Student cohorts

2014 cohort

Alastair Heffernan
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.

Clare McCormack
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.

Joel Hellewell
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. 

Lilith Whittles
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.

Malebogo Tlhajoane
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. 

Tamsin Dewé
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. 

I am in the first cohort of the Wellcome Trust Four Year PhD Programme, but am currently in my final year, having taken time off for maternity leave. 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.

2015 cohort

Finlay Campbell
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. 

Isobel Routledge
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).

Lucia Cilloni
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’ve been working 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.

Matthew Dixon
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.  

I am currently completing my PhD, focussed on understanding transmission dynamics of Taenia solium taeniasis and cysticercosis infection dynamics in pigs and humans, and the impact of interventions.  The PhD has included interdisciplinary research using epidemiological, mathematical and statistical modelling techniques. I am collaborating 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) involves comparison of the T. solium transmission model developed at Imperial College, EPICYST, to another transmission model, cystiSim. Our work is ultimately aiming to support the development of post 2020 World Health Organization targets for T. solium.

Oliver Watson
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 my PhD I will be continuing working on malaria genetic approaches with Prof Jeffrey Bailey at Brown University. 

Robin Schaefer
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.

2016 cohort

Amy Dighe
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.

Constanze Ciavarella
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.

Saskia Ricks
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. 

Sreejith Radhakrishnan
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.

2017 cohort

Ben Jeffrey
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. At LSHTM I specialised in statistical and mathematical methods for studying infectious diseases and then spent 10 weeks in the Philippines working on my dissertation: an analysis of the distribution and dissemination of antibiotic resistance phenotypes of bacterial pathogens.

Following my MSc at I moved to the Sanger Institute where I was employed in the group of Dr David Aanensen. My role involved learning a range of computational and bioinformatic techniques to support the development of software packages for the surveillance of infectious disease. I was responsible for curating and maintaining several large databases of whole genome sequence data and then assisting in the analysis of these data to describe how bacterial pathogens, and particularly hyper-virulent and multi-drug resistant strains, are spreading globally.

I am now beginning the second year of my PhD, after doing two research projects in the MRes year on the transmission dynamics of dengue virus in Colombia; and the evolutionary factors which determine population structure in diverse bacterial species. So far the focus of my PhD work has been on developing spatial and temporal models for forecasting the spread of antibiotic resistance, however I am now moving on to applying machine learning techniques to proteomics data with the aim of identifying new vaccine targets for the bacterium: Streptococcus pneumoniae.

Daniela Olivera Mesa
Before starting the Wellcome Trust PhD programme, I completed two undergraduate degrees in Microbiology and Chemical Engineering from Universidad de los Andes in Colombia as well as a masters degree 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, especially in Colombia where the incidence of tropical diseases is high. This led me to the Wellcome Trust programme at Imperial in Epidemiology, Evolution and control of Infectious diseases.  

During the first year of the programme, I had the opportunity to learn about the work done in the department and  rotate across two different groups. The first half of the year 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. 

For my PhD, I am working under the supervision of Prof. Azra Ghani, Dr. Katharina Hauck ad Dr. Peter Winskill. My research project aims to integrate different components of dynamic transmission models from epidemiology and economic evaluation strategies in order to improve disease eradication planning.   

Hannah Edwards
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 my second year of a PhD project supervised by Prof. Matthew Fisher looking at the molecular epidemiology and population genomics of Cryptococcus fungi. The project offers a great mix of field, lab and computational work as well as cutting across aspects of epidemiology, ecology, genomics and evolutionary biology. This is very different to what I was doing previously and it is one of the benefits of the programme that you get opportunity to, and are encouraged to, try out new topics of research and develop new skills.

Janetta Skarp
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.

So far during my PhD (I have just started my second year) I have been working on elucidating how the combination of outbreak response capacity strength and emerging infectious disease outbreak risk affects the countries' emerging infectious disease burden globally. 

Joshua D'Aeth
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.

