2020 applicants
Postgraduate Research Opportunities

Design of advanced coding and random access techniques for DNA storage

Details

Title: SCH34: Design of advanced coding and random access techniques for DNA storage

Funding: A full Home/EU fee waiver or equivalent fee discount for overseas students  (£5,103 in 2020-21) (further fee details - international students will need to pay the balance of their fees) plus a doctoral stipend equivalent to the RCUK Minimum Doctoral Stipend (£15,285 in 2020-21).

Application deadline: Tuesday 31 March 2020

Start date: October 2020

Duration: 3 years (full time)

Location: Colchester Campus

Based in: School of Computer Science and Electronic Engineering (in collaboration with School of Life Sciences and Department of Mathematical Sciences)

This opportunity is now closed. View our open opportunities.

Overview

The unprecedented growth of digital information creates an increasingly growing demand for new ways of data storage.

DNA molecules can be an excellent medium for data storage, due to its potentially high information density (over 1000 millions gigabyte of data per mm3) and extreme durability (half-life of over 500 years).

The project

This project aims to develop efficient error-correcting codes (ECCs) and random access techniques for DNA storage.

By viewing DNA storage as a communication channel, we will design robust ECCs and their associated decoding schemes to combat the errors (e.g., insertion, deletion, and substitution) that arise in DNA synthesis and sequencing processes.

A key research problem we will address is how to carefully tailor ECCs to match to the specific characteristics of modern bio-chemical machines and processes.

Proposed ECCs will be optimised by DNA data analysis using modern machine learning algorithms (such as convolutional neural network and deep learning).

We will design uncorrelated DNA addresses (primers) to enable accurate random access of a desired data file in large sized DNA storage. Orthogonal sequence design approaches for wireless communications may be modified to design such uncorrelated primers.

We will also carry out hands-on experiments for channel measurement and validation of the proposed schemes.

Additional information

This PhD program will be in collaboration with Coding Theorist Prof Wai Ho Mow in Hong Kong University of Science and Technology (HKUST). The candidate will be encouraged to apply for an International Visiting Internship to HKUST for up to 6 months, during which an additional allowance of about USD 1,500 per month may be provided by HKUST as the internship organiser.

Funding

The award consists of a full Home/EU fee waiver or equivalent fee discount for overseas students (further fee details), a doctoral stipend equivalent to the Research Councils UK National Minimum Doctoral Stipend (£15,285 in 2020-21), plus £2,500 training bursary via Proficio funding, which may be used to cover the cost of advanced skills training including conference attendance and travel.

Supervisor

Dr Nikolaos Thomos

Co-supervisor

School of Computer Science and Electronic Engineering, University of Essex

Nikolaos Thomos is a Reader in CSEE and the CSEE deputy director of research. Before that, he was senior researcher at EPFL, Switzerland. He was awarded the highly esteemed Ambizione career award from Swiss National Science Foundation (SNSF) in 2008 and 2011 for carrying out research on low computational complexity network coding for collaborative video streaming. His research interests include machine learning for communications, multimedia communications, network coding, and joint source and channel coding.

Professor Alex Dumbrell

Co-supervisor

School of Life Sciences, University of Essex

Alex Dumbrell is a Professor in School of Life Sciences since 2019. He received his PhD from University of York in 2006. His research interests include spatial and temporal patterns of biodiversity, next generation sequencing technology and bioinformatics in ecological research, and theoretical ecology (focus on models of biodiversity). He has co-authored over 50 journal papers, 7 books and 10 book chapters.

Dr Jessica Claridge

Co-supervisor

Department of Mathematical Sciences, University of Essex

Jessica Claridge has been a Lecturer in the Mathematics Department and Essex Parthways Department at the University of Essex since 2016. She received a PhD in the Mathematics from Royal Holloway, University of London in 2017. Her research interests include combinatorics and applications in coding theory and information theory.

Criteria

The candidate is required to have a degree in electrical engineering with solid background in mathematics.

The candidate is also expected to have basic knowledge from biochemistry and have experience in hands-on lab experiments.

How to apply

You can apply for this postgraduate research opportunity online.

Please include your CV, covering letter, personal statement, and transcripts of UG and Masters degrees in your application.

The University has moved to requiring only one reference for PhD applications and these can be received after a conditional offer has been made so the absence of these will not hold up the recruitment process.

Instruction to applicants

When you apply online you will be prompted to fill out several boxes in the form:

  • For "Course title" please put "Electronic Systems Engineering", tick "postgraduate research" and hit "search". This will bring up a list of matching courses, select the one marked "full time" and "PhD".
  • For "Proposed research topic or area of research" please put the title of this studentship (SCH34: Design of advanced coding and random access techniques for DNA storage)
  • For "If you have contacted a potential supervisor..." please put the name of the lead supervisor (Dr Zilong Liu).

If you have any informal queries about this opportunity please email the lead supervisor, Dr Zilong Liu (zilong.liu@essex.ac.uk).

You can find the terms and conditions of this studentship here (PDF).

Student and academic working at a board together
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