Gillet, Val, Professor

Professor Val Gillet

MA (Cambridge); MSc (��«Ӱҵ); PhD (��«Ӱҵ)

Information School

Professor of Chemoinformatics

v.gillet@sheffield.ac.uk
+44 114 222 2652

Room C221, The Wave

Full contact details

Professor Val Gillet
Information School
Room C221
The Wave
2 Whitham Road
��«Ӱҵ
S10 2AH

Profile

After completing a degree in Natural Sciences at Cambridge, I took a short term research post in the Department of Information Studies (as the Information School was then called) and contributed to the building of a database of generic chemical structures as found in the patent literature. This post fueled my interest in computing and I took the MSc in Information Science, returning to the generic structures project for my master’s dissertation and subsequent PhD - this time developing novel search algorithms to retrieve structural information from the database. I then moved to the Chemistry Department at Leeds University where I led a team working on de novo design (that is, the in-silico design of chemical compounds to fit a set of constraints such as a protein binding site) before returning to ��«Ӱҵ in the mid-nineties and taking up an academic post.

University Responsibilities

Head of School 2012-2016 & 2019-2023
REF Coordinator 2017-
Deputy Director of Research 2017-
Director of Research 2010-2012
Member of School’s Strategy Group 2009-
Member of School Promotions Panel
Workload Allocation Model lead 2010-2016.
Programme Coordinator for the MSc (Res) in Chemoinformatics (formerly the MSc in Chemoinformatics) 2000-2010.
Departmental EPSRC DTG Coordinator.
Staff Review and Development Scheme reviewer.
School Research Ethics Coordinator 2008-2010.
Chair of Staff/Student Committee from 2004 to 2007.
School Representative on Teaching Affairs Committee, Pure Science, 1999-2004.
Editor of School Newsletter, 1999-2004.

Research interests

My research interests are focussed on the development and application of chemoinformatics techniques that are used primarily in the design of novel bioactive compounds. I have expertise in data mining and machine learning methods including multiobjective evolutionary algorithms, emerging pattern mining and graph theory. Particular application areas include virtual screening, the identification of structure-activity relationships, toxicity prediction, 3D similarity methods and the de novo design of novel compounds. I also have expertise in developing novel representation methods for chemical structures with recent areas including reduced graphs, spectral geometry, wavelet analysis and reaction vectors.

Much of my research has been carried out in collaboration with pharmaceutical and software companies including: AstraZeneca, Cambridge Crystallographic Data Centre, Eli Lilly, GlaxoSmithKline, Janssen Pharmaceutials, Lhasa Limited, Novartis Pharamceuticals, Pfizer Central Research (UK and US), Sanofi-Aventis and Unilever. I also have collaborators across the University including Dr Beining Chen in the Department of Chemistry, Prof Rob Harrison in the Department of Automatic Control and Systems Engineering, Prof Tanya Whitfield in Biomedical Sciences, Prof Jon Sayers in the Medical School and Dr Heather Mortiboys in SITraN (��«Ӱҵ Institute for Translational Neuroscience).

I am a member of the Chemoinformatics Research Group.

Publications

Books

Chowdhury G, Gillet V, McLeod J & Willett P (2018) Preface.
Lipkowitz KB, Gillet VJ & Cundari TR (2006) Reviews in Computational Chemistry: Preface.
(2006) . John Wiley & Sons, Inc..

