S
Stuart L. Moodie
Researcher at University of Edinburgh
Publications - 36
Citations - 2116
Stuart L. Moodie is an academic researcher from University of Edinburgh. The author has contributed to research in topics: Systems Biology Graphical Notation & Entity–relationship model. The author has an hindex of 18, co-authored 36 publications receiving 1888 citations. Previous affiliations of Stuart L. Moodie include European Bioinformatics Institute & University College London.
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Journal ArticleDOI
The Systems Biology Graphical Notation
Nicolas Le Novère,Michael Hucka,Huaiyu Mi,Stuart L. Moodie,Falk Schreiber,Falk Schreiber,Anatoly Sorokin,Emek Demir,Katja Wegner,Mirit I. Aladjem,Sarala M. Wimalaratne,Frank T Bergman,Ralph Gauges,Peter Ghazal,Hideya Kawaji,Lu Li,Yukiko Matsuoka,Alice Villéger,Sarah Elizabeth Boyd,Laurence Calzone,Mélanie Courtot,Ugur Dogrusoz,Tom C. Freeman,Akira Funahashi,Samik Ghosh,Akiya Jouraku,Sohoung Kim,Fedor A. Kolpakov,Augustin Luna,Sven Sahle,Esther Schmidt,Steven Watterson,Steven Watterson,Guanming Wu,Igor Goryanin,Douglas B. Kell,Chris Sander,Herbert M. Sauro,Jacky L. Snoep,Kurt W. Kohn,Hiroaki Kitano +40 more
TL;DR: The Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists, believes that it will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge.
Journal ArticleDOI
SBML Level 3: an extensible format for the exchange and reuse of biological models
Sarah M. Keating,Sarah M. Keating,Dagmar Waltemath,Matthias König,Fengkai Zhang,Andreas Dräger,Claudine Chaouiya,Claudine Chaouiya,Frank Bergmann,Andrew Finney,Colin S. Gillespie,Tomáš Helikar,Stefan Hoops,Rahuman S Malik-Sheriff,Stuart L. Moodie,Ion I. Moraru,Chris J. Myers,Aurélien Naldi,Brett G. Olivier,Brett G. Olivier,Brett G. Olivier,Sven Sahle,James C. Schaff,Lucian P. Smith,Lucian P. Smith,Maciej J. Swat,Denis Thieffry,Leandro Watanabe,Darren J. Wilkinson,Darren J. Wilkinson,Michael L. Blinov,Kimberly Begley,James R. Faeder,Harold F. Gómez,Thomas M. Hamm,Yuichiro Inagaki,Wolfram Liebermeister,Allyson L. Lister,Daniel Lucio,Eric Mjolsness,Carole J. Proctor,Karthik Raman,Nicolas Rodriguez,Clifford A. Shaffer,Bruce E. Shapiro,Joerg Stelling,Neil Swainston,Naoki Tanimura,John Wagner,Martin Meier-Schellersheim,Herbert M. Sauro,Bernhard O. Palsson,Hamid Bolouri,Hiroaki Kitano,Akira Funahashi,Henning Hermjakob,John Doyle,Michael Hucka,Richard R. Adams,Nicholas Alexander Allen,Bastian R. Angermann,Marco Antoniotti,Gary D. Bader,Jan Červený,Mélanie Courtot,Christopher Cox,Piero Dalle Pezze,Emek Demir,William S. Denney,Harish Dharuri,Julien Dorier,Dirk Drasdo,Ali Ebrahim,Johannes Eichner,Johan Elf,Lukas Endler,Chris T. Evelo,Christoph Flamm,Ronan M. T. Fleming,Martina Fröhlich,Mihai Glont,Emanuel Gonçalves,Martin Golebiewski,Hovakim Grabski,Alex Gutteridge,Damon Hachmeister,Leonard A. Harris,Benjamin D. Heavner,Ron Henkel,William S. Hlavacek,Bin Hu,Daniel R. Hyduke,Hidde de Jong,Nick Juty,Peter D. Karp,Jonathan R. Karr,Douglas B. Kell,Roland Keller,Ilya Kiselev,Steffen Klamt,Edda Klipp,Christian Knüpfer,Fedor A. Kolpakov,Falko Krause,Martina Kutmon,Camille Laibe,Conor Lawless,Lu Li,Leslie M. Loew,Rainer Machné,Yukiko Matsuoka,Pedro Mendes,Huaiyu Mi,Florian Mittag,Pedro T. Monteiro,Kedar Nath Natarajan,Poul M. F. Nielsen,Tramy Nguyen,Alida Palmisano,Jean-Baptiste Pettit,Thomas Pfau,Robert Phair,Tomas Radivoyevitch,Johann M. Rohwer,Oliver A. Ruebenacker,Julio Saez-Rodriguez,Martin Scharm,Henning Schmidt,Falk Schreiber,Michael Schubert,Roman Schulte,Stuart C. Sealfon,Kieran Smallbone,Sylvain Soliman,Melanie I. Stefan,Devin P. Sullivan,Koichi Takahashi,Bas Teusink,David Tolnay,Ibrahim Vazirabad,Axel von Kamp,Ulrike Wittig,Clemens Wrzodek,Finja Wrzodek,Ioannis Xenarios,Anna Zhukova,Jeremy Zucker +146 more
TL;DR: The latest edition of the Systems Biology Markup Language (SBML) is reviewed, a format designed for this purpose that leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models.
Journal ArticleDOI
Systems biology reveals new strategies for personalizing cancer medicine and confirms the role of PTEN in resistance to trastuzumab.
Dana Faratian,Alexey Goltsov,Galina Lebedeva,Anatoly Sorokin,Stuart L. Moodie,Peter Mullen,Charlene Kay,In Hwa Um,Simon P. Langdon,Igor Goryanin,David J. Harrison +10 more
TL;DR: Quantitative PTEN protein expression was found to be the key determinant of resistance to anti-HER2 therapy in silico, which was predictive of unseen experiments in vitro using the PTEN inhibitor bp(V), further compelling evidence that PTEN, appropriately measured in the clinical setting, refines clinical decision making in patients treated with anti- HER2 therapies.
Journal ArticleDOI
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project
Frank 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,Herbert M. Sauro,Martin Scharm,Stian Soiland-Reyes,Dagmar Waltemath,Florent Yvon,Nicolas Le Novère,Nicolas Le Novère +18 more
TL;DR: It is anticipated that the COMBINE Archive will become a significant help for modellers, as the domain moves to larger, more complex experiments such as multi-scale models of organs, digital organisms, and bioengineering.
Journal ArticleDOI
Protein recognition of adenylate: an example of a fuzzy recognition template.
TL;DR: The concept of a fuzzy recognition template is presented, as a useful means of describing the protein/adenylate interactions presented here, which will also be a valuable concept for characterising other protein/ligand interactions.