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Accelerating molecular phylogenetic inference using high performance computing.


   School of Biological Sciences

   Applications accepted all year round  Self-Funded PhD Students Only

Reading United Kingdom Bioinformatics Evolution Molecular Biology Computer Science Statistics

About the Project

 

Molecular phylogenetic inference, constructing evolutionary histories from molecular data, is an activity universal to all biological disciplines. Phylogenetic inference is an essential analytical technique used in almost all areas of biology from virology and immunology, to protein evolution, from protein networks to evaluating extinction risks and from organismal studies to the analysis of gene evolution. The use of molecular phylogenies in the literature has grown rapidly over the past 10 years. The volume of molecular data has grown nearly exponentially, due to a roughly 50,000 fold reduction in sequencing costs. During the same time period the accuracy and complexity of analytical models has increased. The volume of data and increase in model complexity far exceed advances in computing power. This has created a widening gap between data sets and methods researchers would like to use and available computing power and scalable software. While there are currently a number of methods to scale phylogenetic inference tools, they tend to only be effective up to hundreds of cores.  

This project will develop highly scalable algorithms for molecular phylogenetic inference, using a range of techniques, including parallelisation of existing methods, development of highly scalable algorithms and GPU acceleration.  

 School of Biological Sciences, University of Reading:  

The University of Reading, located west of London, England, provides world-class research education programs. The University’s main Whiteknights Campus is set in 130 hectares of beautiful parkland, a 30-minute train ride to central London and 40 minutes from London Heathrow airport.   

Our School of Biological Sciences conducts high-impact research, tackling current global challenges faced by society and the planet. Our research ranges from understanding and improving human health and combating disease, through to understanding evolutionary processes and uncovering new ways to protect the natural world. In 2020, we moved into a stunning new ~£60 million Health & Life Sciences building. This state-of-the-art facility is purpose-built for science research and teaching. It houses the Cole Museum of Zoology, a café and social spaces. 

In the School of Biological Sciences, you will be joining a vibrant community of ~180 PhD students representing ~40 nationalities. Our students publish in high-impact journals, present at international conferences, and organise a range of exciting outreach and public engagement activities. 

During your PhD at the University of Reading, you will expand your research knowledge and skills, receiving supervision in one-to-one and small group sessions. You will have access to cutting-edge technology and learn the latest research techniques. We also provide dedicated training in important transferable skills that will support your career aspirations. If English is not your first language, the University's excellent International Study and Language Institute will help you develop your academic English skills. 

The University of Reading is a welcoming community for people of all faiths and cultures. We are committed to a healthy work-life balance and will work to ensure that you are supported personally and academically. 

 

 


Funding Notes

Eligibility:
Applicants should have a good degree (minimum of a UK Upper Second (2:1) undergraduate degree or equivalent) in Biological Sciences or a strongly-related discipline. Applicants will also need to meet the University’s English Language requirements. We offer pre-sessional courses that can help with meeting these requirements.

How to apply:
Submit an application for a PhD in Biological Sciences at View Website.


References

Please view the academic profile of Dr Andrew Meade:
http://www.reading.ac.uk/biologicalsciences/SchoolofBiologicalSciences/Meetourteam/staff/a-meade.aspx

Further information:
http://www.reading.ac.uk/biologicalsciences/SchoolofBiologicalSciences/PhD/sbs-phd.aspx

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