Journal articles

Walter M, Webb SJ & Gillet VJ (2024) . Journal of Chemical Information and Modeling, 64(9), 3670-3688.
Gillet V, Ghiandoni GM, Flanagan S, Bodkin MJ, Nizi MG, Galera-Prat A, Brai A, Chen B, Wallace J, Hristozov D , Webster J et al (2024) . Molecular Informatics.
Walter M, Allen LN, de la Vega de León A, Webb SJ & Gillet VJ (2022) . Journal of Cheminformatics, 14(1).
Ghiandoni GM, Bodkin MJ, Chen B, Hristozov D, Wallace JEA, Webster J & Gillet VJ (2021) . Molecular Informatics.
Grayson JD, Baumgartner MP, Santos Souza CD, Dawes SJ, El Idrissi IG, Louth JC, Stimpson S, Mead E, Dunbar C, Wolak J , Sharman G et al (2021) . Chemical Science.
Ghiandoni G, Bodkin MJ, Chen B, Hristozov D, Wallace JEA, Webster J & Gillet V (2020) . Journal of Computer-Aided Molecular Design.
Ghiandoni GM, Bodkin MJ, Chen B, Hristozov D, Wallace JEA, Webster J & Gillet V (2019) . Journal of Chemical Information and Modeling, 59(10), 4167-4187.
Seddon MP, Cosgrove DA, Packer MJ & Gillet VJ (2019) . Journal of Chemical Information and Modeling, 59(1), 98-116.
de la Vega de Leon A, Chen B & Gillet V (2018) . Journal of Cheminformatics, 10(-), ---.
Seddon MP, Cosgrove DA & Gillet VJ (2018) . ChemMedChem, 13(6), 607-613.
Martin YC, Abagyan R, Ferenczy GG, Gillet VJ, Oprea TI, Ulander J, Winkler D & Zefirov NS (2016) . Pure and Applied Chemistry, 88(3), 239-264.
Gillet VJ, Holliday JD & Willett P (2015) . Molecular Informatics, 34(9), 598-607.
Gardiner EJ & Gillet VJ (2015) . Journal of Chemical Information and Modeling, 55(9), 1781-1803.
Gan S, Cosgrove DA, Gardiner EJ & Gillet VJ (2014) . Journal of Chemical Information and Modeling, 54(12), 3302-3319.
Coquin L, Canipa SJ, Drewe WC, Fisk L, Gillet VJ, Patel M, Plante J, Sherhod RJ & Vessey JD (2014) . Toxicology Research, 4(1), 46-56.
Sherhod R, Judson PN, Hanser T, Vessey JD, Webb SJ & Gillet VJ (2014) . Journal of chemical information and modeling, 54(7), 1864-1879.
Sherhod R, Gillet VJ, Hanser T, Judson PN & Vessey JD (2013) . Journal of Cheminformatics, 5(S1).
Louth J, Thompson MJ, Evans C, Wright PC, Heath P, Delagadillo JMV, Gillet V & Chen B (2013) Deconvolution of molecular targets for small molecule anti-prion compounds using proteomic and microarray techniques. Prion, 7, 66-66.
Sherhod R, Gillet VJ, Judson PN & Vessey JD (2012) . Journal of Chemical Information and Modeling, 52(11), 3074-3087.
Martin RL, Gardiner EJ, Senger S & Gillet VJ (2012) . Journal of Chemical Information and Modeling, 52(3), 757-769.
Taylor R, Cole JC, Cosgrove DA, Gardiner EJ, Gillet VJ & Korb O (2012) Development and validation of an improved algorithm for overlaying flexible molecules. Journal of Computer-Aided Molecular Design, 1-22.
Louth J, Thompson M, Evans C, Wright P, Heath P, Delgadillo JV, Gillet V & Chen B (2012) Deconvoluting molecular targets for small molecule anti-prion compounds using proteomic and microarray techniques. Prion, 6, 98-98.
Gillet VJ (2011) . Wiley Interdisciplinary Reviews: Computational Molecular Science, 1(4), 580-589.
Hristozov D, Bodkin M, Chen B, Patel H & Gillet VJ (2011) , 29-43.
Birchall K & Gillet VJ (2011) Reduced graphs and their applications in chemoinformatics.. Methods in molecular biology (Clifton, N.J.), 672, 197-212.
Papadatos G, Alkarouri M, Gillet VJ, Willett P, Kadirkamanathan V, Luscombe CN, Bravi G, Richmond NJ, Pickett SD, Hussain J , Pritchard JM et al (2010) . Journal of Chemical Information and Modeling, 50(10), 1872-1886.
Martin RL, Gardiner E, Gillet VJ, Muñoz-Muriedas J & Senger S (2010) . Molecular Informatics, 29(8-9), 603-620.
Gardiner EJ, Cosgrove DA, Taylor R & Gillet VJ (2010) . ChemInform, 41(13).
Leach AR, Gillet VJ, Lewis RA & Taylor R (2010) . Journal of Medicinal Chemistry, 53(2), 539-558.
Whittle M, Gillet VJ & Willett P (2010) , 46-59.
Gardiner EJ, Cosgrove DA, Taylor R & Gillet VJ (2009) . Journal of Chemical Information and Modeling, 49(12), 2761-2773.
Birchall K, Gillet VJ, Willett P, Ducrot P & Luttmann C (2009) . Journal of Chemical Information and Modeling, 49(6), 1330-1346.
Patel H, Gillet VJ, Chen B & Bodkin MJ (2009) . Journal of Chemical Information and Modeling, 49(5), 1163-1184.
Papadatos G, Cooper AW, Kadirkamanathan V, Macdonald SJ, McLay IM, Pickett SD, Pritchard JM, Willett P & Gillet VJ (2009) . Journal of Chemical Information and Modeling, 49(2), 195-208.
Gardiner EJ, Gillet VJ, Haranczyk M, Hert J, Holliday JD, Malim N, Patel Y & Willett P (2009) . Statistical Analysis and Data Mining, 2(2), 103-114.
Patel Y, Gillet VJ, Willett P, Howe T, Pastor J & Oyarzabal J (2008) . Journal of Medicinal Chemistry, 51(23), 7552-7562.
Birchall K, Gillet VJ, Harper G & Pickett SD (2008) . ChemInform, 39(48).
Birchall K, Gillet VJ, Harper G & Pickett SD (2008) . ChemInform, 39(48).
Birchall K, Gillet VJ, Harper G & Pickett SD (2008) . Journal of Chemical Information and Modeling, 48(8), 1543-1557.
Birchall K, Gillet VJ, Harper G & Pickett SD (2008) . Journal of Chemical Information and Modeling, 48(8), 1558-1570.
Moffat K, Gillet VJ, Whittle M, Bravi G & Leach AR (2008) . ChemInform, 39(29).
Gillet VJ (2008) . Current Opinion in Chemical Biology, 12(3), 372-378.
Moffat K, Gillet VJ, Whittle M, Bravi G & Leach AR (2008) . Journal of Chemical Information and Modeling, 48(4), 719-729.
Whittle M, Eaglestone B, Ford N, Gillet VJ & Madden A (2007) . Journal of the American Society for Information Science and Technology, 58(14), 2382-2400.
Gardiner EJ, Gillet VJ, Willett P & Cosgrove David A. CDA (2007) . ChemInform, 38(24).
Gardiner EJ, Gillet VJ, Willett P & Cosgrove DA (2007) . Journal of Chemical Information and Modeling, 47(2), 354-366.
Leach AR & Gillet VJ (2007) . An Introduction To Chemoinformatics, 1-255.
Cottrell SJ, Gillet VJ & Taylor R (2006) . Journal of Computer-Aided Molecular Design, 20(12), 735-749.
Whittle M, Gillet VJ, Willett P & Loesel J (2006) . Journal of Chemical Information and Modeling, 46(6), 2206-2219.
Whittle M, Gillet VJ, Willett P & Loesel J (2006) . Journal of Chemical Information and Modeling, 46(6), 2193-2205.
Whittle M, Eaglestone B, Ford N, Gillet VJ & Madden A (2006) Query transformations and their role in Web searching by the general public. Information Research, 12(1).
Mardikian S, Gillet VJ, Jackson RM & Westhead DR (2006) Using multiobjective optimization to study the strengths of different interaction energies in protein-ligand complexes. Abstracts of Papers of the American Chemical Society, 232, 411-411.
Birchall K, Harper G, Gillet VJ & Pickett S (2006) CINF 22-Evolving reduced graph queries for extracting structure-activity relationships. Abstracts of Papers of the American Chemical Society, 232.
