. (2015) Editorial: Advances in Computational Immunology. Journal of Immunology Research, vol. 2015, Article ID 170920.
  8. Simon,C., Kudahl,U.J., Sun,J., Olsen,L.R., Zhang,G.L., Reinherz,E.L., Brusic,V. (2015) FluKB: A knowledge-based system for influenza vaccine target discovery and analysis of the immunological properties of influenza viruses. Journal of Immunology Research, vol. 2015, Article ID 380975.
  9. Olsen,L.R., Simon,C., Kudahl,U.J., Bagger,F.O., Winther,O., Reinherz,E.L., Zhang,G.L., Brusic,V. (2015) A computational method for identification of vaccine targets from protein regions of conserved human leukocyte antigen binding. BMC Med Genomics, 8 Suppl 4:S1.
  10. Keskin,D.B., Reinhold,B., Zhang,G.L., Ivanove,A.R., Kargere,B.L., Reinherz,E.L. (2015) Reply to van de Sandt and Rimmelzwaan: Matching epitope display with functional avidity. Proceedings of the National Academy of Sciences, 112(19):E2418.
  11. Keskin,D.B., Reinhold,B., Zhang,G.L., Ivanove,A.R., Kargere,B.L., Reinherz,E.L. (2015) Physical detection of influenza A epitopes identifies a stealth subset on human lung epithelium evading natural CD8 immunity. Proceedings of the National Academy of Sciences, 112(7), 2151-2156.
  12. Zhang,G. L., Keskin,D.B., Lin,H.L., Lin,H.H., DeLuca,D.S., Leppanen,S., Milford,E.L., Reinherz,E.L., Brusic,V. (2014) Human Leukocyte Antigen Typing Using a Knowledge Base Coupled with a High Throughput Oligonucleotide Probe Array Analysis. Frontiers in Immunology 5:597.
  13. Sun,J., Zhang,G.L., Li,S., Ivanov,A.R., Fenyo,D., Lisacek,F., Murthy,S.K., Karger,B.L., Brusic,V. (2014) Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells - a benchmarking study. BMC Genomics, 15(Suppl 9):S1.
  14. Zhang,G. L., Sun,J., Chitkushev,L., Brusic,V. (2014) Big data analytics in immunology: a knowledge-based approach. BioMed Research International, vol. 2014, Article ID 437987.
  15. Zhang,G.L., Riemer,A.B., Keskin,D.B., Chitkushev,L., Reinherz,E.L., Brusic,V. (2014) HPVdb: a data mining system for knowledge discovery in human papillomavirus with applications in T cell immunology and vaccinology. Database (Oxford).
  16. Anderson,N.M., Harrold,I., Mansour,M.R., Sanda,T., McKeown,M., Nagykary,N., Bradner,J.E., Zhang,G.L., Look,A., Feng,H. (2013) BCL2-specific inhibitor ABT-199 synergizes strongly with cytarabine against the early immature LOUCY cell line but not more differentiated T-ALL cell lines. Leukemia.
  17. Yamada,T., Muta,E., Kim,J., Azuma,K., Sugawara,S., Zhang,G.L., Matsueda,S., Yamashita,Y., Itoh,K., Hoshino,T., Sasada,T. (2013) EGFR T790M Mutation as a Possible Target for Immunotherapy; Identification of HLA-A*0201-Restricted T Cell Epitopes Derived from the EGFR T790M Mutation. PLoS One. 8(11): e78389.
  18. Olsen,L.R., Kudahl,U.J., Simon,C., Sun,J., Schönbach,C., Reinherz,E.L., Zhang,G.L., Brusic,V. (2013) BlockLogo: Visualization of peptide and sequence motif conservation. J Immunol Methods. 400-401:37-44.
  19. Cai,A., Keskin,D.B., DeLuca,D.S., Alonso,A., Zhang,W. Zhang,G.L., Hammond,N.N., Nardi,V., Stone,R.M., Neuberg,D., Sidney,J., Brusic,V., Wu,C.J. (2012) Mutated BCR-ABL Generates Immunogenic T Cell Epitopes In CML Patients. Clinical cancer research 18(20):5761-72.
  20. Biernacki,M.A., Tai,Y., Zhang,G.L., Alonso,A., Zhang,W., Prabhala,R., Zhang,L., Munshi,N. Neuberg,D., Soiffer,R.J., Ritz,J., Alyea,E.P., Brusic,V., Anderson,K.C., Wu,C.J. (2012) Novel myeloma-associated antigens revealed in the context of syngeneic hematopoietic stem cell transplantation. Blood 119(13):3142-50.
