Department of Biology

Overview

The 2011 cohort welcomes you! 

Introduction

The burden of infectious disease to human health is significant, with parasitic, bacterial and viral diseases representing six of the ten leading causes of mortality world-wide. A major obstacle to the development of new diagnostic, therapeutic and preventative tools to combat these infections is understanding the complexity of the disease processes at the molecular, cellular and organismal level. The CIDCATS programme addresses this challenge by providing graduate training in the quantitative skills required to develop iterative programmes of research that cross discipline boundaries. The last decade has been noted for the development of increasingly powerful experimental technologies (e.g. 2-photon imaging, gene expression analysis, proteomics) that are now providing extensive and detailed data characterizing the structure, dynamics and properties of biological systems. This opens up exciting opportunities for the development of novel data analysis and visualization methods and further, the modelling and simulation of the complex biomolecular and cellular processes that underlie infectious disease.

The CIDCATS programme

The CIDCATS (Combating Infectious Disease: Computational Approaches in Translational Science) interdisciplinary PhD Programme in Infectious Disease is funded by the Wellcome Trust. This four-year PhD training programme will provide students (including those with a strong background in a non-biological science,  engineering or mathematics) with in-depth knowledge of infectious diseases and the interdisciplinary skills necessary to conduct research in one of the following three inter-related research themes, that are central to our ability to combat these infections:

1. Drug Target Development

2. Predictive Modelling of Pathogenesis and Treatment Response

3. Development of Novel Tools for Complex Data Analysis.

The aim is to deliver the next generation of scientists who will drive quantitative biology to support interdisciplinary research in the biomedical sciences. To this end we will train five students per year for the next five years. (2011-2016)

Is this the programme for you?

Do you have a keen interest in biological problems?  

Are you excited at the prospect of impacting on our knowledge and treatment of infectious diseases?

Have you excelled in your undergraduate degree in any of these or closely related disciplines: Computer Science, Mathematics, Physics, Chemistry, Electronics, Engineering, Biology? 

We especially encourage applications from excellent non-biological scientists and mathematicians who seek to impact on  biomedical research.

Research environment

The programme is led and administered by the Department of Biology.  Training and research supervision will be undertaken by staff from Biology, Mathematics, Physics, Chemistry, Computer Science, Electronics, and the Hull York Medical School. 

A number of research centres at the University provide an environment that encourages and fosters interdisciplinary research.   Three of these underpin the interdisciplinary research themes of this programme:

• Centre for Immunology and Infection (CII), a joint centre with the Hull York Medical School, provides the hub for this training programme. The aims of the CII are to integrate the study of basic and clinical immunology, microbiology and parasitology to develop a greater understanding of the processes underlying infection and disease, and thus to develop new approaches to prevention and treatment. 
• York Plasma Institute (YPI) in the Physics Department is a collaboration between the University of York and EPSRC. Its vision is to establish a world-leading interdisciplinary plasma institute for the UK, with an international reputation for fundamental plasma science and related technology, collaborating with industries and universities, and fostering new start-up companies. Our facilities include the main YPI research building, which provides postgraduate teaching facilities, videoconferencing rooms and the Remote Tokamak Control Room. The YPI Laboratories are presently nearing completion.

• York Structural Biology Lab (YSBL) uses and develops methods to determine, analyse and exploit the structure of proteins and their complexes with other molecules. The research contributes powerful insights into biological function and finds application in drug discovery. 

• York Centre for Complex System Analysis harnesses York's extensive theoretical, mathematical and computational expertise in the key areas of data analysis, modeling and simulation of biological, material and engineered systems. 

Additionally, York has key technical facilities that support modern biological research:

• The Technology Facility (TF) provides researchers with supported access to a range of specialised bioscience technology platforms covering: genomics, proteomics, microscopy, flow cytometry, protein expression and purification, molecular interactions, and bioinformatics.  The TF supports staff and students in applying the latest technologies and multi-disciplinary approaches to their work.

