{"entity": "researcher", "timestamp": "2026-08-20T21:19:59.455Z", "family": "Nair", "given": "Anu G", "initials": "AG", "orcid": "0000-0002-1952-9583", "affiliations": ["Department of Neuroscience, Karolinska Institute, 17165, Stockholm, Sweden.", "Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a923f8455b54b32b90949faa67ea90c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a923f8455b54b32b90949faa67ea90c"}}, "publications": [{"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"}, {"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"}]}