Gardiner EJ, Cosgrove DA, Willett P & Gillet VJ (2006) Cluster representation using reduced graphs. Abstracts of Papers of the American Chemical Society, 232, 181-181.
Mardikian S, Gillet VJ, Jackson RM & Westhead DR (2006) CINF 68-Studying the effects of individual interaction energies in a variety of protein-ligand complexes. Abstracts of Papers of the American Chemical Society, 232.
Ganguly M, Brown N, Schuffenhauer A, Ertl P, Gillet VJ & Greenidge PA (2006) . Journal of Chemical Information and Modeling, 46(5), 2110-2124.
Gillet VJ & Willett P (2006) , 187-208.
Birchall K, Gillet VJ, Harper G & Pickett SD (2006) . Journal of Chemical Information and Modeling, 46(2), 577-586.
Barker EJ, Buttar D, Cosgrove DA, Gardiner EJ, Kitts P, Willett P & Gillet VJ (2006) . Journal of Chemical Information and Modeling, 46(2), 503-511.
Reddy TRK, Mutter R, Heal W, Guo K, Gillet VJ, Pratt S & Chen B (2006) . Journal of Medicinal Chemistry, 49(2), 607-615.
Kristam R, Gillet VJ, Lewis RA & Thorner D (2005) . ChemInform, 36(22).
Kristam R, Gillet VJ, Lewis RA & Thorner D (2005) . Journal of Chemical Information and Modeling, 45(2), 461-476.
Cottrell SJ, Gillet VJ, Taylor R & Wilton DJ (2004) . Journal of Computer-Aided Molecular Design, 18(11), 665-682.
Whittle M, Gillet VJ, Willett P, Alex A & Loesel J (2004) . Journal of Chemical Information and Computer Sciences, 44(5), 1840-1848.
Gillet VJ (2004) . ChemInform, 35(18).
Gillet VJ (2004) . Structure and Bonding, 110, 133-152.
Gillet VJ (2004) . Methods in molecular biology (Clifton, N.J.), 275, 335-354.
Gillet VJ, Willett P & Bradshaw J (2003) . ChemInform, 34(21).
Wright T, Gillet VJ, Green DVS & Pickett SD (2003) . ChemInform, 34(21).
Barker EJ, Gardiner EJ, Gillet VJ, Kitts P & Morris J (2003) . Journal of Chemical Information and Computer Sciences, 43(2), 346-356.
Wright T, Gillet VJ, Green DVS & Pickett SD (2003) . Journal of Chemical Information and Computer Sciences, 43(2), 381-390.
Gillet VJ, Willett P & Bradshaw J (2003) . Journal of Chemical Information and Computer Sciences, 43(2), 338-345.
Bishop N, Gillet VJ, Holliday JD & Willett P (2003) . Journal of Information Science, 29(4), 249-267.
Nicolotti O, Gillet VJ, Fleming PJ & Green DVS (2002) . Journal of Medicinal Chemistry, 45(23), 5069-5080.
Patel Y, Gillet VJ, Bravi G & Leach AR (2002) . Journal of Computer-Aided Molecular Design, 16(8-9), 653-681.
Gillet VJ, Willett P, Fleming PJ & Green DVS (2002) . Journal of Molecular Graphics and Modelling, 20(6), 491-498.
Gillet VJ (2002) . Journal of Computer-Aided Molecular Design, 16(5-6), 371-380.
Gillet VJ, Khatib W, Willett P, Fleming PJ & Green DVS (2002) . Journal of Chemical Information and Computer Sciences, 42(2), 375-385.
Gillet VJ & Willett P (2002) . Pharmacochemistry Library, 32(C), 125-133.
Watson P, Willett P, Gillet VJ & Verdonk ML (2001) . Journal of Computer-Aided Molecular Design, 15(9), 835-857.
Verdonk ML, Cole JC, Watson P, Gillet V & Willett P (2001) . Journal of Molecular Biology, 307(3), 841-859.
Gillet VJ (2000) . Molecular Diversity, 5(4), 245-254.
Schuffenhauer A, Gillet VJ & Willett P (2000) Similarity Searching in Files of Three-Dimensional Chemical Structures: Analysis of the BIOSTER Database Using Two-Dimensional Fingerprints and Molecular Field Descriptors.. J. Chem. Inf. Comput. Sci., 40, 295-307.
Gillet VJ & Nicolotti O (2000) . Perspectives in Drug Discovery and Design, 20, 265-287.
Gillet VJ, Willett P, Bradshaw J & Green DVS (1999) . Journal of Chemical Information and Computer Sciences, 39(1), 169-177.
Gillet VJ, Willett P & Bradshaw J (1998) . Journal of Chemical Information and Computer Sciences, 38(2), 165-179.
Gillet VJ, Wild DJ, Willett P & Bradshaw J (1998) . Computer Journal, 41(8), 555-558.
Gillet VJ, Willett P & Bradshaw J (1997) . Journal of Chemical Information and Computer Sciences, 37(4), 731-740.
Mata P, Gillet VJ, Johnson AP, Lampreia J, Myatt GJ, Sike S & Stebbings AL (1995) SPROUT: 3D Structure Generation Using Templates.. J. Chem. Inf. Comput. Sci., 35, 479-493.
Gillet VJ, Myatt G, Zsoldos Z & Johnson AP (1995) . Perspectives in Drug Discovery and Design, 3(1), 34-50.
Holliday JD, Downs GM, Gillet VJ, Lynch MF & Dethlefsen W (1994) . Journal of Chemical Information and Computer Sciences, 34(1), 39-46.
Gillet VJ, Newell W, Mata P, Myatt GJ, Sike S, Zsoldos Z & Johnson AP (1994) SPROUT: Recent developments in the de novo design of molecules.. J. Chem. Inf. Comput. Sci., 34, 207-217.
Holliday JD, Downs GM, Gillet VJ & Lynch MF (1993) . Journal of Chemical Information and Computer Sciences, 33(3), 369-377.
Gillet VJ, Johnson AP, Mata P, Sike S & Williams P (1993) SPROUT: A program for structure generation.. J. Comput. Aided Mol. Des., 7, 127-153.
Holliday JD, Downs GM, Gillet VJ & Lynch MF (1992) . Journal of Chemical Information and Computer Sciences, 32(5), 453-462.
Dethlefsen W, Lynch MF, Gillet VJ, Downs GM, Holliday JD & Barnard JM (1991) . Journal of Chemical Information and Computer Sciences, 31(2), 233-253.
Dethlefsen W, Lynch MF, Gillet VJ, Downs GM, Holliday JD & Barnard JM (1991) . Journal of Chemical Information and Computer Sciences, 31(2), 253-260.
Gillet VJ, Downs GM, Holliday JD, Lynch MF & Dethlefsen W (1991) . Journal of Chemical Information and Computer Sciences, 31(2), 260-270.
Gillet VJ, Johnson AP, Mata P & Sike S (1990) . Tetrahedron Computer Methodology, 3(6), 681-696.
DOWNS GM, GILLET VJ, HOLLIDAY JD & LYNCH MF (1989) . ChemInform, 20(50).
DOWNS GM, GILLET VJ, HOLLIDAY JD & LYNCH MF (1989) . ChemInform, 20(50).
Downs GM, Gillet VJ, Holliday JD & Lynch MF (1989) . Journal of Chemical Information and Computer Sciences, 29(3), 207-214.
Downs GM, Gillet VJ, Holliday JD & Lynch MF (1989) . Journal of Chemical Information and Computer Sciences, 29(3), 215-224.
Downs GM, Gillet VJ, Holliday JD & Lynch MF (1989) . Journal of Chemical Information and Computer Sciences, 29(3), 172-187.
Downs GM, Gillet VJ, Holliday JD & Lynch MF (1989) . Journal of Chemical Information and Computer Sciences, 29(3), 187-206.
Brint AT, Gillet VJ, Lynch MF, Willett P, Manson GA & Wilson GA (1988) . Parallel Computing, 8(1-3), 295-300.
Gillet VJ, Dethlefsen W, Downs GM, Ling A, Lynch F, Venkataram P & Wood JV (1987) . Journal of Chemical Information and Computer Sciences, 27(3), 126-137.
Gillet VJ, Welford SM, Lynch MF, Willett P, Barnard JM, Downs GM, Manson G & Thompson J (1986) . Journal of Chemical Information and Computer Sciences®, 26, 118-126.