•  York Centre of Excellence in Mass Spectrometry and the York Centre for Hyperpolarisation in MRI will support the development and application of analytical methods and protocols. These facilities will support the experimental training component of our interdisciplinary PhD programme in state-of-the-art experimental techniques.

Research Areas

Research areas

PhD thesis research topics within the scope of the programme will be identified and developed by the student at the end of the Foundation year in collaboration with academics drawn from the programme supervisory pool (please see training tab).

An indicative list of interdisciplinary researchers associated with the programme and available as prospective members of the PhD supervisory team are provided below.

Potential Supervisors

Training

Training

CIDCATS is a cross-disciplinary PhD programme that will provide you with the skill set necessary to work across traditional disciplinary boundaries.  The focus is on developing the mathematical, statistical and computational skills to support quantitative biological research in the area of infectious disease.

Programme Structure and Timeline

The programme provides flexible training that is adaptable to your skills and background and to those of other students in your cohort.

It is a 4 year programme consisting of two phases.  The Foundation Phase (Year 1) develops your basic science, research skills and experience in interdisciplinary research as a preparation for your individual research project in the Research Phase (Years 2-4).

Foundation Phase (Year 1)

Core Training. You will receive training in basic science, research skills and thematic topics to enable you to become an effective researcher in the area of Infectious Disease.  The training is provided flexibly through a range of workshops, seminars and practical sessions.  Topics include a practical course in basic laboratory skills in Biomedical research; Immunology and Infection; Modelling and Simulation techniques targeted to bacteriology, parasitology, immunology and virology; Networks and Complex Systems; Bioinformatics; Data analysis and Computer programming; Drug target development and predictive modeling of pathogenesis. Additionally, you will enhance your transferable skills in areas such as Ethics, History of Biomedicine, and Science Communication.

Elective Training. You can supplement and tailor your own training through elective modules from a range of Masters programmes. 

Research Projects. You will undertake 3 research projects (1 group-based, 2 individual) in order to develop your scientific, technical and problem-solving skills in a range of research environments.  The individual projects are “rotations”, allowing you to work within different research groups.  The group project develops the team-working skills essential for effective interdisciplinary biomedical research.

At the end of the Foundation Phase, you will develop (and submit for approval to the programme committee, and the Wellcome Trust) a project proposal for your PhD thesis.  You will have the chance to work with interdisciplinary supervisors drawn from across the University’s departments and research centres.

Research Phase (Years 2-4)

During this phase, you will focus on your PhD research project, submitting your thesis by the end of Year 4.  Your cohort will engage in group activities, (e.g. workshops, journal clubs, research symposia) and you will continue to receive training in scientific skills (technical skills, experimental design, data analysis), as well as oral and written communication skills.  There will also be the opportunity to attend conferences and engage in outreach activities.

Management

Management

Programme Director: Prof Deborah Smith. (Biology/CII)

Associate Director: Prof Reidun Twarock. (Maths/Biology/YCCSA)

Dr Fred Antson (Chemistry/YSBL)

Dr Leo Caves (Biology/YCCSA)

Professor Paul Kaye (HYMS/Biology/CII)

Professor Jon Timmis (Computer Science/Electronics)

Dr Marjan van der Woude (HYMS/Biology/CII)

Dr Roddy Vann (Physics)

Mrs Julie Knox (Biology Graduate School)

How to apply

How to apply 

• Application: Five studentships are available on this prestigious programme for entry in October 2014.  Previous applicants should not reapply.  To be considered you need to provide information on your qualifications, a letter of application explaining your suitability for this programme, and your CV. Applications for entry in October 2014 will open from October 2013 onwards.

• Eligibility:  We welcome applications from all suitably-qualified students (with, or expecting to gain, at least an Upper Second Class Honours degree or equivalent in a relevant discipline), irrespective of their nationality. 

• Short-listing: Shortlisting will take place as soon as possible after the closing date and successful applicants will be notified promptly.  Shortlisted applicants will be required to complete a formal application for entry to postgraduate study at the University of York, details of which will be sent by email.

