Community-driven roadmap for integrated disease maps. - Marek Ostaszewski; Stephan Gebel; Inna Kuperstein; Alexander Mazein; Andrei Yu. Zinovyev; Ugur Dogrusoz; Jan Hasenauer; Ronan M. T. Fleming; Nicolas Le Novère; Piotr Gawron; Thomas S. Ligon; Anna Niarakis; et al. (Briefings Bioinform., 2019)

RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. - Vidisha Singh; George D. Kalliolias; Marek Ostaszewski; Maëva Veyssiere; Eleftherios Pilalis; Piotr Gawron; Alexander Mazein; Eric Bonnet; Elisabeth Petit-Teixeira; Anna Niarakis (Database J. Biol. Databases Curation, 2020)

Automated inference of Boolean models from molecular interaction maps using CaSQ. - Sara Sadat Aghamiri; Vidisha Singh; Aurélien Naldi; Tomás Helikar; Sylvain Soliman; Anna Niarakis; Jinbo Xu (Bioinform., 2020)

A practical guide to mechanistic systems modeling in biology using a logic-based approach. - Anna Niarakis; Tomás Helikar (Briefings Bioinform., 2021)

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)

The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. - Vasundra Touré; Åsmund Flobak; Anna Niarakis; Steven Vercruysse; Martin Kuiper (Briefings Bioinform., 2021)

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. - Andreas Dräger; Tomás Helikar; Matteo Barberis; Marc R. Birtwistle; Laurence Calzone; Claudine Chaouiya; Jan Hasenauer; Jonathan R. Karr; Anna Niarakis; María Rodríguez Martínez; Julio Saez-Rodriguez; Juilee Thakar (Bioinform., 2021)

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. - Anna Niarakis; Dagmar Waltemath; James A. Glazier; Falk Schreiber; Sarah M. Keating; David P. Nickerson; Claudine Chaouiya; Anne Siegel; Vincent Noël; Henning Hermjakob; Tomás Helikar; Sylvain Soliman; et al. (Briefings Bioinform., 2022)

Building digital twins of the human immune system: toward a roadmap. - Reinhard C. Laubenbacher; Anna Niarakis; Tomás Helikar; Gary An; B. Shapiro; Rahuman S. Malik-Sheriff; T. J. Sego; Adam C. Knapp; Paul Macklin; James A. Glazier (npj Digit. Medicine, 2022)

Computational modelling in health and disease: highlights of the 6th annual SysMod meeting. - Anna Niarakis; Juilee Thakar; Matteo Barberis; María Rodríguez Martínez; Tomás Helikar; Marc R. Birtwistle; Claudine Chaouiya; Laurence Calzone; Andreas Dräger (Bioinform., 2022)

Metabolic reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: A hybrid modeling approach. - Sahar Aghakhani; Sylvain Soliman; Anna Niarakis (PLoS Comput. Biol., 2022)

A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance. - Alexander Mazein; Marcio Luis Acencio; Irina Balaur; Adrien Rougny; Danielle Welter; Anna Niarakis; Diana Ramirez Ardila; Ugur Dogrusoz; Piotr Gawron; Venkata P. Satagopam; Wei Gu; Andreas Kremer; et al. (Frontiers Bioinform., 2023)

MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps. - Sahar Aghakhani; Anna Niarakis; Sylvain Soliman (J. Integr. Bioinform., 2024)

Building a modular and multi-cellular virtual twin of the synovial joint in Rheumatoid Arthritis. - Naouel Zerrouk; Franck Augé; Anna Niarakis (npj Digit. Medicine, 2024)

Design specifications for biomedical virtual twins in engineered adoptive cellular immunotherapies. - Ulrike Weirauch; Markus Kreuz; Colin Birkenbihl; Miriam Alb; Maria Quaranta; Laurence Calzone; Sophia Orozco-Ruiz; Stefanie Binder; Luise Fischer; Solène Clavreul; Morine Maguri; Maximilian Ferle; et al. (npj Digit. Medicine, 2025)