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List of works by Tomáš Helikar

A cell simulator platform: the cell collective

scientific article

A comprehensive, multi-scale dynamical model of ErbB receptor signal transduction in human mammary epithelial cells

scientific article

A multi-approach and multi-scale platform to model CD4+ T cells responding to infections

scientific article published on 03 August 2021

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

Bio-Logic Builder: A Non-Technical Tool for Building Dynamical, Qualitative Models ⬇️

scientific article published on October 17, 2012

COMO: a pipeline for multi-omics data integration in metabolic modeling and drug discovery

scientific article published in 2023

Design, Assessment, and in vivo Evaluation of a Computational Model Illustrating the Role of CAV1 in CD4(+) T-lymphocytes.

scientific article

Dynamics of influenza virus and human host interactions during infection and replication cycle

scientific article published on 19 October 2012

Emergent decision-making in biological signal transduction networks

scientific article (publication date: 4 February 2008)

Ergodic sets as cell phenotype of budding yeast cell cycle

scientific article

Integrating interactive computational modeling in biology curricula

scientific article

Integrative computational approach identifies drug targets in CD4<sup>+</sup> T-cell-mediated immune disorders

scientific article published on 22 January 2021

Interactive learning modules with 3D printed models improve student understanding of protein structure-function relationships

scientific article published on 26 June 2020

Logical Modeling and Dynamical Analysis of Cellular Networks

scientific article

Molecular phylogeny and evolutionary dynamics of influenza A nonstructural (NS) gene

scientific article published on 22 October 2013

Programmatic access to logical models in the Cell Collective modeling environment via a REST API.

scientific article published on 14 November 2015

SBML Level 3: an extensible format for the exchange and reuse of biological models

scientific article published on 01 August 2020

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

scientific article

Sensitivity analysis of biological Boolean networks using information fusion based on nonadditive set functions

scientific article

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

scientific article published on 21 April 2020

The Cell Collective: toward an open and collaborative approach to systems biology.

scientific article

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.

scientific article published on 04 September 2015

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5

scientific article published in March 2024

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