ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists. - Tomás Helikar; Jim A. Rogers (BMC Syst. Biol., 2009)

The Cell Collective: Toward an open and collaborative approach to systems biology. - Tomás Helikar; Bryan M. Kowal; Sean McClenathan; Mitchell Bruckner; Thaine W. Rowley; Alex Madrahimov; Benjamin Wicks; Manish Shrestha; Kahani Limbu; Jim A. Rogers (BMC Syst. Biol., 2012)

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. - Claudine Chaouiya; Duncan Bérenguier; Sarah M. Keating; Aurélien Naldi; Martijn P. van Iersel; Nicolas Rodriguez 001; Andreas Dräger; Finja Büchel; Thomas Cokelaer; Bryan M. Kowal; Benjamin Wicks; Emanuel J. V. Gonçalves; et al. (BMC Syst. Biol., 2013)

Sensitivity analysis of biological Boolean networks using information fusion based on nonadditive set functions. - Naomi Kochi; Tomás Helikar; Laura Allen; Jim A. Rogers; Zhenyuan Wang; Mihaela Teodora Matache (BMC Syst. Biol., 2014)

Cooperative development of logical modelling standards and tools with CoLoMoTo. - Aurélien Naldi; Pedro T. Monteiro 001; Christoph Müssel; Hans A. Kestler; Denis Thieffry; Ioannis Xenarios; Julio Saez-Rodriguez; Tomás Helikar; Claudine Chaouiya (Bioinform., 2015)

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1. - Claudine Chaouiya; Sarah M. Keating; Duncan Bérenguier; Aurélien Naldi; Denis Thieffry; Martijn P. van Iersel; Nicolas Le Novère; Tomás Helikar (J. Integr. Bioinform., 2015)

Integrating Interactive Computational Modeling in Biology Curricula. - Tomás Helikar; Christine E. Cutucache; Lauren M. Dahlquist; Tyler A. Herek; Joshua J. Larson; Jim A. Rogers (PLoS Comput. Biol., 2015)

Programmatic access to logical models in the Cell Collective modeling environment via a REST API. - Bryan M. Kowal; Travis R. Schreier; Joseph T. Dauer; Tomás Helikar (Biosyst., 2016)

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)

ccNetViz: a WebGL-based JavaScript library for visualization of large networks. - Ales Saska; David Tichy; Robert Moore; Achilles Rasquinha; Caner Akdas; Xiaodong Zhao; Renato Fabbri; Ana Jelicic; Gaurav Grover; Himanshu Jotwani; Mohamed Shadab; Resa M. K. Helikar; et al. (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)

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)

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4. - Lucian P. Smith; Frank T. Bergmann; Alan Garny; Tomás Helikar; Jonathan R. Karr; David P. Nickerson; Herbert M. Sauro; Dagmar Waltemath; Matthias König 003 (J. Integr. Bioinform., 2021)

A multi-approach and multi-scale platform to model CD4+ T cells responding to infections. - Kenneth Y. Wertheim; Bhanwar Lal Puniya; Alyssa La Fleur; Ab Rauf Shah; Matteo Barberis; Tomás Helikar (PLoS Comput. Biol., 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)

COMO: a pipeline for multi-omics data integration in metabolic modeling and drug discovery. - Brandt Bessell; Josh Loecker; Zhongyuan Zhao; Sara Sadat Aghamiri; Sabyasachi Mohanty; Rada Amin; Tomás Helikar; Bhanwar Lal Puniya (Briefings Bioinform., 2023)

Toward mechanistic medical digital twins: some use cases in immunology. - Reinhard C. Laubenbacher; Fred Adler; Gary An; Filippo Castiglione; Stephen Eubank 002; Luis L. Fonseca; James A. Glazier; Tomás Helikar; Marti Jett-Tilton; Denise Kirschner; Paul Macklin; Borna Mehrad; et al. (Frontiers Digit. Health, 2024)

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5. - Lucian P. Smith; Frank T. Bergmann; Alan Garny; Tomás Helikar; Jonathan R. Karr; David P. Nickerson; Herbert M. Sauro; Dagmar Waltemath; Matthias König 003 (J. Integr. Bioinform., 2024)