2018 cohort

William Green
I completed my BA in Natural Sciences and MSc in Chemistry at Trinity College Cambridge, during which time I conducted research in Organic Synthesis at the University of Oxford and at Harvard University. While I enjoyed organic chemistry, I found lab work to be a little frustrating and repetitive, so decided to follow a rather different passion in infectious diseases. As such, after University I completed an internship at Gavi, working in the policy team on the cost-effectiveness of the RTS,S malaria vaccine. I then worked as a consultant in the Global Polio Eradication Initiative at the WHO headquarters in Geneva, during which time I enjoyed learning about the work of polio modelling groups, particularly around the globally synchronized switch from trivalent to bivalent oral poliovirus vaccine. In April 2016 was deployed to Papua New Guinea as an independent monitor for the switch, which grounded my interest in pursuing a full-time career in infectious diseases. Following my work at WHO, I worked as a consultant at Dalberg Global Development Advisors, first in Geneva and then in London. After two years, having particularly enjoyed the Maths modules in my first two years of the Natural Sciences Tripos, I desired a more rigorous and mathematical approach to infectious disease dynamics, so the Wellcome Trust PhD program in Epidemiology, Evolution and Control of Infectious Diseases was a great fit.

As someone with previously limited experience in programming, the MRes part of the course was particularly useful, allowing me to get a good grounding infectious disease models, improve my coding ability, and gain insight into the research carried out across the department. For my first project I modelled malaria transmission during a mass drug administration trial in Zambia, using the parameter fits to estimate the generation time of P. falciparum malaria. My second project focused on evaluating gravity models for spatio-temporal forecasting of epidemics, comparing simulations of a hypothetical pandemic influenza outbreak in the UK from observed and gravity-model imputed commuting data. In my PhD I am studying how clustering of the uptake of healthcare interventions affects epidemic dynamics, with anticipated application in the ongoing Ebola Virus Disease outbreak in DRC.

Katherine Davis
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 techniques that I will 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. Building on this, I am now exploring the costs and benefits of integration of cervical cancer screening with other services in Kenya, for my PhD.

Olivier Eales

Helen Coupland
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 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. The MRes offered me a chance to explore the different areas of infectious disease research that are conducted in the department as well as the opportunity to improve my academic writing and the possibility of publication. The seminars also allowed me to improve my knowledge of infectious disease epidemiology and to learn about the use of genetic and genomic data within the field. In my PhD, under the supervision of Dr Samir Bhatt, I will be investigating the application of machine learning methods to big healthcare data.

Bimandra Djaafara
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) 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 will continue working with Dr Patrick Walker and in collaboration with Indonesia NMCP. My research aims to further explore the transmission dynamics of malaria in Indonesia and to use mathematical model in formulating malaria elimination strategy for Indonesia.

Jonathan Roberts
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.

In my first year of the programme I completed one project comparing models used to infer chlamydia prevalence in the UK and Australia, and a second project estimating the cost-effectiveness of strategies for preventing the transmission of hepatitis B from mothers to their children in Malawi. Alongside these projects, I attended great MRes seminars given by senior researchers in the department as well as departmental seminars given by experts from outside Imperial College. The MRes year is a fantastic way to experience the breadth of the research areas investigated by the Department of Infectious Disease Epidemiology and contribute to that research yourself with two six-month projects.
This year I'm excited to start work on my PhD project modelling healthcare systems in Malawi.

2020 cohort

Olivia Boyd
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. 

Jack Wardle
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 am now beginning my PhD project during which I will explore the use of different data sources of human mobility in models of international infectious disease spread.

Olanrewaju Edun
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.

For my PhD, I will be studying the consequences and determinants of HIV treatment among adolescents and young adults in sub-Saharan Africa.

Victoria Cox
I studied biochemistry at the University of Oxford and during my master’s year I worked in a molecular virology lab. My main interests became focussed in immunology, virology and host-pathogen interactions. Whilst I loved lab-work, I wanted to move into a computational research role because I felt this would be the best route to become more involved in public health research.

Immediately before starting on the MRes I worked short-term as a Research Assistant in the department’s malaria group, looking at the cost-effectiveness of different interventions. Then for 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.

I had limited coding experience before the MRes and I found the year to be academically challenging, but the department is an incredibly supportive place full of engaged and helpful people from a huge range of backgrounds, so it was possible to learn many new skills quickly. I’m really glad I got to do the MRes before starting the PhD - it enabled me to learn new methods and to explore what I would like to focus my future research on. I’m now working in the arbovirus research group, looking at the impact of climate on the spatiotemporal dynamics of dengue virus in South America.

Iwona Hawryluk
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 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, supervised by Dr Samir Bhatt and Dr Thomas Mellan, I will look at applying deep learning methods to satellite imagery for spatiotemporal mapping of malaria risk in Africa.

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.

Sam Horsfield
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.

For my PhD I am building upon the pangenome methods I developed in the MRes and applying these and other tools to study evolution in diverse bacterial populations.

2020 cohort

Leonhardt Unruh

Jacob Stapley

Dariya Nikitin

Fernando Guntoro