Clare Andradi-Brown (Joined 2018 programme)

Clare Andradi-BrownI studied Biology as an undergraduate and throughout my studies the importance of statistical analysis had been reinforced. I completed a Bioinformatics project from which I gained skills in database searching and visualising protein structures. The proficiencies gained were of additional use for the completion of a Bioinformatics module and subsequently my final year project. Taken together, this demonstrated to me the importance of Bioinformatics and its numerous applications.

I applied to the 4-year PhD programme because I am keen to understand and contribute to the global impact of computational biology. The MSc will provide me with the appropriate skills for further doctoral studies and allow me to focus on the topics required to take forward toward doctoral studies. The PhD programme is a unique chance to enjoy both experimental and theoretical academic supervisors. It offers a wide range of opportunities that will allow one to put particular theories to the test and I am really excited to start this program!


Ivan Croydon-Veleslavov (Joined 2016 programme)

Ivan

Hello, I am a Wellcome Trust PhD student under the supervision of Professor Michael Stumpf and co-supervised by Professor Matthias Merkenschlager. My work centers on developing computational approaches to characterise stem cell dynamics from single-cell data. I am particularly interested in gaining intuition from high-dimensional data and applying statistical learning approaches to biological problems.

Prior to starting the Wellcome Trust programme in Theoretical Systems Biology and Bioinformatics, I completed my undergraduate degree in Biological Sciences here at Imperial. During this time, I began to appreciate how mathematical and computational approaches were being applied to biological data to obtain meaningful insights into complex processes. Whilst initially interested in a broad range of subjects, including evolutionary biology, genomics and statistics, a final year module in Integrative Systems Biology consolidated my initial interest  in the field and encouraged me to apply for the PhD programme. This decision was supported further by my experience as a BBSRC scholar at the Bioinformatics department of the Natural History Museum, where I was able to sequence and annotate the mitochondrial DNA of newly discovered insect species alongside my degree.

During the MSc year, I was introduced to a wide range of mathematical techniques and computing environments. Knowledge fostered during the taught component was applied throughout the subsequent research projects, providing the opportunity to experience different supervisors and research groups.

Whilst demanding, the structure of the course provided me with the necessary skills and expertise to start my PhD in Michael Stumpf’s lab. Really, it has been the broadness of the course material and the diverse academic backgrounds of my peers that have made these past two years so rewarding. I would encourage anyone interested in interdisciplinary research to consider this program, regardless of their chosen subject at undergrad.


Madeleine Hall (Joined 2017 programme)

Madelein

In 2017 I graduated from the University of Edinburgh with a BSc in Mathematics. During my undergraduate degree I was particularly drawn to studying applied mathematics, looking at modelling and describing real-world systems using various mathematical tools. I undertook several research projects outside of my ascribed courses, on topics ranging from image processing to density functional theory, all of which heavily involved computational and numerical skills.

Having developed an affinity for both applied mathematics and computing, and knowing I wanted to pursue further study and academia, I was immediately attracted to the Wellcome Trust programme at Imperial in Bioinformatics. The programme has given me the opportunity to greatly broaden my biological knowledge, especially having not studied the subject since A-level. The research conducted within the institution and throughout the programme is pioneering. The opportunity to immerse in groundbreaking research areas and groups is invaluable.

The skills developed throughout the course of the first year have hugely accelerated my abilities and competence in a range of capacities. The emphasis on programming languages including web design has advanced my confidence and capabilities in computing, data analysis and web development. The support provided by directors of the programme combined with the vast range of areas that can be covered makes this an excellent programme for anyone seeking a very interdisciplinary exposition to research. There is a lot of choice available for projects, allowing candidates to pursue a niche area to deep understanding, or alternatively pursue a variety of topics to become familiar with many aspects of the field. I took advantage of the option to immerse myself in a broad range of research groups, and look forward to pursuing my chosen focus throughout my forthcoming PhD.


Tara Hameed (Joined 2017 programme)

Tara

I am currently a Wellcome trust student just beginning the first year of my PhD. 

I undertook an undergraduate degree in Mathematics and then applied to the 1+3 year program provided by The Wellcome Trust and Imperial College London: Bioinformatics and Theoretical Systems Biology. During the masters year I took varied projects from looking at Gaussian Processes to trying out the field of Biophysics. I decided to do my PhD with Dr. Reiko Tanaka looking at the immune response to inhalation of a mould named A. Fumigatus. The aim is to mathematically model this using a system of ODEs to look at eventually proposing treatments to invasive aspergillosis. 