Chapters

Zhao M, Harvey M, Cameron D, Hopfgartner F & Gillet VJ (2023) In Sserwanga I, Goulding A, Moulaison-Sandy H, Du JT, Soares AL, Hessami V & Frank RD (Ed.), Lecture Notes in Computer Science (pp. 303-311). Springer Nature Switzerland
Puertas-Martín S, Redondo JL, Banegas-Luna AJ, Garzón EM, Pérez-Sánchez H, Gillet VJ & Ortigosa PM (2022) , Computational Science and Its Applications – ICCSA 2022 Workshops (pp. 127-139). Springer International Publishing
Gillet VJ & Willett P (2007) , Comprehensive Medicinal Chemistry II (pp. 167-192). Elsevier
Gillet VJ & Leach AR (2007) , Comprehensive Medicinal Chemistry II (pp. 235-264). Elsevier
Gillet VJ & Willett P (2006) Compound selection using measures of similarity and dissimilarity, Comprehensive Medicinal Chemistry II (pp. 167-191).
Gillet VJ (2003) , Soft Computing Approaches in Chemistry (pp. 1-30). Springer Berlin Heidelberg
Gillet VJ (2000) (pp. 49-69). Wiley
Lynch M, Downs G, Gillet V, Holliday J & Dethlefsen W (1989) , Chemical Information (pp. 161-173). Springer Berlin Heidelberg
Downs GM, Gillet VJ, Holliday J & Lynch MF (1988) , Chemical Structures (pp. 151-167). Springer Berlin Heidelberg
Gillet VJ () , Biomolecular and Bioanalytical Techniques (pp. 17-36). John Wiley & Sons, Ltd
Papadatos G, Gillet VJ, Luscombe CN, McLay IM, Pickett SD & Willett P () , Chemoinformatics for Drug Discovery (pp. 179-204). John Wiley & Sons, Inc
Gillet VJ, Bodkin MJ & Hristozov D () , De novo Molecular Design (pp. 267-285). Wiley-VCH Verlag GmbH & Co. KGaA
Papadatos G, Bodkin MJ, Gillet VJ & Willett P () , Bioisosteres in Medicinal Chemistry (pp. 103-127). Wiley-VCH Verlag GmbH & Co. KGaA