  21. Zhang,G.L., Ansari,H.R., Bradley,P., etc. (2011) Machine Learning Competition in Immunology - Prediction of HLA class I molecules. J Immunol Methods 374(1-2), 1-4.
  22. Zhang,G.L., Lin,H.H., Keskin,D.B., Reinherz,E.L., Brusic,V. (2011) Dana-Farber repository for machine learning in immunology. J Immunol Methods. 374(1-2), 18-25.
  23. Olsen,L.R., Zhang,G.L., Keskin,D.B., Reinherz,E.L., Brusic,V. (2011) Conservation analysis of dengue virus T-cell epitope-based vaccine candidates using peptide block entropy analysis. Front. Immun. 2:69.
  24. Olsen,L.R., Zhang,G.L., Reinherz,E.L., Brusic,V. (2011) FLAVIdB: A data mining system for knowledge discovery in flaviviruses with direct applications in immunology and vaccinology. Immunome Res. 7(3):1-9.
  25. DeLuca,D.S., Keskin,D.B., Zhang,G.L., Reinherz,E.L., Brusic,V. (2011) PB1-F2 Finder: scanning influenza sequences for PB1-F2 encoding RNA segments. BMC Bioinformatics. 12 Suppl 13:S6.
  26. Keskin,D.B., Reinhold,B., Lee,S.Y., Zhang,G.L., Lank,S., O'Connor,D., Berkowitz,R.S., Brusic,V., Kim,S.J., Reinherz,E.L. (2011) Direct identification of an HPV-16 tumor antigen from cervical cancer biopsy specimens. Front. Immun. 2:75.
  27. Zhang,G.L., Deluca,D.S., Keskin,D.B., Chitkushev,L., Zlateva,T., Lund,O., Reinherz,E.L., Brusic,V. (2011) MULTIPRED2: A computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles. J Immunol Methods 374(1-2), 53-61.
  28. Budde,M.L., Lhost,J.J., Burwitz,B.J., Becker,E.A., Burns,C.M., O'Connor,S.L., Karl,J.A., Wiseman,R.W., Bimber,B.N., Zhang,G.L., Hildebrand,W., Brusic,V., O'Connor,D.H. (2011) Transcriptionally Abundant Major Histocompatibility Complex Class I Alleles are Fundamental to Non-Human Primate SIV-specific CD8+ T Cell Responses. J Virol. 85(7), 3250-61.
  29. Riemer,A.B., Keskin,D.B., Zhang,G.L., Handley,M.l, Anderson,K.S., Brusic,V., Reinhold,B., Reinherz,E.L. (2010) A conserved E7-derived CTL epitope expressed on human papillomavirus-16 transformed HLA-A2+ human epithelial cancers. J Biol Chem. 285(38), 29608-22.
  30. Lin,H.H., Zhang,G.L., Tongchusak,S., Reinherz,E.L., Brusic,V. (2008) Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research. BMC Bioinformatics. 9(Suppl 12), S22.
  31. Khan,A.M., Miotto,O., Nascimento,E.J., Srinivasan,K.N., Heiny,A.T., Zhang,G.L., Marques,E.T., Tan,T.W., Brusic,V., Salmon,J., August,J.T. (2008) Conservation and variability of dengue virus proteins: implications for vaccine design. PLoS Negl Trop Dis. 2(8), e272.
  32. Zhang,G.L., Khan,A.M., Srinivasan,K.N., Heiny,A.T., Lee,K.X., Kwoh,C.K., August,J.T., Brusic,V. (2008) Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes. BMC Bioinformatics 9(Suppl 1), S19.
  33. Heiny,A.T., Miotto,O., Srinivasan,K.N., Khan,A.M., Zhang,G.L., Brusic,V., Tan,T.W., August,J.T. (2007) Evolutionarily conserved protein sequences of influenza a viruses, avian and human, as vaccine targets. PLoS ONE 2(11), e1190.
  34. Zhang,G.L., Bozic, I., Kwoh,C.K., August,J.T. Brusic,V. (2007) Prediction of Supertype-Specific HLA Class I Binding Peptides Using Support Vector Machines. J Immunol Methods 320, 143-154.
