{"entity": "researcher", "timestamp": "2026-08-20T20:45:14.534Z", "family": "Trpevski", "given": "Daniel", "initials": "D", "orcid": "0000-0001-9068-6744", "affiliations": ["Science for Life Laboratory, School of Electrical Engineering and Computer Science KTH Royal Institute of Technology  Stockholm"], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/b007cf92b2cb4bc8a4c61436e4e3cefc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/b007cf92b2cb4bc8a4c61436e4e3cefc"}}, "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": 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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": "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": 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"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": "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": "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"}]}