Dave
Thorne

PhD

where London, UK

Projects

Lazarus more…

The Lazarus project uses the research platform aspect of Utopia Documents to provide crowd-sourcing abilities to scientists. It has been slowly building up a picture of the interconnectedness of scientific literature and uses that knowledge to help researchers get more out of their time.

Utopia Documents more…

The creation of a ‘next-generation’ document viewer that could link the reader, simply through the process of reading, with the world at large. Providing lnks to definitions, database entries, citations, and more, it brings documents to life. Utopia Documents is still ongoing and is currently a thriving project.

OpenPHACTS more…

The Open PHACTS Discovery Platform has been developed to reduce barriers to drug discovery in industry, academia and for small businesses.

Semantic Biochemical Journal more…

The semantic Biochemical Journal was a novel and successful attempt to enrich the Biochecmical Journal with more useful semantic information, linking underlying data and public resources to the process of reading an article online.

EMBRACE more…

“European Model for Bioinformatics Research and Community Education” – European Commission FP6 Programme. Research into the uses of web service technologies for aiding large-scale distributed bioinformatics research. This five-year project required much collaboration and frequent trips across Europe both for project meetings and community outreach (workshops and teaching duties).

Protein Folding Fragments more…

PFF sought to compile a list of protein folds and along with the results of various analysis tools in order to try to better predict protein folding.

Publications

S. Pettifer, J. Velterop, T. K. Attwood, L. Harland, J. Marsh, D. Thorne, and A. Tunbridge. Reuniting data and narrative in scientific articles. Insights, 25(3):288-293, November 2012. [ DOI ]
B. Vroling, D. Thorne, P. McDermott, T. K Attwood, G. Vriend, and S. Pettifer. Integrating GPCR-specific information with full text articles. BMC Bioinformatics, 12(362), Sep 2011. [ DOI ]
B. Vroling, D. Thorne, P. McDermott, HJ. Joosten, T. K. Attwood, S. Pettifer, and G. Vriend. Nucleardb: information system for nuclear receptors. Nucleic Acids Research, Nov 2011.
S. Pettifer, P.McDermott, J. Marsh, D. Thorne, A.Villéger, and T. K. Attwood. Ceci n'est pas un hamburger: modelling and representing the scholarly article. Learned Publishing, Jul 2011. [ DOI | http ]
T. K. Attwood, D. B. Kell, P. Mcdermott, J. Marsh, S. R. Pettifer, and D. Thorne. Utopia Documents: linking scholarly literature with research data. Bioinformatics, 26:i540-i546, Sep 2010. [ DOI | http ]
S. Pettifer, J. Ison, M. Kalaš, D. Thorne, P. McDermott, I. Jonassen, A. Liaquat, J. M. Fernández, J. M. Rodriguez, INB-Partners, D. G. Pisano, J. Salzemann, C. Blanchet, V. Breton, M. Uludag, P. Rice, E. Bartaševičiutė, K. Rapacki, M. Hekkelman, O. Sand, H. Stockinger, A. B. Clegg, E. Bongcam-Rudloff, T. K. Attwood, G. Cameron, and G. Vriend. The EMBRACE web service collection. Nucleic Acids Research, 2010. [ DOI | http | http ]
M. L. Hekkelman, T. A. H te Beek, S. R. Pettifer, D. Thorne, T. K. Attwood, and G. Vriend. WIWS: a protein structure bioinformatics web service collection. Nucleic Acids Research, 2010. [ DOI | http ]
S. Pettifer, D. Thorne, P. McDermott, T. Attwood, J. Baran, J. C. Bryne, T. Hupponen, D. Mowbray, and G. Vriend. An active registry for bioinformatics web services. Bioinformatics, 25, 2009. [ DOI | http ]
T. K. Attwood, D. B. Kell, P. Mcdermott, J. Marsh, S. R. Pettifer, and D. Thorne. Calling international rescue: knowledge lost in literature and data landslide! Biochemical Journal, Dec 2009. [ DOI | http ]
S. R. Pettifer, D. Thorne, P. McDermott, J. Marsh, A. Villéger, D. B. Kell, and T. K. Attwood. Visualising biological data: a semantic approach to tool and database integration. BMC Bioinformatics, 16, Jun 2009. [ DOI | http ]

