metaSHARK: a WWW platform for interactive exploration of metabolic networks. - Christopher Hyland; John W. Pinney; Glenn A. McConkey; David R. Westhead (Nucleic Acids Res., 2006)

Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis. - Iain W. Manfield; Chih-Hung Jen; John W. Pinney; Ioannis Michalopoulos; James R. Bradford; Philip M. Gilmartin; David R. Westhead (Nucleic Acids Res., 2006)

An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network. - Brian J. Holden; John W. Pinney; Simon C. Lovell; Grigoris D. Amoutzias; David L. Robertson (BMC Bioinform., 2007)

SHARKview: a tool for the visualization of systems biology data. - John W. Pinney; John M. Starkovich; Peter Li; David L. Robertson (BMC Syst. Biol., 2007)

Methodology capture: discriminating between the "best" and the rest of community practice. - James M. Eales; John W. Pinney; Robert D. Stevens 001; David L. Robertson (BMC Bioinform., 2008)

Identifying the Important HIV-1 Recombination Breakpoints. - John P. Archer; John W. Pinney; Jun Fan; Etienne Simon-Loriere; Eric J. Arts; Matteo Negroni; David L. Robertson (PLoS Comput. Biol., 2008)

JNets: Exploring networks by integrating annotation. - Jamie I. MacPherson; John W. Pinney; David L. Robertson (BMC Bioinform., 2009)

Low-complexity regions within protein sequences have position-dependent roles. - Alain Coletta; John W. Pinney; David Y. Weiss Solís; James Marsh; Steve Pettifer; Teresa K. Attwood (BMC Syst. Biol., 2010)

The biological context of HIV-1 host interactions reveals subtle insights into a system hijack. - Jonathan E. Dickerson; John W. Pinney; David L. Robertson (BMC Syst. Biol., 2010)

Patterns of HIV-1 Protein Interaction Identify Perturbed Host-Cellular Subsystems. - Jamie I. MacPherson; Jonathan E. Dickerson; John W. Pinney; David L. Robertson (PLoS Comput. Biol., 2010)

Simple topological properties predict functional misannotations in a metabolic network. - Rodrigo Liberal; John W. Pinney (Bioinform., 2013)

AMBIENT: Active Modules for Bipartite Networks - using high-throughput transcriptomic data to dissect metabolic response. - William A. Bryant; Michael J. E. Sternberg; John W. Pinney (BMC Syst. Biol., 2013)

Analysis of Metabolic Evolution in Bacteria Using Whole-Genome Metabolic Models. - William A. Bryant; Ali A. Faruqi; John W. Pinney (J. Comput. Biol., 2013)

PathwayBooster: a tool to support the curation of metabolic pathways. - Rodrigo Liberal; Beata K. Lisowska; David J. Leak; John W. Pinney (BMC Bioinform., 2015)