Many students have taken part in programmes at the MRC Centre, learning from leaders in the field across a wide range of research themes and disease areas. Read about the experience of students from the 4-year PhD programme in Epidemiology, Evolution and Control of INfectious Diseases (1+3 MRes and PhD).
During my MRes year I worked on arboviruses. My first project was with Dr Nuno Faria & Dr Ilaria Dorigatti on dengue genomic epidemiology. I then did my second rotation with Dr Katy Gaythorpe on yellow fever seroepidemiology. I really liked working on arboviruses, but I missed the big entomological component that my previous malaria research had. So, I decided to do my PhD with Prof Tom Churcher on modelling the impact of different control strategies on mitigating residual malaria transmission. I had previous worked with Prof Churcher as an RA. I really like the flexibility that the MRes year gave me; I have now worked with several supervisors in the area of vector borne diseases and plan to continue my arbovirus research alongside my PhD. I'm hoping to do some entomological fieldwork in the Bijagos Islands as part of my PhD, and would also be interested in doing an internship at WHO to gain more applied epidemiological skills.
Before starting the 1 + 3 programme, I studied for my MSc in Data Analytics at Queen Mary University of London. During this time, I took up courses on Network Science, and Complex Systems where I first encountered mathematical models of infectious disease transmission. This experience got me interested in the applications of mathematical techniques such as agent-based and network models in epidemiology.
For my first project on the programme, I am worked with Prof Marie-Claude Boily and Dr Romain Silhol to study the potential population-level impact of prophylactic and therapeutic HSV-2 vaccines on genital herpes and HIV in Southeast Brazil. Part of this project is the use of mathematical models to identify key vaccine characteristics to maximise the effect of vaccination programmes, especially in low- and middle-income countries (LMICs).
For my second project, I worked with Dr Ilaria Dorigatti on developing a catalytic model to reconstruct the RSV immunity profile of the population of Lombardy, Italy to better understand heterogeneities in RSV transmission intensity and infer how changes in susceptibility explain the resurgent 2021-2022 RSV season.
The MRes year gave me the chance to learn and apply various computational techniques as I explored different research interests such as sexually transmitted infections, immunisation, and respiratory viruses. For my PhD, I will be working on modelling dengue and the various environmental factors and interventions that can affect its transmission.
Before joining the Epidemiology, Evolution and Control of Infectious Diseases PhD programme I completed a BSc in Biochemistry (Universidad Autonoma de Madrid), and a MSc in Vaccinology (EMJMD LIVE), when I cemented my passion for studying infectious diseases.
Repeatedly during my studies, I sought out opportunities to join different research groups. While I found wet lab experiences very rewarding, with time I became more and more interested in statistics and coding, and I finally pursued my MSc thesis in epidemiology of influenza at Sanofi Pasteur. In the year before the 1+3, I worked at the HPRU in Respiratory Infections at Imperial College, where my research responsibilities contributed to studies assessing SARS-CoV-2 household transmission.
I joined the PhD programme with the aim of further investigating infectious diseases while learning mathematical modelling. During my MRes, I firstly worked on a project assessing the influence of vaccination and sociodemographic factors on the regional variation of COVID-19 transmission in the UK. For my second rotation, I modelled the design of cluster randomised clinical trials to find the optimal design for a typhoid conjugate vaccine cluster randomised trial. I found that the most rewarding experience of the MRes was the exposure to different techniques and projects. I look forward to continuing learning during my PhD, where I will investigate demographic and socioeconomic factors related to vaccine inequality.
I joined the department last year for the MRes course and now a PhD student supervised by Dr Ilaria Dorigatti. My first project was supervised by Dr Ilaria Dorigatti, Dr Juliette Unwin, Dr Sangeeta Bhatia and Megan O’Driscoll. The project is about improving the reproduction number estimation methods at the early stage of an emerging epidemic by incorporating spatially structured data. I worked on malaria for my second project supervised by Professor Tom Churcher and Isaac Stopard. We investigated the effect of location and temperature on the experimental hut trial data. I enjoyed my MRes year very much. I am currently working on understanding different mobility models and other vector-borne diseases.
After completing a BSc in Psychology at Goettingen university, I went on to do an MRes in Cognitive Neuroscience at University College London. During my Masters, I focused on the processes underlying decision making in the human brain, using both experimental studies and computational models. This sparked an increased interest in computational research in me. After my Masters, I worked in industry for a year while deciding on the direction I wanted to take for my PhD. I found out about 1+3 PhD programme at Imperial and after reading several epidemiological papers I decided that this was the area of research I want to pursue. What excited me was the high relevance of both mathematical and biological concepts and methods in the area.
I found the MRes year of the programme extremely useful. Completing two rotations in relatively unrelated areas helped me to better determine my research interests and decide on a final research project. In my first project, I worked with Dr. Leonid Chindelevitch on improving group testing strategies for Covid-19. From there, I moved on to a project on geospatial modelling of malaria with Prof. Samir Bhatt. Both projects gave me the chance to brush up on my mathematical and machine learning knowledge and were great learning experiences. The additional year also gave me time to gain more general expertise in epidemiology. I can highly recommend this programme, especially for anybody coming to epidemiology from a different area where the additional year at the beginning will be very helpful.
In my current project, supervised by Dr Leonid Chindelevitch, I’m working on the development of methods for the analysis of metagenomic samples. My main area of interest is antibiotic resistance and treatment and the many ways in which microbiomes are involved in resistance dissemination.
As an undergraduate, I studied an integrated master’s in biomedical science at the University of Warwick, completing my fourth year in industry with GlaxoSmithKline Consumer Healthcare (now HALEON). I have always held a profound desire to add a quantitatively robust element to my interests in geopolitics and healthcare policy, yet holding a master’s degree which focused on toothpaste, did not naturally lend itself to this 1+3 programme and certainly, in matters mathematical, statistical, and programming-based, I held virtually no experience.
You can therefore trust when I say that the MRes year is a great learning experience. In my first project with Prof. Basáñez, I went from being unable to install R programming software to running and editing a complex stochastic individual-based model to predict the impact of ivermectin treatment on the incidence and prevalence of onchocerciasis-associated epilepsy. Wishing to diversify my skillset as much as possible, my second project with Prof. Gregson and Dr. Eaton focused on statistics, where I employed a series of logistic regression analyses to ascertain the impact of increased antiretroviral therapy coverage on the likelihood of individuals holding HIV stigma.
Returning to onchocerciasis modelling, my PhD research focuses upon understanding hypoendemic transmission of the disease to further elimination efforts across sub-Saharan Africa.
Beyond the modelling and statistical analyses, I've, so far, collaborated with partners in the United States CDC to undertake fieldwork in northern Ghana, gaining rare, first-hand, experience of the realities and impacts of our work. Further collaborations with the Task Force for Global Health in Georgia, USA have enabled me to gather data from a range of colleagues throughout West Africa, from which, the basis of many strands of novel research may develop.
Having recently completed my early-stage assessment (ESA), I look forward to progressing my understanding and research abilities as I enter the third year of the programme.
