{"entity": "researcher", "timestamp": "2026-08-20T20:40:31.284Z", "family": "Hellgren Kotaleski", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-0550-0739", "affiliations": ["Science for Life Laboratory, School of Electrical Engineering and Computer Science KTH Royal Institute of Technology  Stockholm", "Department of Neuroscience Karolinska Institute  Stockholm"], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62"}}, "publications": [{"entity": "publication", "iuid": "8eac5a60871b43c1a0df4de26e89da8d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8eac5a60871b43c1a0df4de26e89da8d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8eac5a60871b43c1a0df4de26e89da8d"}}, "title": "Local, calcium- and reward-based synaptic learning rule that enhances dendritic nonlinearities can solve the nonlinear feature binding problem.", "authors": [{"family": "Khodadadi", "given": "Zahra", "initials": "Z", "orcid": "0000-0001-6124-949X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f4d9f5bc2194a5ebfe98cd6ddcceea5.json"}}, {"family": "Trpevski", "given": "Daniel", "initials": "D", "orcid": "0000-0001-9068-6744", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b007cf92b2cb4bc8a4c61436e4e3cefc.json"}}, {"family": "Lindroos", "given": "Robert", "initials": "R", "orcid": "0000-0002-9134-3601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e27a33b27214884a0563693dc4c96e5.json"}}, {"family": "Hellgren Kotaleski", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}], "type": "journal article", "published": "2025-11-17", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "13", "issn-l": "2050-084X"}, "abstract": "This study investigates the computational potential of single striatal projection neurons (SPNs), emphasizing dendritic nonlinearities and their crucial role in solving complex integration problems. Utilizing a biophysically detailed multicompartmental model of an SPN, we introduce a calcium-based, local synaptic learning rule dependent on dendritic plateau potentials. According to what is known about excitatory corticostriatal synapses, the learning rule is governed by local calcium dynamics from NMDA and L-type calcium channels and dopaminergic reward signals. In order to devise a self-adjusting learning rule, which ensures stability for individual synaptic weights, metaplasticity is also used. We demonstrate that this rule allows single neurons with sufficiently nonlinear dendrites to solve the nonlinear feature binding problem, a task traditionally attributed to neuronal networks. We also detail an inhibitory plasticity mechanism that contributes to dendritic compartmentalization, further enhancing computational efficiency in dendrites. This in silico study highlights the computational potential of single neurons, providing deeper insights into neuronal information processing and the mechanisms by which the brain executes complex computations.", "doi": "10.7554/eLife.97274", "pmid": "41247161", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12622965"}, {"db": "pii", "key": "97274"}], "notes": [], "created": "2026-08-20T13:56:17.083Z", "modified": "2026-08-20T13:56:17.169Z"}, {"entity": "publication", "iuid": "e821c61781074c6f93da5a91df5c0cd4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e821c61781074c6f93da5a91df5c0cd4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e821c61781074c6f93da5a91df5c0cd4"}}, "title": "Local, calcium- and reward-based synaptic learning rule that enhances dendritic nonlinearities can solve the nonlinear feature binding problem", "authors": [{"family": "Khodadadi", "given": "Zahra", "initials": "Z", "orcid": "0000-0001-6124-949X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f4d9f5bc2194a5ebfe98cd6ddcceea5.json"}}, {"family": "Trpevski", "given": "Daniel", "initials": "D", "orcid": "0000-0001-9068-6744", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b007cf92b2cb4bc8a4c61436e4e3cefc.json"}}, {"family": "Lindroos", "given": "Robert", "initials": "R", "orcid": "0000-0002-9134-3601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e27a33b27214884a0563693dc4c96e5.json"}}, {"family": "Hellgren Kotaleski", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}], "type": "journal-article", "published": "2025-11-17", "journal": {"issn": "2050-084X", "volume": "13", "title": "Elife", "issn-l": "2050-084X"}, "abstract": null, "doi": "10.7554/elife.97274.4", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:56:28.056Z", "modified": "2026-08-20T13:56:28.114Z"}, {"entity": "publication", "iuid": "c797720352fa4867ae3dd20d599de456", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c797720352fa4867ae3dd20d599de456.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c797720352fa4867ae3dd20d599de456"}}, "title": "Local, calcium- and reward-based synaptic learning rule that enhances dendritic nonlinearities can solve the nonlinear feature binding problem", "authors": [{"family": "Khodadadi", "given": "Zahra", "initials": "Z", "orcid": "0000-0001-6124-949X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f4d9f5bc2194a5ebfe98cd6ddcceea5.json"}}, {"family": "Trpevski", "given": "Daniel", "initials": "D", "orcid": "0000-0001-9068-6744", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b007cf92b2cb4bc8a4c61436e4e3cefc.json"}}, {"family": "Lindroos", "given": "Robert", "initials": "R", "orcid": "0000-0002-9134-3601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e27a33b27214884a0563693dc4c96e5.json"}}, {"family": "Hellgren Kotaleski", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}], "type": "posted-content", "published": "2025-09-10", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.97274.3", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:56:26.278Z", "modified": "2026-08-20T13:56:26.350Z"}, {"entity": "publication", "iuid": "3c4574b2e8f144a2b67e9e899534b096", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3c4574b2e8f144a2b67e9e899534b096.