{"entity": "researcher", "timestamp": "2026-07-20T00:15:00.548Z", "family": "Bojar", "given": "Daniel", "initials": "D", "orcid": "0000-0002-3008-7851", "affiliations": ["Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden. daniel.bojar@gu.se.", "Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden. daniel.bojar@gu.se."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/f2a9b04a70e34849b1a54b8db3252807.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/f2a9b04a70e34849b1a54b8db3252807"}}, "publications": [{"entity": "publication", "iuid": "81a8ff1347b741339d840038298a8e71", "links": {"self": {"href": "https://publications.scilifelab.se/publication/81a8ff1347b741339d840038298a8e71.json"}, "display": {"href": "https://publications.scilifelab.se/publication/81a8ff1347b741339d840038298a8e71"}}, "title": "Seal milk oligosaccharides rival human milk complexity and exhibit functional dynamics during lactation.", "authors": [{"family": "Jin", "given": "Chunsheng", "initials": "C", "orcid": "0000-0002-0229-102X", "researcher": {"href": "https://publications.scilifelab.se/researcher/458804f3f7274b8a9efe7a90469d0e56.json"}}, {"family": "Lundstr\u00f8m", "given": "Jon", "initials": "J", "orcid": "0000-0003-2733-7124", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e9b642f0bae4a19ba21ed3db3e14d85.json"}}, {"family": "Cori", "given": "Carmen R", "initials": "CR"}, {"family": "Guu", "given": "Shih-Yun", "initials": "SY"}, {"family": "Bennett", "given": "Alexander R", "initials": "AR", "orcid": "0000-0003-4869-9132", "researcher": {"href": "https://publications.scilifelab.se/researcher/becd350a3553463bb37530cc639f281d.json"}}, {"family": "Dannborg", "given": "Mirjam", "initials": "M"}, {"family": "Pomeroy", "given": "Patrick P", "initials": "PP", "orcid": "0000-0003-1603-5630", "researcher": {"href": "https://publications.scilifelab.se/researcher/834269bd43b74cd8bc42aaa3600de72b.json"}}, {"family": "Kennedy", "given": "Malcolm W", "initials": "MW", "orcid": "0000-0002-0970-5264", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1fc8fbe5d748c78ab9fdd182796176.json"}}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications.scilifelab.se/researcher/267ff77d11e04a30bacdd0ae7492bea8.json"}}, {"family": "Hevey", "given": "Rachel", "initials": "R", "orcid": "0000-0002-2649-3427", "researcher": {"href": "https://publications.scilifelab.se/researcher/020432b915a84ec7a643efdfc8ec9e95.json"}}, {"family": "Khoo", "given": "Kay-Hooi", "initials": "KH"}, {"family": "Bojar", "given": "Daniel", "initials": "D", "orcid": "0000-0002-3008-7851", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2a9b04a70e34849b1a54b8db3252807.json"}}], "type": "journal article", "published": "2025-11-25", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "10067", "issn-l": "2041-1723"}, "abstract": "Milk oligosaccharides are crucial for neonatal development and health in mammals. Yet most milk research focuses on humans, or on domesticated mammals that are poor in milk oligosaccharide complexity. Here, we perform an exhaustive mass spectrometry-driven structural characterization of milk oligosaccharides in a wild mammal, female Atlantic grey seals (Halichoerus grypus), throughout their lactation period. Characterizing and quantifying 332 milk oligosaccharides, including 166 unreported structures, we reveal seals to rival human milk in complexity. We report seal free oligosaccharides to reach up to 28 monosaccharides in size. Paired glycomics and metabolomics time course analysis establishes a concerted regulatory process reshaping the seal milk glycome throughout lactation, similar to human milk. Functional analysis of the structures we here characterized reveals anti-biofilm effects and immunomodulatory functions of seal milk oligosaccharides. Our findings challenge long-held assumptions about milk complexity of non-human mammals and enable insights into the functional relevance of complex carbohydrates in milk.", "doi": "10.1038/s41467-025-66075-2", "pmid": "41290693", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12647773"}, {"db": "pii", "key": "10.1038/s41467-025-66075-2"}], "notes": [], "created": "2026-01-27T13:07:39.913Z", "modified": "2026-01-27T13:07:41.170Z"}, {"entity": "publication", "iuid": "e00f6172e9db476b9bfccb664dc53b21", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e00f6172e9db476b9bfccb664dc53b21.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e00f6172e9db476b9bfccb664dc53b21"}}, "title": "O-glycosylation contributes to mammalian glycoRNA biogenesis.", "authors": [{"family": "Porat", "given": "Jennifer", "initials": "J", "orcid": "0000-0002-1709-4635", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2d99766bf064dd08e103cbc67a0dc9d.json"}}, {"family": "Watkins", "given": "Christopher P", "initials": "CP", "orcid": "0009-0000-5045-5001", "researcher": {"href": "https://publications.scilifelab.se/researcher/13fac6fde41a49ec9ebc4c3e051da9db.json"}}, {"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Xie", "given": "Xixuan", "initials": "X", "orcid": "0000-0002-8512-6053", "researcher": {"href": "https://publications.scilifelab.se/researcher/4804e601c34844dc93a4026dad4e3744.json"}}, {"family": "Tan", "given": "Xiao", "initials": "X"}, {"family": "Lebedenko", "given": "Charlotta