After finishing my BA in Natural Sciences at the University of Cambridge, I worked in research, studying host-pathogen interactions and novel antimalarial targets. I realised my interests lay in the global perspective of control of high burden pathogens and undertook an MSc in Control of Infectious Diseases at the London School of Hygiene and Tropical Medicine. My MSc project studied the phylogenetic reconstruction of dengue virus transmission chains. My studies brought together my interests in epidemiology, modelling infectious disease dynamics and how data-driven approaches can influence decision-making and improve control of communicable disease.
The 1+3 PhD programme was a natural next step. It has allowed me to build on my previous experiences and interests whilst providing me with the training required to expand my coding, analytical, and transferrable skills. For my first MRes project I worked with Dr. Ilaria Dorigatti, using mathematical modelling to analyse COVID-19 in real-time and make short-term projections. This gave me insight into the challenges of working with outbreak data as well as the department’s huge involvement with global outbreak responses. My second project was with Prof. Peter White where I used a compartmental model to simulate hypothetical gonorrhoea vaccine effects in a clinical trial and compared this with the impact at scale. This further improved my modelling skills and taught me about the interface between conclusions made by studies and their potential impact on public health policies.
I have finished my first year of the PhD, supervised by Prof. Peter White, Dr. Jeffrey Eaton, and Dr. Lilith Whittles. The work from my first project aim this year has utilised integrated health-economic disease-transmission modelling of gonorrhoea vaccination in MSM in England, taking into consideration vaccine-uptake behaviour and cost-effectiveness with the aim of informing gonococcal vaccine strategy. I look forward to presenting my work at conferences this year such as the European Scientific Conference on Applied Infectious Disease Epidemiology in November 2022.
Originally from Indonesia, I hold a BSc in Virology and Immunology from the University of Bristol and an MSc in Bioinformatics from the University of Edinburgh. Prior to joining the 1+3 PhD programme, I was a research assistant under Prof Simon Mead at the MRC Prion Unit at UCL working to develop a machine learning tool to diagnose human prion diseases based on epigenetic profiles. My current research interests are infectious diseases and machine learning, with a focus in high-through data analysis and visualization. Given my academic background and interests, I was naturally attracted to this programme in Epidemiology, Evolution and Control of Infectious Diseases.
In my first MRes project, I worked together with the COVID-19 Response Team under the supervision of Dr John Lees to optimize inference from compartmental models of infectious diseases using various computational and statistical strategies. For my second project, supervised under Dr Leonid Chindelevitch, I developed an automated pipeline for benchmarking antimicrobial resistance prediction using multiple data representation types and machine learning models, which was accompanied with an interactive dashboard app to visualize the outputs.
The MRes year was an exceptional time to explore the wide range of subjects within the department as well as to acquire as many skills as possible from world-leading experts in epidemiology. I am now excited to begin my PhD, where I will be working with the REACT team aiming to characterise multi-omics signatures and pathways that contribute to SARS-CoV-2 infection and Long COVID.
Before starting the Wellcome Trust 1+3 PhD programme in Epidemiology, Evolution and the Control of Infectious Diseases, completed a BSc in Genetics and Statistics at the University of Western Ontario follow by an MSc in Epidemiology at the London School of Hygiene and Tropical Medicine. During this time period, I realised I wanted to combine my interests in biological sciences and public health with my passion of statistical and mathematical methods. This led me to pursue a career in infectious disease modelling.
Following my MSc in Epidemiology, I started in the Department of Infectious Disease Epidemiology at Imperial College working as a Research Assistant for Jeff Eaton. During this time, I worked on the estimation and modelling of real-time HIV incidence in Malawi, with a focus in adolescent girls and young women (AGYW), aiming to develop novel methods for extrapolating population incidence estimates from surveillance data collected at ante-natal care clinics.
In Fall, 2019, I started on the Wellcome Trust 1+3 PhD programme in DIDE. My first project during the MRes year focused on adapting a hierarchical beta-binomial model to use current presence of serological markers from malarial infection during past pregnancies in women (ages 15-45) to back estimate regional malaria prevalence. My second project was conducted in adjunct with work I completed as part of the phylodynamic COVID-19 response team in Spring, 2020. We developed a phylodynamic model in an epidemiological framework to estimate R, number of introductions and cumulative number infected over time across all regions with sequence data available on GISAID.
While continuing to work in the phylodynamic COVID-19 response team, I have now started on the Wellcome Trust PhD programme in Epidemiology, Evolution and Control of Infectious Diseases under the supervision of Dr. Erik Volz and Dr. Marc Baguelin. My PhD project focuses on developing novel phylodynamic modelling methods for forecasting hot-spots and transmission dynamics in RNA-virus outbreaks, including influenza, HIV and sars-cov-2.
After studying chemistry as an undergraduate at the University of Oxford, I moved away from the lab and spent a few years working at the Government Office for Science, where my role mostly focused on supporting the provision of science advice to government during emergencies. During this time, I became really interested in the threats of infectious disease outbreaks and the insights that epidemiology can provide to aid their control. I went on to study on the MSc in Epidemiology at the London School of Hygiene and Tropical Medicine, and then worked on the surveillance of tuberculosis in England at Public Health England. I decided to apply for the 1+3 PhD programme at Imperial because I was keen to focus on research and gain more experience of mathematical modelling of disease dynamics.
The MRes year provided a great opportunity to learn from the wide range of research going on in the department, as well as picking up some of the techniques and methods that will be useful through the course of the PhD programme. In my first project I used a malaria transmission dynamics model to predict the potential impact of a new vector control method called eave tubes. My second project aimed to quantify the relative risks of importing cases of COVID-19 by air travel.
I have just begun the 3rd year of my PhD which focuses on ways to measure human movement within and between countries, and how these mobility patterns can be used to model the spread of emerging or re-emerging infectious disease outbreaks. In particular I have focused on issues of data availability and the impacts that this might have on predictions of where or when a disease may spread.
Prior to joining the 1 + 3 PhD programme, I had obtained a medical degree from Igbinedion University in Nigeria and worked in the PEPFAR-funded HIV control programme. I subsequently completed an MSc in Control of Infectious Disease at LSHTM, where I got exposed to epidemiology, modelling and their important roles in the global HIV control effort. This led to my interest in the 1 + 3 PhD programme.
The MRes year was extremely useful for me, as I had little experience in programming or modelling. It provided me the opportunity to develop these skills from my supervisors, weekly core sessions and other colleagues in the department. For my first MRes project, I used statistical modelling to study ways in which HIV clinic data sources can be used to estimate population viral suppression. My second project involved the development of a mathematical model of hepatitis B virus (HBV) transmission from an existing framework. This model was used to identify indicators that best reflect continued reductions in chronic HBV infections, to help inform in-country validation of WHO elimination targets.