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3c4574b2e8f144a2b67e9e899534b096"}}, "title": "Author response: Local, calcium- and reward-based synaptic learning rule that enhances dendritic nonlinearities can solve the nonlinear feature binding problem", "authors": [{"family": "Khodadadi", "given": "Zahra", "initials": "Z", "orcid": "0000-0001-6124-949X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f4d9f5bc2194a5ebfe98cd6ddcceea5.json"}}, {"family": "Trpevski", "given": "Daniel", "initials": "D", "orcid": "0000-0001-9068-6744", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b007cf92b2cb4bc8a4c61436e4e3cefc.json"}}, {"family": "Lindroos", "given": "Robert", "initials": "R", "orcid": "0000-0002-9134-3601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e27a33b27214884a0563693dc4c96e5.json"}}, {"family": "Hellgren Kotaleski", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}], "type": "peer-review", "published": "2025-04-24", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.97274.2.sa0", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:56:24.448Z", "modified": "2026-08-20T13:56:24.519Z"}, {"entity": "publication", "iuid": "720df4eed1904229a46ba6e81a23ab1e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/720df4eed1904229a46ba6e81a23ab1e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/720df4eed1904229a46ba6e81a23ab1e"}}, "title": "Local, calcium- and reward-based synaptic learning rule that enhances dendritic nonlinearities can solve the nonlinear feature binding problem", "authors": [{"family": "Khodadadi", "given": "Zahra", "initials": "Z", "orcid": "0000-0001-6124-949X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f4d9f5bc2194a5ebfe98cd6ddcceea5.json"}}, {"family": "Trpevski", "given": "Daniel", "initials": "D", "orcid": "0000-0001-9068-6744", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b007cf92b2cb4bc8a4c61436e4e3cefc.json"}}, {"family": "Lindroos", "given": "Robert", "initials": "R", "orcid": "0000-0002-9134-3601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e27a33b27214884a0563693dc4c96e5.json"}}, {"family": "Hellgren Kotaleski", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}], "type": "posted-content", "published": "2025-04-24", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.97274.2", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:56:22.459Z", "modified": "2026-08-20T13:56:22.493Z"}, {"entity": "publication", "iuid": "e799bf76a2334aad9c686bb13e7bc707", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e799bf76a2334aad9c686bb13e7bc707.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e799bf76a2334aad9c686bb13e7bc707"}}, "title": "The impact of Parkinson's disease on striatal network connectivity and corticostriatal drive: An in silico study.", "authors": [{"family": "Carannante", "given": "Ilaria", "initials": "I", "orcid": "0000-0001-8210-8709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d94ae668884641ec9ba2713e0db64d61.json"}}, {"family": "Scolamiero", "given": "Martina", "initials": "M"}, {"family": "Hjorth", "given": "J J Johannes", "initials": "JJJ", "orcid": "0000-0002-9302-0750", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec9300bb976d4038a766d908fcd0ce86.json"}}, {"family": "Kozlov", "given": "Alexander", "initials": "A"}, {"family": "Bekkouche", "given": "Bo", "initials": "B"}, {"family": "Guo", "given": "Lihao", "initials": "L", "orcid": "0000-0002-9982-6229", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3adb76adf48468092952ae4809796d2.json"}}, {"family": "Kumar", "given": "Arvind", "initials": "A", "orcid": "0000-0002-8044-9195", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf2fe30252074acb8d09f88f6c9b55f3.json"}}, {"family": "Chach\u00f3lski", "given": "Wojciech", "initials": "W", "orcid": "0000-0002-2665-9001", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/59be49fa28984d38ac328e451be56820.json"}}, {"family": "Kotaleski", "given": "Jeanette Hellgren", "initials": "JH", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}], "type": "journal article", "published": "2024-12-10", "journal": {"title": "Netw Neurosci", "issn": "2472-1751", "volume": "8", "issue": "4", "pages": "1149-1172", "issn-l": null}, "abstract": "Striatum, the input stage of the basal ganglia, is important for sensory-motor integration, initiation and selection of behavior, as well as reward learning. Striatum receives glutamatergic inputs from mainly cortex and thalamus. In rodents, the striatal projection neurons (SPNs), giving rise to the direct and the indirect pathway (dSPNs and iSPNs, respectively), account for 95% of the neurons, and the remaining 5% are GABAergic and cholinergic interneurons. Interneuron axon terminals as well as local dSPN and iSPN axon collaterals form an intricate striatal network. Following chronic dopamine depletion as in Parkinson's disease (PD), both morphological and electrophysiological striatal neuronal features have been shown to be altered in rodent models. Our goal with this in silico study is twofold: (a) to predict and quantify how the intrastriatal network connectivity structure becomes altered as a consequence of the morphological changes reported at the single-neuron level and (b) to investigate how the effective glutamatergic drive to the SPNs would need to be altered to account for the activity level seen in SPNs during PD. In summary, we predict that the richness of the connectivity motifs in the striatal network is significantly decreased during PD while, at the same time, a substantial enhancement of the effective glutamatergic drive to striatum is present.", "doi": "10.1162/netn_a_00394", "pmid": "39735495", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11674317"}, {"db": "pii", "key": "netn_a_00394"}], "notes": [], "created": "2026-08-20T12:16:23.614Z", "modified": "2026-08-20T12:16:23.766Z"}, {"entity": "publication", "iuid": "c7e2e6681a1e407ea03342a3ccf6964f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c7e2e6681a1e407ea03342a3ccf6964f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c7e2e6681a1e407ea03342a3ccf6964f"}}, "title": "A GPU-based computational framework that bridges neuron simulation and artificial intelligence.", "authors": [{"family": "Zhang", "given": "Yichen", "initials": "Y", "orcid": "0000-0002-5118-4378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f032857a40b24b359e60624ddd47bc76.json"}}, {"family": "He", "given": "Gan", "initials": "G", "orcid": "0000-0001-5746-8737", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/70924e68f7ef4eb6b3247b95ca708f11.json"}}, {"family": "Ma", "given": "Lei", "initials": "L", "orcid": "0000-0001-6024-3854", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/20cf8debf827450cb872626a47927410.json"}}, {"family": "Liu", "given": "Xiaofei", "initials": "X"}, {"family": "Hjorth", "given": "J J Johannes", "initials": "JJJ"}, {"family": "Kozlov", "given": "Alexander", "initials": "A"}, {"family": "He", "given": "Yutao", "initials": "Y"}, {"family": "Zhang", "given": "Shenjian", "initials": "S"}, {"family": "Kotaleski", "given": "Jeanette