• Interviews: Shortlisted applicants will be invited for an interview to take place at the University of York in the week commencing on Monday 11 February 2013. Video interviews can be arranged for international applicants. Candidates will be asked to give a short presentation before interview by an academic panel. 

• Value: Wellcome Trust 4-year PhD studentships cover tuition fees and include a generous tax-free living allowance.

• Language: There are language requirements for international students wishing to apply to the PhD programme.

• Queries: If you have any queries about the application procedure, please contact biol-cidcats@york.ac.uk

A PhD in York

A PhD in York

• Information on the Research Environment can be found under the tab "Overview" and on Training for Research students for this specific Programme under the tab “Training”.

As a Research student at the University of York, in addition to your Supervisors, you can also expect:

• a Training Advisory Panel of 2 other academic staff to monitor progress and offer advice.
• a programme of training in research and transferable skills tailored to your needs.
• opportunities to attend seminars by leading scientists from around the world, and to present your own work through posters and talks. 

In addition to the excellent research environment specific to this Programme, the University, the city and the environment has much to offer students.

The University of York

The University of York is in the World Top 100 and recently won UK University of the Year 2010/11 at the Times Higher Education awards.  On both the national and international stage, it ranks near the top of nearly every measure of quality – whether this is excellence in teaching, research achievements or the satisfaction of students.  The collegiate system and campus help to form a strong, close-knit community of students and staff.

The University is undergoing an exciting expansion plan, with the £200 million first phase of the new Heslington East development opened in October 2010.  This includes new accommodation for the Departments of Computer Science and Theatre, Film and Television and the York Law and Management Schools, as well as Goodricke College and the Ron Cooke Hub, which houses the York Centre for Complex Systems Analysis. The second phase of this expansion will include the relocation of Langwith College, a new social and catering building, a biomass gasification heat and power energy centre, and new sporting facilities.  The first phase of the new York Sports Village will feature a competition-standard eight lane 25 metre pool, learner pool, 100 station gym, full size 3G astroturf pitch and three further five-a-side pitches.

University links of interest:

General information about the University http://www.york.ac.uk/about/

Research at York http://www.york.ac.uk/research/

Information for visitors http://www.york.ac.uk/about/visitors/

York - the city

York is in the North East of England, ~2 hours north of London by rail.  York is an attractive location; the city is essentially medieval laid out on the original Roman pattern with 80% of the city walls intact and the 12th Century Minster (cathedral) dominating the town. The Roman Emperor Constantine was crowned/ anointed here. This rich history, together with good restaurants, pubs and shops, makes York a very popular tourist destination.  The city has a vibrant music scene, ranging from classical music, to pubs with live jazz and folk music.  There are multiple theatres and cinemas.  Living in York is easy: a good public transportation system, sidewalks and bicycle paths make travelling straightforward, while the surrounding countryside and proximity to the coast provide plenty of opportunities for local travel.  

York can easily be reached by car, train or plane from other parts of the UK.  The city lies on a main train intersection, making Scotland and other parts of Britain very accessible: it is just a 2 hour train trip to London,  Edinburgh or Manchester.  For international travel, there is a direct rail link to Manchester airport (http://www.manchesterairport.co.uk/manweb.nsf#252) and excellent rail links to the London airports and train terminals, for travel to mainland Europe.  Ferries to mainland Europe also depart from Hull, which lies 35 miles from York.

Some websites of interest include:

York tourism: http://www.visityork.org/

National Centre for Early Music: http://www.ncem.co.uk/

The British Music Society of York: http://www.bms-york.org.uk/about.htm

Black Swan Pub: www.blackswanyork.com/

Train schedules: http://www.eastcoast.co.uk/,  and: http://www.thetrainline.com

York- the environment

York is close to the North Yorkshire Moors and not far away from the Yorkshire Dales and the coast. York’s environment therefore offers a wide range of opportunities for pursuing outdoor and cultural activities, including excellent hiking opportunities.  Other activities pursued in the area include road and mountain biking, sailing, climbing and caving. 

Contact

Contact

For enquiries, please contact the Biology Graduate School Office: