Study level

  • PhD
  • Master of Philosophy
  • Honours

Faculty/School

Faculty of Health

School of Biomedical Sciences

Topic status

We're looking for students to study this topic.

Research centre

Centre for Microbiome Research

Supervisors

Associate Professor Luis Pedro Coelho
Position
Senior Research Fellow/Group Leader
Division / Faculty
Faculty of Health
Associate Professor Ben Woodcroft
Position
Principal Research Fellow
Division / Faculty
Faculty of Health

Overview

Metagenomics data is complex, high-volume data and keeps evolving, requiring novel computational method development as the wetlab approaches changes and databases grow. Thus, novel computational methods are required to take advantage of them.

There are several potential projects under this topic, including:

  • using deep learning to improve metagenomics assembly
  • developing better tools to analyse the presence of resistance genes in metagenomics data
  • developing approaches for estimating the quality of genomes from novel generation sequences
  • predicting the function of small sequences using more than just sequence.

Interested applicants are encouraged to contact the supervisor to discuss what exact project best fits their background and interests.

We aim to have our methods be adopted by the wider microbiome research community. Thus, we implement them in high-quality tools to maximise the positive impact of our research.

Research activities

Research activities include (depending on the exact project defined):

  • developing new machine learning-based algorithms
  • developing new string processing algorithms
  • implementing these in a tool using Python or Rust
  • benchmarking the methods against state-of-the-art alternatives
  • collaborating with experimentalists to apply new methods while improving them.

Outcomes

Projects under this topic will result in new algorithms, their implementation in an open source tool for widespread use, and their benchmarking against the state of the art. The results will be published in a scientific journal and communicated at conferences and in online materials.

Skills and experience

The applicant should have programming skills and an interest in learning about biology.

Scholarships

You may be eligible to apply for a research scholarship.

Explore our research scholarships

Keywords

Contact

Contact the supervisor for more information