{"entity": "researcher", "timestamp": "2026-08-20T21:02:20.334Z", "family": "Schw\u00e4mmle", "given": "Veit", "initials": "V", "orcid": "0000-0002-9708-6722", "affiliations": ["Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/158e08b0cfd34f90882f66142d8e62b7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/158e08b0cfd34f90882f66142d8e62b7"}}, "publications": [{"entity": "publication", "iuid": "75d22281ae0c460ab81945d4b6549abe", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/75d22281ae0c460ab81945d4b6549abe.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/75d22281ae0c460ab81945d4b6549abe"}}, "title": "Toward an Integrated Machine Learning Model of a Proteomics Experiment.", "authors": [{"family": "Neely", "given": "Benjamin A", "initials": "BA", "orcid": "0000-0001-6120-7695", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6942cadc06104793927194f19aa57a8d.json"}}, {"family": "Dorfer", "given": "Viktoria", "initials": "V", "orcid": "0000-0002-5332-5701", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b2a0a15b0b2945238e7a39343b5c2a29.json"}}, {"family": "Martens", "given": "Lennart", "initials": "L", "orcid": "0000-0003-4277-658X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/df9a736ba6d04cbdb881a040480bf6f0.json"}}, {"family": "Bludau", "given": "Isabell", "initials": "I"}, {"family": "Bouwmeester", "given": "Robbin", "initials": "R", "orcid": "0000-0001-6807-7029", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd945733eeaf46d895f9d8799b430d66.json"}}, {"family": "Degroeve", "given": "Sven", "initials": "S", "orcid": "0000-0001-8349-3370", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/99e10b1c63144945aa258d810ddbb090.json"}}, {"family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2463c206245a4dbb979cad9d201d73c4.json"}}, {"family": "Gessulat", "given": "Siegfried", "initials": "S"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Palczynski", "given": "Pawel", "initials": "P"}, {"family": "Payne", "given": "Samuel H", "initials": "SH", "orcid": "0000-0002-8351-1994", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe701ec4cf24456980c1902ec61a0ab1.json"}}, {"family": "Rehfeldt", "given": "Tobias Greisager", "initials": "TG", "orcid": "0000-0002-1190-9485", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9671e5e2b13f40e293e935c355e68d2a.json"}}, {"family": "Schmidt", "given": "Tobias", "initials": "T", "orcid": "0000-0002-1883-6514", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d612bc6bfdce4e968b76abbd88a7603d.json"}}, {"family": "Schw\u00e4mmle", "given": "Veit", "initials": "V", "orcid": "0000-0002-9708-6722", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/158e08b0cfd34f90882f66142d8e62b7.json"}}, {"family": "Uszkoreit", "given": "Julian", "initials": "J", "orcid": "0000-0001-7522-4007", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/97c6efaaa4f045a7a718ca2ba376f641.json"}}, {"family": "Vizca\u00edno", "given": "Juan Antonio", "initials": "JA", "orcid": "0000-0002-3905-4335", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81245410f3234e658147bc94f6b3dad2.json"}}, {"family": "Wilhelm", "given": "Mathias", "initials": "M", "orcid": "0000-0002-9224-3258", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2eda8473072c48639cbd09676ed17cfe.json"}}, {"family": "Palmblad", "given": "Magnus", "initials": "M", "orcid": "0000-0002-5865-8994", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80053e2256cd4e55afc7ba916821602c.json"}}], "type": "journal article", "published": "2023-03-03", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "22", "issue": "3", "pages": "681-696", "issn-l": "1535-3893"}, "abstract": "In recent years machine learning has made extensive progress in modeling many aspects of mass spectrometry data. We brought together proteomics data generators, repository managers, and machine learning experts in a workshop with the goals to evaluate and explore machine learning applications for realistic modeling of data from multidimensional mass spectrometry-based proteomics analysis of any sample or organism. Following this sample-to-data roadmap helped identify knowledge gaps and define needs. Being able to generate bespoke and realistic synthetic data has legitimate and important uses in system suitability, method development, and algorithm benchmarking, while also posing critical ethical questions. The interdisciplinary nature of the workshop informed discussions of what is currently possible and future opportunities and challenges. In the following perspective we summarize these discussions in the hope of conveying our excitement about the potential of machine learning in proteomics and to inspire future research.", "doi": "10.1021/acs.jproteome.2c00711", "pmid": "36744821", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9990124"}], "notes": [], "created": "2026-08-20T08:11:44.566Z", "modified": "2026-08-20T08:11:45.110Z"}, {"entity": "publication", "iuid": "9cc984813da147a3b039716d43f3a767", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9cc984813da147a3b039716d43f3a767.