Alumni case study: Matthew Gibb
Cohort
Systems Biology
Job title
CEO/Founder
Company
LendLayer Inc.

In what way was your DPhil important to your employer?

Technical skills, mathematics of finance, software engineering of building our internal and customer-facing products, data science/machine learning of credit prediction, credibility when raising debt and equity financing.

In what ways have the skills and knowledge from your DPhil been useful in your current role?

Technical skills, mathematics of finance, software engineering of building our internal and customer-facing products, data science/machine learning of credit prediction, credibility when raising debt and equity financing.

What do you think has been of most value to you in undertaking a DPhil at Oxford?

Deep technical skills in mathematics, data science, computer science/software engineering

How do you think you benefited from being part of a cohort?

It was absolutely awesome. I and many others would have sunk without it. We all inherited such a wide and deep pool of expertise, creativity and support from each other, the academic team and from other cohorts, which widened everybody's options and made our path to success more robust to difficulties. Huge win, grateful to be part of it and I would recommend it to anybody!

What would you say to someone who was considering doing a DPhil at the DTC?

Do it now! Don’t wait!

Do you have any fond memories about the DTC to share?

My fondest are of the friends I made in the cohort:

  • Having them lend a hand when I didn’t know what an SSH key was or why Matlab would explode with red Java memory exceptions for some reason, and being able to lend a hand with a bit of maths they were stumped on.

  • Going to the Royal Oak and lamenting that our simulations were wrong or would crash.

  • Establishing scientifically after 2 days of wetlab work that Jem Pearson and I were the only pair in the cohort not to have any DNA at all.

Oxford Interdisciplinary Bioscience Networking Event 2017

The Oxford Interdisciplinary Bioscience Networking Event brings together researchers from the seven research organisations involved in the DTP, including the University of Oxford, Oxford Brookes University, The Pirbright Institute, Diamond Light Source, ISIS Neutron and Muon Source, STFC Central Laser Facility and the Research Complex at Harwell, together with researchers from industry and non-academic organisations.

Case study: Vaanathi Sundaresan

Vaanathi’s interest in biomedical imaging arose from the knowledge that few people in rural parts of India have access to medical check-ups or screening procedures that would be considered routine in the developed world. People are unlikely even to recognise the importance of screening which can assist in earlier diagnosis and treatment. Vaanathi realised that biomedical imaging might be able to provide an affordable and non-invasive screening solution, which would promote sustainable healthcare delivery.

This insight led Vaanathi to undertake a Master of Science by research in Electrical Engineering in Madras, focussing on retinal image analysis. Her research involved detecting and characterizing the disease signs that occur in retinal fundus images due to various stages of diabetic retinopathy and age-related macular degeneration. This in turn motivated her to apply for the course at the CDT in Biomedical Imaging.

Vaanathi valued the opportunity to gain knowledge about various imaging modalities and training in many different skillsets during the first year, from programming languages to good clinical practice. Another great advantage, she feels, is that the CDT allows students to undertake two very different projects in the first year. This gave her the chance to work on MRI as one of her options, a field she knew little about before starting her DPhil.

In the first project with Professor Mark Jenkinson (Nuffield Department of Clinical Neurosciences), Vaanathi used MRI images from brain scans to model the distribution of white matter lesions related to dementia. Her second project was on foetal cardiac analysis in ultrasound images – a challenging area, as the foetal heart at 20 weeks (the time of the routine antenatal scan) is small, and the foetus’s orientation varies. The ultimate aim of this research in the group of Professor Alison Noble (Institute of Biomedical Engineering) is antenatal detection of foetal cardiac anomalies and congenital heart diseases. During her rotation projects, Vaanathi had to use the various skills which formed part of the training she received during the first part of the course, especially high-performance computing. Both projects required the processing and analysis of very large amounts of data by accessing high performance clusters.

