{"entity": "researcher", "timestamp": "2026-08-10T16:37:19.549Z", "family": "Swaney", "given": "Danielle L", "initials": "DL", "orcid": "0000-0001-6119-6084", "affiliations": ["Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.", "Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA.", "J. David Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/56317207941d4aaf81ab4d55de5fcba4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/56317207941d4aaf81ab4d55de5fcba4"}}, "publications": [{"entity": "publication", "iuid": "6234890ec4f9490bbc0a7d0677b47d65", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6234890ec4f9490bbc0a7d0677b47d65.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6234890ec4f9490bbc0a7d0677b47d65"}}, "title": "Plasma proteomics for novel biomarker discovery in childhood tuberculosis", "authors": [{"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Wambi", "given": "Peter", "initials": "P"}, {"family": "Jaganath", "given": "Devan", "initials": "D"}, {"family": "Calderon", "given": "Roger", "initials": "R"}, {"family": "Castro", "given": "Robert", "initials": "R"}, {"family": "Mohapatra", "given": "Alexander", "initials": "A"}, {"family": "McKetney", "given": "Justin", "initials": "J"}, {"family": "Luiz", "given": "Juaneta", "initials": "J"}, {"family": "Nerurkar", "given": "Rutuja", "initials": "R"}, {"family": "Nkereuwem", "given": "Esin", "initials": "E"}, {"family": "Franke", "given": "Molly F", "initials": "MF"}, {"family": "Mousavian", "given": "Zaynab", "initials": "Z"}, {"family": "Collins", "given": "Jeffrey M", "initials": "JM", "orcid": "0000-0002-2903-797X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e55c6f4136342ad8c1874d0c0e13924.json"}}, {"family": "Sigal", "given": "George B", "initials": "GB"}, {"family": "Segal", "given": "Mark R", "initials": "MR"}, {"family": "Kampman", "given": "Beate", "initials": "B"}, {"family": "Wobudeya", "given": "Eric", "initials": "E"}, {"family": "Cattamanchi", "given": "Adithya", "initials": "A"}, {"family": "Ernst", "given": "Joel D", "initials": "JD"}, {"family": "Zar", "given": "Heather J", "initials": "HJ"}, {"family": "Swaney", "given": "Danielle L", "initials": "DL", "orcid": "0000-0001-6119-6084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56317207941d4aaf81ab4d55de5fcba4.json"}}], "type": "posted-content", "published": "2024-12-08", "journal": {"title": null, "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2024.12.05.24318340", "pmid": null, "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-18T16:51:17.973Z", "modified": "2025-03-21T13:33:21.345Z"}, {"entity": "publication", "iuid": "442cfbe882b344b6b586a3c9a349c165", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/442cfbe882b344b6b586a3c9a349c165.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/442cfbe882b344b6b586a3c9a349c165"}}, "title": "Multiscale photocatalytic proximity labeling reveals cell surface neighbors on and between cells.", "authors": [{"family": "Lin", "given": "Zhi", "initials": "Z", "orcid": "0000-0001-6662-7330", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/059b4f81da244058a9e7442b149daadf.json"}}, {"family": "Schaefer", "given": "Kaitlin", "initials": "K", "orcid": "0000-0003-4825-1389", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5601fa03584f40e887f7c12e005737ea.json"}}, {"family": "Lui", "given": "Irene", "initials": "I", "orcid": "0000-0002-6171-5443", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1eca2b8ec2d9461b89c962e8f225e192.json"}}, {"family": "Yao", "given": "Zi", "initials": "Z"}, {"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Swaney", "given": "Danielle L", "initials": "DL", "orcid": "0000-0001-6119-6084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56317207941d4aaf81ab4d55de5fcba4.json"}}, {"family": "Palar", "given": "Ajikarunia", "initials": "A", "orcid": "0000-0001-9357-6970", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/155427eafdb8474589a735c36ca9f149.json"}}, {"family": "Sali", "given": "Andrej", "initials": "A", "orcid": "0000-0003-0435-6197", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd70ba581f7e49b886339e8883b7f053.json"}}, {"family": "Wells", "given": "James