Tomás Helikar

21 papers Journal 21
YearRankTypeTitle / Venue / Authors
2024 J jnl
The simulation experiment description markup language (SED-ML): language specification for level 1 version 5.
J. Integr. Bioinform.
Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomás Helikar, Jonathan R. Karr, David P. Nickerson, Herbert M. Sauro, Dagmar Waltemath, Matthias König
2024 J jnl
Toward mechanistic medical digital twins: some use cases in immunology.
Frontiers Digit. Health
Reinhard C. Laubenbacher, Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luis L. Fonseca, James A. Glazier, Tomás Helikar, Marti Jett-Tilton, Denise Kirschner, Paul Macklin, Borna Mehrad, Beth Moore, Virginia Pasour, Ilya Shmulevich, Amber Smith, Isabel Voigt, Thomas E. Yankeelov, Tjalf Ziemssen
2023 J jnl
COMO: a pipeline for multi-omics data integration in metabolic modeling and drug discovery.
Briefings Bioinform.
Brandt Bessell, Josh Loecker, Zhongyuan Zhao, Sara Sadat Aghamiri, Sabyasachi Mohanty, Rada Amin, Tomás Helikar, Bhanwar Lal Puniya
2022 J jnl
Addressing
Briefings Bioinform.
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, Laurence Calzone
2022 J jnl
Building digital twins of the human immune system: toward a roadmap.
npj Digit. Medicine
Reinhard C. Laubenbacher, Anna Niarakis, Tomás Helikar, Gary An, Bruce Shapiro, Rahuman S. Malik-Sheriff, T. J. Sego, Adam C. Knapp, Paul Macklin, James A. Glazier
2022 J jnl
Computational modelling in health and disease: highlights of the 6th annual SysMod meeting.
Bioinform.
Anna Niarakis, Juilee Thakar, Matteo Barberis, María Rodríguez Martínez, Tomás Helikar, Marc R. Birtwistle, Claudine Chaouiya, Laurence Calzone, Andreas Dräger
2021 J jnl
A multi-approach and multi-scale platform to model CD4+ T cells responding to infections.
PLoS Comput. Biol.
Kenneth Y. Wertheim, Bhanwar Lal Puniya, Alyssa La Fleur, Ab Rauf Shah, Matteo Barberis, Tomás Helikar
2021 J jnl
A practical guide to mechanistic systems modeling in biology using a logic-based approach.
Briefings Bioinform.
Anna Niarakis, Tomás Helikar
2021 J jnl
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.
Briefings Bioinform.
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, Aurélien Naldi, Eugenia Oshurko, Ioannis Xenarios, Sylvain Soliman, Claudine Chaouiya, Tomás Helikar, Laurence Calzone
2021 J jnl
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems.
Bioinform.
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
2021 J jnl
The simulation experiment description markup language (SED-ML): language specification for level 1 version 4.
J. Integr. Bioinform.
Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomás Helikar, Jonathan R. Karr, David P. Nickerson, Herbert M. Sauro, Dagmar Waltemath, Matthias König
2020 J jnl
Automated inference of Boolean models from molecular interaction maps using CaSQ.
Bioinform.
Sara Sadat Aghamiri, Vidisha Singh, Aurélien Naldi, Tomás Helikar, Sylvain Soliman, Anna Niarakis, Jinbo Xu
2020 J jnl
ccNetViz: a WebGL-based JavaScript library for visualization of large networks.
Bioinform.
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, Tomás Helikar, Jonathan D. Wren
2016 J jnl
Programmatic access to logical models in the Cell Collective modeling environment via a REST API.
Biosyst.
Bryan M. Kowal, Travis R. Schreier, Joseph T. Dauer, Tomás Helikar
2015 J jnl
Cooperative development of logical modelling standards and tools with CoLoMoTo.
Bioinform.
Aurélien Naldi, Pedro T. Monteiro, Christoph Müssel, Hans A. Kestler, Denis Thieffry, Ioannis Xenarios, Julio Saez-Rodriguez, Tomás Helikar, Claudine Chaouiya
2015 J jnl
Integrating Interactive Computational Modeling in Biology Curricula.
PLoS Comput. Biol.
Tomás Helikar, Christine E. Cutucache, Lauren M. Dahlquist, Tyler A. Herek, Joshua J. Larson, Jim A. Rogers
2015 J jnl
The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.
J. Integr. Bioinform.
Claudine Chaouiya, Sarah M. Keating, Duncan Bérenguier, Aurélien Naldi, Denis Thieffry, Martijn P. van Iersel, Nicolas Le Novère, Tomás Helikar
2014 J jnl
Sensitivity analysis of biological Boolean networks using information fusion based on nonadditive set functions.
BMC Syst. Biol.
Naomi Kochi, Tomás Helikar, Laura Allen, Jim A. Rogers, Zhenyuan Wang, Mihaela Teodora Matache
2013 J jnl
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
BMC Syst. Biol.
Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan M. Kowal, Benjamin Wicks, Emanuel J. V. Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomás Helikar
2012 J jnl
The Cell Collective: Toward an open and collaborative approach to systems biology.
BMC Syst. Biol.
Tomás Helikar, Bryan M. Kowal, Sean McClenathan, Mitchell Bruckner, Thaine W. Rowley, Alex Madrahimov, Benjamin Wicks, Manish Shrestha, Kahani Limbu, Jim A. Rogers
2009 J jnl
ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists.
BMC Syst. Biol.
Tomás Helikar, Jim A. Rogers