Hellgren", "initials": "JH", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}, {"family": "Tian", "given": "Yonghong", "initials": "Y", "orcid": "0000-0002-2978-5935", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/274fbf68d1414851bb2117630dd5875a.json"}}, {"family": "Grillner", "given": "Sten", "initials": "S", "orcid": "0000-0002-8951-3691", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18eacd075f8e45c888e6ed7233928b35.json"}}, {"family": "Du", "given": "Kai", "initials": "K", "orcid": "0000-0002-7505-1561", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a6ec74688d7a43c99d38464701faf7d5.json"}}, {"family": "Huang", "given": "Tiejun", "initials": "T", "orcid": "0000-0002-4234-6099", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f392801ee20d421286e61ac3fb80fd66.json"}}], "type": "journal article", "published": "2023-09-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "5798", "issn-l": "2041-1723"}, "abstract": "Biophysically detailed multi-compartment models are powerful tools to explore computational principles of the brain and also serve as a theoretical framework to generate algorithms for artificial intelligence (AI) systems. However, the expensive computational cost severely limits the applications in both the neuroscience and AI fields. The major bottleneck during simulating detailed compartment models is the ability of a simulator to solve large systems of linear equations. Here, we present a novel Dendritic Hierarchical Scheduling (DHS) method to markedly accelerate such a process. We theoretically prove that the DHS implementation is computationally optimal and accurate. This GPU-based method performs with 2-3 orders of magnitude higher speed than that of the classic serial Hines method in the conventional CPU platform. We build a DeepDendrite framework, which integrates the DHS method and the GPU computing engine of the NEURON simulator and demonstrate applications of DeepDendrite in neuroscience tasks. We investigate how spatial patterns of spine inputs affect neuronal excitability in a detailed human pyramidal neuron model with 25,000 spines. Furthermore, we provide a brief discussion on the potential of DeepDendrite for AI, specifically highlighting its ability to enable the efficient training of biophysically detailed models in typical image classification tasks.", "doi": "10.1038/s41467-023-41553-7", "pmid": "37723170", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10507119"}, {"db": "pii", "key": "10.1038/s41467-023-41553-7"}], "notes": [], "created": "2026-08-20T08:52:53.674Z", "modified": "2026-08-20T08:52:53.977Z"}, {"entity": "publication", "iuid": "336dfbab8d9f4359a6df4d224f9deafa", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/336dfbab8d9f4359a6df4d224f9deafa.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/336dfbab8d9f4359a6df4d224f9deafa"}}, "title": "Multiscale molecular simulations to investigate adenylyl cyclase\u2010based signaling in the brain", "authors": [{"family": "van Keulen", "given": "Siri C", "initials": "SC", "orcid": "0000-0001-6995-8389", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/838c25a32bf64d748878f2e1cd8f6227.json"}}, {"family": "Martin", "given": "Juliette", "initials": "J", "orcid": "0000-0002-4787-0885", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/275f6d37420a4a9686333e3cf5ee0486.json"}}, {"family": "Colizzi", "given": "Francesco", "initials": "F", "orcid": "0000-0001-5601-1452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b77167bd9a574db4aaf988820337fffc.json"}}, {"family": "Frezza", "given": "Elisa", "initials": "E", "orcid": "0000-0003-0122-7859", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1b13ebd77c5e45cf8b5cdd7d20537e4e.json"}}, {"family": "Trpevski", "given": "Daniel", "initials": "D", "orcid": "0000-0001-9068-6744", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b007cf92b2cb4bc8a4c61436e4e3cefc.json"}}, {"family": "Diaz", "given": "Nuria Cirauqui", "initials": "NC", "orcid": "0000-0003-4752-9916", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/23e47b48ccf2426c8d2eb0a43115b7cb.json"}}, {"family": "Vidossich", "given": "Pietro", "initials": "P"}, {"family": "Rothlisberger", "given": "Ursula", "initials": "U", "orcid": "0000-0002-1704-8591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/05288e7d55aa42508609d4e97065edeb.json"}}, {"family": "Hellgren Kotaleski", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}, {"family": "Wade", "given": "Rebecca C", "initials": "RC", "orcid": "0000-0001-5951-8670", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/502d793871ee450e9b3961a027d3199d.json"}}, {"family": "Carloni", "given": "Paolo", "initials": "P", "orcid": "0000-0002-9010-0149", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b0d0a3cc3e0a4f38b52e681b8ee0c6c7.json"}}], "type": "journal-article", "published": "2023-01-00", "journal": {"title": "Wiley Interdiscip Rev Comput Mol Sci", "issn": "1759-0876", "volume": "13", "issue": "1", "issn-l": null}, "abstract": null, "doi": "10.1002/wcms.1623", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T06:35:59.164Z", "modified": "2026-08-20T06:35:59.536Z"}, {"entity": "publication", "iuid": "11a0dcc1f898408fbf3563cc8e393d23", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/11a0dcc1f898408fbf3563cc8e393d23.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/11a0dcc1f898408fbf3563cc8e393d23"}}, "title": "Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows.", "authors": [{"family": "Eriksson", "given": "Olivia", "initials": "O", "orcid": "0000-0003-0740-4318", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/50ed8ead3a804dd28e4e7d5d3b3556d8.json"}}, {"family": "Bhalla", "given": "Upinder Singh", "initials": "US", "orcid": "0000-0003-1722-5188", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cdffabe50ea9416c81b99c91f5b42983.json"}}, {"family": "Blackwell", "given": "Kim T", "initials": "KT", "orcid": "0000-0003-4711-2344", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c810676e03014f6389d2cc79889e77d4.json"}}, {"family": "Crook", "given": "Sharon