Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data. - Tom C. Freeman; Leon Goldovsky; Markus Brosch; Stijn van Dongen; Pierre Mazière; Russell J. Grocock; Shiri Freilich; Janet M. Thornton; Anton J. Enright (PLoS Comput. Biol., 2007)

A logic-based diagram of signalling pathways central to macrophage activation. - Sobia Raza; Kevin A. Robertson; Paul A. Lacaze; David Page; Anton J. Enright; Peter Ghazal; Tom C. Freeman (BMC Syst. Biol., 2008)

The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways. - Tom C. Freeman; Sobia Raza; Athanasios Theocharidis; Peter Ghazal (BMC Syst. Biol., 2010)

Construction of a large scale integrated map of macrophage pathogen recognition and effector systems. - Sobia Raza; Neil McDerment; Paul A. Lacaze; Kevin A. Robertson; Steven Watterson; Ying Chen; Michael Chisholm; George Eleftheriadis; Stephanie Monk; Maire O'Sullivan; Arran Turnbull; Douglas Roy; et al. (BMC Syst. Biol., 2010)

Visualisation of BioPAX Networks using BioLayout Express3D. - Derek W. Wright; Tim Angus; Anton J. Enright; Tom C. Freeman (F1000Research, 2014)

A promoter-level mammalian expression atlas. - Fantom Consortium; RIKEN PMII; RIKEN CLST (DGT); Alistair R. R. Forrest; Hideya Kawaji; Michael Rehli; J. Kenneth Baillie; Michiel J. L. de Hoon; Vanja Haberle; Timo Lassmann; Ivan V. Kulakovskiy; Marina Lizio; et al. (Nat., 2014)

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. - J. Kenneth Baillie; Andrew Bretherick; Christopher S. Haley; Sara Clohisey; Alan Gray; Lucile P. A. Neyton; Jeffrey Barrett; Eli A. Stahl; Albert Tenesa; Robin Andersson; J. Ben Brown; Geoffrey J. Faulkner; et al. (PLoS Comput. Biol., 2018)

Setting the basis of best practices and standards for curation and annotation of logical models in biology - highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. - Anna Niarakis; Martin Kuiper; Marek Ostaszewski; Rahuman S. Malik-Sheriff; Cristina Casals-Casas; Denis Thieffry; Tom C. Freeman; Paul D. Thomas; Vasundra Touré; Vincent Noël; Gautier Stoll; Julio Saez-Rodriguez; et al. (Briefings Bioinform., 2021)

A graph-based approach for the visualisation and analysis of bacterial pangenomes. - Josh Harling-Lee; Jamie Gorzynski; Gonzalo Yebra; Tim Angus; J. Ross Fitzgerald; Tom C. Freeman (BMC Bioinform., 2022)

Graphia: A platform for the graph-based visualisation and analysis of high dimensional data. - Tom C. Freeman; Sebastian Horsewell; Anirudh Patir; Josh Harling-Lee; Tim Regan; Barbara B. Shih; James G. D. Prendergast; David A. Hume; Tim Angus (PLoS Comput. Biol., 2022)