Publications

2022

Liu,M., Tayob,N., Penter,L., Sellars,M., Tarren,A., Chea,V., Carulli,I., Huang,T., Li,S., Cheng,S., Le,P., Frackiewicz,L., Fasse,J., Qi,C., Liu,J.F., Stover,E.H., Curtis,J., Livak,K.J., Neuberg,D., Zhang,G.L., Matulonis,U.A., Wu,C.J., Keskin,D.B., Konstantinopoulos,P.A. (2022) Improved T cell immunity following neoadjuvant chemotherapy in ovarian cancer. Clin Cancer Res.

Ji,L., Li,Z., Lucas,M., Vodenska,I., Chitkushev,L., Zhang,G.L., Pregnancy outcomes in women with pregestational diabetes. EAI Conference on Computer Science and Education in Computer Science, June 24-27, 2022.

2021

Wang, T., Gan, Y., Arena, S. D., Chitkushev, L. T., Zhang, G., & Rawassizadeh, R. (2021). Advances for indoor fitness tracking, coaching, and motivation: A review of existing technological advances. IEEE Systems, Man, and Cybernetics Magazine, 7(1), 4-14.

Zhang, G., Chitkushev, L., Olsen, L. R., Keskin, D. B., & Brusic, V. (2021). TANTIGEN 2.0: a knowledge base of tumor T cell antigens and epitopes. BMC bioinformatics, 22, 1-8.

2020

Keshavarz, H., Abadeh, M. S., & Rawassizadeh, R. (2020). Sefr: A fast linear-time classifier for ultra-low power devices. arXiv preprint arXiv:2006.04620.

Javaheri, T., Homayounfar, M., Amoozgar, Z., Reiazi, R., Homayounieh, F., Abbas, E., … & Rawassizadeh, R. (2020). Covidctnet: An open-source deep learning approach to identify covid-19 using ct image. arXiv preprint arXiv:2005.03059.

Dehghani, M., Tsui, K. L., Zwetsloot, I. M., & Rawassizadeh, R. (2020). What are the perceived experiences of health fitness trackers for the elderly? A qualitative post-adoption study. International Journal of Technology Marketing, 14(2), 181-198.

Hosseinzadeh, M., Koohpayehzadeh, J., Bali, A. O., Asghari, P., Souri, A., Mazaherinezhad, A., … & Rawassizadeh, R. (2021). A diagnostic prediction model for chronic kidney disease in internet of things platform. Multimedia Tools and Applications, 80, 16933-16950.

Javaheri, A., Moghadamnejad, N., Keshavarz, H., Javaheri, E., Dobbins, C., Momeni-Ortner, E., & Rawassizadeh, R. (2020). Public vs media opinion on robots and their evolution over recent years. CCF Transactions on Pervasive Computing and Interaction, 2, 189-205.

Homayounfar, M., Malekijoo, A., Visuri, A., Dobbins, C., Peltonen, E., Pinsky, E., … & Rawassizadeh, R. (2020). Understanding smartwatch battery utilization in the wild. Sensors, 20(13), 3784.

Aras,P., Zhang,G.L., Rawassizadeh,R., Vodenska,I., Chitkushev,L. Data Quality Assessment of Medical Insurance Claims. The 16th Annual International Conference on Computer Science and Educations in Computer Science, Sept. 5, 2020.

Davchev, J., Mishev, K., Vodenska, I., Chitkushev, L., & Trajanov, D. (2020, September). Bitcoin price prediction using transfer learning on financial micro-blogs. In The 16th Annual International Conference on Computer Science and Education in Computer Science.

Sarkizova,S., Klaeger,S., Le,P.M., Li,L.W., Oliveira,G., Keshishian,H., Hartigan,C.R., Zhang,W., Braun,D.A., Ligon,K.L., Bachireddy,P., Zervantonakis,I.K., Rosenbluth,J.M., Ouspenskaia,T., Law,T., Justesen,S., Stevens,J., Lane,W.J., Eisenhaure,T., Zhang,G.L., Clauser,K.R., Hacohen,N., Carr,S.A., Wu,C.J., Keskin,D.B. (2020) A large peptidome dataset improves HLA class I epitope prediction across most of the human population. Nature Biotechnology, 1-11.

