Molecules for memory: modelling CaMKII. - Melanie I. Stefan; Nicolas Le Novère (BMC Syst. Biol., 2007)

Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters. - Melanie I. Stefan; Stuart J. Edelstein; Nicolas Le Novère (BMC Syst. Biol., 2009)

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. - Chen Li 011; Marco Donizelli; Nicolas Rodriguez 001; Harish Dharuri; Lukas Endler; Vijayalakshmi Chelliah; Lu Li 002; Enuo He; Arnaud Henry; Melanie I. Stefan; Jacky L. Snoep; Michael Hucka; et al. (BMC Syst. Biol., 2010)

Ten Simple Rules for Getting Help from Online Scientific Communities. - Giovanni Marco Dall'Olio; Jacopo Marino; Michael Schubert; Kevin L. Keys; Melanie I. Stefan; Colin S. Gillespie; Pierre Poulain; Khader Shameer; Robert Sugar; Brandon M. Invergo; Lars Juhl Jensen; Jaume Bertranpetit; et al. (PLoS Comput. Biol., 2011)

Cooperative Binding. - Melanie I. Stefan; Nicolas Le Novère (PLoS Comput. Biol., 2013)

Ten Simple Rules for Finishing Your PhD. - Jacopo Marino; Melanie I. Stefan; Sarah Blackford (PLoS Comput. Biol., 2014)

Multi-state Modeling of Biomolecules. - Melanie I. Stefan; Thomas M. Bartol; Terrence J. Sejnowski; Mary B. Kennedy (PLoS Comput. Biol., 2014)

The Quantitative Methods Boot Camp: Teaching Quantitative Thinking and Computing Skills to Graduate Students in the Life Sciences. - Melanie I. Stefan; Johanna L. Gutlerner; Richard T. Born; Michael Springer (PLoS Comput. Biol., 2015)

The systems biology format converter. - Nicolas Rodriguez 001; Jean-Baptiste Pettit; Piero Dalle Pezze; Lu Li 002; Arnaud Henry; Martijn P. van Iersel; Gaël Jalowicki; Martina Kutmon; Kedar Nath Natarajan; David Tolnay; Melanie I. Stefan; Chris T. A. Evelo; et al. (BMC Bioinform., 2016)

Cooperative binding mitigates the high-dose hook effect. - Ranjita Dutta Roy; Christian Rosenmund; Melanie I. Stefan (BMC Syst. Biol., 2017)

Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology. - Kevin S. Bonham; Melanie I. Stefan (PLoS Comput. Biol., 2017)

FindSim: A Framework for Integrating Neuronal Data and Signaling Models. - Nisha A. Viswan; Gubbi Vani HarshaRani; Melanie I. Stefan; Upinder S. Bhalla (Frontiers Neuroinformatics, 2018)

A multi-state model of the CaMKII dodecamer suggests a role for calmodulin in maintenance of autophosphorylation. - Matthew C. Pharris; Neal M. Patel; Tyler G. VanDyk; Thomas M. Bartol; Terrence J. Sejnowski; Mary B. Kennedy; Melanie I. Stefan; Tamara Kinzer-Ursem (PLoS Comput. Biol., 2019)

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). - Dagmar Waltemath; Martin Golebiewski; Michael L. Blinov; Padraig Gleeson; Henning Hermjakob; Michael Hucka; Esther Thea Inau; Sarah M. Keating; Matthias König 003; Olga Krebs; Rahuman S. Malik-Sheriff; David P. Nickerson; et al. (J. Integr. Bioinform., 2020)

Validation Through Collaboration: Encouraging Team Efforts to Ensure Internal and External Validity of Computational Models of Biochemical Pathways. - Richard Fitzpatrick; Melanie I. Stefan (Neuroinformatics, 2022)

Ten simple rules for failing successfully in academia. - Stefan Gaillard; Tara van Viegen; Michele Veldsman; Melanie I. Stefan; Veronika Cheplygina (PLoS Comput. Biol., 2022)