Tomas Helikar
Tomas Helikar
Susan J Rosowski Associate Professor, Department of Biochemistry, University of Nebraska - Lincoln
Verified email at - Homepage
Cited by
Cited by
Emergent decision-making in biological signal transduction networks
T Helikar, J Konvalina, J Heidel, JA Rogers
Proceedings of the National Academy of Sciences 105 (6), 1913-1918, 2008
Logical modeling and dynamical analysis of cellular networks
W Abou-Jaoudé, P Traynard, PT Monteiro, J Saez-Rodriguez, T Helikar, ...
Frontiers in genetics 7, 94, 2016
The Cell Collective: Toward an open and collaborative approach to systems biology.
T Helikar, B Kowal, S McClenathan, M Bruckner, T Rowley, B Wicks, ...
BMC Systems Biology 6 (1), 96, 2012
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
C Chaouiya, D Bérenguier, SM Keating, A Naldi, MP Van Iersel, ...
BMC systems biology 7 (1), 1-15, 2013
SBML Level 3: an extensible format for the exchange and reuse of biological models
SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ...
Molecular systems biology 16 (8), e9110, 2020
Cooperative development of logical modelling standards and tools with CoLoMoTo.
A Naldi, PT Monteiro, C Müssel, HA Kestler, D Thieffry, I Xenarios, ...
Bioinformatics 31 (7), 2015
ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists
T Helikar, JA Rogers
BMC systems biology 3 (1), 1-15, 2009
The CoLoMoTo interactive notebook: accessible and reproducible computational analyses for qualitative biological networks
A Naldi, C Hernandez, N Levy, G Stoll, PT Monteiro, C Chaouiya, ...
Frontiers in physiology 9, 680, 2018
A comprehensive, multi-scale dynamical model of ErbB receptor signal transduction in human mammary epithelial cells
T Helikar, N Kochi, B Kowal, M Dimri, M Naramura, SM Raja, V Band, ...
PloS one 8 (4), e61757, 2013
Integrating Interactive Computational Modeling in Biology Curricula
T Helikar, CE Cutucache, LA Dahlquist, TA Herek, JJ Larson, JA Rogers
PLoS Computational Biology, 2015
Boolean modeling of biochemical networks
T Helikar, N Kochi, J Konvalina, JA Rogers
Open Bioinformatics Journal 5, 16, 2011
COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms
M Ostaszewski, A Niarakis, A Mazein, I Kuperstein, R Phair, ...
Molecular systems biology 17 (10), e10387, 2021
Automated inference of Boolean models from molecular interaction maps using CaSQ
SS Aghamiri, V Singh, A Naldi, T Helikar, S Soliman, A Niarakis
Bioinformatics 36 (16), 4473-4482, 2020
A cell simulator platform: the cell collective
T Helikar, B Kowal, JA Rogers
Clinical Pharmacology & Therapeutics 93 (5), 393-395, 2013
Ergodic Sets as Cell Phenotype of Budding Yeast Cell Cycle
R Todd, T Helikar
Plos One 7 (10), e45780, 2012
Simulation of stimulation: cytokine dosage and cell cycle crosstalk driving timing-dependent T cell differentiation
M Barberis, T Helikar, P Verbruggen
Frontiers in Physiology 9, 879, 2018
A mechanistic computational model reveals that plasticity of CD4+ T cell differentiation is a function of cytokine composition and dosage
BL Puniya, RG Todd, A Mohammed, DM Brown, M Barberis, T Helikar
Frontiers in physiology, 878, 2018
Dynamics of Influenza Virus and Human Host Interactions During Infection and Replication Cycle
A Madrahimov, T Helikar, B Kowal, G Lu, J Rogers
Bulletin of Mathematical Biology, 2012
Student understanding of DNA structure–function relationships improves from using 3D learning modules with dynamic 3D printed models
ME Howell, CS Booth, SM Sikich, T Helikar, RL Roston, BA Couch, ...
Biochemistry and Molecular Biology Education 47 (3), 303-317, 2019
The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.
C Chaouiya, SM Keating, D Berenguier, A Naldi, D Thieffry, MP van Iersel, ...
Journal of Integrative Bioinformatics 12 (2), 2015
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