Conference proceedings papers

de Leon ADLV & Gillet V (2018) Phenotypic screening aided by multitask prediction methods. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, Vol. 256
de Leon ADLV & Gillet V (2017) Using deep neural networks with heterogeneous chemical data to support phenotypic assay campaigns. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, Vol. 254
Seddon M, Cosgrove D, Packer M & Gillet V (2017) Application of spectral and diffusion geometry descriptors to shape-based virtual screening. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, Vol. 253
Seddon M, Cosgrove D, Packer M & Gillet V (2017) Spectral and diffusion geometry descriptions of molecular shape. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, Vol. 253
Kannas C, Read W, Ruddock N, Fletcher M, Jackson T, Stevens R, Winter J, Willett P & Gillet V (2015) Multiobjective transformation based de novo design: A case study of surfactants. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, Vol. 250
Valencia J, Chen B & Gillet V (2012) Searching putative targets in silico for anti-prion compounds. Abstracts of Papers of the American Chemical Society, Vol. 243
Gan S, Gillet VJ, Gardiner EJ & Cosgrove DA (2012) Spectral clustering of chemical data: A Lanczos-based approach. Abstracts of Papers of the American Chemical Society, Vol. 243
Gillet VJ, Allen B, Bodkin M, Chen B, Cole J, Hristozov D, Liebeschuetz J & Patel H (2012) De novo design of synthetically accessible compounds: Application to fragment-based drug design. Abstracts of Papers of the American Chemical Society, Vol. 243
Gillet V (2011) Pharmacophore methods: Past, present, and future. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, Vol. 242
Gillet V, Martin R, Gardiner E & Senger S (2010) Applications of wavelets in virtual screening. Abstracts of Papers of the American Chemical Society, Vol. 240
Gillet VJ, Patel H, Bodkin M & Chen BN (2009) De novo design using reaction vectors: Application to library design. Abstracts of Papers of the American Chemical Society, Vol. 237
Mott IP, Gedeck P & Gillet VJ (2009) Multiobjective approach to optimizing scoring functions for docking. Abstracts of Papers of the American Chemical Society, Vol. 237
Cole JC, Gardiner EJ, Gillet VJ & Taylor R (2009) Development of test systems for pharmacophore elucidation. Abstracts of Papers of the American Chemical Society, Vol. 237
Martin RL, Gardiner EJ, Gillet VJ & Senger S (2009) Wavelet compression of GRID fields for similarity searching and virtual screening. Abstracts of Papers of the American Chemical Society, Vol. 237
Gillet VJ, Holliday J & Willett P (2008) CINF 72-Graduate training in chemoinformatics at the University of ��«Ӱҵ. Abstracts of Papers of the American Chemical Society, Vol. 235
Cosgrove DA, Gardiner EJ, Gillet VJ & Taylor R (2008) COMP 97-Combining clique-detection, MOGUL and MOGA for pharmacophore generation. Abstracts of Papers of the American Chemical Society, Vol. 235
Patel Y, Gillet VJ, Willet P, Pastor J, Howe T & Oyarzabal J (2008) COMP 270-Assessment of additive/nonadditive effects in SAR: Implications in the drug discovery iterative process. Abstracts of Papers of the American Chemical Society, Vol. 235
Gillet VJ & Willett P (2008) CINF 32-Academic-industrial collaboration in chemoinformatics: Experiences from the UK. Abstracts of Papers of the American Chemical Society, Vol. 235
Patel H, Gillet VJ, Chen BN & Bodkin M (2008) CINF 53-Structure generation using reaction vectors. Abstracts of Papers of the American Chemical Society, Vol. 235
Gillet VJ, Cottrell S & Taylor R (2006) Generation of multiple pharmacophore hypotheses using a multiobjective optimization algorithm. Abstracts of Papers of the American Chemical Society, Vol. 231
Gillet VJ (2004) Virtual screening using reduced graphs.. Abstracts of Papers of the American Chemical Society, Vol. 228 (pp U362-U363)
Bayley MJ, Gillet VJ, Willett P, Bradshaw J & Green DVS (1999) . Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB (pp 321-330)
Gillet VJ, Downs GM, Holliday JD, Lynch MF & Dethlefsen W (1993) . Chemical Structures 2 (pp 87-103)

Preprints

Zhao M, Harvey M, Cameron D, Hopfgartner F & Gillet VJ (2023) , arXiv.
Walter M, Allen LN, de León ADLV, Webb SJ & Gillet VJ (2022) , Research Square Platform LLC.

