{"entity": "researcher", "timestamp": "2026-11-12T14:49:39.821Z", "family": "Li", "given": "Yuping", "initials": "Y", "orcid": "0000-0003-2057-3271", "affiliations": ["Department of Immunology and Microbiology, University of California San Francisco, San Francisco, 94158, CA, USA."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4958e5be5fb489d93350357e471d548.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4958e5be5fb489d93350357e471d548"}}, "publications": [{"entity": "publication", "iuid": "d24496ff298042db99f2c7999a565fe1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d24496ff298042db99f2c7999a565fe1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d24496ff298042db99f2c7999a565fe1"}}, "title": "Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping.", "authors": [{"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Mozumdar", "given": "Deepto", "initials": "D"}, {"family": "Kokontis", "given": "Claire", "initials": "C"}, {"family": "M\u00e8ndez-Moran", "given": "Melissa", "initials": "M", "orcid": "0000-0003-0817-7292", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/90d7c50c904f4c71be76e0ec228c04bc.json"}}, {"family": "Nieweglowska", "given": "Eliza", "initials": "E", "orcid": "0000-0002-9204-3002", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c23665a0824d4896a58e4d9115bbbca9.json"}}, {"family": "Pelin", "given": "Adrian", "initials": "A"}, {"family": "Li", "given": "Yuping", "initials": "Y", "orcid": "0000-0003-2057-3271", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4958e5be5fb489d93350357e471d548.json"}}, {"family": "Guo", "given": "Baron", "initials": "B"}, {"family": "Krogan", "given": "Nevan J", "initials": "NJ", "orcid": "0000-0003-4902-337X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bf20e1447b9643f599f94d983b2bd9dd.json"}}, {"family": "Agard", "given": "David A", "initials": "DA", "orcid": "0000-0003-3512-695X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/acf4cd7f71944afbbe8f579e36f6dd23.json"}}, {"family": "Bondy-Denomy", "given": "Joseph", "initials": "J", "orcid": "0000-0002-4909-9481", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4ac66d863ed429f85fefcfc5dab6666.json"}}, {"family": "Swaney", "given": "Danielle L", "initials": "DL", "orcid": "0000-0001-6119-6084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56317207941d4aaf81ab4d55de5fcba4.json"}}], "type": "journal article", "published": "2023-08-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "5156", "issn-l": "2041-1723"}, "abstract": "Host-pathogen interactions are pivotal in regulating establishment, progression, and outcome of an infection. While affinity-purification mass spectrometry has become instrumental in characterizing such interactions, it suffers from limitations in scalability and biological authenticity. Here we present the use of co-fractionation mass spectrometry for high throughput analysis of host-pathogen interactions from native viral infections of two jumbophages (\u03d5KZ and \u03d5PA3) in Pseudomonas aeruginosa. This approach enabled the detection of > 6000 unique host-pathogen interactions for each phage, encompassing > 50% of their respective proteomes. This deep coverage provided evidence for interactions between KZ-like phage proteins and the host ribosome, and revealed protein complexes for previously undescribed phage ORFs, including a \u03d5PA3 complex showing strong structural and sequence similarity to \u03d5KZ non-virion RNA polymerase. Interactome-wide comparison across phages showed similar perturbed protein interactions suggesting fundamentally conserved mechanisms of phage predation within the KZ-like phage family. To enable accessibility to this data, we developed PhageMAP, an online resource for network query, visualization, and interaction prediction ( https://phagemap.ucsf.edu/ ). We anticipate this study will lay the foundation for the application of co-fractionation mass spectrometry for the scalable profiling of host-pathogen interactomes and protein complex dynamics upon infection.", "doi": "10.1038/s41467-023-40724-w", "pmid": "37620325", "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10449902"}, {"db": "pii", "key": "10.1038/s41467-023-40724-w"}], "notes": [], "created": "2026-11-06T08:03:13.304Z", "modified": "2026-11-06T08:03:13.672Z"}]}