A model integrating the cerebellar granule neuron excitability and calcium signaling pathways. - Marja-Leena Linne; Tiina Manninen; Tuula O. Jalonen (Neurocomputing, 2004)

Simulation tools for biochemical networks: evaluation of performance and usability. - Antti Pettinen; Tommi Aho; Olli-Pekka Smolander; Tiina Manninen; Antti Saarinen; Kaisa-Leena Taattola; Olli Yli-Harja; Marja-Leena Linne (Bioinform., 2005)

Discrete stochastic simulation of cell signaling: comparison of computational tools. - Tiina Manninen; Eeva Makiraatikka; Antti Ylipää; Antti Pettinen; Kalle Leinonen; Marja-Leena Linne (EMBC, 2006)

Developing Itô stochastic differential equation models for neuronal signal transduction pathways. - Tiina Manninen; Marja-Leena Linne; Keijo Ruohonen (Comput. Biol. Chem., 2006)

A novel approach to model neuronal signal transduction using stochastic differential equations. - Tiina Manninen; Marja-Leena Linne; Keijo Ruohonen (Neurocomputing, 2006)

Comparison of discrete- and continuous-state stochastic methods to model neuronal signal transduction. - Tiina Manninen; Daniel X. Keller (BCB, 2010)

Postsynaptic Signal Transduction Models for Long-Term Potentiation and Depression. - Tiina Manninen; Katri Hituri; Jeanette Hellgren Kotaleski; Kim T. Blackwell; Marja-Leena Linne (Frontiers Comput. Neurosci., 2010)

Computational study of noise in a large signal transduction network. - Jukka Intosalmi; Tiina Manninen; Keijo Ruohonen; Marja-Leena Linne (BMC Bioinform., 2011)

Modeling Signal Transduction Leading to Synaptic Plasticity: Evaluation and Comparison of Five Models. - Tiina Manninen; Katri Hituri; Eeva Toivari; Marja-Leena Linne (EURASIP J. Bioinform. Syst. Biol., 2011)

Modeling Neuron-Astrocyte Interactions: Towards Understanding Synaptic Plasticity and Learning in the Brain. - Riikka Havela; Tiina Manninen; Ausra Saudargiene; Marja-Leena Linne (ICIC (2), 2017)

Reproducibility and Comparability of Computational Models for Astrocyte Calcium Excitability. - Tiina Manninen; Riikka Havela; Marja-Leena Linne (Frontiers Neuroinformatics, 2017)

Sustainable computational science: the ReScience initiative. - Nicolas P. Rougier; Konrad Hinsen; Frédéric Alexandre; Thomas Arildsen; Lorena A. Barba; Fabien C. Y. Benureau; C. Titus Brown; Pierre de Buyl; Ozan Caglayan; Andrew P. Davison; Marc-André Delsuc; Georgios Detorakis; et al. (PeerJ Comput. Sci., 2017)

Computational Models for Calcium-Mediated Astrocyte Functions. - Tiina Manninen; Riikka Havela; Marja-Leena Linne (Frontiers Comput. Neurosci., 2018)

Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures. - Tiina Manninen; Jugoslava Acimovic; Riikka Havela; Heidi Teppola; Marja-Leena Linne (Frontiers Neuroinformatics, 2018)

Astrocyte-mediated spike-timing-dependent long-term depression modulates synaptic properties in the developing cortex. - Tiina Manninen; Ausra Saudargiene; Marja-Leena Linne (PLoS Comput. Biol., 2020)

Analysis of Network Models with Neuron-Astrocyte Interactions. - Tiina Manninen; Jugoslava Acimovic; Marja-Leena Linne (Neuroinformatics, 2023)

CellRemorph: A Toolkit for Transforming, Selecting, and Slicing 3D Cell Structures on the Road to Morphologically Detailed Astrocyte Simulations. - Laura Keto; Tiina Manninen (Neuroinformatics, 2023)