Currently in the third year of my PhD, which focuses on understanding the determinants of HIV treatment success amongst adolescents and using modelling to quantify the contribution of low-level viremia to new HIV infections. This project involves the use of data from longitudinal cohort studies, complex HIV surveys and routine HIV programme data. I have had the opportunity to develop skills in advanced regression, longitudinal data analysis and mathematical modelling. Look forward to developing these further and applying to my research.
Before joining the 1+3 PhD programme in the Department of Infectious Disease Epidemiology (DIDE), I studied biochemistry at the University of Oxford. During my final year I worked in a molecular virology lab and my main interests became focussed in immunology, virology and host-pathogen interactions. Whilst I loved lab-work, I decided to apply for computational research PhDs because I felt this would be the best route to become more involved in public health research.
When I first joined DIDE I worked as a Research Assistant in the department’s malaria group, looking at the cost-effectiveness of different interventions. Then during the MRes year I completed two research projects: the first comparing modelling methods to estimate the force of infection of dengue virus transmission, and the second modelling the spatiotemporal dynamics of hand-foot-and-mouth disease in Malaysia. Before the MRes I had limited coding experience and I found the year to be academically challenging, but the department is an incredibly supportive place where I was able to learn new methods quickly and benefit from working with researchers from a wide range of backgrounds.
Since starting the PhD, I work in the arbovirus research group, looking primarily at the impact of climate on the spatiotemporal dynamics of different arboviruses, for example dengue, zika and chikungunya virus in Brazil and West Nile virus in Italy. I am also working on a modelling project analysing the relationships between climate factors and mosquito life traits, which govern mosquito survival, reproduction, development and feeding behaviours. After the PhD my current aim is to stay in research, either in an academic or public policy context.
My interest in mathematical modelling started during my undergraduate degree in Mathematics in Poland. Driven by that, I completed an MSc in Applied Mathematics specialising in Mathematical Biology at the University of Helsinki, Finland. I learned about many different ecological and epidemiological models there and wrote my dissertation on the dynamics of a disease occurring in a structured host population of amphibians. During my studies, I developed a passion for programming and mathematical modelling and wanted to get a bit more practical experience, so I spent 2 years working in the industry as a data scientist. I then decided to return to academia and to my interest in infectious diseases and applied to this 1+3 PhD programme.
In my first MRes project, I had the chance to contribute to a large multi-disease model, by implementing a new module for schistosomiasis transmission and investigating the benefits of preventive chemotherapy among children in Malawi. My second project focused on model selection techniques in Bayesian statistics and their applications for COVID-19 models. In my PhD, I’m further developing statistical methods for quantifying the severity and modelling the spread of COVID-19. I'm also interested in modern machine learning methods, and I'm involved in a collaborative project in which we apply deep learning methods to satellite imagery for spatiotemporal mapping of malaria risk in Africa. Recently I completed a 3-months industry internship in cybersecurity, which allowed me to use the skills learnt during the PhD programme outside the field of epidemiology.
This programme has so far given me an excellent opportunity to develop my skills lying in a cross-section of epidemiology, statistics, mathematics and computer science, all while being supervised by world-renowned experts in the field.
Before joining the programme, I completed an MSci in Biochemistry at the University of Birmingham. During my degree, I undertook a placement at the Earlham Institute in Norwich, where I became interested in applying next generation sequencing technologies to study bacterial genomics and epidemiology. Following my time at Birmingham, I joined the biotech company, Illumina, where I developed new sequencing platforms for broad genomic applications.
From my experiences during my degree and in industry, I pursued MRes projects that were focused on applying cutting-edge genomic analyses to study bacterial pathogen epidemiology. In my first project, I developed a novel sequencing method for environmental detection of Salmonella Typhi, the causative agent of Typhoid fever. For my second project, I benchmarked population genome analysis methods, known as pangenome graphs, and developed a tool to aid in using these graphs in the epidemiological study of bacterial pathogens.
Over the first two years of my PhD, I have developed skills in software engineering and statistical learning, producing tools and analyses focused on the study of evolution and epidemiology of diverse bacterial pathogens. I’ve presented this work at national and international conferences, and I have collaborated with groups outside of Imperial on a number of different projects. In my final year, I am putting the finishing touches on this work, and I hope to get a Post-Doctoral position in the field of bacterial evolutionary epidemiology.
I am a final-year PhD student with Neil Ferguson and Anne Cori in the Department of Infectious Disease Epidemiology, funded by the Wellcome Trust. My current research focusses on the inference of viral load kinetics and epidemic dynamics using Ct-value distributions from the REACT data set, and community testing data from the UK. My previous projects have included (i) inference of the reproduction number in heterogeneous epidemics, published in the Royal Society Interface; (ii) evaluation of gravity models for spatio-temporal forecasting of epidemics and (iii) modelling malaria transmission during a mass drug administration trial to estimate the generation time of P. falciparum malaria.
During my studies at Imperial, I took an 8-month break of studies to work full-time on the Covid pandemic, which included working in the World Health Organization’s Emergencies Program to set up data analytics infrastructure; working in the Imperial Covid-modelling team assessing intervention strategies in Latin America; and working for the UK Cabinet Office leading on presentation of infection indicators for briefings to senior stakeholders and ministers. In September 2020 I was seconded to the Joint Biosecurity Centre in the Department of Health and Social Care, where I lead on projects including (i) analysis of the efficacy of the Test and Trace program; (ii) modelling testing and isolation strategies in schools; (iii) forecasting the reproduction number based on age-prioritised vaccination roll-out, vaccine coverage and efficacy, and age-based transmission matricies.
Prior to beginning my studies at Imperial I was a consultant at Dalberg Global Development Advisors, working with a number of clients in the global health space on projects including market-sizing, strategy development and program evaluations. I also worked at the Global Polio Eradication Initiative at the WHO headquarters in Geneva, during which time I was deployed to Papua New Guinea as an independent monitor for the global polio vaccine switch.
I am a graduate of Trinity College Cambridge, where I obtained an MSc in Chemistry (1st class) and a BA in Natural Sciences (1st class, ranked 4th/102).
Before I started the Wellcome Trust 4-Year PhD Programme in Epidemiology, Evolution and Control of Infectious Diseases, I studied Biological Sciences at the University of Oxford. During my undergraduate degree, I enjoyed modules focused on infectious diseases and so I chose a final year project quantifying changes in tick-borne disease prevalence in the south-west of England. After completing my BA, I pursued my growing interest in epidemiology and studied an MSc in Control of Infectious Diseases at the London School of Hygiene and Tropical Medicine. At the London School, I developed my statistical skills and explored infectious disease dynamics in more detail. My final project assessed the use of novel rapid diagnostic tests for detecting intestinal schistosomiasis and cemented my fascination with identifying the best techniques to deploy in disease control.
Following my MSc, I was involved in a variety of projects, including performing a process evaluation of the implementation of a targeted approach to HIV testing for children and adolescents in Zimbabwe. I also acted as a member of the International Society of Neglected Tropical Diseases press core, interviewing researchers in a variety of fields, and worked with the HIV charity Sophia Forum, supporting their advocacy for women living with HIV in the UK. However, I was keen to return to academia and address epidemiological questions in more detail. As a result, I applied for the 4-year programme at Imperial.