M", "initials": "SM", "orcid": "0000-0003-1659-0749", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b169ae29de4474a271926f09e8889f.json"}}, {"family": "Keller", "given": "Daniel", "initials": "D", "orcid": "0000-0003-3280-6255", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/815355e0fa8f4a02913e758c3d296bf5.json"}}, {"family": "Kramer", "given": "Andrei", "initials": "A", "orcid": "0000-0002-3828-6978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8181305816dc47afbd6a2bb17b9bab63.json"}}, {"family": "Linne", "given": "Marja-Leena", "initials": "ML", "orcid": "0000-0003-2577-7329", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4bb446e2144a4f22afc2bb5c38769282.json"}}, {"family": "Saudargien\u0117", "given": "Ausra", "initials": "A", "orcid": "0000-0003-2768-3334", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd194515e38a4230a32c995136ab2395.json"}}, {"family": "Wade", "given": "Rebecca C", "initials": "RC", "orcid": "0000-0001-5951-8670", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/502d793871ee450e9b3961a027d3199d.json"}}, {"family": "Hellgren Kotaleski", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}], "type": "journal article", "published": "2022-07-06", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "11", "issn-l": "2050-084X"}, "abstract": "Modeling in neuroscience occurs at the intersection of different points of view and approaches. Typically, hypothesis-driven modeling brings a question into focus so that a model is constructed to investigate a specific hypothesis about how the system works or why certain phenomena are observed. Data-driven modeling, on the other hand, follows a more unbiased approach, with model construction informed by the computationally intensive use of data. At the same time, researchers employ models at different biological scales and at different levels of abstraction. Combining these models while validating them against experimental data increases understanding of the multiscale brain. However, a lack of interoperability, transparency, and reusability of both models and the workflows used to construct them creates barriers for the integration of models representing different biological scales and built using different modeling philosophies. We argue that the same imperatives that drive resources and policy for data - such as the FAIR (Findable, Accessible, Interoperable, Reusable) principles - also support the integration of different modeling approaches. The FAIR principles require that data be shared in formats that are Findable, Accessible, Interoperable, and Reusable. Applying these principles to models and modeling workflows, as well as the data used to constrain and validate them, would allow researchers to find, reuse, question, validate, and extend published models, regardless of whether they are implemented phenomenologically or mechanistically, as a few equations or as a multiscale, hierarchical system. To illustrate these ideas, we use a classical synaptic plasticity model, the Bienenstock-Cooper-Munro rule, as an example due to its long history, different levels of abstraction, and implementation at many scales.", "doi": "10.7554/eLife.69013", "pmid": "35792600", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9259018"}, {"db": "pii", "key": "69013"}], "notes": [], "created": "2026-08-20T13:53:50.356Z", "modified": "2026-08-20T13:53:51.537Z"}, {"entity": "publication", "iuid": "e4c0dcf88cb74becad02b58b03f9db12", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e4c0dcf88cb74becad02b58b03f9db12.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e4c0dcf88cb74becad02b58b03f9db12"}}, "title": "A GPU-based computational framework that bridges Neuron simulation and Artificial Intelligence", "authors": [{"family": "Zhang", "given": "Yichen", "initials": "Y"}, {"family": "He", "given": "Gan", "initials": "G"}, {"family": "Liu", "given": "Xiaofei", "initials": "X"}, {"family": "Hjorth", "given": "J J Johannes", "initials": "JJJ"}, {"family": "Kozlov", "given": "Alexander", "initials": "A"}, {"family": "He", "given": "Yutao", "initials": "Y"}, {"family": "Zhang", "given": "Shenjian", "initials": "S"}, {"family": "Ma", "given": "Lei", "initials": "L"}, {"family": "Kotaleski", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}, {"family": "Tian", "given": "Yonghong", "initials": "Y"}, {"family": "Grillner", "given": "Sten", "initials": "S", "orcid": "0000-0002-8951-3691", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18eacd075f8e45c888e6ed7233928b35.json"}}, {"family": "Du", "given": "Kai", "initials": "K"}, {"family": "Huang", "given": "Tiejun", "initials": "T"}], "type": "posted-content", "published": "2022-06-15", "journal": {"issn-l": null}, "abstract": null, "doi": "10.21203/rs.3.rs-1749714/v1", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T12:58:16.065Z", "modified": "2026-08-20T12:58:16.127Z"}, {"entity": "publication", "iuid": "9d48d65709524fd7a4a4de2acd909918", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9d48d65709524fd7a4a4de2acd909918.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9d48d65709524fd7a4a4de2acd909918"}}, "title": "A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience.", "authors": [{"family": "Santos", "given": "Jo\u00e3o P G", "initials": "JPG", "orcid": "0000-0002-0395-039X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57b4d19321b146e4be78794b7ea69ad6.json"}}, {"family": "Pajo", "given": "Kadri", "initials": "K", "orcid": "0000-0003-2110-7889", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e7288dc0795e49129c8d5b79b0ff1f90.json"}}, {"family": "Trpevski", "given": "Daniel", "initials": "D", "orcid": "0000-0001-9068-6744", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b007cf92b2cb4bc8a4c61436e4e3cefc.json"}}, {"family": "Stepaniuk", "given": "Andrey", "initials": "A", "orcid": "0000-0002-2543-4820", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e95615d8a854b60a3f70821cfeddb8c.json"}}, {"family": "Eriksson", "given": "Olivia", "initials": "O", "orcid": "0000-0003-0740-4318", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/50ed8ead3a804dd28e4e7d5d3b3556d8.json"}}, {"family": "Nair", "given": "Anu G", "initials": "AG", "orcid": "0000-0002-1952-9583", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a923f8455b54b32b90949faa67ea90c.json"}}, {"family": "Keller", "given": "Daniel", "initials": "D", "orcid": "0000-0003-3280-6255", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/815355e0fa8f4a02913e758c3d296bf5.json"}}, {"family": "Hellgren Kotaleski", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}, {"family": "Kramer", "given": "Andrei", "initials": "A", "orcid": "0000-0002-3828-6978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8181305816dc47afbd6a2bb17b9bab63.json"}}], "type": "journal article", "published": "2022-01-00", "journal": {"title": "Neuroinformatics", "issn": "1559-0089", "volume": "20", "issue": "1", "pages": "241-259", "issn-l": null}, "abstract": "Neuroscience