Anderson WD, Makadia HK, Vadigepalli R. (2016). Molecular variability elicits a tunable switch with discrete neuromodulatory response phenotypes. Journal of computational neuroscience. 40 [PubMed]

• Cell signaling/ion channel variability effects on neuronal response (Anderson, Makadia, et al. 2015) [Model]

Antunes G, De Schutter E. (2012). A stochastic signaling network mediates the probabilistic induction of cerebellar long-term depression. The Journal of neuroscience : the official journal of the Society for Neuroscience. 32 [PubMed]

• Cerebellar long-term depression (LTD) (Antunes and De Schutter 2012) [Model]

Antunes G, Simoes-de-Souza FM. (2018). AMPA receptor trafficking and its role in heterosynaptic plasticity. Scientific reports. 8 [PubMed]

• AMPA receptor trafficking and its role in heterosynaptic plasticity (Antunes et al 2018) [Model]

Ashhad S, Narayanan R. (2013). Quantitative interactions between the A-type K+ current and inositol trisphosphate receptors regulate intraneuronal Ca2+ waves and synaptic plasticity. The Journal of physiology. 591 [PubMed]

• Calcium waves and mGluR-dependent synaptic plasticity in CA1 pyr. neurons (Ashhad & Narayanan 2013) [Model]

Basak R, Narayanan R. (2018). Active dendrites regulate the spatiotemporal spread of signaling microdomains. PLoS computational biology. 14 [PubMed]

• Active dendrites shape signaling microdomains in hippocampal neurons (Basak & Narayanan 2018) [Model]

Bell M, Bartol T, Sejnowski T, Rangamani P. (2019). Dendritic spine geometry and spine apparatus organization govern the spatiotemporal dynamics of calcium. The Journal of general physiology. 151 [PubMed]

• Dendritic spine geometry, spine apparatus organization: spatiotemporal Ca dynamics (Bell et al 2019) [Model]

Chen W, De Schutter E. (2014). Python-based geometry preparation and simulation visualization toolkits for STEPS. Frontiers in neuroinformatics. 8 [PubMed]

• Python-based toolkits for STEPS (Chen and De Schutter 2014) [Model]

Evans RC et al. (2012). The effects of NMDA subunit composition on calcium influx and spike timing-dependent plasticity in striatal medium spiny neurons. PLoS computational biology. 8 [PubMed]

• NMDA subunit effects on Calcium and STDP (Evans et al. 2012) [Model]

García-Grajales JA, Rucabado G, García-Dopico A, Peña JM, Jérusalem A. (2015). Neurite, a finite difference large scale parallel program for the simulation of electrical signal propagation in neurites under mechanical loading. PloS one. 10 [PubMed]

• Neurite: electrophysiological-mechanical coupling simulation framework (Garcia-Grajales et al 2015) [Model]

Hituri K, Linne ML. (2013). Comparison of models for IP3 receptor kinetics using stochastic simulations. PloS one. 8 [PubMed]

• IP3R model comparison (Hituri and Linne 2013) [Model]

Hjorth JJJ et al. (2020). The microcircuits of striatum in silico. Proceedings of the National Academy of Sciences of the United States of America. 117 [PubMed]

• The microcircuits of striatum in silico (Hjorth et al 2020) [Model]

Kim M et al. (2011). Colocalization of protein kinase A with adenylyl cyclase enhances protein kinase A activity during induction of long-lasting long-term-potentiation. PLoS computational biology. 7 [PubMed]

• Hippocampus CA1: Simulations of LTP signaling pathways (Kim M et al. 2011) [Model]

Makadia HK et al. (2015). Multiscale model of dynamic neuromodulation integrating neuropeptide-induced signaling pathway activity with membrane electrophysiology. Biophysical journal. 108 [PubMed]

• Model of AngII signaling and membrane electrophysiology (Makadia, Anderson, Fey et al., 2015) [Model]

Manninen T, Hituri K, Kotaleski JH, Blackwell KT, Linne ML. (2010). Postsynaptic signal transduction models for long-term potentiation and depression. Frontiers in computational neuroscience. 4 [PubMed]

Manninen T, Saudargiene A, Linne ML. (2020). Astrocyte-mediated spike-timing-dependent long-term depression modulates synaptic properties in the developing cortex. PLoS computational biology. 16 [PubMed]

• A synapse model for developing somatosensory cortex (Manninen et al 2020) [Model]

Mattioni M, Le Novère N. (2013). Integration of biochemical and electrical signaling-multiscale model of the medium spiny neuron of the striatum. PloS one. 8 [PubMed]

• Multiscale simulation of the striatal medium spiny neuron (Mattioni & Le Novere 2013) [Model]

Migliore M, De Simone G, Migliore R. (2015). Effect of the initial synaptic state on the probability to induce long-term potentiation and depression. Biophysical journal. 108 [PubMed]

• Effect of the initial synaptic state on the probability to induce LTP and LTD (Migliore et al. 2015) [Model]

Neymotin SA et al. (2015). Neuronal calcium wave propagation varies with changes in endoplasmic reticulum parameters: a computer model. Neural computation. 27 [PubMed]

• Neuronal dendrite calcium wave model (Neymotin et al, 2015) [Model]