  35. Chong,A., Zhang,Z., Choi,K.P., Choudhary,V., Djamgoz,M.B., Zhang,G.L., Bajic,V.B. (2007) Promoter profiling and coexpression data analysis identifies 24 novel genes that are coregulated with AMPA receptor genes, GRIAs. Genomics. 89(3), 378-84.
  36. Rajapakse,M., Zhang,G.L., Srinivasan,K.N., Schmidt,B., Petrovsky,N., Brusic,V. (2006) PREDNOD, a prediction model for peptide binding to the H-2g7 haplotype of the non-obese diabetic mouse. Autoimmunity 39(8), 645-50.
  37. Zhang,Z.H., Koh,J.L.Y., Zhang,G.L., Choo,K.H., Tammi,M.T., Tong,J.C. (2006) AllerTool: A Web Server for Predicting Allergenicity and Allergic Cross-Reactivity in Proteins. Bioinformatics. 23(4), 504-6.
  38. Zhang,G.L., Petrovsky,N., Kwoh,C.K., August,J.T., Brusic,V. (2006) PREDTAP: a system for prediction of peptide binding to the human transporter associated with antigen processing. Immunome Res. 2(1):3.
  39. Cocquet,J., Chong,A., Zhang,G.L., Veitia,R.A. (2006) Reverse transcriptase template switching and false alternative transcripts. Genomics. 88(1),127-31.
  40. Tong,J.C., Zhang,G.L., Tan,T.W., August,J.T., Brusic,V., Ranganathan,S. (2006) Prediction of HLA-DQ3.2? Ligands: evidence of multiple registers in class II binding peptides. Bioinformatics, 22, 1232-1238.
  41. Zhang,G.L., Khan,A.M., Srinivasan,K.N., August,J.T., Brusic,V. (2005) Neural Models for Predicting Viral Vaccine Targets. J Bioinform Comput Biol 3(5), 1207-1225.
  42. Zhang,G.L., Khan,A.M., Srinivasan,K.N., August,J.T. aBrusic,V. (2005) MULTIPRED: a computational system for prediction of promiscuous HLA binding peptides. Nucleic Acids Res. 33, W172 -W179.
  43. Zhang,G.L., Srinivasan,K.N., Veeramani,A., August,J.T., Brusic,V. (2005) PREDBALB/c: a system for prediction of peptide binding to the H2d molecules, a haplotype of the BALB/c mouse. Nucleic Acids Res. 33, W180 -W183.
  44. Srinivasan,K.N., Zhang,G.L., Khan,A.M., August,J.T., Brusic,V. (2004). Predictions of Class I T-cell epitopes: Evidence of presence of immunological hot spots inside antigens. Bioinformatics 20 Suppl 1, i297-i302.
  45. Chong,A.*, Zhang,G.L.*, Bajic,V.B. (2004). ICE (Information for the Coordinates of Exons): A Human Splice Sites Database. Genomics 84, 762-766. (*These authors contributed equally to the work)
  46. Chong,A., Zhang,G.L., Bajic,V.B. (2003). FIE2: A program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes, Nucleic Acids Res. 31(13), 3546-3553.
  47. Chong,A., Zhang,G.L., Bajic,V.B. (2002). Information and Sequence Extraction around 5'-end and Translation Initiation Site of Human Genes, In Silico Biology 2, 462-465.
  48. Brusic,V., Petrovsky,N., Zhang,G.L., Bajic,V.B. (2002). Prediction of promiscuous peptides that bind HLA class I molecules. Immunology and Cell Biology 80(3), 280-285.
  49. Bajic,V.B., Seah,S.H., Chong,A., Zhang,G.L., Koh,J.L.Y., Brusic,V. (2002). Dragon Promoter Finder: recognition of vertebrate RNA Polymerase II promoters. Bioinformatics 18(1), 198-199.
  50. Abeyratne,U.R., Zhang,G.L., Saratchandran,P. (2001). EEG Source Localization: A Comparative Study of Classical and Neural Network Methods. International Journal of Neural Systems 11(4), 349-359.
  51. Tun,A.K., Lye,N.T., Zhang,G.L., Abeyratne,U.R. and Saratchandran,P. (2000) RBF networks for source localization in quantitative electrophysiology. Critical Reviews in Biomedical Engineering 28, 463-472.
Abstracts

  1. Nishijima,M., Zhang,G.L., Vodenska,I. and Mori,F. Evaluating the primary health decentralization on Diabetes indicators: The Brazilian HiperDia program for diabetes case. The 12th World Congress of the International Health Economics Association. July 8-11, 2017, Boston, USA.