incorporates knowledge from a range of scales, from single molecules to brain wide neural networks. Modeling is a valuable tool in understanding processes at a single scale or the interactions between two adjacent scales and researchers use a variety of different software tools in the model building and analysis process. Here we focus on the scale of biochemical pathways, which is one of the main objects of study in systems biology. While systems biology is among the more standardized fields, conversion between different model formats and interoperability between various tools is still somewhat problematic. To offer our take on tackling these shortcomings and by keeping in mind the FAIR (findability, accessibility, interoperability, reusability) data principles, we have developed a workflow for building and analyzing biochemical pathway models, using pre-existing tools that could be utilized for the storage and refinement of models in all phases of development. We have chosen the SBtab format which allows the storage of biochemical models and associated data in a single file and provides a human readable set of syntax rules. Next, we implemented custom-made MATLAB\u00ae scripts to perform parameter estimation and global sensitivity analysis used in model refinement. Additionally, we have developed a web-based application for biochemical models that allows simulations with either a network free solver or stochastic solvers and incorporating geometry. Finally, we illustrate convertibility and use of a biochemical model in a biophysically detailed single neuron model by running multiscale simulations in NEURON. Using this workflow, we can simulate the same model in three different simulators, with a smooth conversion between the different model formats, enhancing the characterization of different aspects of the model.", "doi": "10.1007/s12021-021-09546-3", "pmid": "34709562", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9537196"}, {"db": "pii", "key": "10.1007/s12021-021-09546-3"}], "notes": [], "created": "2026-08-20T06:40:27.397Z", "modified": "2026-08-20T06:40:27.743Z"}, {"entity": "publication", "iuid": "0ef018dbfcbc4441a4d908a5dec3466d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0ef018dbfcbc4441a4d908a5dec3466d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0ef018dbfcbc4441a4d908a5dec3466d"}}, "title": "AKAP79 enables calcineurin to directly suppress protein kinase A activity.", "authors": [{"family": "Church", "given": "Timothy W", "initials": "TW", "orcid": "0000-0002-5958-6304", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e26b2111b4b4c6ba6787264ca9776e8.json"}}, {"family": "Tewatia", "given": "Parul", "initials": "P", "orcid": "0000-0002-3096-1318", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dec4cd7664574a838d799cfe51c0d69b.json"}}, {"family": "Hannan", "given": "Saad", "initials": "S", "orcid": "0000-0003-4594-0808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04f95bdddc73499090cb716c87be442f.json"}}, {"family": "Antunes", "given": "Jo\u00e3o", "initials": "J", "orcid": "0000-0001-9635-5145", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9d002305993408ca13309f401a9fdff.json"}}, {"family": "Eriksson", "given": "Olivia", "initials": "O", "orcid": "0000-0003-0740-4318", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/50ed8ead3a804dd28e4e7d5d3b3556d8.json"}}, {"family": "Smart", "given": "Trevor G", "initials": "TG", "orcid": "0000-0002-9089-5375", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a1f0334101f45458e091596c118d1b2.json"}}, {"family": "Hellgren Kotaleski", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}, {"family": "Gold", "given": "Matthew G", "initials": "MG", "orcid": "0000-0002-1281-0815", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c3986f4801b34bef99163503a3297e16.json"}}], "type": "journal article", "published": "2021-10-06", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "10", "issn-l": "2050-084X"}, "abstract": "Interplay between the second messengers cAMP and Ca2+ is a hallmark of dynamic cellular processes. A common motif is the opposition of the Ca2+-sensitive phosphatase calcineurin and the major cAMP receptor, protein kinase A (PKA). Calcineurin dephosphorylates sites primed by PKA to bring about changes including synaptic long-term depression (LTD). AKAP79 supports signaling of this type by anchoring PKA and calcineurin in tandem. In this study, we discovered that AKAP79 increases the rate of calcineurin dephosphorylation of type II PKA regulatory subunits by an order of magnitude. Fluorescent PKA activity reporter assays, supported by kinetic modeling, show how AKAP79-enhanced calcineurin activity enables suppression of PKA without altering cAMP levels by increasing PKA catalytic subunit capture rate. Experiments with hippocampal neurons indicate that this mechanism contributes toward LTD. This non-canonical mode of PKA regulation may underlie many other cellular processes.", "doi": "10.7554/eLife.68164", "pmid": "34612814", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8560092"}, {"db": "pii", "key": "68164"}], "notes": [], "created": "2026-08-20T13:53:42.578Z", "modified": "2026-08-20T13:53:42.701Z"}, {"entity": "publication", "iuid": "b3c5a34d9afc4b5c8febfa44e3feae9d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b3c5a34d9afc4b5c8febfa44e3feae9d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b3c5a34d9afc4b5c8febfa44e3feae9d"}}, "title": "Predicting Synaptic Connectivity for Large-Scale Microcircuit Simulations Using Snudda.", "authors": [{"family": "Hjorth", "given": "J J Johannes", "initials": "JJJ", "orcid": "0000-0002-9302-0750", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec9300bb976d4038a766d908fcd0ce86.json"}}, {"family": "Hellgren Kotaleski", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}, {"family": "Kozlov", "given": "Alexander", "initials": "A", "orcid": "0000-0003-3994-0799", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bcd020bb912c4ff59b2cd86e28ac8d5c.json"}}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "Neuroinformatics", "issn": "1559-0089", "volume": "19", "issue": "4", "pages": "685-701", "issn-l": null}, "abstract": "Simulation of large-scale networks of neurons is an important approach to understanding and interpreting experimental data from healthy and diseased brains. Owing to the rapid development of simulation software and the accumulation of quantitative data of different neuronal