Find contact details and further information about the Innate2Adaptive team.
Professor of Immunology
I have worked for many years on the biology of the antigen presenting cell, especially on the mechanisms of antigen processing in dendritic cells. In the last few years 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 major pathogens including HIV and Mycobacterium tuberculosis. The research’s major aim is to understand the fundamental rules which regulate the host-pathogen interface. But the research questions are shaped by an awareness of current clinical priorities and challenges, articulated through our close links with UCL Hospitals, the Institute for Immunity and Transplantation and the Bloomsbury Centre for Pathogen Research.
Professor of Infectious Diseases
I am a clinician scientist and a consultant in Infectious Diseases. I undertook an MRC PhD fellowship to study the role of acute phase responses in anti bacterial host defence, followed by a Wellcome Trust fellowship on the impact of HIV 1 infection on innate immune host-pathogen interactions in macrophages. This led to the study of HIV TB co-infection and my current focus on immunological determinants of outcome in tuberculosis. My group combines molecular, cellular and systems level approaches to investigate host microbial interactions in order to inform novel approaches for diagnosis, patient stratification, and identification of rational targets for therapeutic intervention. I lead the Infection Clinical Research Hub. I am the Infection lead for the UCL Academic Careers Office and the director for the UCL Wellcome Trust Clinical PhD Programme.
I am an MRC Clinician Scientist in the Division of Infection and Immunity at University College London and an Honorary Consultant in Respiratory Medicine at University College London Hospital. I hold a medical degree from Edinburgh University and undertook postgraduate medical training in Glasgow and London. I began my specialist respiratory medicine training in Glasgow, and subsequently undertook translational immunology research using genome‑wide molecular profiling to understand inflammatory processes in respiratory disease, leading to the award of a PhD at UCL. My current research integrates human and zebrafish models to understand host factors that calibrate a balanced immune response in tuberculosis.
Clinical Postdoctoral Research Fellow
My clinical training speciality is in infectious diseases and microbiology, and during this time I developed an interest in better understanding immunity to tuberculosis, a pathogen that has circulated in the human population for centuries, and yet still has a significant impact on morbidity and mortality worldwide.
In 2013 I was awarded a Wellcome Trust Postdoctoral Clinical Research Fellowship to study correlates of protection to tuberculosis, making use of both human in vivo challenge models and in vitro models of macrophage-tuberculosis interaction. The project was largely based in the laboratory of Professor Mahdad Noursadeghi (UCL) and involved recruitment of individuals infected with tuberculosis both in the UK and in Peru, in collaboration with Professor David Moore (London School of Hygiene and Tropical Medicine).
I am now an NIHR Clinical Lecturer in Medical Microbiology at UCL, bringing together the observations made in my Postdoctoral Fellowship to workup future studies that aim to harness knowledge of the host immune response in tuberculosis infections to generate novel host-directed therapies.
My work touches on two core themes in the group, namely investigating human immune responses to tuberculosis infection and improving comparative analysis of whole genome transcriptional data. I have focused particularly on the use of transcriptional modules (a.k.a. signatures) to deconvolute biological information from multicellular transcriptional datasets, developing software that ranks modules based on their sensitivity and specificity for their annotated functions.
I joined the Innate2Adaptive research group at UCL as post-doctoral research associate in 2014. Beforehand, I undertook a PhD in Biological Sciences at the MRC Human Nutrition Research Institute at Cambridge University, investigating immune responses to gastrointestinal nanoparticles. As post-doc I have been involved in research in the field of inflammation and human tuberculosis infection, conducting cellular immunology experiments, transcriptional profiling, T cell receptor repertoire sequencing and bioinformatics analyses. My current projects focus on exploring the T cell responses at mycobacterial challenge sites; and studying the effect of ageing on antigen-specific primary immune responses.
I did my PhD at Rajiv Gandhi Centre for Biotechnology in India investigating the role of histone modifications in regulating bacterially-provoked host immune responses during Mycobacterium tuberculosis infection. During this time I obtained a Newton-Bhabha fellowship to work develop a collaboration with Johnjoe McFadden’s TB research group at the University of Surrey in the UK, which I then joined for my first Postdoctoral position. In 2018, I joined UCL to study human immune response variation in TB, aiming to identify functional immune correlates of protection and pathogenesis, combining genomics, transcriptomics and host-pathogen interactions in macrophages.
Matthew VX Whelan
I joined the Innate2Adaptive research group as a post-doctoral research associate in 2020. Before this, I undertook a BSc in Cell and Molecular Biology in University College Dublin, Ireland. In 2015, I was awarded the Government of Ireland Postgraduate Research Scholarship (IRC) to carryout a PhD in ‘Infection Biology’. My PhD investigated the effect of DNA supercoiling mediated epigenetic regulation on biofilm formation and host-cell entry by the pathogen Campylobacter jejuni. My research projects revolve around developing fluorescence imaging based approaches to observe and measure host-pathogen interactions. My current interests include characterising viral (SARS-CoV-2, HIV) and bacterial (Mycobacterium tuberculosis) intracellular trafficking/escape and immune modulation.