Duncan Ingram (Joined 2016 programme)

Ingram, Duncan (Joined 2016 programme)My interest in science spans biology to physics, so the use of interdisciplinary approaches to scientific problems has always fascinated me on a fundamental level. My BSc in biochemistry introduced me to ‘systems biology’ which explored how merging biology with quantitation is vital for tackling many complex yet pertinent problems. This was challenging yet hugely rewarding, and spurred me to apply for this programme at Imperial.

As computation and maths were not focuses of my degree, the MSc was excellent grounding for immersing me in these important areas. In addition, the other students had a variety of backgrounds which encouraged us all to engage and learn different skills that were necessary for tackling the course’s content. I quickly felt that coding and statistics were as natural to me as biochemistry was during my BSc, and I was excited to apply these during the three diverse projects offered during the course.

My PhD project is with the Stan group in bioengineering, and it focuses on using whole-cell models to understand the complex interactions between genetic constructs and host organisms. I’m currently developing a tool that allows users to annotate their constructs and model their effects on host cells. This has been very engaging, and alongside the support from Wellcome and Imperial, I look forward to tackling the remaining years!


Jonathan Ish-Horowitz (Joined 2017 programme)

JonathanI completed an undergraduate degree in Physics at Manchester followed by a Masters in Mathematical Modelling at UCL, where I developed an interest in machine learning. I was fascinated by the ability of Deep Learning to extract features from complex data and wanted to apply these methods to interesting problems, of which there are many in biology.

I chose the Wellcome Trust PhD in Theoretical Systems Biology and Bioinformatics because it offered the opportunity to start with high-quality lecture courses in biology, which I needed having come from a physical sciences background. The chance to work on different topics in the first year projects was also very useful and I gained experience of software development, data mining and statistical machine learning in a biological context.

I am continuing my final project for my PhD and knowing that I enjoy the topic and get on well with my supervisor before starting have made the process far easier. I will be working on methods to provide interpretability for machine learning models like kernel methods and neural networks. Currently these models operate as "black-boxes", meaning that how their inputs are used in computing an output is unknown. This limits their usefulness in research, as understanding the internal workings of a model is essential for extracting biological insight. We then plan to use this method to understand how interactions between genes influence the development of asthma and lung cancer.


Heather Jackson (Joined 2017 programme)

Heather

My undergraduate studies were in Biology at the University of Manchester. During my degree I studied a wide range of modules spanning various fields of Biology and I found them all equally interesting. My final year project acted as an introduction to Bioinformatics and it was through this that my interest in the field grew. I was particularly drawn to Bioinformatics as the skill set that it requires can be applied extensively, which is perfect for someone who cannot decide on a particular biological discipline, like myself.

I was attracted to the Wellcome Trust 1+3 programme in Bioinformatics and Theoretical Systems Biology due to the interdisciplinary nature of the course and the taught component at the beginning of the master’s year. Mixing students from different academic backgrounds is a strong advantage of the programme as everybody is always willing to help one another. Furthermore, the three short research projects are great for exposure to different research groups and developing new skills. This is also a really unique opportunity to work with different supervisors with whom you can potentially do your PhD. Although I had limited experience of mathematics and computing prior to the course, after having completed the taught component and the three projects I now feel well prepared to start my Doctoral studies. 

I am looking forward to starting my PhD under the supervision of Dr. Myrsini Kaforou in the Department of Medicine. I will be integrating multiple levels of molecular and clinical data (multi-level ‘omics) from patients with infectious diseases. The aim of this integrated approach is to better understand and diagnose infectious diseases.


Klara Kaleb (Joined 2018 programme)

Klara KalebI studied Biomedical Sciences at the undergraduate level at University College London. Due to the versatile nature of the degree, I got to take modules in various fields of biology, from pharmacology and embryology to mammalian physiology and finally cell and molecular biology, which I decided to specialise in. In addition to this, I also took modules in statistics and computing. Naturally, I wanted to combine the two and that is when I discovered the fields of bioinformatics and systems biology. Eager to learn more, I reached out to one of my lecturers and got to do an internship in a computational biology group after my second year. This further enhanced my interest towards quantitative and interdisciplinary approaches to studying biological systems and so upon my internship completion, I immediately started looking for the PhD opportunities available.

I chose the Wellcome Trust PhD in Theoretical Systems Biology and Bioinformatics due to its flexibility and highly interdisciplinary nature, as well as the opportunity to get more comphrehensive foundation in quantitative skills during the lectures in the first term. I very much look forward to starting in October!


