{"entity": "researcher", "timestamp": "2026-08-20T20:37:11.717Z", "family": "Bonet", "given": "David Fern\u00e1ndez", "initials": "DF", "orcid": "0000-0001-5402-6917", "affiliations": ["Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/4137a3467a924e3ca44e7e09277e410a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/4137a3467a924e3ca44e7e09277e410a"}}, "publications": [{"entity": "publication", "iuid": "ac0652984bb2418391760e337cc32f0b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ac0652984bb2418391760e337cc32f0b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ac0652984bb2418391760e337cc32f0b"}}, "title": "Hidden network preserved in Slide-tags data allows reference-free spatial reconstruction.", "authors": [{"family": "Dahlberg", "given": "Simon K", "initials": "SK", "orcid": "0009-0004-1327-5721", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6292b48f802f4fd3a81e84628af9cf43.json"}}, {"family": "Bonet", "given": "David Fern\u00e1ndez", "initials": "DF", "orcid": "0000-0001-5402-6917", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4137a3467a924e3ca44e7e09277e410a.json"}}, {"family": "Franz\u00e9n", "given": "Lovisa", "initials": "L", "orcid": "0000-0003-3755-718X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/496c1998b3dd4c33a89b38bed7dea4d1.json"}}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL", "orcid": "0000-0002-2207-7370", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/132000c8241249d9b2c4cfeb4a058862.json"}}, {"family": "Hoffecker", "given": "Ian T", "initials": "IT", "orcid": "0000-0001-6941-4576", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d1a249b0d0d34c6e827dc2b15eb33a9f.json"}}], "type": "journal article", "published": "2025-10-31", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "9652", "issn-l": "2041-1723"}, "abstract": "Spatial transcriptomics technologies aim to spatially map gene expression in tissues and typically use oligonucleotide array surfaces that have undergone spatial indexing. These arrays are used to capture nucleic acids diffusing from adjacently placed tissues, allowing subsequent sequencing to reveal both gene and position. Slide-tags is a recently developed method by Russell et al. that inverts this principle. Instead of capturing molecules released from the tissue, probes are detached from a pre-decoded bead array and diffused into tissues, tagging nuclei with spatial barcodes. In this work we reanalyze this data and discover a latent, spatially informative cell-bead network formed incidentally from barcode diffusion and the biophysical properties of the tissue. This allows us to treat Slide-tags as a network-based imaging-by-sequencing approach. By optimizing spatial constraints encoded in the cell-bead network structure, we can achieve unassisted tissue reconstruction, a fundamental shift from classical spatial technologies based on pre-indexed arrays.", "doi": "10.1038/s41467-025-65295-w", "pmid": "41173855", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12579210"}, {"db": "pii", "key": "10.1038/s41467-025-65295-w"}], "notes": [], "created": "2026-08-20T08:54:08.092Z", "modified": "2026-08-20T08:54:08.319Z"}, {"entity": "publication", "iuid": "dde8f6c0d4904f5aad158dbc2b7cdfe7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/dde8f6c0d4904f5aad158dbc2b7cdfe7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/dde8f6c0d4904f5aad158dbc2b7cdfe7"}}, "title": "Spatial Coherence in DNA Barcode Networks", "authors": [{"family": "Bonet", "given": "David Fernandez", "initials": "DF", "orcid": "0000-0001-5402-6917", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4137a3467a924e3ca44e7e09277e410a.json"}}, {"family": "Blumenthal", "given": "Johanna I", "initials": "JI"}, {"family": "Lang", "given": "Shuai", "initials": "S", "orcid": "0000-0001-8091-0570", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e625ab3a1b048b5ae02eb562c2bf044.json"}}, {"family": "Dahlberg", "given": "Simon K", "initials": "SK", "orcid": "0009-0004-1327-5721", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6292b48f802f4fd3a81e84628af9cf43.json"}}, {"family": "Hoffecker", "given": "Ian T", "initials": "IT", "orcid": "0000-0001-6941-4576", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d1a249b0d0d34c6e827dc2b15eb33a9f.json"}}], "type": "posted-content", "published": "2024-05-14", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.05.12.593725", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:54:52.027Z", "modified": "2026-08-20T10:54:52.158Z"}, {"entity": "publication", "iuid": "1a54a1110cc7481194b194be0307ac54", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1a54a1110cc7481194b194be0307ac54.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1a54a1110cc7481194b194be0307ac54"}}, "title": "Image recovery from unknown network mechanisms for DNA sequencing-based microscopy.", "authors": [{"family": "Fernandez Bonet", "given": "David", "initials": "D", "orcid": "0000-0001-5402-6917", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4137a3467a924e3ca44e7e09277e410a.json"}}, {"family": "Hoffecker", "given": "Ian T", "initials": "IT", "orcid": "0000-0001-6941-4576", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d1a249b0d0d34c6e827dc2b15eb33a9f.json"}}], "type": "journal article", "published": "2023-05-11", "journal": {"title": "Nanoscale", "issn": "2040-3372", "volume": "15", "issue": "18", "pages": "8153-8157", "issn-l": "2040-3364"}, "abstract": "Imaging-by-sequencing methods are an emerging alternative to conventional optical micro- or nanoscale imaging. In these methods, molecular networks form through proximity-dependent association between DNA molecules carrying random sequence identifiers. DNA strands record pairwise associations such that network structure may be recovered by sequencing which, in turn, reveals the underlying spatial relationships between molecules comprising the network. Determining the computational reconstruction strategy that makes the best use of the information (in terms of spatial localization accuracy, robustness to noise, and scalability) in these networks is an open problem. We present a graph-based technique for reconstructing a diversity of molecular network classes in 2 and 3 dimensions without prior knowledge of their fundamental generation mechanisms. The model achieves robustness by obtaining an unsupervised sampling of local and global network structure using random walks, making use of minimal prior assumptions. Images are recovered from networks in two stages of dimensionality reduction first with a structural discovery step followed by a manifold learning step. By breaking the process into stages, computational complexity could be reduced leading to fast and accurate performance. Our method represents a means by which diverse molecular network generation scenarios can be unified with a common reconstruction framework.", "doi": "10.1039/d2nr05435c", "pmid": "37078374", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10173253"}], "notes": [], "created": "2026-08-20T09:27:34.827Z", "modified": "2026-08-20T09:27:34.905Z"}, {"entity": "publication", "iuid": "3b89288d7b83481c8e903dd3237a1699", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3b89288d7b83481c8e903dd3237a1699.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3b89288d7b83481c8e903dd3237a1699"}}, "title": "Image recovery from unknown network mechanisms for DNA sequencing-based microscopy", "authors": [{"family": "Bonet", "given": "David Fernandez", "initials": "DF", "orcid": "0000-0001-5402-6917", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4137a3467a924e3ca44e7e09277e410a.json"}}, {"family": "Hoffecker", "given": "Ian T", "initials": "IT", "orcid": "0000-0001-6941-4576", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d1a249b0d0d34c6e827dc2b15eb33a9f.json"}}], "type": "posted-content", "published": "2022-09-30", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.09.29.510142", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:41:08.827Z", "modified": "2026-08-20T10:41:08.909Z"}]}