Vaanathi found both projects extremely interesting and had difficulty choosing between them. In the end, however, she chose to focus on MRI analysis, as she was keen to learn more about MR physics, MR scanning procedure, different types of MR images and their analysis. The long-term aim of her DPhil research in the group of Professor Mark Jenkinson at the FMRIB Centre is to improve white matter lesion detection and to analyse signs including microbleeds and perivascular spaces related to different brain diseases. These signs, if identified in the early stage, could lead to timely treatment and even prevention of progression of various neurodegenerative diseases. From an imaging point of view, detection and characterization of these signs is highly challenging due to their subtle appearance, low contrast and variation in their sizes.

In future Vaanathi would like to gain exposure to industrial research so that she can learn more about the development of affordable imaging equipment, image analysis software and tools and the feasibility of their implementation in a developing research environment. She has been inspired by the collaborations taking place at Oxford between academics, clinicians and industry, and hopes to be able to take this model of working back to India when she completes her DPhil.

Chemical synthesis and molecular biology related to the thymus, a key component of the immune system.

During his MChem degree at Warwick, Oliver spent a year on an industrial placement at Pfizer working on synthetic methodology research. The experience was challenging, unlike anything he had ever done before, but also very rewarding, and kindled his interest in synthesis for biology and medicine.

Beyond this general interest and a desire to work at the interface of chemistry and biology, Oliver was not sure exactly what he wanted to study at DPhil level. A major attraction of the SBM CDT course was that he could apply without having to specify a particular research topic. In his view the first four months at the SBM CDT represented the best taught course he has ever taken. He had not studied any biology since GCSE level and the modules gave him the biology grounding he needed in addition to a superb coverage of all aspects of synthesis. One of his first year rotations was in Professor Ben Davis’s group and led to Oliver appearing as an author on a paper published in Science – a significant achievement.

It was his other rotation with Professor Chris Schofield and Dr Akane Kawamura, however, which enabled Oliver to find a research area to pursue for 3 years. During this project he worked on a new technique for the design of cyclic peptides as chemical probes for different protein targets. Chemical probes can bind to domains in the target protein and affect its function, allowing the researcher to learn more about how the protein works and its associated biology. Previously Oliver had no idea that this area of work with cyclic peptides existed – but it ended up becoming the focus of his DPhil.

Oliver counts himself very lucky to have had excellent supervisors who took the time to help him find the right research topic, and also values the fact that students can try projects without commitment in their first year. His DPhil subject is strongly influenced by personal experience: Oliver has ulcerative colitis, an autoimmune disease which has resulted in serious illness. As a result, he is applying his interest in chemical synthesis and molecular biology to an immunological problem, as well as other targets in epigenetics.

Oliver is the only SBM CDT student working in this area, and he stresses that his research is not typical; one of the CDT’s great benefits is that it enables a wide range of choices, and it is quite possible to do a DPhil in pure synthetic chemistry. He regards having access to experts as another enormous benefit; Oliver collaborates with Professor Georg Hollander, an immunologist at the Weatherall Institute of Molecular Medicine, and is also mentored by Dr Hitesh Sanganee, the Director of Emerging Innovations at AstraZeneca.

Finally, it is the relationship with other students at the SBM CDT that Oliver really appreciates. Because everyone studies together during the first few months, it builds up an excellent support network of colleagues who are equally enthusiastic about the subject area, and who can give each other help and advice throughout the DPhil. It is also, as Oliver points out, a lot of fun – and despite the long hours there is nothing he would rather be doing.

‘Real world application’ of synthetic biology

It was the ‘real world application’ of synthetic biology that attracted Kyle to the programme at the Synthetic Biology CDT. He studied microbiology at undergraduate level and completed an MRes in Biophysics, during which time he developed a keen interest in astrobiology and secured a placement at the NASA Space Life Sciences Laboratory. Kyle’s colleagues at NASA had an emergent interest in synthetic biology, especially in applications that could be used to support longer space missions, and it was this that persuaded Kyle to apply for the Synthetic Biology DPhil programme.