  2. Keskin,D.B., Sarkizova,S., Abelin,J.G., Keshishian,H., Zhang,G.L., Li,L., Clauser,K.R., Rooney,M.S., Ott,P.A., Chitkushev,L.T., Hacohen,N., Carr,S.A., Wu,C.J.. MS-based discovery of the HLA peptidome: applications to algorithm development, neo-epitope discovery and analysis of immunotherapy. The Institute for Cancer Vaccines & Immunotherapy 3rd International Symposium on Immunotherapy, May 12-13, 2017, London, UK.
  3. Andre J., Lu C., Zhang Y., Chayka B., Huff M., Shi W., Xue Y., Liu Y., Huang Y., Zhang Y., Brusic V., Zhang,G.L., Chitkushev L. (2015) T2DMS: An Online Education System for Type II Diabetes Management, Proceedings of CSECS 2015, July 20-23, Boston, MA, USA.
  4. Long,J., Zhang,Y., Chitkushev,L., Brusic,V., Zhang,G.L. (2014) Antidote Application: an educational system for treatment of common toxin overdose, Proceedings of ACM-BCB 2014.
  5. Finstad,S.L., Zhang,G.L., Linde,C., Muik,A., Hermann,F., Evans,V., de la Rosa,M, Zahn,R, Gaufin,T., Reimann,K., Apetrei,C., Miller,C., McCune,J., Picker,L., Veazey,R., Brusic,V., Letvin,N., Schmitz,J. (2010) Influence of FC Gamma-receptor polymorphisms on efficacy of antibody-mediated lymphocyte depletion in rhesus macaques. Journal of medical primatology 39(4), 279 -280.
  6. Biernacki,M., Alonso,A., Zhang,G.L., Zhang,L., Zhang,W.D., Tai,Y.T., Munshi,N., Alyea,E.P., Soiffer,R.J., Brusic,V., Ritz,J., Anderson,K.C., Wu,C.J. (2009) DAPK2 and PIM1 Are Myeloma-Associated Antigens That Elicit Coordinated B and T Cell Immunity After Syngeneic HSCT. Blood (ASH Annual Meeting Abstracts) 114(22), 2445.
  7. Biernacki,M., Zhang,G.L., Zhang,W.D., Brusic,V., Soiffer,R.J., Neuberg,D., Alyea,E.P., Tai,Y.T., Munshi,N.C., Ritz,J., Anderson,K.C., Wu,C.J. (2008) Novel Myeloma-Associated Antigens Revealed in the Context of Successful Syngeneic Hematopoietic Stem Cell Transplantation. Blood (ASH Annual Meeting Abstracts), 112(11), 815.
Book Chapters

  1. Zhang,G.L., DeLuca,D.S., Brusic,V. (2011) Database resources for proteomics-based analysis of cancer. Protein Microarrays for Disease Analysis: Methods and Protocols, Methods in Molecular Biology, Springer, 723, 349-64.
  2. DeLuca,D.S., Marina,O., Ray,S., Zhang,G.L., Wu,C.J., Brusic,V. (2011) Data processing and analysis for protein microarrays. Protein Microarrays for Disease Analysis: Methods and Protocols, Methods in Molecular Biology, Springer, 723, 337-47.
  3. Handoko,S.D., Kwoh,C.K., Ong,Y.S., Zhang,G.L., Brusic,V. (2006) Extreme Learning Machine for Predicting HLA-Peptide Binding. Lecture Notes in Computer Science, Springer, 3973, 716-721.
  4. Bozic,I., Zhang,G.L., Brusic,V. (2005) Predictive Vaccinology: Optimisation of Predictions Using Support Vector Machine Classifiers. Lecture Notes in Computer Science, Springer, 3578, 375-381.
  5. Zhang,G.L., Abeyratne,U.R., Lee,T.H. (2001) A Systematic Comparison of Classical and Neural Network Techniques in EEG Source Localization. Computer Methods in Biomechanics & Biomedical Engineering -3 , Middleton, J., Jones,M.L. and Pande,G.N. (eds.), Gordon and Breach Science Publishers, Amsterdam, Netherland.
Conference Articles

  1. Long,J., Zhang,Y., Brusic,V., Chitkushev,L., Zhang,G.L. Antidote Application: an educational system for treatment of common toxin overdose. ACM-BCB 2017, Aug 20-23, Boston, USA.
