Tomás Helikar

According to our database, Tomás Helikar authored at least 21 papers between 2009 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

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

J. Integr. Bioinform., 2024

Toward mechanistic medical digital twins: some use cases in immunology.

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

Frontiers Digit. Health, 2024

2023

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., September, 2023

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., October, 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

Addressing <i>barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology</i>.

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

Briefings Bioinform., 2022

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

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

J. Integr. 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

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, Aurélien Naldi, Eugenia Oshurko, Ioannis Xenarios, Sylvain Soliman, Claudine Chaouiya, Tomás Helikar, Laurence Calzone

Briefings Bioinform., 2021

A practical guide to mechanistic systems modeling in biology using a logic-based approach.

Anna Niarakis, Tomás Helikar

Briefings Bioinform., 2021

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, Tomás Helikar, Jonathan D. Wren

Bioinform., 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

2016

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

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

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

Cooperative development of logical modelling standards and tools with CoLoMoTo.

Aurélien Naldi, Pedro T. Monteiro, Christoph Müssel, Hans A. Kestler, Denis Thieffry, Ioannis Xenarios, Julio Saez-Rodriguez, Tomás Helikar, Claudine Chaouiya

Bioinform., 2015

2014

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

2013

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, 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

BMC Syst. Biol., 2013

2012

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

2009

ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists.

Tomás Helikar, Jim A. Rogers

BMC Syst. Biol., 2009