New graph algorithms for analysis of the genomes and pangenomes of bacteria and their mobile elements.

This project is one of a number that are in competition for funding from the University of Bath URSA competition, for entry in September 2025.

PLEASE BE AWARE: Applications for this project may close earlier than the advertised deadline if a suitable candidate is found. We therefore recommend that you contact the lead supervisor prior to applying and submit your formal application as early as possible.

Overview of the Research:

“Genome assembly” is a classical algorithmic problem in computational biology that has been worked on intensively over the last 20 years, with the aim of reconstructing a genome (a string of characters A,C,G,T) from multiple error-prone observations of random substrings (“reads”) of the genome. The problem is generally formulated in terms of a graph constructed from those reads, and the goal is to infer the true genome, which is some path through the graph.

 A key to success is being able to combine a good graph-formulation and algorithmic idea with the constraints implied by the biology – e.g.   

–         the difference between the length distribution of the reads, and the length distribution of repeated elements in the genome has a major effect on the complexity of the problem. If the reads are too short, then the problem is not soluble.

–         in real data often the reads are sampled from more than 1 genome (eg humans have two copies of their genome, one from each parent),

–         the error process in the equipment generating the reads makes a non-trivial difference.

Modern data, produces extremely long reads compared to what was previously possible (10x-1000x longer), but it is still not possible to reliably reconstruct near-perfect bacterial genomes without manual curation. We want to fix this, and to do it we will reformulate the problem.

A common factor amongst almost all previous approaches, is that everything is done at the level of DNA. However, recently new approaches have been developed which “zoom out” in one way or another. In the Iqbal research group, we have developed and prototyped one such new formulation and have been able to prove that this is a viable approach.

The goal of this PhD project is to build on this new graph formulation and combine with some prior biological knowledge about bacterial genomes, to

1. develop new efficient genome assembly algorithms and implement them efficiently (in C++ or rust)
2. extend these ideas to analysing large scale differences between different genomes in the same species
3. combine the above to study variation in “hitch-hiking” secondary genomes that exist inside bacteria.

Project keywords: Pangenome, genome assembly, algorithm, data structure, bacteria, graph theory, networks

Candidate Requirements:

Applicants should hold, or expect to receive, a First Class or Upper Second Class UK Honours degree (or the equivalent) in a relevant subject. Either extensive coding experience ideally including a compiled language, or some mathematical/algorithmic maturity (e.g. through a maths or computer science degree) would be a distinct advantage. No biological experience needed, but interest in learning about biology as well as algorithms is essential.

Non-UK applicants must meet the programme’s English language requirement by the application deadline.

Enquiries and Applications:

Informal enquiries are encouraged and should be directed to Zamin Iqbal: zi245@bath.ac.uk

Formal applications should be submitted via the University of Bath’s online application form for a PhD in Biology prior to the closing date of this advert.

IMPORTANT:

When completing the application form:

1. In the Funding your studies section, select ‘University of Bath URSA’ as the studentship for which you are applying.
2. In the Your PhD project section, quote the project title of this project and the name of the lead supervisor in the appropriate boxes.

Failure to complete these two steps will cause delays in processing your application and may cause you to miss the deadline.

More information about applying for a PhD at Bath may be found on our website. 

PLEASE BE AWARE: Applications for this project may close earlier than the advertised deadline if a suitable candidate is found. We therefore recommend that you contact the lead supervisor prior to applying and submit your formal application as early as possible.

Equality, Diversity and Inclusion:

We value a diverse research environment and aim to be an inclusive university, where difference is celebrated and respected. We welcome and encourage applications from under-represented groups.

If you have circumstances that you feel we should be aware of that have affected your educational attainment, then please feel free to tell us about it in your application form. The best way to do this is a short paragraph at the end of your personal statement.