Emergence and Its Place in Nature: A Case Study of Biochemical Networks. - Fred C. Boogerd; Frank J. Bruggeman; Robert C. Richardson; A. Stephan; Hans V. Westerhoff (Synth., 2005)

Noise Management by Molecular Networks. - Frank J. Bruggeman; Nils Blüthgen; Hans V. Westerhoff (PLoS Comput. Biol., 2009)

Formal Methods in Molecular Biology (Dagstuhl Seminar 11151). - Rainer Breitling; Frank J. Bruggeman; Corrado Priami; Adelinde M. Uhrmacher (Dagstuhl Reports, 2011)

ITFoM - The IT Future of Medicine. - Hans Lehrach; Ralf Sudbrak; Peter Boyle; Markus Pasterk; Kurt Zatloukal; Heimo Müller; Tim Hubbard; Angela Brand; Mark A. Girolami; Daniel Jameson; Frank J. Bruggeman; Hans V. Westerhoff (FET, 2011)

Fast Flux Module Detection Using Matroid Theory. - Arne C. Reimers; Frank J. Bruggeman; Brett G. Olivier; Leen Stougie (J. Comput. Biol., 2015)

Interplay between Constraints, Objectives, and Optimality for Genome-Scale Stoichiometric Models. - Timo R. Maarleveld; Meike T. Wortel; Brett G. Olivier; Bas Teusink; Frank J. Bruggeman (PLoS Comput. Biol., 2015)

Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism. - Katja N. Rybakova; Frank J. Bruggeman; Aleksandra Tomaszewska; Martijn J. Moné; Carsten Carlberg; Hans V. Westerhoff (PLoS Comput. Biol., 2015)

Maintaining maximal metabolic flux by gene expression control. - Robert Planqué; Josephus Hulshof; Bas Teusink; Johannes C. Hendriks; Frank J. Bruggeman (PLoS Comput. Biol., 2018)

Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield. - Meike T. Wortel; Elad Noor; Michael Ferris 001; Frank J. Bruggeman; Wolfram Liebermeister (PLoS Comput. Biol., 2018)

The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates. - Daan H. de Groot; Coco van Boxtel; Robert Planqué; Frank J. Bruggeman; Bas Teusink (PLoS Comput. Biol., 2019)

The Fundamental Equations of Change in Statistical Ensembles and Biological Populations. - Steven A. Frank; Frank J. Bruggeman (Entropy, 2020)

Elementary Growth Modes provide a molecular description of cellular self-fabrication. - Daan H. de Groot; Josephus Hulshof; Bas Teusink; Frank J. Bruggeman; Robert Planqué (PLoS Comput. Biol., 2020)

Unlocking Elementary Conversion Modes: ecmtool Unveils All Capabilities of Metabolic Networks. - Tom J. Clement; Erik B. Baalhuis; Bas Teusink; Frank J. Bruggeman; Robert Planqué; Daan H. de Groot (Patterns, 2021)

Is distance from equilibrium a good indicator for a reaction's flux control? - David D. van Niekerk; Erik Rust; Frank J. Bruggeman; Hans V. Westerhoff; Jacky L. Snoep (Biosyst., 2023)

Whole-cell metabolic control analysis. - Frank J. Bruggeman; Maaike Remeijer; Maarten Droste; Luis Salinas; Meike T. Wortel; Robert Planqué; Herbert M. Sauro; Bas Teusink; Hans V. Westerhoff (Biosyst., 2023)