{"entity": "researcher", "timestamp": "2026-08-20T20:36:19.031Z", "family": "Jafari", "given": "Rozbeh", "initials": "R", "orcid": "0000-0002-3396-4709", "affiliations": ["Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden. rozbeh.jafari@ki.se."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/95546f158dde40709fbfbb822a8f89c5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/95546f158dde40709fbfbb822a8f89c5"}}, "publications": [{"entity": "publication", "iuid": "d2d49f05d7904b3bad53fde048184fbf", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d2d49f05d7904b3bad53fde048184fbf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d2d49f05d7904b3bad53fde048184fbf"}}, "title": "Pathway activation model for personalized prediction of drug synergy", "authors": [{"family": "Trac", "given": "Quang Thinh", "initials": "QT", "orcid": "0000-0003-2429-0287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13e232680de04f55b195706785e79988.json"}}, {"family": "Huang", "given": "Yue", "initials": "Y"}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Bohlin", "given": "Anna", "initials": "A"}, {"family": "\u00d6sterroos", "given": "Albin", "initials": "A"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e443cdb01cc44a7fa786941b5c0b62d6.json"}}, {"family": "Jafari", "given": "Rozbeh", "initials": "R", "orcid": "0000-0002-3396-4709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/95546f158dde40709fbfbb822a8f89c5.json"}}, {"family": "Siavelis", "given": "Ioannis", "initials": "I"}, {"family": "B\u00e4ckvall", "given": "Helena", "initials": "H"}, {"family": "Kiviluoto", "given": "Santeri", "initials": "S"}, {"family": "Orre", "given": "Lukas M", "initials": "LM"}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}, {"family": "Pawitan", "given": "Yudi", "initials": "Y"}, {"family": "Vu", "given": "Trung Nghia", "initials": "TN", "orcid": "0000-0001-7945-5750", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c68ab75cfd4458aaa0cff82a637a24b.json"}}], "type": "posted-content", "published": "2025-05-20", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.100071.3", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:50:38.643Z", "modified": "2026-08-20T13:50:38.705Z"}, {"entity": "publication", "iuid": "2d9b1475f2a74141957ffa60c7cde513", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2d9b1475f2a74141957ffa60c7cde513.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2d9b1475f2a74141957ffa60c7cde513"}}, "title": "Pathway activation model for personalized prediction of drug synergy", "authors": [{"family": "Trac", "given": "Quang Thinh", "initials": "QT", "orcid": "0000-0003-2429-0287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13e232680de04f55b195706785e79988.json"}}, {"family": "Huang", "given": "Yue", "initials": "Y"}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Bohlin", "given": "Anna", "initials": "A"}, {"family": 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"https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}, {"family": "Pawitan", "given": "Yudi", "initials": "Y"}, {"family": "Vu", "given": "Trung Nghia", "initials": "TN", "orcid": "0000-0001-7945-5750", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c68ab75cfd4458aaa0cff82a637a24b.json"}}], "type": "posted-content", "published": "2025-03-20", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.100071.2", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:50:34.946Z", "modified": "2026-08-20T13:50:35.029Z"}, {"entity": "publication", "iuid": "abf636b1b12940748f1d797a8dbeb225", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/abf636b1b12940748f1d797a8dbeb225.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/abf636b1b12940748f1d797a8dbeb225"}}, "title": "Author response: Pathway activation model for personalized prediction of drug synergy", "authors": [{"family": "Trac", "given": "Quang Thinh", "initials": "QT", "orcid": "0000-0003-2429-0287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13e232680de04f55b195706785e79988.json"}}, {"family": "Huang", "given": "Yue", "initials": "Y"}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Bohlin", "given": "Anna", "initials": "A"}, {"family": "\u00d6sterroos", "given": "Albin", "initials": "A"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e443cdb01cc44a7fa786941b5c0b62d6.json"}}, {"family": "Jafari", "given": "Rozbeh", "initials": "R", "orcid": "0000-0002-3396-4709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/95546f158dde40709fbfbb822a8f89c5.json"}}, {"family": "Siavelis", "given": "Ioannis", "initials": "I"}, {"family": "B\u00e4ckvall", "given": "Helena", "initials": "H"}, {"family": "Kiviluoto", "given": "Santeri", "initials": "S"}, {"family": "Orre", "given": "Lukas M", "initials": "LM"}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}, {"family": "Pawitan", "given": "Yudi", "initials": "Y"}, {"family": "Vu", "given": "Trung Nghia", "initials": "TN", "orcid": "0000-0001-7945-5750", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c68ab75cfd4458aaa0cff82a637a24b.json"}}], "type": "peer-review", "published": "2025-03-20", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.100071.2.sa0", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:50:36.794Z", "modified": "2026-08-20T13:50:36.879Z"}, {"entity": "publication", "iuid": "20224117c77c4cf1825278ed9767b7d1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/20224117c77c4cf1825278ed9767b7d1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/20224117c77c4cf1825278ed9767b7d1"}}, "title": "Functional proteoform group deconvolution reveals a broader spectrum of ibrutinib off-targets.", "authors": [{"family": "Leo", "given": "Isabelle Rose", "initials": "IR", "orcid": "0000-0002-7627-6690", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21801296760147b78e11b2a0ddcfd0e1.json"}}, {"family": "Kunold", "given": "Elena", "initials": "E"}, {"family": "Audrey", "given": "Anastasia", "initials": "A", "orcid": "0000-0002-8172-8575", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/436d3f91960447c384d04bf8535b35a9.json"}}, {"family": "Tampere", "given": "Marianna", "initials": "M"}, {"family": "Eirich", "given": "J\u00fcrgen", "initials": "J", "orcid": "0000-0003-0963-1872", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3070defe1f614b57ab391fa9a15c39a2.