types, it is possible to predict both computational and dynamical properties of local microcircuits in a 'bottom-up' manner. Simulated data from these models can be compared with experiments and 'top-down' modelling approaches, successively bridging the scales. Here we describe an open source pipeline, using the software Snudda, for predicting microcircuit connectivity and for setting up simulations using the NEURON simulation environment in a reproducible way. We also illustrate how to further 'curate' data on single neuron morphologies acquired from public databases. This model building pipeline was used to set up a first version of a full-scale cellular level model of mouse dorsal striatum. Model components from that work are here used to illustrate the different steps that are needed when modelling subcortical nuclei, such as the basal ganglia.", "doi": "10.1007/s12021-021-09531-w", "pmid": "34282528", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8566446"}, {"db": "pii", "key": "10.1007/s12021-021-09531-w"}], "notes": [], "created": "2026-08-20T06:40:25.552Z", "modified": "2026-08-20T06:40:25.705Z"}, {"entity": "publication", "iuid": "4babeaa6eb34404ab2077c091fadde14", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4babeaa6eb34404ab2077c091fadde14.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4babeaa6eb34404ab2077c091fadde14"}}, "title": "Author response: AKAP79 enables calcineurin to directly suppress protein kinase A activity", "authors": [{"family": "Church", "given": "Timothy W", "initials": "TW", "orcid": "0000-0002-5958-6304", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e26b2111b4b4c6ba6787264ca9776e8.json"}}, {"family": "Tewatia", "given": "Parul", "initials": "P", "orcid": "0000-0002-3096-1318", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dec4cd7664574a838d799cfe51c0d69b.json"}}, {"family": "Hannan", "given": "Saad", "initials": "S", "orcid": "0000-0003-4594-0808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04f95bdddc73499090cb716c87be442f.json"}}, {"family": "Antunes", "given": "Jo\u00e3o", "initials": "J", "orcid": "0000-0001-9635-5145", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9d002305993408ca13309f401a9fdff.json"}}, {"family": "Eriksson", "given": "Olivia", "initials": "O", "orcid": "0000-0003-0740-4318", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/50ed8ead3a804dd28e4e7d5d3b3556d8.json"}}, {"family": "Smart", "given": "Trevor G", "initials": "TG", "orcid": "0000-0002-9089-5375", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a1f0334101f45458e091596c118d1b2.json"}}, {"family": "Hellgren Kotaleski", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}, {"family": "Gold", "given": "Matthew G", "initials": "MG", "orcid": "0000-0002-1281-0815", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c3986f4801b34bef99163503a3297e16.json"}}], "type": "peer-review", "published": "2021-09-29", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.68164.sa2", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:53:44.479Z", "modified": "2026-08-20T13:53:44.570Z"}, {"entity": "publication", "iuid": "93f150f40d0145e4bc4fc2c746510f4b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/93f150f40d0145e4bc4fc2c746510f4b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/93f150f40d0145e4bc4fc2c746510f4b"}}, "title": "Predicting synaptic connectivity for large-scale microcircuit simulations using Snudda", "authors": [{"family": "Hjorth", "given": "J J Johannes", "initials": "JJJ", "orcid": "0000-0002-9302-0750", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec9300bb976d4038a766d908fcd0ce86.json"}}, {"family": "Kotaleski", "given": "Jeanette Hellgren", "initials": "JH", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}, {"family": "Kozlov", "given": "Alexander", "initials": "A", "orcid": "0000-0003-3994-0799", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bcd020bb912c4ff59b2cd86e28ac8d5c.json"}}], "type": "posted-content", "published": "2021-04-15", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.04.15.439985", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:03:59.797Z", "modified": "2026-08-20T10:03:59.860Z"}, {"entity": "publication", "iuid": "45cb181d297749bba1ef1d84aa001856", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/45cb181d297749bba1ef1d84aa001856.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/45cb181d297749bba1ef1d84aa001856"}}, "title": "Reciprocal interaction between striatal cholinergic and low-threshold spiking interneurons - A computational study.", "authors": [{"family": "Frost Nyl\u00e9n", "given": "Johanna", "initials": "J", "orcid": "0000-0001-6863-8893", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2b679645c02544e9947f45d55cfeb813.json"}}, {"family": "Carannante", "given": "Ilaria", "initials": "I", "orcid": "0000-0001-8210-8709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d94ae668884641ec9ba2713e0db64d61.json"}}, {"family": "Grillner", "given": "Sten", "initials": "S", "orcid": "0000-0002-8951-3691", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18eacd075f8e45c888e6ed7233928b35.json"}}, {"family": "Hellgren Kotaleski", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}], "type": "journal article", "published": "2021-04-00", "journal": {"title": "Eur. J. Neurosci.", "issn": "1460-9568", "volume": "53", "issue": "7", "pages": "2135-2148", "issn-l": "0953-816X"}, "abstract": "The striatum is the main input stage of the basal ganglia receiving extrinsic input from cortex and thalamus. The striatal projection neurons (SPN) constitute 95% of the neurons in the striatum in mice while the remaining 5% are cholinergic and GABAergic interneurons. The cholinergic (ChIN) and low-threshold spiking interneurons (LTS) are spontaneously active and form a striatal subnetwork involved in salience detection and goal-directed learning. Activation of ChINs has been shown to inhibit LTS via muscarinic receptor type 4 (M4R) and LTS in turn can modulate ChINs via nitric oxide (NO) causing a prolonged depolarization. Thalamic input prefentially excites ChINs, whereas input from motor cortex favours LTS, but can also excite ChINs. This varying extrinsic input with intrinsic reciprocal, yet opposing, effects raises the possibility of a slow input-dependent modulatory subnetwork. Here, we simulate this subnetwork using multicompartmental neuron models that incorporate data regarding known ion channels and detailed morphological reconstructions. The modelled connections replicate the experimental data on muscarinic (M4R) and nitric oxide modulation onto LTS and ChIN, respectively, and capture their physiological interaction. Finally, we show that the cortical and thalamic inputs triggering the opposing modulation within the network induce periods of increased and decreased spiking activity in ChINs and LTS. This could provide different temporal windows for selective modulation by acetylcholine and nitric oxide, and the possibility of interaction with the wider striatal microcircuit.", "doi": "10.1111/ejn.14854", "pmid": "32511809", "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:17:42.703Z", "modified": "2026-08-20T11:17:42.814Z"}, {"entity": "publication", "iuid": "ae565990469145588d6314f332884309", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ae565990469145588d6314f332884309.