Research group

Current Researchers

Emma Armstrong: De Novo Design using Evolutionary Strategies
Toby King: Investigations of AI techniques in Drug Discovery

Current PhD students

Terence Egbelo: Use of Knowledge Graphs in Drug Discovery
Hanz Tantiango: Data Augmentation in De Novo Design
James Middleton: Alignment-free Molecular Design Methods

Completed PhD students

Christina Founti: New machine learning methods for the analysis and modelling of pharmaceutical data
Gian Marco Ghiandoni: Reaction-based molecule design
Jess Stacey: Data Mining for Lead Optimisation
Moritz Walter: Understanding artificial intelligence models for toxicity prediction
James Webster: Decision-theoretic methods for de novo design
Matthew Seddon: Development of novel techniques for assessing bio-isosteric similarity of chemical fragments.
Sonny Gan: The application of spectral clustering in drug discovery.
Jorge Valencia Delgadillo: Multiobjective design of novel antiprion compounds.
James Wallace: Reaction network for De Novo design
Georgios Papadatos: Data Mining for Lead Optimisation
Yogendra Patel: The Prediction of Molecular Properties Using Similarity Searching and Free-Wilson Analysis
P Watson: Calculating the Knowledge-Based Similarity and Complementarity of Functional Groups based on their Non-Bonded Interactions
Edward Barker: Chemical Similarity Searching Using Reduced Graphs
Kristian Birchall: Reduced Graph Approaches to Analysing High- Throughput Screening Data
Simon Cottrell: Generation of Multiple Pharmacophore Hypotheses Using Multiobjective Optimisation Techniques
Sally Mardikian: The Application of Multiobjective Optimisation to Protein-Ligand Docking
Richard Martin: Wavelet Approximation of GRID Fields for Virtual Screening
Kirstin Moffat: Development Of Computational Methods For 3D Similarity And Structure-Based Design Techniques In Lead Optimisation
Hina Patel: Patient and Practitioner Understanding of Traditional and Western Medical Acupuncture in Practice: A Qualitative Study
Richard Sherhod: Development of a Data Mining Tool for the Identification of Toxicophores
Trudi Wright: Multiobjective Optimisation of Combinatorial Libraries
Tummala Reddy: Design, Synthesis and SAR Studies Of Pyridine Dicarbonitriles As Potential Prion Therapeutics

Grants

Research Projects

EPSRC CASE studentship with GSK

Engineering and Physical Sciences Research Council

Principal Investigator

£81,792

1 October 2015

48 months

BBSRC CASE studentship with Evotec (UK) Ltd.

Biotechnology and Biological Sciences Research Council

Principal Investigator

£98,212

1 October 2017

48 months

BBSRC CASE studentship

Biotechnology and Biological Sciences Research Council

Principal Investigator

£70,000

1 October 2015

36 months

Bio-renewable Formulation - 6 month extension

Unilever

Principal Investigator

£49,171

1 February 2015

12 months

Diagnostic and Drug Discovery Initiative for Alzheimer's Disease

European Commission

Investigator

£739,714

1 October 2014

48 months

Alzheimer's disease (AD) is the major cause of dementia which has no cure at the moment. The overall aim of the project is to create a long-term strategic partnership between ��«Ӱҵ University (UK), Lisbon University (Portugal), Eli Lilly (UK) and Biofordrug (Italy) in order to develop chemical biology tools for better understanding the role of PrPC in AD and harnessing this understanding to develop novel chemical entities for diagnostic and therapeutics applications. Our proposed programme will lead to major increases in the knowledge and capacity of all consortium members, achieved through significant intersectoral exchange of personnel between the partners over the duration of the project (total 134 person months) and through temporary recruitment of 5 new experienced researchers (total 114 person months). The project will thus underpin a substantial programme of intersectoral knowledge transfer and research training and lead to significant innovation and advances in several areas of basic research as well as diagnostics and therapeutics development. These activities will strongly enhance EU standing and international competitiveness in this extremely challenging and increasingly important technological area.

Bio-renewable Formulation Information and Knowledge Management System

Technology Strategy Board

Investigator

£24,992

1 April 2014

24 months

Innovative ICT can play a crucial role in many innovation processes, but its potential is not always exploited in many industries. A route to innovation in formulated product industries is the exploitation of materials in what would otherwise be lost to waste streams from current manufacturing processes. This is exciting both in terms of realising additional value from manufacturing, but also in reduced utilisation of unsustainable material sources and exploitation of novel feedstocks for novel functional materials with new application benefits. This project will develop an information system based on highly innovative information technologies with the capability to rapidly identify the feedstock and functional material opportunities for formulated products, and demonstrate its value in rapid bio-derived surfactant discovery. It aims to support chemical using industries where environmental impact, sustainability and materials security are increasingly significant drivers of innovation alongside improved performance in formulated products.

Project partners are Unilever, British Sugar, Croda, Cybula, University of Manchester and University of Liverpool.

N8 Biohub Information and Knowledge Management System

Technology Strategy Board

Investigator

£131,128

1 October 2013

28 months

The overall aim of this project is to build, and demonstrate the value of, an information system (IS) to support the creation of a "Bio-Hub" centred on the N8 university group. The IS will demonstrate how functional ingredients from simple transformations of sustainable plant & waste feedstocks can be identified more quickly and recommend the best feedstocks for a particular function. It will address two big data problems using clever algorithms: semantic extraction of the available domain literature (terabytes) and optimised global search algorithms to explore the combinatorially large number of transformation products (up to petabytes). The innovations are in the creation of robust enough algorithms to run semi-autonomously in an information system and in bringing these together with all the other components. The value will be demonstrated for specific feedstocks and applications, but the ICTs will be selected for simple extension to, and maintenance of, the overall information domain. Project partners are Unilever, British Sugar, Croda, Cybula and University of Manchester.

