{"entity": "researcher", "timestamp": "2026-08-20T20:54:29.693Z", "family": "Volpe", "given": "Giovanni", "initials": "G", "orcid": "0000-0001-5057-1846", "affiliations": ["Department of Physics, University of Gothenburg, Origov\u00e4gen 6B, SE-41296, Gothenburg, Sweden. giovanni.volpe@physics.gu.se.", "Science for Life Laboratory, Department of Physics, University of Gothenburg, Origov\u00e4gen 6B, SE-41296, Gothenburg, Sweden. giovanni.volpe@physics.gu.se."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ddeb3190b974af1997601b0a1377c7a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ddeb3190b974af1997601b0a1377c7a"}}, "publications": [{"entity": "publication", "iuid": "98b497b8af874ced92acc6c98e00e70f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/98b497b8af874ced92acc6c98e00e70f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/98b497b8af874ced92acc6c98e00e70f"}}, "title": "Myxococcus xanthus for active matter studies: a tutorial for its growth and potential applications.", "authors": [{"family": "Ant\u00fanez Dom\u00ednguez", "given": "Jesus Manuel", "initials": "JM", "orcid": "0000-0003-1410-5930", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/32b315e2705f4d6e89a44155914a0288.json"}}, {"family": "P\u00e9rez Garc\u00eda", "given": "Laura", "initials": "L"}, {"family": "Rivera-Yoshida", "given": "Natsuko", "initials": "N", "orcid": "0000-0001-5721-0621", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c45f9d2cc6fe46c386ddaa0de2c94214.json"}}, {"family": "Di Franco", "given": "Jasmin", "initials": "J", "orcid": "0009-0001-5563-1913", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a6aba479d78a457db0fa617b3f98632c.json"}}, {"family": "Steiner", "given": "David", "initials": "D", "orcid": "0009-0009-7113-5694", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d301969dd3b4b1880fac10267430654.json"}}, {"family": "Arzola", "given": "Alejandro V", "initials": "AV"}, {"family": "Ben\u00edtez", "given": "Mariana", "initials": "M", "orcid": "0000-0002-4901-2833", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92ed517b26324e88a0a7010f7f0bd118.json"}}, {"family": "Blomqvist", "given": "Charlotte Hamngren", "initials": "CH"}, {"family": "Cerbino", "given": "Roberto", "initials": "R", "orcid": "0000-0003-0434-7741", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ab4450c3dad46a7a9a5a81bd40d590a.json"}}, {"family": "Adiels", "given": "Caroline Beck", "initials": "CB", "orcid": "0000-0002-2403-2213", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3ef0e0bf73fd4d87b6d3a49f57c9a059.json"}}, {"family": "Volpe", "given": "Giovanni", "initials": "G", "orcid": "0000-0001-5057-1846", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ddeb3190b974af1997601b0a1377c7a.json"}}], "type": "journal article", "published": "2025-11-19", "journal": {"title": "Soft Matter", "issn": "1744-6848", "volume": "21", "issue": "45", "pages": "8602-8623", "issn-l": null}, "abstract": "Myxococcus xanthus is a unicellular organism known for its capacity to move and communicate, giving rise to complex collective properties, structures and behaviors. These characteristics have contributed to position M. xanthus as a valuable model organism for exploring emergent collective phenomena at the interface of biology and physics, particularly within the growing domain of active matter research. Yet, researchers frequently encounter difficulties in establishing reproducible and reliable culturing protocols. This tutorial provides a detailed and accessible guide to the culture, growth, development, and experimental sample preparation of M. xanthus. In addition, it presents several exemplary experiments that can be conducted using these samples, including motility assays, fruiting body formation, predation, and elasticotaxis-phenomena of direct relevance for active matter studies.", "doi": "10.1039/d5sm00284b", "pmid": "41211965", "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T09:28:18.196Z", "modified": "2026-08-20T09:28:18.556Z"}, {"entity": "publication", "iuid": "ff559de4b9d347229ff638a93972cb02", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ff559de4b9d347229ff638a93972cb02.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ff559de4b9d347229ff638a93972cb02"}}, "title": "Enhanced spatial clustering of single-molecule localizations with graph neural networks.", "authors": [{"family": "Pineda", "given": "Jes\u00fas", "initials": "J", "orcid": "0000-0002-9197-3451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b726263fbc7e4be28cf0450b30769d1c.json"}}, {"family": "Mas\u00f3-Orriols", "given": "Sergi", "initials": "S", "orcid": "0000-0002-4310-5545", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/54fdb72785c345aaa22a203e2019ebd1.json"}}, {"family": "Masoliver", "given": "Montse", "initials": "M"}, {"family": "Bertran", "given": "Joan", "initials": "J"}, {"family": "Goks\u00f6r", "given": "Mattias", "initials": "M"}, {"family": "Volpe", "given": "Giovanni", "initials": "G", "orcid": "0000-0001-5057-1846", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ddeb3190b974af1997601b0a1377c7a.json"}}, {"family": "Manzo", "given": "Carlo", "initials": "C", "orcid": "0000-0002-8625-0996", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5e49022c9a54f49a4db4f9f59485cae.json"}}], "type": "journal article", "published": "2025-11-03", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "9693", "issn-l": "2041-1723"}, "abstract": "Single-molecule localization microscopy generates point clouds corresponding to fluorophore localizations. Spatial cluster identification and analysis of these point clouds are crucial for extracting insights about molecular organization. However, this task becomes challenging in the presence of localization noise, high point density, or complex biological structures. Here, we introduce MIRO (Multifunctional Integration through Relational Optimization), an algorithm that uses recurrent graph neural networks to transform the point clouds in order to improve clustering efficiency when applying conventional clustering techniques. We show that MIRO supports simultaneous processing of clusters of different shapes and at multiple scales, demonstrating improved performance across varied datasets. Our comprehensive evaluation demonstrates MIRO's transformative potential for single-molecule localization applications, showcasing its capability to revolutionize cluster analysis and provide accurate, reliable details of molecular architecture. In addition, MIRO's robust clustering capabilities hold promise for applications in various fields such as neuroscience, for the analysis of neural connectivity patterns, and environmental science, for studying spatial distributions of ecological data.", "doi": "10.1038/s41467-025-65557-7", "pmid": "41184315", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12583556"}, {"db": "pii", "key": "10.1038/s41467-025-65557-7"}], "notes": [], "created": "2026-08-20T08:54:16.231Z", "modified": "2026-08-20T08:54:16.424Z"}]}