David Gilbert's research projects (Bioinformatics Research Centre, University of Glasgow)


  • "Movement and communication in multiscale/multilevel models of biological systems", Leverhulme Trust Emeritus Fellowship. July 2021, 24 months.


  • "Petri nets for multiscale Systems Biology", 2011, 7 months. David Gilbert, PI. Monika Heiner, Visiting Professor. Funded by EPSRC (RC Grant reference: EP/I036168/1). Project website.

  • "EFACTS: European Friedreich's Ataxia Consortium for Translational Studies", 2010, 4 years. Mark Pook, Xaiohui Liu, David Gilbert. Funded by the European Union FP7. 15 partners overall, led by ULB Belgium.

  • Member of the SynBioNT - a Synthetic Biology Network for Modelling and Programming Cell-Chell Interactions,

  • Member of the Synthetic Biology Standards Network.

  • Member of the EVIMalaR (European Virtual Institute of malaria research).

  • SysTryp: Metabolomic systems biology analysis of differentiation in trypanosomes Mike Barrett and Fabien Jourdan (PIs), 3 others (including myself) and 7 partners. BBSRC and ANR (France), January 2008, 3 years.

  • The Molecular Nose EPSRC, Oct 2007, 4 years University of Glasgow: Walter Kolch (PI) (Beatson Institute for Cancer Research), Andy Pitt (Molecular and Cell Biology), Jon Cooper (Bionanotechnology and Microfluidics), Muffy Calder (Computing Science), David Gilbert (Computing Science), Mark Girolami (Bioinformatics and Computational Science). University of Strathclyde: Duncan Graham (Pure and Applied Chemistry), Karen Faulds (Raman Spectroscopy). MRC Genetics Unit: Howard Cooke (Molecular Biology and mouse models) (Edinburgh).

  • SIMAP: Simulation modelling of the MAP kinase pathway, David Gilbert (PI), European Union FP6, January 2006, 3 years (Consortium of 9 members, led by Compugen, Israel).

  • "Glasgow iGEM", international Genetically engineered Machines Competition, David Gilbert and Susan Rosser (PIs). Funding from the European Union and Scottish Enterprise. July-November 2007.

  • "Scottish Bioinformatics Research Network (SBRN)"
    Comprising the Universities of Dundee (lead institution), Edinburgh and Glasgow, the Scottish Crop Research Institute (SCRI), Biomathematics and Statistics Scotland (BIOSS) and the Scottish Bioinformatics Forum. Funding from the Scottish Higher Education Funding Council (SHEFC), the Scottish Executive Environment and Rural Affairs Department (SEERAD), and Scottish Enterprise for four years 2005.

  • "Biochemical Network Data Mined from Scientific Texts", Bioinformatics Research Centre, University of Glasgow and MD Biosciences. Tamara Polajnar (PhD student), David Gilbert (PI), Iadh Ounis, Paul Garside (MD Biosciences). PhD Industrial Studentship, funded by Scottish Enterprise through their Life Sciences programme, 36 months from November 2005.

  • SB(R)Net -- Systems Biology Regional Network. Partner institutions: University of Ulster (Co-ordinator), University of Liverpool, University of Wales -- Aberystwyth, University of Wales -- Bangor, Queen's University Belfast, University College Dublin, University of Glasgow.

  • Anna Dominiczak (BHF Blood Pressure Group, Medicine and Theraputics), Malcolm Atkinson and David Gilbert,
    " Cardiovascular Functional Genomics", funded by the Wellcome Trust, collaboration between 5 large research groupings in the UK, 5 years from August 2002.

  • "Modelling, Inference and Analysis for Biological Systems up to the Cellular Level" BBSRC Research Equipment Grant, David Gilbert (PI), December 2005.

  • "Graph based methods for the analysis of biochemical structures" Juris Viksna, EPSRC Visiting Research Fellow, David Gilbert (PI), April 2005 for 1 year

  • David Gilbert (PI), Muffy Calder, Walter Kolch, Keith van Rijsbergen:
    "A Software Tool for the Simulation and Analysis of Biochemical Networks".
    Funding is for 4 years provided by the Department of Trade and Industry UK, under the Beacon scheme.
    Partners: Bioinformatics Research Centre - Department of Computing Science and the Beatson Institute, University of Glasgow.

  • "Inter-residue Interactions in Protein Structures", Bioinformatics Research Centre, University of Glasgow and the Computational Biology Research Center, Tokyo, Japan. David Gilbert (PI), Pawel Herzyk, Makiko Suwa and Michael Gromiha, funded by the DAIWA Anglo-Japanese Foundation, 12 months from January 2004

  • "BRIDGES: BioMedical Research Informatics Delivered by Grid Enabled Services". National e-Science Centre: Malcolm Atkinson (PI), Bioinformatics Research Centre, University of Glasgow: David Gilbert (PI Glasgow), IBM UK Life Sciences: David White. EPSRC, UK e-Science Core Programme project, 23 months.

  • "Incorporating sequence and interaction information in topological models of protein structure" Mallika Veeramalai, PhD student.

  • "Assigning function to genes using a variety of data sources by combining predications with varying levels of uncertainty", Ali Al-Shahib, PhD student.

  • "Automatic extraction of rules for protein classification", Juris Viksna and David Gilbert (PI Glasgow), 2000-2003, funded by the Wellcome Trust. City University (contractor) and University College London (Department of Biochemistry); European Bioinformatics Institute (associated institution). Continuation funding by the University of Glasgow to April 2005.

  • "Machine learning of protein structure and function", Aik Choon Tan, PhD student.

  • "Patterns, functions and structures on a protein topology database", funded by the BBSRC/EPSRC Bioinformatics Initiative, 2 years from January 2001, David Gilbert (PI Glasgow) and Gilleain Torrance, joint project with David Westhead and Ioannis Michalopoulos, Leeds University (Department of Biochemistry & Molecular Biology). Continuation funding by the University of Glasgow to September 2004.

  • Mathis Riehle, David Gilbert, Chris Wilkinson and Stephen Yarwood, " Engineering Cell Form and Function with Nanometric Surfaces", a collaboration between the Centre for Cell Engineering and the Bioinformatics Research Centre. Funded by the Royal Society Wolfson Foundation Laboratory Refurbishment Scheme, February 2003 for 1 year

  • Yves Deville and David Gilbert, Application of constraint satisfaction for the analysis of biochemical networks September 2002 for 1 year, funded by the EPSRC

  • "Structural patterns in the composite regulatory regions of genomes", Olivier Sand Marie Curie 30 Research Fellow, 2 years from 2001.

  • "Pattern discovery for protein classification", David Gilbert (Leverhulme Trust Research Fellow), August 2000, 6 months, held at the Department of Biochemistry, University College London (Professor Janet Thornton).

  • "Protein topology pattern matching", D. Gilbert and Dr. Juris Viksna (Institute of Mathematics and Computer Science, University of Latvia), funded by the Royal Society, 1999.

  • Protein Function and Biochemical Pathways European Bioinformatics Institute, industry programme. David Gilbert acts as a consultant/programmer.

  • "Formalising TOPS cartoons, and the development of an interactive similarity search mechanism over TOPS databases", David Gilbert (EPSRC Visiting Research Fellow at the European Bioinformatics Institute) with David Westhead (EBI) and Janet Thornton (EBI, UCL, Birkbeck), 1998

  • "The Design and Implementation of a Constraint-based Pattern Recognition System for DNA and Proteins" funded by the British Council & the Research Council of Norway. 1996-97