Targeted dual drug screening in patient tissue to identify new treatments for Parkinson's

Parkinsons UK

Investigator

£249,795

2 September 2013

36 months

The number of patients with Parkinson's disease (PD) will double by 2030. Almost all current treatments focus on replacing the brain chemical, dopamine, which is lost in the disease. These treatments are effective at masking the motor symptoms of PD but they lose effectiveness over time and cause troublesome side effects. There is a lack of treatments which slow or stop disease progression; so called disease modifying therapies which alter the underlying disease causing pathwas. To date drug screens have not proven effective at getting new drugs through discovery and safety testing into the clinic. Therefore alternative drug screening strategies should be explored. Drug re-positioning which identifies new activities/uses of currently licensed drugs has been successful in other diseases. The aim of this study is to design and carry out a re-positioning drug screen in order to identify lead drugs which (i) show beneficial effects on the two most important underlying pathways leading to cell death in PD patient tissue and (ii) are already clinically licensed. The project is being led by Dr. Heather Mortiboys in the Division of Neuroscience. My role is to provide Chemoinformatics support to enable the in silico design of a library of drug compounds for screening.

AstraZeneca Collaboration - Belief Theory

AstraZeneca

Investigator

£70,000

22 November 2010

14 months

This project is focused on developing probabilistic similarity searching methods for searching databases of chemical structures. The aim is to develop computational tools that will support the application of similarity searching methods within AstraZeneca workflows, including effective ways of combining different search methods.

Knowledge Transfer Project - Lhasa Ltd

Technology Strategy Board

Principal Investigator

£132,024

1 October 2010

24 months

Lhasa Ltd. is a not-for-profit software development company whose core business is the development of knowledge about the relationship between chemical structure and toxicity. The aim of the project is to develop data mining methods to automate the discovery of knowledge about chemical structure-toxicity relationships. Knowledge discovery is traditionally done by domain experts who manually examine data sets of chemical structures and their related toxicology, in a very time consuming process. New methods will be developed based on emerging pattern mining which can lead to signficant reductions in the time required to augment the knowledge base.

De Novo Design

Cambridge Crystallographic Data Centre

Principal Investigator

£120,576

1 April 2009

24 months

The project involved the development of an evolutionary algorithm for the de novo design of novel chemical compounds to fit a variety of constraints. The project was a collaboration with the Cambridge Crystallographic Data Centre and Eli Lilly that addressed a key challenge in de novo design, which is ensuring that the compounds that are designed are synthetically accessibility. This was achieved by deriving the the molecular transformations used to generate novel structure from a knowledge-base of reactions and is not limited by reaction type or complexity.

CCDC Pharmacophore Collaboration

Cambridge Crystallographic Data Centre

Principal Investigator

£66,192

1 July 2008

11 months

The project was a continuation of the "AstraZeneca Collaboration - Pharmacophores" project and involved the development of a new multiobjective optimisation method for pharmacophore identification from sets of active compounds. A pharmacophore describes the three-dimensional arrangement of chemical features required for a small molecule to bind to a receptor and the aim of this project was to deduce the pharmacophore from a series of active compounds in the absence of the structure of the receptor itself. This involves superposing the compounds so that their common features are overlaid.

AstraZeneca Collaboration - Pharmacophores

AstraZeneca

Principal Investigator

£74,512

1 January 2007

12 months

The project involved the development of a new multiobjective optimisation method for pharmacophore identification from sets of active compounds. A pharmacophore describes the three-dimensional arrangement of chemical features required for a small molecule to bind to a receptor and the aim of this project was to deduce the pharmacophore from a series of active compounds in the absence of the structure of the receptor itself. This involves superposing the compounds so that their common features are overlaid.

Sanofi-��«Ӱҵ collaboration

Sanofi-Aventis

Investigator

£92,421

1 January 2007

12 months

Array design for lead optimisation in pharmaceutical research

GlaxoSmithKline

Principal Investigator

£252,000

23 October 2006

48 months

This EPSRC-funded project focused on the development of tools to assist medicinal chemists in the design of compound arrays during the lead optimisation stage of drug discovery. Lead optimisation is a complex, time-consuming task, in which chemists seek to obtain a promising balance among potency, off-target interactions, toxicity, and pharmacokinetic behaviour, to identify a candidate molecule to progress to clinical trials. The focus has been on inverse QSAR, that is, determining the structural change necessary to achieve a desired change in property. This has been approached through retrospective studies of lead optimisation projects within the GSK archive and the development of computational tools that can be applied in prospective array design to inform decision making by chemists. These included a novel context-sensitive approach to matched molecular-pairs analysis.

Novartis KTP

Knowledge Transfer Partnership

Principal Investigator

£143,754

1 May 2006

36 months

The project involved the development of multiobjective optimisation methods to improve the accuracy with which predictions can be made about the properties of molecules in the early stages of the drug discovery process. The project focused on protein-ligand docking which is a technique that is widely used to prioritise compounds for biological testing but which is limited in its effectiveness due to inadequacies in the scoring functions that are used to drive the procedure. Several of the known limitations of scoring functions were investigated including: the prediction of the binding-pose of a known ligand; the docking of ligands to non-native proteins; and the re-ranking of a dataset of ligands to correlate more closely with known binding affinities.