The programme offered me an opportunity to familiarise myself with the department’s work, and the techniques that I would require for my research, during the MRes year, which I have found highly valuable. For my first MRes project, I performed a cross-sectional analysis of chlamydia burden and testing behaviour in Bristol. My second MRes project addressed the epidemiology of hypertension and barriers to seeking care in Zimbabwe. This provided a strong knowledge base as I started my PhD.
The project I have chosen for my PhD focuses on exploring the links between HIV, mental health, and quality of life in sub-Saharan Africa. For example, I have used quantitative data from a large cluster randomised trial in Zambia and South Africa (HPTN 071: PopART) to explore the effect of universal test and treat policies on quality of life among people living with HIV. As well as analyses centred on Zambia and South Africa, I have also employed data from a long-running cohort study in Manicaland, Zimbabwe, to examine associations between depression, HIV transmission and HIV care outcomes. I am now using my results to inform mathematical modelling of the impact of therapy for depression on the HIV epidemic in Manicaland.
In early 2022, I paused my PhD research for three months to complete a Fellowship in the Parliamentary Office for Science and Technology (POST), funded by the Nuffield Foundation. During my Fellowship, I researched and wrote a briefing on innovation in adult social care. It was a great opportunity to learn more about how scientific evidence is used in policymaking, and I returned to my PhD project with useful insights about how to ensure that science is used by decision makers.
I completed my MMath in Mathematical Sciences at Durham University, during this time I became increasingly interested in mathematical and statistical modelling methodologies and their application to real-world problems. The prospect of influencing international policy and positively impacting people’s lives attracted me to modelling within public health settings. This led me to conduct my masters thesis exploring alternative approaches for modelling the spread of the Black Death during the 1347-1350 epidemic. After concluding my degree, I began working as a research assistant in the Department of Infectious Disease Epidemiology at Imperial College London under the supervision of Prof Marie-Claude Boily. In collaboration with the World Health Organization, London School of Hygiene and Tropical Medicine and the University of Bristol, I predominantly focused on evaluating the impact of Herpes Simplex-2 Virus on global HIV prevalence using mathematical modelling techniques. I thoroughly enjoyed my time as a research assistant and therefore I decided to apply for the Wellcome Trust PhD Programme in Epidemiology, Evolution and Control of Infectious Diseases.
In my first MRes project, I developed a new methodology designed to be integrated into the current surveillance systems of “malaria-free” countries to assess the threat posed by malaria cases imported from other countries. My second project aimed to improve existing maps of HIV prevalence in Mozambique using a joint-learning neural network model to leverage the spatial and temporal information in antenatal clinic data as well as DHS data. To build my knowledge of using cutting-edge deep learning methods to explore disease dynamics I chose to undertake my PhD with Samir Bhatt looking at the effects and interactions of different exposures over time to increase an individuals risk of respiratory tract infection. I am working in collaboration with Naja Hulvej Rod at the University of Copenhagen using Danish registry data.
I did a BSc in statistics with minor in financial mathematics at Bogor Agricultural University, Indonesia. After graduated, I joined an IT consultancy company as a statistical software developer for a year. With the aim of pursuing a career in science, I then joined Dr Iqbal Elyazar’s geospatial analysis group at Eijkman-Oxford Clinical Research Unit (EOCRU, now OUCRU Indonesia) in Jakarta as a statistician. I was involved in a project on estimating human mobility using mobile phone data and the risk of inter-region malaria importations in Indonesia. I took one-year break to do an MSc in epidemiology at Imperial where I did my first project in mathematical modelling of infectious disease, using population movement estimates from mobile phone data and a simple malaria model to estimate reproduction numbers in a connected network of districts in Indonesia, with Dr Michael White and Prof Azra Ghani. After my MSc, I rejoined EOCRU for another two years before moving back to Imperial to do the 1+3 Wellcome Trust PhD program.
In my first MRes project, I developed a modelling framework to define the end of an outbreak of infectious diseases with Dr Anne Cori, Dr Natsuko Imai and Prof Christl Donnelly, in collaboration with WHO AFRO region. For my second project, supervised by Dr Patrick Walker and Prof Azra Ghani, I worked closely with the National Malaria Control Program (NMCP) of Indonesia to model the impact of malaria control efforts on the feasibility of Plasmodium falciparum elimination in the Papua region of Indonesia using the established Imperial malaria model. The MRes year was a fantastic opportunity to explore our interests in various research topics that are conducted in the department.
For my PhD, I am focusing my work on utilisation of disease surveillance data and mathematical modelling techniques to understand infectious disease transmission dynamics, to evaluate control and intervention programs, and to finally inform infectious disease control programs in Indonesia. During the first two years of COVID-19 pandemic, I joined the department’s COVID response team. I worked on several projects related to COVID, one of them is analysing the transmission dynamics of COVID-19 in Jakarta, Indonesia through syndromic-based mortality data in collaborations with Jakarta Department of Health. For the 2nd half of PhD, I continued working on analysing a decade-worth of malaria data in collaborations with the Indonesia NMCP. I am currently on the writing phase of my thesis.
In 2022, I received the Student Award for Outstanding Achievement medal from Imperial College London for my contributions in extramural activities that bring credit to the College.
Before starting the 1+3 MRes and PhD programme I finished a BSc in theoretical and computational physics at Cardiff University. Whilst at Cardiff I did an undergraduate project in network science, which drew me to towards studying epidemiology. I began the MRes with minimal knowledge of epidemiological modelling, but I found the department to be a really enthusiastic and friendly environment to learn more about the field. My learning has been well supported by the department's facilities and travel opportunities, we were all given powerful laptops to work on at the very start of the MRes year and towards the end of the MRes year I presented the work I did in my first project at a conference in Canada.
Before joining the 1 +3 Wellcome Trust PhD program in Epidemiology, Evolution and Control of Infectious Disease I studied Biology at the University of Oxford. After completing my undergrad I moved to the London School of Hygiene and Tropical Medicine (LSHTM) to study for an MSc in The Control of Infectious Diseases, and then spent a year working as a Research Assistant at the Sanger Institute.
I am now in the final year of my PhD, which has focussed on the application of statistical modelling and machine learning to the study of bacterial disease. Specifically, I am developing methods to predict bacterial phenotype from genomic and proteomic data, and modelling how the most serious bacterial pathogens are likely to spread within healthcare settings.
It has taken me longer than expected to reach this stage of my PhD, as I have twice taken time out to do industry internships. I firstly spent 3 months working at Benevolent AI (a medium sized health tech company based in London) during the summer of 2020, and then I completed a second internship at a Silicon Valley based startup called The Public Health Company, in the summer of 2021. Since the conclusion of my second internship, I have continued working part time at The Public Health Company as a Machine Learning Engineer.
To anyone reading this who is considering applying for the EECID PhD programme: I cannot recommend it enough. Whatever your interests, you will have the opportunity to explore them in depth and learn from some of the very best in people in the world in your field.
