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Professor of Cell & Molecular Biology
Research area
Computational immunology.
Research programme
Research summary
I have worked for many years on the biology of the antigen presenting cell, especially on the mechanisms of antigen processing in dendritic cells. More recently I have become interested in developing mathematical, statistical and computational tools which will help us to integrate and make sense of the huge amounts of data generated by the functional genomics revolution.
My research group is now concentrating on using high throughput sequencing to study the regulation of T and B cell receptor repertoire diversity. We focus on the immune response to cancer, and to major pathogens including HIV and Mycobacterium tuberculosis.
The research's major aim is to understand the fundamental rules which regulate the protective immune response. But the research questions are shaped by an awareness of current clinical priorities and challenges, articulated through close links with UCL Hospitals, and the Institute for Immunity and Transplantation.
Publications
- Selected publications
- 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;8:1267
- Joshi K, Chain BM, Peggs KS, Quezada SA. The "Achilles Heel" of Cancer and Its Implications for the Development of Novel Immunotherapeutic Strategies. Cold Spring Harb Perspect Med. 2017;pii: a027086
- Sun Y, Best K, Cinelli M, Heather JM, Reich-Zeliger S, Shifrut E, Friedman N, Shawe-Taylor J, Chain B. Specificity, Privacy, and Degeneracy in the CD4 T Cell Receptor Repertoire Following Immunization. Front Immunol. 2017;8:430
- Oakes T, Popple AL, Williams J, Best K, Heather JM, Ismail M, Maxwell G, Gellatly N, Dearman RJ, Kimber I, Chain B. The T Cell Response to the Contact Sensitizer Paraphenylenediamine Is Characterized by a Polyclonal Diverse Repertoire of Antigen-Specific Receptors. Front Immunol. 2017;8:162
- Heather JM, Ismail M, Oakes T, Chain B. High-throughput sequencing of the T-cell receptor repertoire: pitfalls and opportunities. Brief Bioinform. 2017;pii:bbw138
- Cinelli M, Sun Y, Best K, Heather JM, Reich-Zeliger S, Shifrut E, Friedman N, Shawe-Taylor J, Chain B. Feature selection using a one dimensional naïve Bayes' classifier increases the accuracy of support vector machine classification of CDR3 repertoires. Bioinformatics. 2017;33:951-955
- Pollara G, Murray MJ, Heather JM, Byng-Maddick R, Guppy N, Ellis M, Turner CT, Chain BM, Noursadeghi M. Validation of Immune Cell Modules in Multicellular Transcriptomic Data. PLoS One. 2017;12:e0169271
- Roe JK, Thomas N, Gil E, Best K, Tsaliki E, Morris-Jones S, Stafford S, Simpson N, Witt KD, Chain B, Miller RF, Martineau A, Noursadeghi M. Blood transcriptomic diagnosis of pulmonary and extrapulmonary tuberculosis. JCI Insight. 2016;1:e87238
- Kundu R, Theodoraki A, Haas CT, Zhang Y, Chain B, Kriston-Vizi J, Noursadeghi M, Khoo B. Cell-type-specific modulation of innate immune signalling by vitamin D in human mononuclear phagocytes. Immunology. 2017;150:55-63
- Pike R, Thomas N, Workman S, Ambrose L, Guzman D, Sivakumaran S, Johnson M, Thorburn D, Harber M, Chain B, Stauss HJ. PD1-Expressing T Cell Subsets Modify the Rejection Risk in Renal Transplant Patients. Front Immunol. 2016;7:126.
- View all publications
RPS Widget Placeholderhttps://research-reports.ucl.ac.uk/RPSDATA.SVC/pubs/BMCHA43?orderby=year