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ORCIDTomás Helikar
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- unicode name: Tomáš Helikar
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Journal Articles
- 2024
[j21]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)- [j20]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) - 2023
- [j19]Brandt Bessell, Josh Loecker, Zhongyuan Zhao, Sara Sadat Aghamiri, Sabyasachi Mohanty, Rada Amin, Tomás Helikar, Bhanwar Lal Puniya:
COMO: a pipeline for multi-omics data integration in metabolic modeling and drug discovery. Briefings Bioinform. 24(6) (2023) - 2022
- [j18]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:
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. Briefings Bioinform. 23(4) (2022) - [j17]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): 4990-4993 (2022) - [j16]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) - 2021
- [j15]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): 1848-1859 (2021) - [j14]Anna Niarakis, Tomás Helikar:
A practical guide to mechanistic systems modeling in biology using a logic-based approach. Briefings Bioinform. 22(4) (2021) - [j13]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:
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinform. 37(21): 3702-3706 (2021) - [j12]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) - [j11]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) - 2020
- [j10]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): 4473-4482 (2020) - [j9]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): 4527-4529 (2020) - 2016
- [j8]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: 12-16 (2016) - 2015
- [j7]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): 1154-1159 (2015) - [j6]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) - [j5]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) - 2014
- [j4]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: 92 (2014) - 2013
- [j3]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: 135 (2013) - 2012
- [j2]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: 96 (2012) - 2009
- [j1]Tomás Helikar, Jim A. Rogers:
ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists. BMC Syst. Biol. 3: 58 (2009)
Coauthor Index
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