Daniela Olivera Mesa
Before starting the programme, I studied Microbiology and Chemical Engineering at Universidad de los Andes in Colombia as well as a MSc in Computational Biology. These studies gave me the tools to work at the intersection between engineering and biology. During the end of my masters’ studies, I became passionate about eco-epidemiological models because of their real-world applications. This led me to 4-Year PhD Programme in Epidemiology, Evolution and Control of Infectious Diseases.
During the MRes year, I had the opportunity to learn about the work done in the department. For my first project, I worked with machine learning methods to find associations of environmental and microbial variables with the immune phenotype of infants in India. For my second project, I investigated the public health impact of malaria transmission blocking vaccines. I developed a mathematical framework to define antibody dynamics following vaccination and included them in the deterministic model of malaria transmission developed by the Malaria Group in the department. In my PhD project, I was supervised by Prof, Azra Ghani, Prof, Katharina Hauck and Dr. Peter Winskill. My research was focused on exploring metapopulation models dynamics and investigating the economic optimisations and trade-offs of infectious disease control. For this project I’ve had the opportunity to work in different diseases like measles, malaria and COVID-19. Additionally, during the COVID-19 pandemic I took an interruption of studies for two months. During this time, I had the opportunity to work with the COVID response team in the department. I was involved in data collection for the early outbreak in China and the analysis of early non-pharmaceutical interventions in Latin America.
I have recently finished my PhD and now I am working as a Technical Analyst in the department. In this role, I work in the interface between research and public policy. I study disease dynamics and interventions, implementing mathematical models. Then, I translate the science to answer public health policy questions from organizations like WHO and GAVI.
Prior to starting the programme, my background was predominantly in biology, epidemiology and public health. Having completed an undergraduate in Biological Sciences at the University of Edinburgh and an MSc in Control of Infectious Disease at LSHTM, I then worked for several years with Malaria Consortium in Asia working on regional epidemiological and operational research projects related to malaria elimination and providing technical support to local governments. I loved gaining practical experience in endemic settings and seeing how research could be applied to inform policy targeted at helping vulnerable populations. I was drawn to the 1 + 3 programme because I was keen to develop further as a scientist and incorporate either modelling or evolutionary biology into my study of infectious disease epidemiology. During the first MRes year I completed a project modelling the impact of a new treatment regimen on community onchocerciasis prevalence, supervised by Prof. Maria-Gloria Basanez, and a project looking at methods of phylogeographic analysis as applied to clinical and environmental poliovirus data from Pakistan, supervised by Prof. Erik Volz and Prof. Nick Grassly. Despite my interest in vector borne disease, it was the opportunity to study the evolution of microbial pathogens that I wanted to develop during my PhD.
I am now in the final year of my PhD supervised by Prof. Matthew Fisher looking at the molecular epidemiology and population genomics of environmental Cryptococcus neoformans and Cryptococcus gattii in Zambia. The project has been very multidisciplinary, involving field work, laboratory methods, species distribution modelling and bioinformatics. The aim is to have a better understanding of what variants of each species exist in the environment and where to inform epidemiology and exposure risk, and to analyse genomic and phenotypic differences between environmental and clinical isolates for insights into virulence and drug resistance.
Before starting the Wellcome PhD programme at DIDE, I completed a BSc in Zoology here at Imperial College and moved on to do my MSc in Epidemiology at the London School of Hygiene & Tropical Medicine. The MRes year of the programme was a great opportunity to find out more about the different research groups, try out a couple of different topics, and think about what area of research interests me most.
I started my PhD in 2018 (supervised by Dr Anne Cori), but took an interruption of studies from December 2020 to September 2021 for maternity leave. For my PhD, I have been estimating countries' outbreak response capacities and investigating how they related to countries' COVID-19 responses, researched the costs of non-pharmaceutical interventions as outbreak response, and evaluated the costs of Ebola stockpiling for various outbreak scenarios.
After my PhD, I am aiming to continue my work on Ebola vaccine stockpiling, if I am successful at obtaining funding for the project.
Before I started on the Wellcome programme, I completed my undergrad in Biology during which I was exposed to a range of different topic areas in the life sciences, from cellular immunology to marine ecology, but the area I became most fascinated with during my studies was infectious disease epidemiology. This topic seemed to contain everything that I enjoyed studying in Biology, with evolution, ecology and immunology all interweaved. The interest I had in the topic was cemented when I chose to undertake my undergraduate project in modelling the evolution of bacteriocin diversity in Streptococcus pneumoniae, which was the most enjoyable part of my undergraduate studies.
That interest in infectious disease biology was the key reason why I applied to the Wellcome trust programme in epidemiology, evolution and control of infectious diseases, a course that allows me to go into the topic in a much a greater depth, while also working in a department that has world leading researchers in the field. During the MRes year of the course I first worked on the emergence of antimicrobial resistance (AMR) among two lineages of S. pneumoniae. I built up skills in phylogenetic and genomic techniques, using these to try and understand how resistance evolves and moves through these populations. For the second project I worked on modelling the HIV epidemic using case report data. This involved both working on simulated and real world data in Brazil to gauge the most effective modelling practice for the HIV epidemic outside sub-Saharan Africa.
For my PhD project, I've continued on the work of my first MRes project, looking again at how AMR can arise and spread through bacterial populations. Utilizing a large international collection of whole genome sequences for S. pneumoniae, I aim to understand how mobile genetic elements can spread through populations and across species, acting as important vectors for AMR genes.
Since finishing my PhD in the summer of 2022, I have taken up a role as bioinformatician at the UKHSA. This work is focusing on respiratory and vaccine preventable bacteria, in particular still working with large pneumococcal datasets.
After completing my undergraduate degree in Natural Science at the University of Cambridge, I worked with the Vaccine Implementation team at GAVI the Global Vaccine Alliance in Geneva before joining the Department of Infectious Disease Epidemiology at Imperial.
I really valued the MRes year at the beginning of the Wellcome Trust 1 + 3 year studentship, as this gave me some exposure to coding and mathematical modelling, with which I had no prior experience. During the MRes period, my interests became more focused on the dynamics of emerging zoonotic infectious diseases. I am now entering the final year of my PhD investigating the dynamics of Middle East Respiratory Coronavirus (MERS-CoV) in dromedary camels, and the potential impact of animal vaccination with Neil Ferguson and Thibaut Jombart.
Being part of such a large group of supportive students and post docs, with plenty of encouragement to get involved in wider departmental life has made such a positive difference to my PhD experience so far. I would definitely recommend the department to prospective PhD students.
In 2020 Amy interrupted her final year of studies for several months to support the department’s COVID-19 response team. On completion of her PhD in 2022 Amy took up a postdoctoral position at Johns Hopkins.
After pursuing a BSc and MSc in pure mathematics in Italy, I was ready to branch out into more practical applications. The interdisciplinary character of epidemiology allowed me to combine my academic interests in mathematics, coding and logic with the chance of improving our understanding of public health.