Kyle defines synthetic biology as ‘the design and redesign of biological parts and systems’ – similar to engineering design, but using DNA and transcriptional regulators instead of circuit boards. In his view the major strength of the CDT programme is the training year, because it gives students the opportunity to try out different projects and potentially change their minds about the focus of their DPhil. Kyle chose to do his DPhil in an area that started out as his second choice project – the group of Professor Phil Poole in the Department of Plant Sciences.

Phil Poole’s group is working on a large and ambitious project to enable cereal crops to fix nitrogen in the same way that plants such as beans and peas do. This involves the design and development of synthetic symbioses between nitrogen-fixing bacteria and plants such as wheat or rice. Achieving this would free the world’s farmers from their dependence on nitrogen-based fertilisers, which are both expensive and extremely destructive to the environment.

As part of this project, Kyle is working with the bacteria that live naturally amongst the roots of cereal crops. By harnessing the natural process of enzyme-catalysed nitrogen-fixation, he is aiming to create genetic circuitry within the bacteria that will provide fertiliser to the target crop. He likens this process to wiring up a lightbulb: the lightbulb will only work with the correct circuitry; and will only turn on when you want it to.

The Synthetic Biology CDT is tripartite, which Kyle feels is extremely beneficial; it gives students exposure to ideas at other universities (in this case Warwick and Bristol) and enables them to exchange strategies. For example, Kyle is using similar gene-editing techniques to a student at Bristol who is working on red blood cells rather than bacteria, so they have been able to problem-solve together – something that Kyle regards as a very valuable aspect of the programme.

The techniques involved in Kyle’s research are cutting-edge and NASA is extremely interested in their potential. In the coming decades NASA seriously envisages the possibility of developing colonies on the Moon and on Mars. By using the kind of engineering that Kyle is engaged in, it should be possible to create bacteria that can optimise plant growth in lunar or Martian soils, or bacteria that can regenerate significant amounts of oxygen. Advances like these would represent a huge improvement in both efficiency and sustainability over processes which at the moment are largely chemically-based, and might well have knock-on benefits for life on earth as well.

Kyle feels that the CDT’s scientific support team really allows students to focus on their key mission. During his DPhil course he has spent more time at NASA, looking at their life support capsules and how synthetic biology might be used to make them more self-sustaining.

Scientific Director, Elucidata Corporation
Cohort
Systems Approaches to Biomedical Science
Job title
Scientific Director
Company
Elucidata Corporation

In what way was your DPhil important to your employer?

Not specific wet/dry lab techniques but transferrable skills.

In what ways have the skills and knowledge from your DPhil been useful in your current role?

Knowledge of adjacent disciplines, inter-personal skills, problem solving, collaboration with industry.

What do you think has been of most value to you in undertaking a DPhil at Oxford?

Quality of training and network created.

How do you think you benefited from being part of a cohort?

Those who undertook different career directions can be easily asked about their experiences.

What would you say to someone who was considering doing a DPhil at the DTC?

If your thinking is flexible and you grasp new concepts easily, you will love it. There is a lot to learn: not only different interdisciplinary techniques, but importantly the ability to formulate and address biological questions from different perspectives. Keep your mind open. If instead you prefer to focus more exclusively on a narrow subject then perhaps consider a traditional DPhil or PhD.

Do you have any fond memories about the DTC to share?

It has been a great to share the experience with the DTC-fellows, especially from the same cohort but also across the years. No matter how simple or hard the assignment was, there was a lot of mutual support. It's really the intellectual development and social bonding that made the DTC so special for me.

Alumni case study: Lydia Harriss
Science adviser, UK Parliament
Alumni case study: Robin Ryder
Associate professor in Applied Mathematics, Universite Paris-Dauphine
Alumni case study: Xavier Didelot
Senior Lecturer, Imperial College London