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9cc984813da147a3b039716d43f3a767"}}, "title": "CoExpresso: assess the quantitative behavior of protein complexes in human cells.", "authors": [{"family": "Chalabi", "given": "Morteza H", "initials": "MH"}, {"family": "Tsiamis", "given": "Vasileios", "initials": "V"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L"}, {"family": "Vandin", "given": "Fabio", "initials": "F"}, {"family": "Schw\u00e4mmle", "given": "Veit", "initials": "V", "orcid": "0000-0002-9708-6722", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/158e08b0cfd34f90882f66142d8e62b7.json"}}], "type": "journal article", "published": "2019-01-09", "journal": {"title": "BMC Bioinformatics", "issn": "1471-2105", "volume": "20", "issue": "1", "pages": "17", "issn-l": "1471-2105"}, "abstract": "Translational and post-translational control mechanisms in the cell result in widely observable differences between measured gene transcription and protein abundances. Herein, protein complexes are among the most tightly controlled entities by selective degradation of their individual proteins. They furthermore act as control hubs that regulate highly important processes in the cell and exhibit a high functional diversity due to their ability to change their composition and their structure. Better understanding and prediction of these functional states demands methods for the characterization of complex composition, behavior, and abundance across multiple cell states. Mass spectrometry provides an unbiased approach to directly determine protein abundances across different cell populations and thus to profile a comprehensive abundance map of proteins.\n\nWe provide a tool to investigate the behavior of protein subunits in known complexes by comparing their abundance profiles across up to 140 cell types available in ProteomicsDB. Thorough assessment of different randomization methods and statistical scoring algorithms allows determining the significance of concurrent profiles within a complex, therefore providing insights into the conservation of their composition across human cell types as well as the identification of intrinsic structures in complex behavior to determine which proteins orchestrate complex function. This analysis can be extended to investigate common profiles within arbitrary protein groups. CoExpresso can be accessed through http://computproteomics.bmb.sdu.dk/Apps/CoExpresso .\n\nWith the CoExpresso web service, we offer a potent scoring scheme to assess proteins for their co-regulation and thereby offer insight into their potential for forming functional groups like protein complexes.", "doi": "10.1186/s12859-018-2573-8", "pmid": "30626316", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6327379"}, {"db": "pii", "key": "10.1186/s12859-018-2573-8"}], "notes": [], "created": "2026-08-20T12:19:29.949Z", "modified": "2026-08-20T12:19:30.012Z"}, {"entity": "publication", "iuid": "f2b02680fd3f4eb3b2572762de32adb2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f2b02680fd3f4eb3b2572762de32adb2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f2b02680fd3f4eb3b2572762de32adb2"}}, "title": "Quantitative behavior of protein complexes in human cells", "authors": [{"family": "Chalabi", "given": "Morteza H", "initials": "MH", "orcid": "0000-0002-2039-2676", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a81d04ffa5c64ecda6adfc0e0600a3e4.json"}}, {"family": "Tsiamis", "given": "Vasileios", "initials": "V"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Vandin", "given": "Fabio", "initials": "F", "orcid": "0000-0003-2244-2320", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/75672b522dde4d979568a931eada5c6a.json"}}, {"family": "Schw\u00e4mmle", "given": "Veit", "initials": "V", "orcid": "0000-0002-9708-6722", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/158e08b0cfd34f90882f66142d8e62b7.json"}}], "type": "posted-content", "published": "2018-07-11", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/367227", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:10:44.214Z", "modified": "2026-08-20T11:10:44.326Z"}]}