Books and Chapters

T. Attwood, S. Pettifer, and D. Thorne. Bioinformatics Challenges at the Interface of Biology and Computer Science: Mind the Gap. Wiley, October 2016. ISBN: 978-0-470-03548-1. [ http ]
D. Thorne. Various entries. In J. M. Hancock and M. J. Zvelebil, editors, Concise Encyclopaedia of Bioinformatics and Computational Biology, 2nd Edition. Wiley, January 2014. ISBN: 978-0-470-97871-9. [ http ]
S. Pettifer, T. Attwood, J. Marsh, and D. Thorne. Utopia documents: Transforming how industrial scientists interact with the scientific literature. In L. Harland and M. Foster, editors, Open source software in life science research: Practical solutions to common challenges in the pharmaceutical industry and beyond. Springer-Verlag, November 2012. ISBN-10: 1907568972. [ http ]

Workshop and Conference Proceedings

S. R. Pettifer, T. K. Attwood, C. Goble, J. Marsh, R. Stevens, and D. Thorne. Project Lazarus: Resurrecting knowledge from the scientific literature by crowdsourcing. Presented at ISMB/ECCB 2017 , Prague, Czech Republic, Jul 2017.
D. Thorne. Citations in Utopia Documents. Presented at EXCITE Workshop 2017: Challenges in Extracting and Managing References, Köln, Germany, Mar 2017.
T. K. Attwood, D. B. Kell, P. Mcdermott, J. Marsh, S. R. Pettifer, and D. Thorne. Utopia Documents: linking scholarly literature with research data. In Proceedings of 9th European Conference on Computational Biology, Ghent, Belgium, Sep 2010.
S. Pettifer, K. Wolstencroft, P. Alper, T. Attwood, A. Coletta, C. Goble, P. Li, P. McDermott, J. Marsh, T. Oinn, J. Sinnott, and D. Thorne. mygrid and UTOPIA: an integrated approach to enacting and visualising in silico experiments in the life sciences. Springer, June 2007. 59-70.
P. McDermott, J. Sinnott, D. Thorne, S. Pettifer, and T. Attwood. An architecture for visualisation and interactive analysis of proteins. In Proceedings of 4th International Conference on Coordinated and Multiple Views in Exploratory Visualization (CMV06), pages 55-65, Jul 2006. London, UK.
D. Thorne and S. Pettifer. Unifying abstract and physical molecular model interaction. In Proceedings of EGUK Theory and Practice of Computer Graphics Conference 2005 (TPCG05), pages 75-82, Jun 2005. Canterbury, UK.

Miscellaneous

T. K. Attwood, D. B. Kell, P. Mcdermott, J. Marsh, S. R. Pettifer, and D. Thorne. Utopia Documents and The Semantic Biochemical Journal experiment. EMBNet News, Mar 2010. [ http ]
T. K. Attwood, D. B. Kell, P. Mcdermott, J. Marsh, S. R. Pettifer, and D. Thorne. Knowledge lost in literature and data landslide: calling international rescue! The Biochemist, Dec 2009. [ .pdf ]
S. Pettifer, D. Thorne, P. McDermott, T. Attwood, J. Baran, J. C. Bryne, T. Hupponen, and G. Vriend. The EMBRACE registry. EMBNet News, January 2009. [ .html ]
M. Corpas, J. Sinnott, D. Thorne, S. Pettifer, and T. Attwood. PFF - an integrated database of residues and fragments critical for protein folding. BMC Systems Biology (online journal), 2007. doi:10.1186/1752-0509-1-SI-P48.