A", "initials": "JA", "orcid": "0000-0001-8267-5519", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0c1fc2f2b584824bd489884424e333c.json"}}], "type": "journal article", "published": "2024-07-19", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "385", "issue": "6706", "pages": "eadl5763"}, "abstract": "Proximity labeling proteomics (PLP) strategies are powerful approaches to yield snapshots of protein neighborhoods. Here, we describe a multiscale PLP method with adjustable resolution that uses a commercially available photocatalyst, Eosin Y, which upon visible light illumination activates different photo-probes with a range of labeling radii. We applied this platform to profile neighborhoods of the oncogenic epidermal growth factor receptor and orthogonally validated more than 20 neighbors using immunoassays and AlphaFold-Multimer prediction. We further profiled the protein neighborhoods of cell-cell synapses induced by bispecific T cell engagers and chimeric antigen receptor T cells. This integrated multiscale PLP platform maps local and distal protein networks on and between cell surfaces, which will aid in the systematic construction of the cell surface interactome, revealing horizontal signaling partners and reveal new immunotherapeutic opportunities.", "doi": "10.1126/science.adl5763", "pmid": "39024454", "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-18T16:51:05.008Z", "modified": "2025-03-21T13:32:58.593Z"}, {"entity": "publication", "iuid": "0effefb552b64f16b9d47b8e0bd4482f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0effefb552b64f16b9d47b8e0bd4482f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0effefb552b64f16b9d47b8e0bd4482f"}}, "title": "Characterization of a lipid-based jumbo phage compartment as a hub for early phage infection.", "authors": [{"family": "Mozumdar", "given": "Deepto", "initials": "D"}, {"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Stevenson", "given": "Erica", "initials": "E"}, {"family": "Guan", "given": "Jingwen", "initials": "J"}, {"family": "Nieweglowska", "given": "Eliza", "initials": "E"}, {"family": "Rao", "given": "Sanjana", "initials": "S"}, {"family": "Agard", "given": "David", "initials": "D"}, {"family": "Swaney", "given": "Danielle L", "initials": "DL", "orcid": "0000-0001-6119-6084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56317207941d4aaf81ab4d55de5fcba4.json"}}, {"family": "Bondy-Denomy", "given": "Joseph", "initials": "J"}], "type": "journal article", "published": "2024-07-10", "journal": {"title": "Cell Host Microbe", "issn": "1934-6069", "issn-l": "1931-3128", "volume": "32", "issue": "7", "pages": "1050-1058.e7"}, "abstract": "Viral genomes are most vulnerable to cellular defenses at the start of the infection. A family of jumbo phages related to phage \u03a6KZ, which infects Pseudomonas aeruginosa, assembles a protein-based phage nucleus to protect replicating phage DNA, but how it is protected prior to phage nucleus assembly is unclear. We find that host proteins related to membrane and lipid biology interact with injected phage protein, clustering in an early phage infection (EPI) vesicle. The injected virion RNA polymerase (vRNAP) executes early gene expression until phage genome separation from the vRNAP and the EPI vesicle, moving into the nascent proteinaceous phage nucleus. Enzymes involved in DNA replication and CRISPR/restriction immune nucleases are excluded by the EPI vesicle. We propose that the EPI vesicle is rapidly constructed with injected phage proteins, phage DNA, host lipids, and host membrane proteins to enable genome protection, early transcription, localized translation, and to ensure faithful genome transfer to the proteinaceous nucleus.", "doi": "10.1016/j.chom.2024.05.016", "pmid": "38870941", "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS2004244"}, {"db": "pmc", "key": "PMC11239273"}, {"db": "pii", "key": "S1931-3128(24)00188-4"}], "notes": [], "created": "2025-03-18T16:51:13.029Z", "modified": "2025-03-21T13:20:33.888Z"}]}