Tomas Helikar
Tomas Helikar
Associate Professor, Department of Biochemistry, University of Nebraska - Lincoln
Verified email at unl.edu - Homepage
Title
Cited by
Cited by
Year
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
1812008
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
1232013
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
1172016
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
1132012
ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists
T Helikar, JA Rogers
BMC systems biology 3 (1), 58, 2009
642009
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
532015
Boolean modeling of biochemical networks
T Helikar, N Kochi, J Konvalina, J A Rogers
The Open Bioinformatics Journal 5 (1), 2011
392011
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
382013
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
282018
A cell simulator platform: the cell collective
T Helikar, B Kowal, JA Rogers
Clinical Pharmacology & Therapeutics 93 (5), 393-395, 2013
282013
Integrating Interactive Computational Modeling in Biology Curricula
T Helikar, CE Cutucache, LA Dahlquist, TA Herek, JJ Larson, JA Rogers
PLoS Computational Biology, 2015
252015
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
252012
Ergodic Sets as Cell Phenotype of Budding Yeast Cell Cycle
R Todd, T Helikar
Plos One 7 (10), e45780, 2012
232012
Bio-Logic Builder: A Non-Technical Tool for Building Dynamical, Qualitative Models
T Helikar, B Kowal, A Madrahimov, M Shrestha, J Pedersen, K Limbu, ...
PLoS ONE 7 (10), e46417, 2012
202012
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
192015
Design, assessment, and in vivo evaluation of a computational model illustrating the role of CAV1 in CD4+ T-lymphocytes
BD Conroy, TA Herek, TD Shew, M Latner, JJ Larson, L Allen, PH Davis, ...
Frontiers in immunology 5, 599, 2014
162014
Molecular phylogeny and evolutionary dynamics of influenza A nonstructural (NS) gene
J Xu, HA Zhong, A Madrahimov, T Helikar, G Lu
Infection, Genetics and Evolution 22, 192-200, 2014
152014
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 9, 878, 2018
132018
Computational systems biology approach for the study of rheumatoid arthritis: From a molecular map to a dynamical model
V Singh, M Ostaszewski, GD Kalliolias, G Chiocchia, R Olaso, ...
Genomics and computational biology 4 (1), 2018
122018
Identification of potential tissue-specific cancer biomarkers and development of cancer versus normal genomic classifiers
A Mohammed, G Biegert, J Adamec, T Helikar
Oncotarget 8, 85692-85715, 2017
122017
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Articles 1–20