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Clustering in bioinformatics

There are many bioinformatics datasets available publically. Extracting consistent information from these require development of novel techniques and tools. This has many applications in medical (and biological) fields with direct consequences for developing drugs, helping doctors to deliver services, and finally curing patients.

Clustering analysis has a growing role in the study of co-expressed genes for gene discovery. Conventional binary and fuzzy clustering do not embrace the biological reality that some genes may be irrelevant for a problem and not be assigned to a cluster, while other genes may participate in several biological functions and should simultaneously belong to multiple clusters. In addition, most algorithms cannot generate tight clusters that focus on their cores or wide clusters that overlap and contain all possibly relevant genes. The primary aim is to develop a clustering paradigm with better performance specifically for biological studies with a view to gene discovery.

This project will involve programming, signal processing, machine learning, mathematical analysis, and good writing ability for presentation of technical work. An ideal candidate will have a very good Master degree or a First Class Bachelor degree. Below are some publications from my group. These will give you some indications of the work we have done already.

  1. B Abu Jamous, R Fa, and A K Nandi, "Integrative Cluster Analysis in Bioinformatics", Published by John Wiley & Sons, Chichester, West Sussex, UK, 2015 (ISBN 978-1-118-90653-8).
  2. B Abu Jamous, F M Buffa, A L Harris, and A K Nandi, “In vitro downregulated hypoxia transcriptome is associated with poor prognosis in breast cancer", Molecular Cancer, DOI: 10.1186/s12943-017-0673-0, vol. 16, no. 105, (19 pages), 2017.
  3. B Abu Jamous, R Fa, D J Roberts, and A K Nandi, “UNCLES: method for the identification of genes differentially consistently co-expressed in a specific subset of datasets", BMC Bioinformatics, DOI: 10.1186/s12859-015-0614-0, vol. 16, no. 184, 2015.
  4. B Abu Jamous, R Fa, D J Roberts, and A K Nandi, “Comprehensive analysis of forty yeast microarray datasets reveals a novel subset of genes (APha-RiB) consistently negatively associated with ribosome biogenesis", BMC Bioinformatics, DOI: 10.1186/1471-2105-15-322, vol. 15, no. 322, 2014.
  5. B Abu Jamous, R Fa, D J Roberts, and A K Nandi, “Paradigm of tunable clustering using binarization of consensus partition matrices (Bi-CoPaM) for gene discovery", PLoS ONE vol. 8, no. 2, doi:10.1371/journal.pone.0056432, 2013.
  6. B Abu Jamous, R Fa, D J Roberts, and A K Nandi, “Yeast gene CMR1/YDL156W is consistently co-expressed with genes participating in DNA-metabolic processes in a variety of stringent clustering experiments", J. R. Soc. Interface, vol. 10, no. 81, doi: 10.1098/rsif.2012.0990, 2013.

This project will involve programming, signal processing, machine learning, mathematical analysis and require good writing ability for presentation of technical work.

An ideal candidate will have a very good Master degree or a First Class Bachelor degree.

How to apply

If you are interested in applying for the above PhD topic please follow the steps below:

  1. Contact the supervisor by email or phone to discuss your interest and find out if you woold be suitable. Supervisor details can be found on this topic page. The supervisor will guide you in developing the topic-specific research proposal, which will form part of your application.
  2. Click on the 'Apply here' button on this page and you will be taken to the relevant PhD course page, where you can apply using an online application.
  3. Complete the online application indicating your selected supervisor and include the research proposal for the topic you have selected.

Good luck!

This is a self funded topic

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%.

Meet the Supervisor(s)


Asoke Nandi - In April 2013, Professor Nandi moved to Brunel University London to become the Head of Electronic and Computer Engineering from the University of Liverpool where he held the David Jardine Chair of Signal Processing in the Department of Electrical Engineering and Electronics. At Liverpool he was the Head of the Signal Processing and Communications Research Group which he established in 1999. Professor Nandi received his PhD from the University of Cambridge. Subsequently, he held positions in Rutherford Appleton Laboratory, CERN, Queen Mary University of London, the University of Oxford, Imperial College London, University of Strathclyde, and the University of Liverpool. Professor Nandi has published over 250 papers in refereed international journals (total: 600 technical papers) with an h-index of 80 (all citation figures are from Google Scholar) and the ERDOS number of 2. He co-discovered the three particles known as W+, W-, and Z0 - three of the four quanta of the electroweak force. This discovery verified the unification of the electromagnetic force and the nuclear weak force. In its recognition the 1984 Nobel Prize for Physics was awarded to his two leaders for their decisive role in this project. He has made pioneering theoretical and applied contributions to statistical signal processing, wireless communications, machine learning, and biomedical signal processing, image processing, genomic signal processing, brain signal processing, and Big Data. Professor Nandi is a Fellow of the Royal Academy of Engineering as well as seven other institutions. He was an IEEE Distinguished Lecturer (EMBS, 2018-2019)