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University of Rochester Center for Biodefense Immune Modeling

The goal of University of Rochester’s Center for Biodefense Immune Modeling (CBIM) is to develop comprehensive, quantitative models of the within host immune response to influenza A infection and vaccination, conduct lab experiments to validate models, and create computational tools to explore model perturbations in silico. Funded since 2005 by the National Institute of Allergy and Infectious Diseases (NIAID) (HHSN272201000055C), the Center is comprised of seven laboratories, mathematical modeling, statistical, bioinformatics, and data management cores, and hosts periodic workshops and symposia on computational immunology. The CBIM represents a multidisciplinary collaboration of human and mouse immunologists, virologists, mathematical modelers, engineers, computer scientists, statisticians and data managers.  
Tools & Resources Selected Publications
CBIM Data icon

Datasets for mathematical modeling produced by CBIM labs

Canini L, Conway JM, Perelson AS, Carrat F. Impact of different oseltamivir regimes on treating influenza A virus infection and resistance emergence: insights from a modeling study. PLoS Comp Biol. 2014;[in press].

Henn AD, Wu S, Qiu X, Ruda M, Stover M, Yang H, Liu Z, Welle SL, Holden-Wiltse J, Wu H, Zand MS. High-resolution temporal response patterns to influenza vaccine reveal a distinct human plasma cell gene signature. Sci Rep. Jul 31 2013;3:2327. PMC3728595

De Boer RJ, Perelson AS. Antigen-stimulated CD4 T cell expansion can be limited by their grazing of peptide-MHC complexes. J Immunol. Jun 1 2013;190(11):5454-5458.PMID:23606541

Wu S, Wu H. More Powerful Significant Testing for Time Course Gene Expression Data Using Functional Principal Component Analysis Approaches. BMC Bioinformatics 2013;14(1):6. PMC3617096

Pawelek KA, Huynh GT, Quinlivan M, Cullinane A, Rong L, Perelson AS. Modeling within-host dynamics of influenza virus infection including immune responses. PloS Comput Biol. 2012;8(6):e1002588. PMC3386161

Wu H, Kumar A, Miao H, Holden-Wiltse J, Mosmann TR, Livingstone A, Belz GT, Perelson AS, Zand MS, Topham DJ. Modeling of influenza-specific CD8+ T cells during the primary response indicates that the spleen is a major source of effectors. Journal of Immunology 2011; 187(9):4474-82. PMC3197949

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DED Discover icon

DEDiscover is a software tool for developing, exploring, and applying differential equation models for infectious diseases.

D-Netweaver icon

D-NetWeaver is a software tool for constructing gene expression dynamic networks from time course experiments.



IMC portal icon

IMC Portal features news and resources relevant to investigators interested in immune response modeling for infectious disease research.

BLIS icon

BLIS is a Web-based Data Management System for Immunologic Research.


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