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ae565990469145588d6314f332884309"}}, "title": "Predicting complex spikes in striatal projection neurons of the direct pathway following neuromodulation by acetylcholine and dopamine.", "authors": [{"family": "Lindroos", "given": "Robert", "initials": "R", "orcid": "0000-0002-9134-3601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e27a33b27214884a0563693dc4c96e5.json"}}, {"family": "Hellgren Kotaleski", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}], "type": "journal article", "published": "2021-04-00", "journal": {"title": "Eur. J. Neurosci.", "issn": "1460-9568", "volume": "53", "issue": "7", "pages": "2117-2134", "issn-l": "0953-816X"}, "abstract": "The input structure of the basal ganglia, striatum, receives dense neuromodulatory input in the form of dopamine and acetylcholine. The two systems are tightly connected, for example, synchronized activity of cholinergic interneurons, leading to increased acetylcholine release, has been shown to directly trigger dopamine release from dopaminergic terminals in striatum. Both signals are further needed for induction of locomotion. High dopamine concentration leads to increased excitability of the direct pathway striatal projection neurons. High cholinergic tone inhibits various potassium channels further increasing the excitability of striatal projection neurons. Here, we investigate the combined effect of concurrent high acetylcholine and dopamine using biophysically detailed models based on rodent data. The aim of the study is to investigate how neuromodulation affects dendritic integration. The result shows that neuromodulation paired with synaptic activation of dendrites can give rise to complex spiking patterns, resembling spike shapes seen in the hippocampus. In the hippocampus, these complex spikes are associated with behavioral time scale plasticity and place cell tuning. We further investigate the mechanisms behind the complex spikes and find that there are two components, one axo-somatic and one dendritic in origin.", "doi": "10.1111/ejn.14891", "pmid": "32609903", "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:17:44.496Z", "modified": "2026-08-20T11:17:44.601Z"}, {"entity": "publication", "iuid": "5883df4a0a1149b986c31fa77b8cae5e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5883df4a0a1149b986c31fa77b8cae5e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5883df4a0a1149b986c31fa77b8cae5e"}}, "title": "AKAP79 enables calcineurin to directly suppress protein kinase A activity", "authors": [{"family": "Church", "given": "Timothy W", "initials": "TW", "orcid": "0000-0002-5958-6304", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e26b2111b4b4c6ba6787264ca9776e8.json"}}, {"family": "Tewatia", "given": "Parul", "initials": "P"}, {"family": "Hannan", "given": "Saad", "initials": "S", "orcid": "0000-0003-4594-0808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04f95bdddc73499090cb716c87be442f.json"}}, {"family": "Antunes", "given": "Jo\u00e3o", "initials": "J", "orcid": "0000-0001-9635-5145", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9d002305993408ca13309f401a9fdff.json"}}, {"family": "Eriksson", "given": "Olivia", "initials": "O"}, {"family": "Smart", "given": "Trevor G", "initials": "TG", "orcid": "0000-0002-9089-5375", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a1f0334101f45458e091596c118d1b2.json"}}, {"family": "Kotaleski", "given": "Jeanette Hellgren", "initials": "JH", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}, {"family": "Gold", "given": "Matthew G", "initials": "MG", "orcid": "0000-0002-1281-0815", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c3986f4801b34bef99163503a3297e16.json"}}], "type": "posted-content", "published": "2021-03-15", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.03.14.435320", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:03:12.874Z", "modified": "2026-08-20T10:03:13.091Z"}, {"entity": "publication", "iuid": "27b6126f8f3c4511acab6ef1075f069f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/27b6126f8f3c4511acab6ef1075f069f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/27b6126f8f3c4511acab6ef1075f069f"}}, "title": "A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience", "authors": [{"family": "Santos", "given": "Jo\u00e3o P G", "initials": "JPG", "orcid": "0000-0002-0395-039X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57b4d19321b146e4be78794b7ea69ad6.json"}}, {"family": "Pajo", "given": "Kadri", "initials": "K", "orcid": "0000-0003-2110-7889", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e7288dc0795e49129c8d5b79b0ff1f90.json"}}, {"family": "Trpevski", "given": "Daniel", "initials": "D", "orcid": "0000-0001-9068-6744", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b007cf92b2cb4bc8a4c61436e4e3cefc.json"}}, {"family": "Stepaniuk", "given": "Andrey", "initials": "A", "orcid": "0000-0002-2543-4820", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e95615d8a854b60a3f70821cfeddb8c.json"}}, {"family": "Eriksson", "given": "Olivia", "initials": "O"}, {"family": "Nair", "given": "Anu G", "initials": "AG", "orcid": "0000-0002-1952-9583", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a923f8455b54b32b90949faa67ea90c.json"}}, {"family": "Keller", "given": "Daniel", "initials": "D", "orcid": "0000-0003-3280-6255", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/815355e0fa8f4a02913e758c3d296bf5.json"}}, {"family": "Kotaleski", "given": "Jeanette Hellgren", "initials": "JH", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}, {"family": "Kramer", "given": "Andrei", "initials": "A", "orcid": "0000-0002-3828-6978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8181305816dc47afbd6a2bb17b9bab63.json"}}], "type": "posted-content", "published": "2020-11-18", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.11.17.385203", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T09:59:52.437Z", "modified": "2026-08-20T10:00:11.436Z"}, {"entity": "publication", "iuid": "bf713b4be054448b837f0f3744038238", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bf713b4be054448b837f0f3744038238.