Melpi Kasapi (Joined 2018 programme)

MelpiI studied Biology at Davidson College in the USA and my main research experience did not involve extensive computational efforts because of the strong immunological focus in a wet lab context. However, a final year module in genomics and my professional experience at the National Human Genome Research Institute (NHGRI) inspired my appreciation of bioinformatics. Through my involvement in big-scale sequencing projects like The Cancer Genome Atlas (TCGA) I got to see the diversity of analyses, findings, and studies that are dependent on bioinformatics. I also valued working with scientists from different backgrounds and fields, and experienced team science at its best. 

The Wellcome Trust PhD seemed the perfect choice because of its interdisciplinary nature and the MSc integration which will enable me to develop a strong foundation of computational skills. In addition, the prospect of developing methods that could improve diagnostics and could have a more direct influence to clinical care is very appealing to me. I look forward to working in such an inspiring environment and with my colleagues help move science forward. 


Istvan Kleijn (Joined 2016 programme)

Istvan

How do ants go about their lives? What's inside an atom, or outside the galaxy? What happened on earth before anyone was around to record it? Initially, my interest in science led me to study mathematics and physics, at Utrecht University. For my undergraduate research, I applied spectroscopy methods to bacterial chemotaxis. This experience taught me how approaches from physics can be applied to advance general scientific interest. I went on to pursue a Master's degree in theoretical physics, where I practised my abilities in quantification (but never got the hang of quantisation). An Erasmus semester in Stockholm, studying biophysics and biochemistry, rekindled my interest in biology. I was then given the opportunity to carry out my Master's research project in theoretical biology, working on stochastic models of bacterial gene expression and growth. Looking to develop my modelling skills while studying the complexity of life, I applied to this graduate program, and was very happy when I was offered a place.

Although I had gathered bits and pieces of biological knowledge through project work, the MSc finally gave me a formal background in and understanding of systems biology and bioinformatics. The courses provided a comprehensive foundation and prepared well for the three projects that followed. In these projects, I took the opportunity to work in three very different research groups with both hands. Through this experience, I discovered what I like best about theoretical biology: the search for a global understanding of complex biological systems, where insights from modelling and observations from the laboratory are combined.

At the end of the MSc, I was excited to continue my second project and expand it into a full PhD. Supervised by Vahid Shahrezaei (Dept. of Mathematics) and Sam Marguerat (London Institute of Medical Sciences), I am investigating cell-scale allocation strategies in fission yeast. So far, it has been really rewarding work, gaining skills in both experiments and data analysis, and collaborating with people from many backgrounds. We are currently expanding our data set, and I have been given the opportunity to be involved in the entire scientific process: from planning the experiments, to performing them, to analysing the data and providing an understanding that can guide the next iteration. I cannot wait to find out what my cells can come up with!


Jonas MacKerodt (Joined 2016 programme)

Jonas

As part of my undergraduate and following it, I worked in the field of tumour immunology where I developed a passion for the immune system and its intricate interactions. Coming from an experimental background, I became increasingly interested in the unique insights and more holistic pictures computational and quantitative approaches can provide us.

The MSc course gave me the opportunity to transit from experimental research into the field of quantitative sciences. The course introduced me to a wide-range of techniques of today's Systems Biology and Bioinformatics field and gave me the chance to become familiar with a variety of programming languages. The projects, in particular, gave me the opportunity to apply and further develop my new skills and choose my PhD supervisor and topic.

Combining my interest in the immune system and the Systems Biology, I am conducting my doctoral research in the Mathematical Immunology research group of Dr Becca Asquith. We investigate human T cell lineage dynamics and the dynamics of T cell memory formation applying a variety of theoretical and experimental approaches. By combining mathematical modelling, bioinformatical analysis and wet-lab experiments, this project allows me to build on my experimental experience while at the same time further my knowledge and develop expertise in quantitative biology.


Léonie Strömich (Joined 2017 programme)

Leonie

My background is a rather wet lab oriented one: my bachelor and master studies in Molecular Biotechnology at the University of Heidelberg were split into three different fields of research: Drug Discovery, Biophysical Chemistry and Bioinformatics. I was always in the field of wet lab work, even working on a plant biotech project during my bachelor thesis. But somehow in the course of my master studies I got more and more attracted to Bioinformatics. During my computational projects and my master thesis in Heidelberg I always had the feeling that coming from a biological background benefits me when trying to access a bioinformatical problem. And I found the last year which was following the MSc Bioinformatics and Theoretical Systems Biology course, proved that interdisciplinarity is a major advantage. While learning a lot of new things in fields I was previously unfamiliar with, my biological knowledge always allowed me to see the bigger picture. Additionally, working together with my course mates which have such different backgrounds and research interests further pushed me to explore more theoretical fields.