G", "initials": "CG", "orcid": "0000-0002-9891-9247", "researcher": {"href": "https://publications.scilifelab.se/researcher/a08ba15f170f48508c1139957c7855aa.json"}}, {"family": "Hemberger", "given": "Helena", "initials": "H", "orcid": "0009-0007-4535-5859", "researcher": {"href": "https://publications.scilifelab.se/researcher/5903355624f24408a3bd400eac3701b5.json"}}, {"family": "Shin", "given": "Woojung", "initials": "W", "orcid": "0000-0002-1780-0317", "researcher": {"href": "https://publications.scilifelab.se/researcher/519e26f9761c4ca1914d0846c4f66e73.json"}}, {"family": "Chai", "given": "Peiyuan", "initials": "P", "orcid": "0000-0002-9203-8975", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8053916ad104f6189d940a2e8d44a48.json"}}, {"family": "Collins", "given": "James J", "initials": "JJ"}, {"family": "Garcia", "given": "Benjamin A", "initials": "BA"}, {"family": "Bojar", "given": "Daniel", "initials": "D", "orcid": "0000-0002-3008-7851", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2a9b04a70e34849b1a54b8db3252807.json"}}, {"family": "Flynn", "given": "Ryan A", "initials": "RA", "orcid": "0000-0001-5013-0442", "researcher": {"href": "https://publications.scilifelab.se/researcher/9904ad50d52a42018a0dbace87a63016.json"}}], "type": "journal article", "published": "2024-08-29", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "There is an increasing appreciation for the role of cell surface glycans in modulating interactions with extracellular ligands and participating in intercellular communication. We recently reported the existence of sialoglycoRNAs, where mammalian small RNAs are covalently linked to N-glycans through the modified base acp3U and trafficked to the cell surface. However, little is currently known about the role for O-glycosylation, another major class of carbohydrate polymer modifications. Here, we use parallel genetic, enzymatic, and mass spectrometry approaches to demonstrate that O-linked glycan biosynthesis is responsible for the majority of sialoglycoRNA levels. By examining the O-glycans associated with RNA from cell lines and colon organoids we find known and previously unreported O-linked glycan structures. Further, we find that O-linked glycans released from small RNA from organoids derived from ulcerative colitis patients exhibit higher levels of sialylation than glycans from healthy organoids. Together, our work provides flexible tools to interrogate O-linked glycoRNAs (O-glycoRNA) and suggests that they may be modulated in human disease.", "doi": "10.1101/2024.08.28.610074", "pmid": "39257776", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11384000"}, {"db": "pii", "key": "2024.08.28.610074"}], "notes": [], "created": "2025-10-23T12:25:28.900Z", "modified": "2025-10-23T12:25:31.699Z"}, {"entity": "publication", "iuid": "1c82fe6271894373810a4f34aa2f37be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c82fe6271894373810a4f34aa2f37be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c82fe6271894373810a4f34aa2f37be"}}, "title": "Predicting glycan structure from tandem mass spectrometry via deep learning.", "authors": [{"family": "Urban", "given": "James", "initials": "J"}, {"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Thomsson", "given": "Kristina A", "initials": "KA"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG", "orcid": "0000-0002-3045-2628", "researcher": {"href": "https://publications.scilifelab.se/researcher/62e0b7440ff1447c9611d938d185fbc7.json"}}, {"family": "Ives", "given": "Callum M", "initials": "CM", "orcid": "0000-0003-0511-1220", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bbf92bfc8f047a3bce5b86918755dae.json"}}, {"family": "Fadda", "given": "Elisa", "initials": "E"}, {"family": "Bojar", "given": "Daniel", "initials": "D", "orcid": "0000-0002-3008-7851", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2a9b04a70e34849b1a54b8db3252807.json"}}], "type": "journal article", "published": "2024-07-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "21", "issue": "7", "pages": "1206-1215", "issn-l": "1548-7091"}, "abstract": "Glycans constitute the most complicated post-translational modification, modulating protein activity in health and disease. However, structural annotation from tandem mass spectrometry (MS/MS) data is a bottleneck in glycomics, preventing high-throughput endeavors and relegating glycomics to a few experts. Trained on a newly curated set of 500,000 annotated MS/MS spectra, here we present CandyCrunch, a dilated residual neural network predicting glycan structure from raw liquid chromatography-MS/MS data in seconds (top-1 accuracy: 90.3%). We developed an open-access Python-based workflow of raw data conversion and prediction, followed by automated curation and fragment annotation, with predictions recapitulating and extending expert annotation. We demonstrate that this can be used for de novo annotation, diagnostic fragment identification and high-throughput glycomics. For maximum impact, this entire pipeline is tightly interlaced with our glycowork platform and can be easily tested at https://colab.research.google.com/github/BojarLab/CandyCrunch/blob/main/CandyCrunch.ipynb . We envision CandyCrunch to democratize structural glycomics and the elucidation of biological roles of glycans.", "doi": "10.1038/s41592-024-02314-6", "pmid": "38951670", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11239490"}, {"db": "pii", "key": "10.1038/s41592-024-02314-6"}], "notes": [], "created": "2024-11-27T15:30:37.956Z", "modified": "2025-10-23T12:26:27.666Z"}]}