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bf713b4be054448b837f0f3744038238"}}, "title": "Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals.", "authors": [{"family": "Bruce", "given": "Neil J", "initials": "NJ", "orcid": "0000-0002-2735-3215", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3533ee5106064d07a14f9bf6334de21e.json"}}, {"family": "Narzi", "given": "Daniele", "initials": "D"}, {"family": "Trpevski", "given": "Daniel", "initials": "D"}, {"family": "van Keulen", "given": "Siri C", "initials": "SC", "orcid": "0000-0001-6995-8389", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/838c25a32bf64d748878f2e1cd8f6227.json"}}, {"family": "Nair", "given": "Anu G", "initials": "AG", "orcid": "0000-0002-1952-9583", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a923f8455b54b32b90949faa67ea90c.json"}}, {"family": "R\u00f6thlisberger", "given": "Ursula", "initials": "U"}, {"family": "Wade", "given": "Rebecca C", "initials": "RC", "orcid": "0000-0001-5951-8670", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/502d793871ee450e9b3961a027d3199d.json"}}, {"family": "Carloni", "given": "Paolo", "initials": "P", "orcid": "0000-0002-9010-0149", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b0d0a3cc3e0a4f38b52e681b8ee0c6c7.json"}}, {"family": "Hellgren Kotaleski", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}], "type": "journal article", "published": "2019-10-00", "journal": {"title": "PLoS Comput Biol", "issn": "1553-7358", "volume": "15", "issue": "10", "pages": "e1007382", "issn-l": "1553-734X"}, "abstract": "Long-term potentiation and depression of synaptic activity in response to stimuli is a key factor in reinforcement learning. Strengthening of the corticostriatal synapses depends on the second messenger cAMP, whose synthesis is catalysed by the enzyme adenylyl cyclase 5 (AC5), which is itself regulated by the stimulatory G\u03b1olf and inhibitory G\u03b1i proteins. AC isoforms have been suggested to act as coincidence detectors, promoting cellular responses only when convergent regulatory signals occur close in time. However, the mechanism for this is currently unclear, and seems to lie in their diverse regulation patterns. Despite attempts to isolate the ternary complex, it is not known if G\u03b1olf and G\u03b1i can bind to AC5 simultaneously, nor what activity the complex would have. Using protein structure-based molecular dynamics simulations, we show that this complex is stable and inactive. These simulations, along with Brownian dynamics simulations to estimate protein association rates constants, constrain a kinetic model that shows that the presence of this ternary inactive complex is crucial for AC5's ability to detect coincident signals, producing a synergistic increase in cAMP. These results reveal some of the prerequisites for corticostriatal synaptic plasticity, and explain recent experimental data on cAMP concentrations following receptor activation. Moreover, they provide insights into the regulatory mechanisms that control signal processing by different AC isoforms.", "doi": "10.1371/journal.pcbi.1007382", "pmid": "31665146", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6821081"}, {"db": "pii", "key": "PCOMPBIOL-D-19-00529"}], "notes": [], "created": "2026-08-20T12:42:51.464Z", "modified": "2026-08-20T12:42:51.559Z"}, {"entity": "publication", "iuid": "88edb039cd174b03ac6dfcc22087c414", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/88edb039cd174b03ac6dfcc22087c414.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/88edb039cd174b03ac6dfcc22087c414"}}, "title": "Untangling Basal Ganglia Network Dynamics and Function: Role of Dopamine Depletion and Inhibition Investigated in a Spiking Network Model.", "authors": [{"family": "Lindahl", "given": "Mikael", "initials": "M"}, {"family": "Hellgren Kotaleski", "given": "Jeanette", "initials": "J", "orcid": "0000-0002-0550-0739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a920517bd1c142878f03bee05e843b62.json"}}], "type": "journal article", "published": "2017-01-12", "journal": {"title": "eNeuro", "issn": "2373-2822", "volume": "3", "issue": "6", "issn-l": null}, "abstract": "The basal ganglia are a crucial brain system for behavioral selection, and their function is disturbed in Parkinson's disease (PD), where neurons exhibit inappropriate synchronization and oscillations. We present a spiking neural model of basal ganglia including plausible details on synaptic dynamics, connectivity patterns, neuron behavior, and dopamine effects. Recordings of neuronal activity in the subthalamic nucleus and Type A (TA; arkypallidal) and Type I (TI; prototypical) neurons in globus pallidus externa were used to validate the model. Simulation experiments predict that both local inhibition in striatum and the existence of an indirect pathway are important for basal ganglia to function properly over a large range of cortical drives. The dopamine depletion-induced increase of AMPA efficacy in corticostriatal synapses to medium spiny neurons (MSNs) with dopamine receptor D2 synapses (CTX-MSN D2) and the reduction of MSN lateral connectivity (MSN-MSN) were found to contribute significantly to the enhanced synchrony and oscillations seen in PD. Additionally, reversing the dopamine depletion-induced changes to CTX-MSN D1, CTX-MSN D2, TA-MSN, and MSN-MSN couplings could improve or restore basal ganglia action selection ability. In summary, we found multiple changes of parameters for synaptic efficacy and neural excitability that could improve action selection ability and at the same time reduce oscillations. Identification of such targets could potentially generate ideas for treatments of PD and increase our understanding of the relation between network dynamics and network function.", "doi": "10.1523/ENEURO.0156-16.2016", "pmid": "28101525", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC5228592"}, {"db": "pii", "key": "eN-NWR-0156-16"}], "notes": [], "created": "2026-08-20T12:51:23.062Z", "modified": "2026-08-20T12:51:23.120Z"}]}