My PhD research aimed to describe the generic systems used within the biological computational research field. By recognising and extracting the resources (databases and software names) used within journal articles, I was able to provide a proxy for the abstract in silico method used within each paper. By performing this extraction on a large scale (full PubMed Central corpus), I could provide an overview of the methods and resources used within the domain. This research potetially has wider implications in community "best" and "common" practice. You can access my final thesis here.
This project was jointly supervised by:
- Geraint Duck, Goran Nenadic, Michele Filannino, Andy Brass, David L. Robertson, and Robert Stevens. A survey of bioinformatics database and software usage through mining the literature. PLoS ONE (2016) Full Text
- Geraint Duck, Aleksandar Kovacevic, David L. Robertson, Robert Stevens, and Goran Nenadic. Ambiguity and variability of database and software names in bioinformatics. Journal of Biomedical Semantics (2015) Full Text
- Geraint Duck, Goran Nenadic, Andy Brass, David L. Robertson, and Robert Stevens. Extracting patterns of database and software usage from the bioinformatics literature. Bioinformatics (2014) Full Text
- Dumontier, M. et al. The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. Journal of Biomedical Semantics (2014)
- Katayama, T., et al. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in the life sciences. Journal of Biomedical Semantics (2014) Full Text
- Geraint Duck, Goran Nenadic, Andy Brass, David L. Robertson, and Robert Stevens. bioNerDS: exploring bioinformatics' database and software use through literature mining. BMC Bioinformatics (2013) Full Text
- Geraint Duck, Robert Stevens, David Robertson, and Goran Nenadic. Ambiguity and variability of database and software names in bioinformatics. In SMBM 2012, pages 2-9. Paper Proceedings
POSTERS AND PRESENTATIONS:
- Presentation, Strasbourg, ECCB 2014
- Poster, Berlin, ISMB 2013
- Presentation, Manchester, The University of Manchester Symposium 2012
- Poster, Basel, ECCB 2012
- Presentation, Zurich, SMBM 2012 [Presented by Goran Nenadic]
- Attendence at BioHackathon 2012 in Toyama, Japan ["Hacked" together BioInterchange]
- Poster, Manchester, The University of Manchester Symposium 2011
- My MSc project developed and tested a methodology for the statistical comparison within a given sequence alignment. The idea was the define how "treelike" a given dataset was through a parametric bootstrap approach resulting in a packaged Java based piece of software to do such a test. This project was supervised by Dr Simon Whelan
- My BSc final year project was to develop a simulator system in Java using the Repast library to help test the spread of an infection within an agent based, closed, system. The agents were allowed to move, needed to eat, and also reproduce. Infection could be spread through food or agent proximity. This project was supervised by Dr Nathan Griffiths
- I graduated from my MSc in Computational Molecular Biology (Bioinformatics) from the University of Manchester in December 2010, receiving a Distinction for both the course work and dissertation components.
- I have also achieved a First Class Undergraduate degree in Computer Science from the University of Warwick in July 2009 with a 78% average.
- I love to travel and try to visit as many places and countries as I can. Of particular note, however, was my trip to Japan as part of an exchange program where I spent 10 days living with a Japanese family. I also spent 2 weeks aiding research into the local wildlife in the Kalahari desert as a part of the Kalahari Meerkat Project.