PDQ Wizard: automated prioritization and characterization of gene and protein lists using biomedical literature. - G. R. Grimes; T. Q. Wen; Muriel Mewissen; Robert M. Baxter; Stuart L. Moodie; J. S. Beattie; Peter Ghazal (Bioinform., 2006)

A Graphical Notation to describe the Logical Interactions of Biological Pathways. - Stuart L. Moodie; Anatoly A. Sorokin; Igor Goryanin; Peter Ghazal (J. Integr. Bioinform., 2006)

Quantifying the implicit process flow abstraction in SBGN-PD diagrams with Bio-PEPA - Laurence Loewe; Stuart L. Moodie; Jane Hillston (COMPMOD, 2009)

Translation from the Quantified Implicit Process Flow Abstraction in SBGN-PD Diagrams to Bio-PEPA Illustrated on the Cholesterol Pathway. - Laurence Loewe; Maria Luisa Guerriero; Steven Watterson; Stuart L. Moodie; Peter Ghazal; Jane Hillston (Trans. Comp. Sys. Biology, 2011)

Software support for SBGN maps: SBGN-ML and LibSBGN. - Martijn P. van Iersel; Alice Villéger; Tobias Czauderna; Sarah E. Boyd; Frank T. Bergmann; Augustin Luna; Emek Demir; Anatoly A. Sorokin; Ugur Dogrusöz; Yukiko Matsuoka; Akira Funahashi; Mirit I. Aladjem; et al. (Bioinform., 2012)

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. - Frank T. Bergmann; Richard R. Adams; Stuart L. Moodie; Jonathan Cooper; Mihai Glont; Martin Golebiewski; Michael Hucka; Camille Laibe; Andrew K. Miller; David P. Nickerson; Brett G. Olivier; Nicolas Rodriguez 001; et al. (BMC Bioinform., 2014)

COMBINE archive: One File To Share Them All. - Frank T. Bergmann; Richard Adams; Stuart L. Moodie; Jonathan Cooper; Mihai Glont; Martin Golebiewski; Michael Hucka; Camille Laibe; Andrew K. Miller; David P. Nickerson; Brett G. Olivier; Nicolas Rodriguez 001; et al. (CoRR, 2014)

Implementing a Domain-specific Language for Model-based Drug Development. - Natallia Kokash; Stuart L. Moodie; Mike K. Smith; Nick Holford (EUSPN/ICTH, 2015)

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2 . - Huaiyu Mi; Falk Schreiber; Stuart L. Moodie; Tobias Czauderna; Emek Demir; Robin Haw; Augustin Luna; Nicolas Le Novère; Anatoly A. Sorokin; Alice Villéger (J. Integr. Bioinform., 2015)

Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3. - Stuart L. Moodie; Nicolas Le Novère; Emek Demir; Huaiyu Mi; Alice Villéger (J. Integr. Bioinform., 2015)

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2. - Anatoly A. Sorokin; Nicolas Le Novère; Augustin Luna; Tobias Czauderna; Emek Demir; Robin Haw; Huaiyu Mi; Stuart L. Moodie; Falk Schreiber; Alice Villéger (J. Integr. Bioinform., 2015)

Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0. - Adrien Rougny; Vasundra Touré; Stuart L. Moodie; Irina Balaur; Tobias Czauderna; Hanna Borlinghaus; Ugur Dogrusoz; Alexander Mazein; Andreas Dräger; Michael L. Blinov; Alice Villéger; Robin Haw; et al. (J. Integr. Bioinform., 2019)

Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1. - Lucian P. Smith; Stuart L. Moodie; Frank T. Bergmann; Colin S. Gillespie; Sarah M. Keating; Matthias König 003; Chris J. Myers; Maciek J. Swat; Darren J. Wilkinson; Michael Hucka (J. Integr. Bioinform., 2020)