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Mathematical modelling of epistasis in proteins using network analysis and statistical learning


   Computer Science

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  Dr A Pandini, Dr Sarath Dantu  Applications accepted all year round  Self-Funded PhD Students Only

About the Project

Proteins are biopolymers composed of repetitive units (residues) from a set of 20 amino acids that form complex three-dimensional topologies. Protein topologies/structures undergo conformational changes over picosecond to millisecond timescales.

These changes are important for biological function and arise from inter and intra residue interactions and interactions with the solvent. These conformational changes can be modelled, using computer simulations and well-established software, generating millions of 3D structures that are saved as time-dependent trajectories.

To design proteins for novel functions or enhance their existing biological activity, advances in computational protocols for protein design are desired. Towards this goal, understanding the epistasis at the protein level, i.e. networks of synergistic interactions between residues that contribute to the function is the first step.

In this project, using the molecular dynamics simulations and sequence analysis data of a test protein system, the doctoral researcher will develop a mathematical formalism to analyse the complex network of interactions between the protein residues using time series network analysis, which can handle multiple densities of states;

  • use graph convolutional networks to learn and predict effects of mutations on structural dynamics
  • contributing to biological function 
  • integrate this method to select design sites into our computational protocol for the selection of design sites.

The ideal candidate will have BSc and/or MSc degree in mathematics and/or computer science. Knowledge of C/Python and R will be highly desirable.

Research in Computer Science at Brunel is internationally recognised, ranked 5th in the UK in the Performance Ranking of Scientific Papers for World Universities and 1st in the UK for H-index (source NTU 2018). We have particular strengths in research into computing methodologies (Intelligent data analysis, artificial intelligence, simulation and modelling), software engineering, human centred computing (HCI and interactive multimedia systems) and digital economy (including IOT, trust, privacy and cybersecurity). Our research delivers creative computing solutions to industrial and societal challenges, with applications including healthcare, overseas development, education, ecology, finance and manufacturing.

Research journey

Doctoral research programmes (PhDs) take a proud place in the world-class research environment and community at Brunel. PhD students are recognised and valued by their supervisors as an essential part of their departments and a key component of the university's overall strategy to develop and deliver world-class research.

A PhD programme is expected to take 3 years full-time or 6 years part-time, with intakes starting in January, April or October.

The general University entrance requirement for registration for a research degree is normally a First or Upper Second Class Honours degree (1st or 2:1) or an international equivalent. A Masters degree is a welcome, but not required, qualification for entry.

Find out how to apply for a PhD at Brunel

Research support

Excellent research support and training

The Graduate School provides a range of personal, professional and career development opportunities. This includes workshops, online training, coaching and events, to enable you to enhance your professional profile, refine your skills, and plan your next career steps as part of the Researcher Development Programme. The researcher development programme (RDP) offers workshops and seminars in a range of areas including progression, research management, research dissemination, and careers and personal development. You will also be offered a number of online, self-study courses on BBL, including Research Integrity, Research Skills Toolkit, Research Methods in Literature Review and Principles of Research Methods.

Library services

Brunel's Library is open 24 hours a day, has 400,000 books and 250,000 ebooks, and an annual budget of almost £2m. Subject information Specialists train students in the latest technology, digital literacy, and digital dissemination of scholarly outputs. As well as the physical resources available in the Library, we also provide access to a wealth of electronic resources. These include databases, journals and e-books. Access to these resources has been bought by the Library through subscription and is limited to current staff and students. 

Dedicated research support staff provide guidance and training on open access, research data management, copyright and other research integrity issues.

Find out more: Brunel Library

Careers support

You will receive tailored careers support during your PhD and for up to three years after you complete your research at Brunel. We encourage you to actively engage in career planning and managing your personal development right from the start of your research, even (or perhaps especially) if you don't yet have a career path in mind. Our careers provision includes online information and advice, one-to-one consultations and a range of events and workshops. The Professional Development Centre runs a varied programme of careers events throughout the academic year. These include industry insight sessions, recruitment fairs, employer pop-ups and skills workshops.


Funding Notes

Brunel offers a number of funding options to research students that help cover the cost of their tuition fees, contribute to living expenses or both. See more information here: https://www.brunel.ac.uk/research/Research-degrees/Research-degree-funding. The UK Government is also offering Doctoral Student Loans for eligible students, and there is some funding available through the Research Councils. Many of our international students benefit from funding provided by their governments or employers. Brunel alumni enjoy tuition fee discounts of 15%.

How good is research at Brunel University London in Computer Science and Informatics?


Research output data provided by the Research Excellence Framework (REF)

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