I am a postdoctoral research associate working at UCL since 2017. Having a PhD in genetic epidemiology, my interests lie in genetic and genomic studies of complex diseases. My work funded by Cancer Research UK is to look at T cell receptor sequencing (TCR-seq) in lung cancer patients recruited by TRACERx. In addition to NGS-based assay and data processing for the in-house TCR-seq pipeline, my studies extend to the TCR transduction pipeline using phoenix-derived retrovirus. Data analyses on TCR-seq and Single Cell RNA-seq are a major focus of my recent work.
Jose Afonso Guerra-Assuncao
I am postdoctoral research associate working as part of the Noursadeghi and Breuer research groups. I completed my PhD at the University of Cambridge on the evolutionary analysis of animal microRNAs. I did my first postdoc at the London School of Hygiene and Tropical Medicine where I researched tuberculosis transmission and drug resistance. I have joined UCL in 2016 at the Cancer Institute, working on the Personal Genome Project UK and developing single-cell RNA sequencing methodology at the bioinformatics core facility. I have been at the Division of Infection and Immunity since 2019. I am currently working on Adenovirus genomics, evolution and transmission as well functional analysis of RNA sequencing experiments and their use for biomarker discovery. I also work as the core bioinformatician of the Pathogen Genomics Unit (PGU).
PhD Students and Research Assistants
I am a PhD student working between the Division of Infection & Immunity and CoMPLEX. Prior to joining the division, I completed a masters in physics - with a specialisation in neutrino physics - at the University of Warwick, worked for a short time in the software industry, and then undertook an interdisciplinary research masters in biological complexity with CoMPLEX at UCL. My work focuses on modelling T cell receptor (TCR) recognition of antigens at both the molecular and repertoire levels. I help to maintain and extend the capabilities of the Decombinator software that we use in the Innate2Adaptive group to extract TCR abundances from raw sequence data. I am also interested in computational docking methods in the context of bound TCR-pMHC complex prediction from corresponding unbound TCR and pMHC structures.
NIHR Doctoral Research Fellow
Rishi is an academic trainee in respiratory medicine and an NIHR-funded clinical research fellow based between UCL Institute for Global Health and the innate2adaptive lab. He is interested in combining epidemiological and ‘omics approaches to improve diagnosis and prognosis of respiratory infections (particularly TB and SARS-CoV-2). His methodological interests include individual participant data meta-analysis, risk prediction, and systematic evaluations of prediction models and next generation biomarkers.
Wellcome Trust Clinical Training Fellow
Marc Robert de Massy
I am a CRUK Bioinformatics PhD candidate in the Immune Regulation and Tumour Immunotherapy Research Group of UCL Cancer Institute since 2017. I am interested in the relationship between tumour neo-antigens and expansion of T-Cell receptors (TCRs) using a combination of single-cell RNA-seq, TCR repertoire sequencing, flow cytometry data and immune staining data in the context of the TRACERx (TRAcking Cancer Evolution through therapy (Rx)) study. My PhD project aims to leverage machine learning and/or deep learning solutions in order to understand what shapes TCR repertoire of tumour infiltrating lymphocytes.
In October 2018 I joined Innate2Adaptive working as a research technician for Professor Mahdad Noursadeghi. My primary role is working on human immune response variation in Tuberculosis, involving transcriptomic analysis of a latent TB patient cohort to identify the immune responses that are associated with increased risk of active TB, and in October 2020 began a closely related part-time PhD in the group. Before joining I obtained a BSc in Biomedical Science at King’s College London followed by an MSc in Immunology at Imperial College London.
I am a biochemist with an interest in structural biology and cancer immunology and I aim to work at the interface between experimental and computational biology. I obtained my degree from Imperial College and worked at the Institute of Cancer Research during my placement year. I joined the Innate2Adaptive group as a PhD student under the supervision of Prof Benny Chain and Prof Sergio Quezada at the UCL Cancer Institute.
My PhD project contributes towards our understanding of the polyclonal T cell response in the context of cancer immune response. I use computational and experimental tools to explore T cell specificity and affinity, with a focus on defining which physical interactions drive recognition of foreign peptides and T cell activation. My aim is to build a picture of how different T cells respond to the same antigen and collaborate during an immune response, in order to understand whether it can be predictive of patient outcome or can be improved therapeutically.
NIHR Academic Clinical Fellow
I am an NIHR Academic Clinical Fellow and specialist registrar in Infectious Diseases and Microbiology. I completed my medical degree at the University of Cambridge (2009-2015) and subsequently moved to London for clinical training where I completed the Academic Foundation Programme and Core Medical Training in the North West Thames Deanery before being awarded my Academic Clinical Fellowship at UCL. I am currently working to develop a project to investigate the implications of T cell and macrophage interaction in TB infection with the aim of obtaining a Clinical Research Training Fellowship to complete a PhD.
I am a Biologist with a BSc from Queen Mary University of London, with a biomedical sciences MPhil from the University of Cambridge. I have previously worked as a Research Assistant (MRC Toxicology Unit) working as part of an immunology group at the University of Cambridge. My previous work focused on patients with rare primary immunodeficiency and working on a novel transgenic mouse model. I have joined the Innate2Adaptive research group as a Research Assistant in 2020. My current project explores blood transcriptional biomarkers for Tuberculosis.