Benny Chain

Benny Chain

Professor of Computational Immunology








Network Investigator


Research Keywords: 

TCR repertoire in chronic infection and cancer



I obtained a PhD in comparative electrophysiology at the University of Cambridge, and then studied comparative invertebrate immunology at the Sloan Kettering Institute in New York. I joined Prof. Av Mitchison at UCL in 1982, becoming Professor of Immunology in 1996, and holding a joint appointment in Computer Science as Professor of Computational Immunology since 2018. I hold a visiting professorship at the Weizmann Institute, Israel, working with the systems immunology group led by Prof. Nir. Friedman.

I worked for most of my career on antigen processing and presentation by dendritic cells. More recently, I have realigned my research program to exploit mathematical and computational approaches to make sense of the data explosion generated by the functional genomics revolution. My research focuses on using high throughput sequencing to analyse and model the T cell receptor repertoire, in order to understand and manipulate the immune response to HIV and Mycobacterium tuberculosis, and to cancer.


Related Websites: 

Profile page at UCL


Key Publications:

Chain BM, Kay PM, Feldmann M. The cellular pathway of antigen presentation: biochemical and functional analysis of antigen processing in dendritic cells and macrophages. Immunology. 1986 Jun;58(2):271-6. PubMed PMID: 3086221; PubMed Central PMCID: PMC1452653.

Levine TP, Chain BM. Endocytosis by antigen presenting cells: dendritic cells are as endocytically active as other antigen presenting cells. ProcNatlAcadSci U S A. 1992 Sep 1;89(17):8342-6. PubMed PMID: 1355605; PubMed Central PMCID: PMC49914.

Bennett K, Levine T, Ellis JS, Peanasky RJ, Samloff IM, Kay J, Chain BM. Antigen processing for presentation by class II major histocompatibility complex requires cleavage by cathepsin E. Eur J Immunol. 1992 Jun;22(6):1519-24. PubMed PMID: 1601038.
Ibrahim MA, Chain BM, Katz DR. The injured cell: the role of the dendritic cell system as a sentinel receptor pathway. Immunol Today. 1995 Apr;16(4):181-6. Review. PubMed PMID:
Prokopowicz ZM, Arce F, Biedro R, Chiang CL, Ciszek M, Katz DR, Nowakowska M,Zapotoczny S, Marcinkiewicz J, Chain BM. Hypochlorous acid: a natural adjuvant that facilitates antigen processing, cross-priming, and the induction of adaptive immunity. J Immunol. 2010 Jan 15;184(2):824-35. Epub 2009 Dec 16. PubMed PMID:20018624.
Creusot RJ, Thomsen LL, Tite JP, Chain BM. Local cooperation dominates over competition between CD4+ T cells of different antigen/MHC specificity. J Immunol.2003 Jul 1;171(1):240-6. PubMed PMID: 12817004.
Thomas N, Best K, Cinelli M, Reich-Zeliger S, Gal H, Shifrut E, Madi A, Friedman N, Shawe-Taylor J, Chain B. Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence. Bioinformatics. 2014 ;30(22):3181-8. doi: 10.1093/bioinformatics/btu523.
Oakes T, Heather JM, Best K, Byng-Maddick R, Husovsky C, Ismail M, Joshi K, Maxwell G, Noursadeghi M, Riddell N, Ruehl T, Turner CT, Uddin I, Chain B. Quantitative Characterization of the T Cell Receptor Repertoire of Naïve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile. Front Immunol. 2017 Oct 12;8:1267.
Polonsky M, Rimer J, Kern-Perets A, Zaretsky I, Miller S, Bornstein C, David E, Kopelman NM, Stelzer G, Porat Z, Chain* B, Friedman N. Induction of CD4 T cell memory by local cellular collectivity. Science. 2018 Jun 15;360(6394). * joint senior author Zhang C, Zhou S, Groppelli E, Pellegrino P, Williams I, Borrow P, Chain BM, Jolly C. Hybrid Spreading Mechanisms and T Cell Activation Shape the Dynamics of HIV-1 Infection. PLoS Comput Biol. 2015 Apr 2;11(4):e1004179. doi:10.1371/ journal.pcbi.1004179.
Kroopa J, de Massy, R, Ismail, M. , Reading, J.L. , Uddin, I,  Woolston, A,  Hatipoglu, E, Oakes, T. , Rosenthal, R. , Peacock, T, Ronel, T, Noursadeghi, M , Turati, V, Furness, AJS, Georgiou, A, Wong, YNS, Ben Aissa, A, Sunderland, MW, Jamal-Hanjani, M , Veeriah,S, Birkbak, NJ, Wilson, GA, Hiley, CT, Ghorani, E, Guerra-Assunção, J-A, Herrero, J, Enver, T, Hadrup, SR, Hackshaw, A, Peggs, KS, McGranahan, N, Swanton, C on behalf of the TRACERx consortium, Quezada, SA and Chain, BM Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer. Nat. Med. (2019) 25.