The MRes course preceding the PhD allowed for a smooth transition between the highly theoretical study of maths and the applied research in epidemiology carried out in this department. During that period I worked on two different projects covering different areas of the field, which allowed me to make an informed choice for my PhD project.
I'm now in my third and last year of the PhD studying the role of seasonal population movements in malaria transmission and control under the supervision of Prof Neil Ferguson and Prof Azra Ghani. The broad spectrum of the project allowed me to develop skills in big data analysis and high-performance parallel computing in the context of epidemiological modelling. Pursuing this degree challenged me in many ways, but ultimately pushed me to develop great independence, project and time management skills which will be valuable for my future career. I have also had the opportunity to partner with another research institution in the UK and to attend a number of conferences both in the UK and overseas.
In 2020 Constanze interrupted her final year of studies for several months to support the department’s COVID-19 response team, and in 2021 she took up a position in the Infectious Disease Epidemiology and Analytics (IDEA) Unit at Institut Pasteur as a mathematical modeller working primarily on Plasmodium vivax.
Prior to starting the Wellcome Trust programme, I read biology here at Imperial. During my degree, I became particularly fascinated by infectious diseases. I decided to stay at Imperial to do an MSc in Epidemiology in order to learn more about modelling the spread of disease. Following my MSc, I applied for the 1+3 Wellcome Trust PhD programme.
The MRes year of the PhD programme was a good opportunity to rotate across two different groups within the department and further develop my skills. My first project used a mathematical model to investigate the impact a hypothetical biomarker test targeting fast-progressors may have on the TB epidemic in India. My second project involved statistical analyses to investigate the association between social capital and the likelihood of initiation ART in Zimbabwe.
I am now in the final year of my PhD under the supervision of Dr. Nimalan Arinaminpathy and Prof. Timothy Hallett. My PhD aims to elucidate the optimum use of new and emerging technologies for TB control in South Africa and India, through the use of mathematical models.
In June 2021 Saskia took up a position at Baccuico as a data scientist.
After training as a veterinarian in India and specializing in wildlife medicine from the Royal Veterinary College, London, I dabbled in lots of things including hardcore molecular biology research, working in government service as a veterinary clinician, a two-year stint as a wildlife vet in a tiger reserve and teaching at my alma mater in Kerala, India.
During my work in the field in India, I developed an interest in infectious disease epidemiology, particularly of zoonoses. I have a particular interest in rabies (and other lyssavirus infections), an entirely preventable disease that still accounts for over 60,000 human deaths annually, with the majority of these reported from India. Rabies accounts for over 20,000 annual human deaths in India, with most human exposures occurring through the bite of infected free-roaming dogs. In the absence of timely post-exposure vaccination, most individuals who develop symptoms inevitably die. Mass vaccination of dog populations against rabies is recommended as the most cost-effective means of reducing human deaths from this disease.
For my PhD, under the supervision of Professor Christl Donnelly, Imperial College London, Dr. Pierre Nouvellet, University of Sussex and Dr. Abi Tamim Vanak, Ashoka Trust for Research on Ecology and the Environment (ATREE), I am currently conducting fieldwork in Kerala, south India to evaluate immunological responses in free-roaming and owned dogs after vaccination against rabies. I've also conducted dog population surveys and plan to radio-collar a few free-roaming dogs to understand movement patterns and home ranges, and to estimate dog population densities. From November 2019, I'll also be conducting household surveys to assess dog ownership practices, public awareness about rabies and attitudes towards stray dogs. The information gathered from fieldwork will be used to inform mathematical models of the feasibility of vaccinating dogs as a means of rabies control and elimination.
On completion of his PhD, Sree moved to LSHTM as a Research Fellow in Vaccine Modelling.
I studied Natural Sciences at the University of Cambridge, with a focus on genetics in my last year. My interests lay in the application of statistical and computational methods in biological research, more specifically in developing mathematical models capable of describing the complexities of biological systems. After conducting a research project with Professor Gilligan in the Epidemiology and Modelling group, I realised that the field of epidemiology combined my interest in biology with a rigorous analytical approach to research in a way I found very exciting.
I am very happy I decided to apply for a PhD as part of the 1+3 Wellcome Trust PhD programme in Evolution, Epidemiology and Control of Infectious Disease. The first year of the programme allowed me to explore various fields of research and decide which direction I wanted to take my research career in, as well as letting me choose a supervisor I felt was a good match for me. I decided on a project with Thibaut Jombart and Neil Ferguson, focusing on the development of computational and statistical tools for the reconstruction of transmission trees in densely sampled infectious disease outbreaks. Though the learning curve was steep, my PhD was very fulfilling, letting me work with some of the best scientists in the field, explore my academic interests me and accumulate a wide variety of skills.
Upon completing my PHD, I accepted a post doc position in the department with Thibaut Jombart to continue developing methods for outbreak analysis. In 2020, Finlay moved to WHO headquarters in Geneva as a Data Manager for Health Emergencies, working on Ebola and potentially COVID-19.
Before starting the Wellcome Trust PhD programme at DIDE, I completed an undergraduate degree in Biological Sciences at Oxford University. During my degree I became fascinated by the dynamics and interactions between diseases, hosts and their environment, both from a theoretical perspective and applied to policy and health intervention design. I also became interested in the use of models and quantitative methods in ecology and evolution, especially applied to the ecological and evolutionary dynamics of social interactions - my undergraduate thesis explored the evolution and dynamics of "spiteful" phenotypes in bacteria! I then worked in science communication and policy for a year, which gave me a perspective on the interactions between epidemiological research and policy makers.
I was attracted to this PhD programme as I was keen to carry out research in an area that could inform real world decision making, whilst being able to explore interactions between infectious disease, the environment and social factors. During my MRes year I gained much needed skills in mathematical modelling, statistical analysis and programming. During this time, I explored spatial patterns in transmissibility of the 2009 UK flu pandemic and modelled the impact of vector control on the population dynamics of blackflies, which vector River Blindness. I combined the insights gained from the two projects - quantifying transmission and its variation over time and space and developing models of vector borne disease - in my PhD project, supervised by Samir Bhatt and Azra Ghani. My PhD explored ways to make use of disease surveillance data to quantify malaria transmission in near elimination settings and how this varies over time and space. Since completing my PhD I have accepted a post doc position at the University of California San Francisco (UCSF).
Prior to starting at Imperial College London, I pursued my love for mathematics and completed a BSc in Mathematics from Newcastle University. During my bachelors, I developed a strong interest for how mathematics and statistics could be applied to medical research and this pushed me to apply to Cambridge University for an MPhil in Computational Biology. My masters allowed me to develop and strengthen my computational skills, while also showing me the wide range of possible applications for all the skills that were being taught.
The 1+3 PhD program offered by Imperial College was perfect for me because it gave me the chance to understand whether research was the right path for me. During my MRes I worked on polio vaccine trial data and on building a household flu transmission model, and this made me understand that disease modelling was what I wanted to pursue further. Having a supervisor who could push me and who I felt comfortable with was very important for me and the MRes year was the perfect way to get to know the people in the department, hear about their work and finding potential research ideas. The department has an extremely diverse pool of expertise and backgrounds and it’s a great environment to share your research and get constructive feedback either during to the lunch-time seminars or simply during lunch-time in the kitchen.
