Tomás Helikar

Publication Activity (10 Years)

Years Active: 2009-2024
Publications (10 Years): 13

Top Topics

Systems Biology

Computational Model

Markup Language

Signal Transduction

Top Venues

Briefings Bioinform.

J. Integr. Bioinform.

PLoS Comput. Biol.

Publications

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
Toward mechanistic medical digital twins: some use cases in immunology. Frontiers Digit. Health 6 (2024)
Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomás Helikar, Jonathan R. Karr, David P. Nickerson, Herbert M. Sauro, Dagmar Waltemath, Matthias König
The simulation experiment description markup language (SED-ML): language specification for level 1 version 5. J. Integr. Bioinform. 21 (1) (2024)
Anna Niarakis, Juilee Thakar, Matteo Barberis, María Rodríguez Martínez, Tomás Helikar, Marc R. Birtwistle, Claudine Chaouiya, Laurence Calzone, Andreas Dräger
Computational modelling in health and disease: highlights of the 6th annual SysMod meeting. Bioinform. 38 (21) (2022)
Anna Niarakis, Dagmar Waltemath, James Glazier, Falk Schreiber, Sarah M. Keating, David P. Nickerson, Claudine Chaouiya, Anne Siegel, Vincent Noël, Henning Hermjakob, Tomás Helikar, Sylvain Soliman, Laurence Calzone
. Briefings Bioinform. 23 (4) (2022)
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
Building digital twins of the human immune system: toward a roadmap. npj Digit. Medicine 5 (2022)
Anna Niarakis, Tomás Helikar
A practical guide to mechanistic systems modeling in biology using a logic-based approach. Briefings Bioinform. 22 (4) (2021)
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
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. 22 (2) (2021)
Kenneth Y. Wertheim, Bhanwar Lal Puniya, Alyssa La Fleur, Ab Rauf Shah, Matteo Barberis, Tomás Helikar
A multi-approach and multi-scale platform to model CD4+ T cells responding to infections. PLoS Comput. Biol. 17 (8) (2021)
Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomás Helikar, Jonathan R. Karr, David P. Nickerson, Herbert M. Sauro, Dagmar Waltemath, Matthias König
The simulation experiment description markup language (SED-ML): language specification for level 1 version 4. J. Integr. Bioinform. 18 (3) (2021)
Andreas Dräger, Tomás Helikar, Matteo Barberis, Marc Birtwistle, Laurence Calzone, Claudine Chaouiya, Jan Hasenauer, Jonathan R. Karr, Anna Niarakis, María Rodríguez Martínez, Julio Saez-Rodriguez, Juilee Thakar
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinform. 37 (21) (2021)
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
ccNetViz: a WebGL-based JavaScript library for visualization of large networks. Bioinform. 36 (16) (2020)
Sara Sadat Aghamiri, Vidisha Singh, Aurélien Naldi, Tomás Helikar, Sylvain Soliman, Anna Niarakis, Jinbo Xu
Automated inference of Boolean models from molecular interaction maps using CaSQ. Bioinform. 36 (16) (2020)
Bryan M. Kowal, Travis R. Schreier, Joseph T. Dauer, Tomás Helikar
Programmatic access to logical models in the Cell Collective modeling environment via a REST API. Biosyst. 139 (2016)
Aurélien Naldi, Pedro T. Monteiro, Christoph Müssel, Hans A. Kestler, Denis Thieffry, Ioannis Xenarios, Julio Saez-Rodriguez, Tomás Helikar, Claudine Chaouiya
Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinform. 31 (7) (2015)
Tomás Helikar, Christine E. Cutucache, Lauren M. Dahlquist, Tyler A. Herek, Joshua J. Larson, Jim A. Rogers
Integrating Interactive Computational Modeling in Biology Curricula. PLoS Comput. Biol. 11 (3) (2015)
Claudine Chaouiya, Sarah M. Keating, Duncan Bérenguier, Aurélien Naldi, Denis Thieffry, Martijn P. van Iersel, Nicolas Le Novère, Tomás Helikar
The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1. J. Integr. Bioinform. 12 (2) (2015)
Naomi Kochi, Tomás Helikar, Laura Allen, Jim A. Rogers, Zhenyuan Wang, Mihaela Teodora Matache
Sensitivity analysis of biological Boolean networks using information fusion based on nonadditive set functions. BMC Syst. Biol. 8 (2014)
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
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst. Biol. 7 (2013)
Tomás Helikar, Bryan M. Kowal, Sean McClenathan, Mitchell Bruckner, Thaine W. Rowley, Alex Madrahimov, Benjamin Wicks, Manish Shrestha, Kahani Limbu, Jim A. Rogers
The Cell Collective: Toward an open and collaborative approach to systems biology. BMC Syst. Biol. 6 (2012)
Tomás Helikar, Jim A. Rogers
ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists. BMC Syst. Biol. 3 (2009)