Janssen MSc Summer Placement

Janssen-Cilag Spain

Principal Investigator

£1,500

5 May 2005

4 months

Analysis of ADMET models

Janssen-Cilag Spain

Principal Investigator

£1,500

15 June 2004

15 months

Support tools for automatic pharmacophore generation

Pfizer

Principal Investigator

£71,467

1 March 2004

22 months

Johnson and Johnson PhD

Janssen Pharmaceuticals N.V.

Investigator

£76,305

1 January 2004

36 months

Tuning Parameters for Multiobjective Library Design

GlaxoSmithKline

Principal Investigator

£4,277

1 December 2003

2 months

Novel methods for the association of chemical similarity with biological response

GlaxoSmithKline

Principal Investigator

£21,000

1 October 2003

36 months

Mining molecular bioassay data

GlaxoSmithKline

Principal Investigator

£21,000

1 October 2002

36 months

The development of computational methods for 3D similarity and structure-based design techniques in lead optimisation

Pfizer

Investigator

£125,016

1 January 2003

24 months

Novel methods for the alignment of flexible molecules

GlaxoSmithKline

Principal Investigator

£21,000

1 October 2002

36 months

Multiple flexible alignment of molecules

Cambridge Crystallographic Data Centre

Principal Investigator

£19,500

1 May 2002

36 months

Teaching interests

My teaching interests are in applied computational techniques including data mining and machine learning. I played a central role in the curriculum design of the MSc Data Science which was launched in the School in September 2014 and currently I coordinate the module INF6028: Data Mining and Data Visualisation as well as supervising dissertations in data science.

I have a particular interest in applying data science techniques to the processing of chemical structures for applications such as drug design: a field which has become known as Chemoinformatics. I teach INF105: Introduction to Chemoinformatics and INF215: Introduction to Computer Aided Drug Design to first and second year chemistry undergraduates, respectively. I organised and ran an annual short course on a Practical Introduction to Chemoinformatics for many years which attracted PhD students and industrial delegates from across the globe.

Teaching activities

INF325 - Building AI Applications

INF6027 - Introduction to Data Science

INF6028 - Data Mining

INF6060 - Information Retrieval: Search Engines and Digital Libraries

Professional activities and memberships

Membership of professional bodies

Trustee. Molecular Graphics and Modelling Society, 2005 -
Committee member of UK QSAR and Chemoinformatics Group, 2005 -

Editorial board membership

Member of Editorial Board of Journal of Cheminformatics, 2008 -
Member of Editorial Advisory Board of Journal of Chemical Information and Modeling, 2005 -
Editor of Reviews in Computational Chemistry, 2005-2006

Committee and advisory group membership

Member of the Advisory Board of AI3SD: AI for Chemical Discovery EPSRC Network
Trustee of Lhasa Limited, 2014-to date
Governor of the Cambridge Crystallographic Data Centre, Dec 2006-May 2013. Vice-Chair of board of Governors May 2013-2014
Member of Scientific Advisory Committee of the triennial International Conference on Chemical Structures at Noordwijkerhout held in the Netherlands, 2005-to-date
Member of the American Chemical Society, 2001 to date
Member of Scientific Advisory Board of EBI Chemistry Services, 2016-2017. Chair of board 2017-to date
Member of Strategy Advisory Board of EPSRC Prosperity Partnership grant to the Universities of Strathclyde and Nottingham and GlaxoSmithKline (GSK) on “Accelerated Discovery and Development of New Medicines” 2019-
Member of Management Advisory Panel of EPSRC funded Physical Sciences Data Science service, 2019-

Invited presentations

“Applications of Machine Learning in Molecular Design: Learning from Bioactivity and Reaction Databases” Summer School on Machine Learning, Leuven, Belgium. Aug. 2018
“Molecular Shape Matching using Spectral Geometry Techniques.” GlaxoSmithKline. July 5, 2017
“From Spectral Clustering to Spectral Geometry: Applications in Chemoinformatics.” Computational Chemistry Kitchen, Oxford, Mar 16, 2017
“De Novo Design: from Drugs to the Design of Sustainable Cleaning Agents,” University of Leeds, Jan. 2017
“De Novo Design: from Drug Discovery to the Design of Novel Chemicals from Biomasses” German Chemoinformatics Conference, Nov, 2016
“Perspectives on De Novo Design”, Keynote at Third Oxford Meeting on Drug Design, University of Oxford, 2014.
“Multiobjective Design of Drug-like Molecules” at Multi-disciplinary Integration and Optimisation in Science and Engineering. UCL, London, 2012
“Applications of Wavelets in Virtual Screening” at Journal of Chemical Information and Modeling 50th Anniversary Symposium, American Chemical Society, Boston, 2010

Other roles

Reviewer of research funding proposals for the Austrian Science Fund, BBSRC, EPSRC, Leverhulme Visiting Professorship Scheme, Medical Research Council, Royal Society, Science Foundation Ireland and the Wellcome Trust
External examiner for PhD theses at the universities of Cambridge, Leeds, Imperial College, Manchester, Newcastle, Portsmouth, York and Cyprus
Organiser and Chair of the triennial International Conferences in Chemoinformatics held in ��«Ӱҵ since 1998 Chair of 2018 iConference in ��«Ӱҵ.