During my PhD I been worked on modelling the impact of routine active case-finding interventions on the transmission of TB in high-burden settings, with a focus on India, which I had the chance to visit for various collaborations and to gain first-hand experience of real-life implementation of case-finding efforts.
On completion of her PhD, Lucia returned to the department to work as part of the COVID-19 response team. In 2021 , Lucia moved to Johns Hopkins Bloomberg School of Public Health as a postdoctoral research fellow.
My research interests lie in the area of One Health, with a focus on the control of infectious diseases that impact both human and animals, where the environment also plays a role in transmission. I have previously worked in the Centre on Global Health and Security at Chatham House and the Royal Veterinary College on projects directed at zoonotic diseases within the One Health theme. My interests also involve understanding the development of scientific evidence that can best support policy, and have worked in the parliamentary office at Public Health England, and at Wellcome Trust on the ebola emergency funding call to give me a better insight into these processes.
My PhD focussed on understanding transmission dynamics of Taenia solium taeniasis and cysticercosis infection dynamics in pigs and humans, and the impact of interventions. It included interdisciplinary research using epidemiological, mathematical and statistical modelling techniques. I collaborated externally with a number of institutions including the Statens Serum Institut (Copenhagen); Sciensano (Brussels); Ghent University; Institute of Tropical Medicine (Antwerp); Royal Veterinary College (London), Technical University Munich; University of Oslo, University of Copenhagen, Schistosomiasis Control Initiative Foundation and the Ministry of Public Health in Madagascar. This coalition of partners (CystiTeam) involved comparison of the T. solium transmission model developed at Imperial College, EPICYST, to another transmission model, cystiSim. The work ultimately aimed to support the development of post 2020 World Health Organization targets for T. solium.
Since completing his PhD Matt has taken up a position as a Monitoring, Evaluation and Research Advisor, at One Health, Schistosomiasis Control Initiative Foundation. He also remains a visiting researcher with Imperial College.
Before starting within the department, I studied Natural Sciences at Pembroke College, Cambridge before completing a master's degree in Systems Biology. During this I was fortunate enough to work both with Dr Pietro Lio on multi-omic computational methods for identifying new biochemical reactions indicative of disease and with Dr Nik Cunniffe looking at using select plant species as an early warning system within plant infectious disease systems. This was my first exposure to infectious disease modelling after which I decided to apply for the Wellcome Trust 1+3 PhD Epidemiology, Evolution and Control of Infectious Disease at Imperial College London.
For the MRes year of the programme I conducted two projects exploring firstly the capability of popular Bayesian phylogenetic tools for inferring the origin of influenza outbreaks, and secondly the drivers of the spread of Plasmodium falciparum pfhrp2 gene deletions in sub-Saharan Africa. Without having to take any exams as part of this year I really had the opportunity to spend a lot of time learning to program in R, which was nice to know before starting on my PhD.
During my PhD I continued working within the malaria group by integrating genetic information into malaria transmission modelling. This work seeks to extend malaria transmission models that have been used in creating global technical strategies for malaria control by including parasite genetic information. These extensions have helped to demonstrate how interventions shape the genetic diversity of the P. falciparum parasite and characterises how parasite genetics could be used for malaria surveillance. After his PhD OJ continued to work on malaria genetic approaches with Prof Jeffrey Bailey at Brown University before being awarded a Schmidt Science Fellowship in 2020 to work on drug resistant malaria. OJ received exceptional permission to delay the start of his placement while he returned to the department to support the COVID-19 response team.
I completed my PhD in 2019 under the 1+3 Wellcome Trust programme of Epidemiology, Evolution and Control of Infectious Diseases. I have a background in social sciences (my undergraduate was in human sciences) and did a Masters in Public Health before joining the department for the MRes. My PhD focused on prevention of HIV in sub-Saharan Africa (a topic I’ve been working on since my undergraduate). I was involved in a large-scale project that looks into how we can organise concepts and data on HIV prevention along a theoretical framework of a cascade of necessary steps to prevent HIV infections. Since such a framework was very successful for HIV treatment, we hope that this can improve both routine monitoring of HIV prevention programmes as well as advocacy for HIV prevention – an area neglected in the past decade. It was a great opportunity to be involved in this project from the start, gaining experience in development of research projects, field work, and data analysis. After completing the PhD, I started as a Research Advisor at Action Against Hunger UK. As part of the No Wasted Lives initiative, I review evidence on the treatment of severe acute malnutrition among children and provide advice on how to align programmes with this evidence and how to fill critical knowledge gaps with new research.
As an undergraduate, I repeatedly jumped degrees, moving from biology to chemistry to physics to mathematical physics (I graduated in the last one). Theoretical physics interested me most and I began a PhD in that area. Problem was, while learning maths and physics was immensely enjoyable, carrying out research in the field did not engage me; I wanted to work on problems with concrete applications.
So, I applied to Imperial for a 4 year (1+3) graduate programme in infectious disease epidemiology. In this discipline, I could take all the quantitative skills I had developed and put them to use on public health problems that directly influence policy. As a Master’s (MRes) student, I worked on a cost-effectiveness analysis of HIV diagnostics, publishing my work the following year. I also performed ecological modelling of rabies in African wild dogs and took part in a domestic dog vaccination programme in central Kenya.
As a PhD student, I developed a global model of the hepatitis C epidemic in Timothy Hallett’s Global Health Analytics group, and investigated the attainability of WHO elimination targets. I presented my methods at a conference in Egypt in 2016 and initial results at a conference in São Paulo in November 2017. In my third year, in addition to extending my global analysis, I developed a hepatitis C model of Yunnan province, China. I returned to the province to present results of an economic analysis, which could potentially be used by local health officials to advocate for increased access to highly effective new drugs.
The 1+3 year doctoral training programme involved doing two research projects before entering the PhD. This was critical in determining what I wanted to do, and in developing those intangible research skills that matter so much in a 3-year research project. The Department of Infectious Disease Epidemiology provided regular lectures in the first year, and an almost year-round set of seminars that are open to all research students. These have helped me expand my knowledge of the field as a whole. In addition, the funding available through my Wellcome Studentship has facilitated travelling across the world to carry out, and present, my work. In short, through a generous funding package and the structure of the programme offered by Imperial, I was given a fantastic platform upon which to complete my PhD research.
Since completing his PhD, Alastair has gone on to take up a position at the National Audit Office in Newcastle.
Before joining the PhD programme, I completed an undergraduate degree in mathematics at Trinity College Dublin and a master’s degree in mathematics at the University of Cambridge. While I studied a variety of topics during this time, I was always primarily interested in exploring real-world applications of mathematical modelling, and so joining this programme gave me the opportunity to learn about how mathematical modelling and epidemiological analysis can be used to understand the transmission and control of infectious diseases. I particularly love the interdisciplinary nature of the research carried out in the department and enjoyed being part of a cohort of PhD students, all with different backgrounds, experiences and research interests.