2019

Zhang,G.L., Keskin,B.D., Chitkushev,L. (2019). Extraction of Immune Epitope Information. In:Ranganathan, S., Nakai, K., Schönbach C. and Gribskov, M. (eds.), Encyclopedia of Bioinformatics and Computational Biology, vol. 3, pp. 39–46. Oxford: Elsevier.

Nishijima,M., Sarti,F.M., Vodenska,I., Zhang,G. (2019) Effects of decentralization of primary health care on diabetes mellitus in Brazil. Public health, 166:108-20.

Shaikh,R.A., Zhong,J., Lyu,M., Lin,S., Keskin,D., Zhang,G.L., Chitkushev,L., Brusic,V. Classification of Five Cell Types from PBMC Samples using Single Cell Transcriptomics and Artificial Neural Networks. The 3rd International Workshop on Computational Methods for the Immune System Function, IEEE BIBM, Nov 18-21, 2019, San Diego, CA.

Zhang,G.L., Chitkushev,L. Keskin,D., Brusic,V. TANTIGEN 2.0: an online database and analysis platform for tumor T cell antigens. The 3rd International Workshop on Computational Methods for the Immune System Function, IEEE BIBM, Nov 18-21, 2019, San Diego, CA.

Yan,W., Gangineni,S., Zhang,Y., Wang,J., Zhang,G.L., Chitkushev,L. Medical expenditures of diabetes-related hospitalizations in the United States. The 15th Annual International Conference on Computer Science and Educations in Computer Science, June 28 – July 2, 2019, Fulda, Germany.

2018

Huiting,L.N.,Samaha,Y., Zhang,G.L., Roderick,J.E., Li,B., Anderson,N.M., Wang,Y.W., Wang,L., Laroche, F.J.F., Choi, J.W., Liu,C.T., Kelliher,M.A., Feng,H. (2018) UFD1 contributes to MYC-mediated leukemia aggressiveness through suppression of the proapoptotic unfolded protein response. Leukemia, 25.

2017

Zhang,G.L., Keskin,D., Chitkushev,L. Brusic,V. MCVdb: a database for knowledge discovery in Merkel cell polyomavirus with applications in T cell immunology and vaccinology. The 1st International Workshop on Computational Methods for the Immune System Function, IEEE BIBM, Nov 13-16, 2017, Kansas City, MO.

Zhang,G.L., Brusic,V., Chitkushev,L. Data Analytics Based Positioning of Health Informatics Programs. The 13th Annual International Conference on Computer Science and Educations in Computer Science, June 30 – July 3, 2017, Albena, Bulgaria.

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, 32(3), 752.

Yoshizawa, A., Bi, K., Keskin, D. B., Zhang, G., Reinhold, B., & Reinherz, E. L. (2018). TCR‐pMHC encounter differentially regulates transcriptomes of tissue‐resident CD8 T cells. European journal of immunology, 48(1), 128-150.

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 Immunol.

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.

 

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.

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.

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., (2017) Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction. Immunity, 46, 315-326.

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.

2016

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.

2015

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.

Pappalardo,F., Brusic,V., Pennisi,M., Zhang,G.L. (2015) Editorial: Advances in Computational Immunology. Journal of Immunology Research, vol. 2015, Article ID 170920.

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.

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.

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.

Keskin,D.B., Reinhold,B.B., Zhang,G. L., Ivanov,A.R., Karger,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.

2014

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. Front Immunol.5:597.

Long,J., Zhang,Y., Chitkushev,L., Brusic,V., Zhang,G.L. Antidote Application: an educational system for treatment of common toxin overdose, Proceedings of ACM-BCB, 2014 September 20-23, Newport Beach, CA, USA.

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.

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).

2013

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.

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.

2012

Alekha,S, Kalathur,S, Zhang,GL, Olsen,LR, Zlateva,T, Chitkushev,LT, Brusic,V. Interactive blocklogo tool for visualization of peptide conservation. 2012 Boston University Science and Engineering Research Symposium.

2011

Kalathur,S, Zhang,GL, 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.

Dilek,E., Zhang,GL, Lee,JY, 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.

Zhang,GL, Deluca,DS, 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.

2010

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.