| 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 | 284 | 2012 |
| 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 | 263 | 2020 |
| 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 | 261 | 2016 |
| 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 | 245 | 2008 |
| 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, 1-15, 2013 | 201 | 2013 |
| Building digital twins of the human immune system: toward a roadmap R Laubenbacher, A Niarakis, T Helikar, G An, B Shapiro, RS Malik-Sheriff, ... NPJ digital medicine 5 (1), 64, 2022 | 109 | 2022 |
| 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 | 106 | 2018 |
| 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 | 101 | 2021 |
| 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 | 98 | 2015 |
| ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists T Helikar, JA Rogers BMC systems biology 3, 1-15, 2009 | 77 | 2009 |
| 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 | 70 | 2020 |
| Integrating Interactive Computational Modeling in Biology Curricula T Helikar, CE Cutucache, LA Dahlquist, TA Herek, JJ Larson, JA Rogers PLoS Computational Biology, 2015 | 57 | 2015 |
| 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 | 53 | 2013 |
| Recent applications of quantitative systems pharmacology and machine learning models across diseases SS Aghamiri, R Amin, T Helikar Journal of pharmacokinetics and pharmacodynamics, 1-19, 2022 | 51 | 2022 |
| 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 | 49 | 2019 |
| 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 | 49 | 2018 |
| Boolean modeling of biochemical networks T Helikar, N Kochi, J Konvalina, J A Rogers | 49 | 2011 |
| 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 | 48 | 2018 |
| Two heads are better than one: current landscape of integrating QSP and machine learning: an ISoP QSP SIG white paper by the working group on the integration of quantitative … T Zhang, IP Androulakis, P Bonate, L Cheng, T Helikar, J Parikh, ... Journal of Pharmacokinetics and Pharmacodynamics 49 (1), 5-18, 2022 | 42 | 2022 |
| Using concept maps to characterise cellular respiration knowledge in undergraduate students HE Bergan-Roller, NJ Galt, T Helikar, JT Dauer Journal of Biological Education 54 (1), 33-46, 2018 | 40 | 2018 |
Claudine ChaouiyaI2M UMR 7373, Aix Marseille University (France)Verified email at univ-amu.fr
