Joe Mullen

PhD Student

I am a PhD student in the School for Computing Science, Newcastle University. My PhD is in collaboration with GlaxoSmithKline. The aim of my work is the identification of potential drug repurposing targets. This will be achieved using data integration and the development of novel data mining techniques. My primary supervisors at Newcastle University are Professor Anil Wipat and Dr Simon Cockell.

 

Research Interests

  • Data Integration
  • Graph Mining
  • Network Pharmacology
  • Drug Discovery/ Repurposing

Publications

  • [DOI] G. Misirli, A. Wipat, J. Mullen, K. James, M. Pocock, W. Smith, N. Allenby, and J. S. Hallinan, “BacillOndex: an integrated data resource for systems and synthetic biology,” J integr bioinform, vol. 10, iss. 2, p. 224, 2013.
    [Bibtex]
    @article{Misirli:2013:J-Integr-Bioinform:23571273,
    abstract = {{BacillOndex} is an extension of the Ondex data integration system, providing a semantically annotated, integrated knowledge base for the model Gram-positive bacterium Bacillus subtilis. This application allows a user to mine a variety of B. subtilis data sources, and analyse the resulting integrated dataset, which contains data about genes, gene products and their interactions. The data can be analysed either manually, by browsing using Ondex, or computationally via a Web services interface. We describe the process of creating a {BacillOndex} instance, and describe the use of the system for the analysis of single nucleotide polymorphisms in B. subtilis Marburg. The Marburg strain is the progenitor of the widely-used laboratory strain B. subtilis 168. We identified 27 {SNPs} with predictable phenotypic effects, including genetic traits for known phenotypes. We conclude that {BacillOndex} is a valuable tool for the systems-level investigation of, and hypothesis generation about, this important biotechnology workhorse. Such understanding contributes to our ability to construct synthetic genetic circuits in this organism.},
    author = {Misirli, G. and Wipat, A. and Mullen, J. and James, K. and Pocock, M. and Smith, W. and Allenby, N. and Hallinan, J. S.},
    citeulike-article-id = {12296710},
    citeulike-linkout-0 = {http://www.hubmed.org/display.cgi?uids=23571273},
    citeulike-linkout-1 = {http://dx.doi.org/10.2390/biecoll-jib-2013-224},
    doi = {10.2390/biecoll-jib-2013-224},
    journal = {J Integr Bioinform},
    number = {2},
    pages = {224},
    posted-at = {2013-05-08 12:15:18},
    priority = {2},
    title = {{BacillOndex}: An Integrated Data Resource for Systems and Synthetic Biology},
    url = {http://www.hubmed.org/display.cgi?uids=23571273},
    volume = {10},
    year = {2013}
    }

Publications

Contact

Address: Room 924, Claremount Tower, School of Computing Science, University of Newcastle upon Tyne, Newcastle upon tyne, NE1 7RU

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