  2. Ruth,C, Yu,EA, Huey,S, Chitkushev,L, Mehta,SL, Zhang,GL (2016). ConnEDCt: A Development Framework for Mobile Electronic Data Capture in Disconnected Communities. Computer Science and Education in Computer Science, 12, 219-233.
  3. Zhang,G.L., Keskin,D., Chitkushev,L., Reinherz,E., Brusic,V. EBVdb: a data repository and analysis platform for knowledge discovery in Epstein-Barr virus with applications in T cell immunotherapy. ICSI3 2015, July 17-18, Taomina, Italy.
  4. Sun,J., Zhang,G.L., Li,S., Ivanov,A.R., Fenyo,D., Lisacek,F., Murthy,S.K., Karger,B.L., Brusic,V.. Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells – a benchmarking study. Proceedings of InCob, 2014 July 31- August 2; Sydney, Australia.
  5. Zhang,P., Chitkushev,L., Brusic,V., Zhang,G.L. Biomarkers in immunology: from concepts to applications. Proceedings of ACM-BCB, 2013 Sep 22-25; Washington DC, USA.
  6. Sun,J., Zhang,G.L., Olsen,L.R., Reinherz,E.L., Brusic,V. Landscape of neutralizing assessment of monoclonal antibodies against dengue virus. Proceedings of ACM-BCB, 2013 Sep 22-25; Washington DC, USA.
  7. Zhang,G.L., Keskin,D.B., Reinherz,E.L., Brusic,V. A cDNA microarray for rapid and economical identification of HLA profiles of individuals. Proceedings of BIBM, 2011 Nov 12-15; Atlanta, GA, USA. p. 677?679.
  8. Dilek,E., Zhang,G.L., Lee,J.Y., Zlateva,T., Chitkushev,L., Brusic,V. Probe design optimization of HLA microarray. Proceedings of BIBM, 2011 Nov 12-15; Atlanta, GA, USA. p. 680?682.
  9. Kalathur,S., Zhang,G.L., Zlateva,T., Brusic,V., Chitkushev,L. Visualization tools for presenting and analysis of global landscapes of vaccine targets. Proceedings of BIBM, 2011 Nov 12-15; Atlanta, GA, USA. p. 683?688.
  10. Zhang,G.L., Budde,M.L., Lhost,J.J., O'Connor,D.H., Hildebrand,W., Brusic,V. PREDmafa: a system for prediction of peptide binding to several MHC class I molecules in cynomolgus macaques. Proceedings of the second Immunoinformatics and Computational Immunology Workshop (ICIW 2011), 2011 Aug. 1-3; Chicago, USA.
  11. Chitkushev,L., Zlateva,T., DeLuca,D., Zhang,G.L., Brusic,V. Integrated health informatics curricula within information technology programs. Proceedings of 6th Annual International Conference on Computer Science and Education in Computer Science, 2010 June 26-29; Munich, Germany. p. 204?216.
  12. Zhang,G.L., Tong,J.C., Zhang,Z.H., Zheng,Y., August,J.T., Kwoh,C.K., Brusic,V. Computational models for identifying promiscuous HLA-B7 binders based on information theory and support vector machine. Proceedings of International Conference on Biomedical and Pharmaceutical Engineering; 2006 Dec. 11-14; Singapore. p. 319-23.
  13. Zhang,G.L., Kwoh,C.K., August,J.T., Brusic,V. Performance Evaluation of MULTIPRED1 on Prediction of MHC Class I Binders. Proceedings of International Conference on Biomedical and Pharmaceutical Engineering; 2006 Dec. 11-14; Singapore. p. 307-13.
  14. Zhang,G.L., Abeyratne,U.R., Saratchandra,P. Comparing RBF & BPN Neural Networks in Dipole Localization. In: Blanchard SM, editor. Proceedings of the First Joint BMES/EMES Conference: Serving Humanity, Advancing Technology; 1999 Oct. 13-16; Atlanta, GA. USA. p. 939.
  15. Adnan,S.M., Abeyratne,U.R., Zhang,G.L. Position selective stimulation of a multifascicular nerve. In: Blanchard SM, editor. Proceedings of the First Joint BMES/EMES Conference: Serving Humanity, Advancing Technology; 1999 Oct. 13-16; Atlanta, GA. USA. p. 480.