I am now looking forward to starting my thesis in the lab of Sophia Yaliraki, where I will apply computational models based on graph theory to explore proteins in the cancer setting, Imperial College provides a great working environment for the most interesting interdisciplinary collaboration which can only be of benefit for a computational thesis.


Scott Ward (Joined 2016 programme)

Scott

I completed a four year mathematics undergraduate degree at Imperial College London. During this time I developed an appreciation of different mathematical and statistical methodologies with a particular emphasis on their application to bioinformatics data. During my third year I decided to do a course in mathematical biology which piqued my interest in the bridge between mathematics and biology which was followed by a project in phylogentics in the final year of my undergraduate degree. These two experiences, combined, confirmed my interest in mathematical biology and was my reasoning for applying to Wellcome Trusts 1+3 year PhD course in Theoretical Systems Biology and Bioinformatics.

What was of particular attraction to me was the opportunity to study a number of areas in systems biology and bioinformatics through the MSc year. Although challenging, it was an extremely rewarding experience. I learnt vast amounts of biology in the lectures provided in the first term, whilst also understanding how statistical methodologies are applied to biological data in current literature.

I have since moved to the Statistics department and am conducting research on the type 6 secretion system (T6SS) of Pseudomonas aeruginosa (P. aeruginosa). P. aeruginosa is a gram negative bacterium that is a leading cause of chronic infections in hospitals and our work hopes to gain greater insight and the potential to guide future drug development against this pathogen. Currently, I am analysing multimodal microscopy images to extract shape descriptors of P. aeruginosa. and localise the T6SS. Using this data we are working on approaches to model the spatial distribution of the T6SS on the cell membrane of P. aeruginosa and examine whether there exist preferential regions where this mechanism assembles.


Ming-Hei Wong (Joined 2018 programme)

Thomas WongI am Thomas Wong, an Imperial undergraduate mathematics student returning for four more years for the Wellcome Trust programme.

In my undergraduate studies, I have done various projects in statistics, studying network traffic data with exploratory data analysis. With programming skills in Python, R and Matlab, I have done two software engineering internships, working on database and web applications.

I am interested in different aspects of data science, from developing machine learning models to implementing database infrastructures. Biology is a recent area that is applying more quantitative methods in research and there are lots of interesting problems for data scientists. The Welcome Trust programme has a wide range of projects that allow students to choose from. Leveraging my industrial experiences in data science, I would like to research in the more computational aspects of bioinformatics, such as proposing and verifying statistical and stochastic models with experimental data, building software packages in R and Python. I hope to have the chance to collaborate with the industry which allows my work to make an impact in medical research and biotechnology. 

The Wellcome Trust programme is a Well-structured program which allows students from different backgrounds to develop skills to succeed in modern biological research. With three projects offered at the second-half of the first year, including computational and numerical elements, they provide a solid training for students to be Well-rounded researchers. It is one of the few programmes that have an intensive and structured framework in the UK to develop tomorrow's researchers. I am looking forward to joining other students from different backgrounds in October. 


Tony Yang (Joined 2018 programme)

Tony YangI graduated from Imperial College London with a MSci in Chemistry. I chose chemistry due to my interest in experimental work, especially organic synthesis. Having been introduced to Python in my first and second year of study, I began to develop an interest in programming and data science because of its problem solving nature. After my penultimate year, I had the opportunity to conduct a summer research project in UCLA (IROP), and worked on computational organic chemistry in Prof. Kendall Houk's group. This project gave me a whole new perspective on organic chemistry and I started to appreciate how modern computational methods can provide another level of fidelity to science.

Wanting to combine computational techniques with a natural science subject, the Wellcome Trust programme in Bioinformatics immediately attracted my interest. Having not coming from a biological science or computer science background, I liked the idea of starting with a taught master year, which will give me a more systematic introduction to both biology and computer science. This summer I participated in Google Summer of Code 2018, during which I worked with the Ensembl team from European Bioinformatics Institute. My project aimed to develop an automated workflow for analysing newly reported genomic sequences. This real world exposure to bioinformatics further deepened my understanding of this subject, and now I am looking forward even more to learning different aspects of bioinformatics and meeting all my peers from different academic backgrounds.