Dr John Holliday

Senior Research Manager

BSc (Staffordshire), PhD (Sheffield)

Teaching

I am the module coordinator for the Content Management Systems module, taught at postgraduate and level-3 undergraduate levels. Content Management Systems provide tools for the management, access, storage, retrieval, publication and archiving of content. Content can be any web or enterprise asset, such as an image, block of text, database table, template file, etc.

I am responsible for practical support for the Chemoinformatics modules taught in the iSchool. In addition, I teach on and provide technical support for the annual three day course entitled ‘A Practical Introduction to Chemoinformatics’.

Professional standing

• Trustee of the Chemical Structure Association Trust (2001-)
• Organising Committee for triennial Joint Sheffield Conferences on Chemoinformatics (2001-)
• Member of Editorial Board for Scientific Reports

Research interests

Chemoinformatics

Chemoinformatics is the application of computer-based techniques to the field of chemistry, notably relating to the discovery processes in the pharmaceutical and agrochemical industries. My main role within the iSchool is as Research Manager for the chemoinformatics research group, a role which includes management of the group’s specialist software, hardware and databases, as well as research supervision. Within Chemoinformatics, my main research areas include:

• chemical database diversity and compound selection;
• evolutionary programming methods;
• comparison of similarity coefficients and data fusion techniques.

Geographical Information Systems

Geographical Information Systems (GIS) is the application of computer-based techniques to the field of geography; the representation, management and analysis of spatial data found in geographical information. My main research area is the analysis and representation of linguistic data (geolinguistics).

Project Management

I am the Project Manager of Sheffield Uni-Tech trainee technician programme. The programme provides training and hands-on experience in ICT for local unemployed people.

Uni-Tech

Key publications

Haranczyk, M. & Holliday, J. Comparison of Similarity Coefficients for Clustering and Compound Selection, Journal of Chemical Information and Modeling 48, 2008, 498-508

Holliday, J.D., Salim, N. & Willett, P. On the magnitudes of coefficient values in the calculation of chemical similarity and dissimilarity, American Chemical Society Symposium Series 894, 2005, 77-95

Holliday, J.D., Rodgers, S.L., Willett, P., Chen, M.-Y., Mahfouf, M., Lawson, K. & Mullier, G. Clustering files of chemical structures using the fuzzy k-means clustering method, Journal of Chemical Information and Computer Sciences 44, 2004, 894-902

Salim, N., Holliday, J.D. & Willett, P. Combination of fingerprint-based similarity coefficients using data fusion, Journal of Chemical Information and Computer Sciences 43, 2003, 435-442

Holliday, J.D., Jelfs, S.P., Willett, P. & Gedeck, P. Calculation of inter-substituent similarity using R-group descriptors, Journal of Chemical Information and Computer Sciences 43, 2003, 406-411

Holliday, J.D., Hu, C.-Y. & Willett, P. Grouping of coefficients for the calculation of inter-molecular similarity and dissimilarity using 2D fragment bit-strings, Combinatorial Chemistry and High-Throughput Screening 5, 2002, 155-166

Edgar, S.J., Holliday, J.D. & Willett, P. Effectiveness of retrieval in similarity searches of chemical databases: a review of performance measures, Journal of Molecular Graphics and Modelling 18, 2000, 343-357

Gardiner, E.J., Holliday, J.D., Willett, P., Wilton, D.J. & Artymiuk, P.J. Selection of reagents for combinatorial synthesis using clique detection, Quantitative Structure-Activity Relationships 17, 1998, 232-236

Holliday, J.D. & Lynch, M.F. Computer storage and retrieval of generic chemical structures in patents Part 16 The refined search: an algorithm for matching components of generic chemical structures at the atom-bond level, Journal of Chemical Information and Computer Sciences 35, 1995, 1-7

Holliday, J.D. & Lynch, M.F. Computer storage and retrieval of generic chemical structures in patents Part 17 Evaluation of the Refined Search, Journal of Chemical Information and Computer Sciences 35, 1995, 659-662

Holliday, J.D., Ranade, S.S. & Willett, P. A fast algorithm for selecting sets of dissimilar structures from large chemical databases, Quantitative Structure-Activity Relationships 14, 1995, 501-506

Holliday, J.D., Downs, G.M., Gillet, V.J. & Lynch, M.F. Computer Storage and Retrieval of Generic Chemical Structures in Patents 15 Generation of Topological Fragment Descriptors from Nontopological Representations of Generic Structure Components, Journal of Chemical Information and Computer Sciences 33, 1993, 369-377

Holliday, J.D., Downs, G.M., Gillet, V.J. & Lynch, M.F. Computer Storage and Retrieval of Generic Chemical Structures in Patents 14 Fragment Generation from Generic Structures, Journal of Chemical Information and Computer Sciences 32, 1992, 453-462

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Last updated: 28 October 2012