About the Project
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.
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.
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