As I hadn’t studied infectious disease epidemiology previously, I found the MRes part of the programme particularly helpful. It allowed me to gain an understanding of core concepts, an overview of the wide range of research carried out in the department, programming and other technical skills, and very much helped me to decide which area of research I wanted to pursue for my PhD. My PhD, completed under the supervision of Neil Ferguson and Azra Ghani, focussed on modelling mosquito populations at fine spatial scales and exploring how the underlying spatial structure of these populations affects the dynamics observed. I also examined the results of a small-scale field study testing the use of the bacterium Wolbachia for mosquito population control in Singapore.
On completion of my PhD in 2018, I took up a post-doctoral position in the department with Neil Ferguson.
I did an undergraduate in Mathematics and Philosophy as well as a Masters in Statistics before joining the Wellcome Trust programme. I applied because I wanted to use my statistical skills to make a positive change in the world. I spent a lot of my first year at Imperial getting to grips with the biological side of infectious disease modelling - working on a complex Bayesian model that tries to reproduce the transmission events in outbreaks from epidemiological and genetic data, as well as on a project to determine whether some genetic clones of the P. falciparum malaria parasite are more transmissible than others.
In the final year of my PhD course, I researched the use of the prevalence of infection in pregnant women as an alternative measure of malaria burden over time in humanitarian settings. I was supervised by Thomas Churcher and Azra Ghani, and this particular project was attractive to me because I worked closely with Médecins Sans Frontières (MSF) to make sure that my work could help guide them to make decisions in their operations. Looking back, I am very glad that I applied for this studentship. It was hard work but I have had the opportunity to work with some of the best scientists in their fields, the department is busy and professional, and I feel that I have developed all of the skills that I need to continue my career as a researcher.
On completion of his PhD Joel initially took up a short post-doctoral position in the department with Tom Churcher, and in April 2019 moved to the London School of Hygiene Tropical Medicine (LSHTM) to take up a post-doctoral position with Sebastian Funk in infectious disease modelling.
I applied for the PhD programme after spending five years working as a consultant actuary in central London. My background is in mathematics and I was keen to use the skills I had learnt during my degree creatively to solve practical problems with broad public health benefits.
The 1+3 year structure of the program was perfect for someone who, like me, was changing disciplines. The two projects I worked on during my MRes year, combined with the intensive training sessions, allowed me to make an informed decision about my final PhD project, as well as developing excellent working relationships with my supervisors, Professors Xavier Didelot and Peter White. There is always a diverse and interesting range of projects on offer. Mine ranged from studying the potential impact of voluntary male circumcision to prevent HIV in men who have sex with men, to a Bayesian analysis of a 1665 plague outbreak in the Derbyshire village of Eyam, which was picked up by mainstream media outlets and featured on BBC Radio 4’s Inside Science. During my PhD I worked on mathematically modelling the spread of antibiotic resistance in gonorrhoea, using a wide array of techniques: from Markov Chain Monte Carlo methods to sexual network simulations, and phylogenetic analysis of genomic data. I have had the opportunity to publish peer-reviewed studies in leading academic journals, as well as presenting at conferences around the world.
After completing my PhD I accepted a postdoc position in the department, continuing to work with Peter White, working for the past five years in a department at the forefront of the global effort to control infectious diseases has been rewarding and inspiring. I thoroughly recommend it.
Lilith was awarded a Sir Henry Wellcome Fellowship in early 2020, but deferred her start date to support the departments COVID-19 response team. Lilith remains in the department and started her fellowship in October 2021.
I completed an undergraduate degree in the Biological Sciences at Union College in Schenectady, USA. While at Union College, I worked on a number of molecular biology research projects with a focus on cell cycle regulation and neurobiology. Immediately after, I was awarded a fellowship to complete a placement at the McCord hospital in Durban, South Africa. There I coordinated a paediatric HIV funding programme and served as a part of a multidisciplinary research team within the antenatal care department where we appraised the hospitals PMTCT (Prevention of Mother to Child Transmission of HIV) programme. I then went on to obtain an MSc degree in the Control of Infectious Diseases from the London School of Hygiene and Tropical Medicine (LSHTM) in 2013. Prior to joining the Wellcome Trust PhD programme I served as a research assistant with a research group at the University of Botswana that was developing randomised control trials to evaluate the scale-up of proven interventions aimed at combatting inter-generational relationships in my native Botswana.
My PhD research was centred on health care delivery within low-income country settings, entitled “From Policy to Practice: Heath Systems and the Provision of HIV Care and Treatment in eastern Zimbabwe”. My key interests lay in better understanding health system limitations as well as the economic and epidemiological factors that may impede the success of specific healthcare interventions in developing countries. Specifically, I investigated the provision of HIV care and treatment in eastern Zimbabwe, a low-income country with a generalised HIV epidemic.
I was particularly drawn to the Wellcome PhD training programme within the Department for Infectious Disease Epidemiology at Imperial College because of the wealth of knowledge and expertise in HIV research within the department. In addition, the specialist MRes course enabled me to enhance my skills in medical statistics while also exploring other aspects of epidemiology that were of interest to me, including infectious disease modelling and bioinformatics.
On completion of his PhD in 2018, Malebogo took up a position at Public Health England (PHE) as an HIV/STI Surveillance and Prevention Scientist.
I developed a special interest in infectious diseases during the five years I spent practicing as an equine veterinarian in Australia, South Africa and the UK. Infectious disease control was a regular part of veterinary practice in South Africa in particular, where my patients included horses infected with viral diseases such as West Nile Fever (a zoonosis) and African Horse Sickness (which has a case fatality rate of around 90%). Wanting to combat infectious diseases at the population rather than individual level led me to an MSc in Control of Infectious Diseases at the Royal Veterinary College. I subsequently spent two years working in infectious disease risk analysis, as a consultant to various research agencies and public health departments in the UK and internationally. I learnt to code while developing a risk model for zoonotic avian influenza infection at what is now the Animal and Plant Health Agency (APHA) and decided to pursue modelling further.
For my project, under the supervision of Dr Nick Croucher and Professor Christophe Fraser (now at the Big Data Institute, University of Oxford), I am examining the evolutionary dynamics of antimicrobial resistance (AMR) in bacterial populations. To do this, I have built an individual-based model that simulates interactions between hosts, bacteria, mobile genetic elements, and resistance genes. Having disentangled these interactions, I hope to ultimately quantify the effect of control measures in one host population (for example, farm animals) on the evolution and spread of AMR in another host population (such as humans). It has been a pleasure to be part of such a friendly and high-achieving department, and to benefit from the excellent support of the Wellcome Trust.
Tamsin was in the first cohort of the Wellcome Trust Four Year PhD Programme, and having taken time off for maternity leave, in 2021 took up a position at the Veterinary Medicines Directorate leading on AMR surveillance and evidence for Defra.