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Jafari", "given": "Rozbeh", "initials": "R", "orcid": "0000-0002-3396-4709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/95546f158dde40709fbfbb822a8f89c5.json"}}], "type": "journal article", "published": "2025-02-25", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "1948", "issn-l": "2041-1723"}, "abstract": "Proteome-wide profiling has revealed that targeted drugs can have complex protein interaction landscapes. However, it's a challenge to profile drug targets while systematically accounting for the dynamic protein variations that produce populations of multiple proteoforms. We address this problem by combining thermal proteome profiling (TPP) with functional proteoform group detection to refine the target landscape of ibrutinib. In addition to known targets, we implicate additional specific functional proteoform groups linking ibrutinib to mechanisms in immunomodulation and cellular processes like Golgi trafficking, endosomal trafficking, and glycosylation. Further, we identify variability in functional proteoform group profiles in a CLL cohort, linked to treatment status and ex vivo response and resistance. This offers deeper insights into the impacts of functional proteoform groups in a clinical treatment setting and suggests complex biological effects linked to off-target engagement. These results provide a framework for interpreting clinically observed off-target processes and adverse events, highlighting the importance of functional proteoform group-level deconvolution in understanding drug interactions and their functional impacts with potential applications in precision medicine.", "doi": "10.1038/s41467-024-54654-8", "pmid": "40000607", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11862126"}, {"db": "pii", "key": "10.1038/s41467-024-54654-8"}], "notes": [], "created": "2026-08-20T08:53:42.430Z", "modified": "2026-08-20T08:53:42.664Z"}, {"entity": "publication", "iuid": "d0e2a79c0a384ecfa7c2f9617353d66c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d0e2a79c0a384ecfa7c2f9617353d66c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d0e2a79c0a384ecfa7c2f9617353d66c"}}, "title": "Pathway activation model for personalized prediction of drug synergy", "authors": [{"family": "Trac", "given": "Quang Thinh", "initials": "QT", "orcid": "0000-0003-2429-0287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13e232680de04f55b195706785e79988.json"}}, {"family": "Huang", "given": "Yue", "initials": "Y"}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Bohlin", "given": "Anna", "initials": "A"}, {"family": "\u00d6sterroos", "given": "Albin", "initials": "A"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e443cdb01cc44a7fa786941b5c0b62d6.json"}}, {"family": "Jafari", "given": "Rozbeh", "initials": "R", "orcid": "0000-0002-3396-4709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/95546f158dde40709fbfbb822a8f89c5.json"}}, {"family": "Siavelis", "given": "Ioannis", "initials": "I"}, {"family": "B\u00e4ckvall", "given": "Helena", "initials": "H"}, {"family": "Kiviluoto", "given": "Santeri", "initials": "S"}, {"family": "Orre", "given": "Lukas M", "initials": "LM"}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}, {"family": "Pawitan", "given": "Yudi", "initials": "Y"}, {"family": "Vu", "given": "Trung Nghia", "initials": "TN", "orcid": "0000-0001-7945-5750", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c68ab75cfd4458aaa0cff82a637a24b.json"}}], "type": "posted-content", "published": "2024-08-09", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.100071.1", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:50:33.150Z", "modified": "2026-08-20T13:50:33.234Z"}, {"entity": "publication", "iuid": "64edbdbeaa8d4bbfbec29969c29f6262", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/64edbdbeaa8d4bbfbec29969c29f6262.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/64edbdbeaa8d4bbfbec29969c29f6262"}}, "title": "Pathway activation model for personalized prediction of drug synergy", "authors": [{"family": "Trac", "given": "Quang Thinh", "initials": "QT", "orcid": "0000-0003-2429-0287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13e232680de04f55b195706785e79988.json"}}, {"family": "Huang", "given": "Yue", "initials": "Y"}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Bohlin", "given": "Anna", "initials": "A"}, {"family": "\u00d6sterroos", "given": "Albin", "initials": "A"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e443cdb01cc44a7fa786941b5c0b62d6.json"}}, {"family": "Jafari", "given": "Rozbeh", "initials": "R", "orcid": "0000-0002-3396-4709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/95546f158dde40709fbfbb822a8f89c5.json"}}, {"family": "Siavelis", "given": "Ioannis", "initials": "I"}, {"family": "B\u00e4ckvall", "given": "Helena", "initials": "H"}, {"family": "Kiviluoto", "given": "Santeri", "initials": "S"}, {"family": "Orre", "given": "Lukas M", "initials": "LM"}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}, {"family": "Pawitan", "given": "Yudi", "initials": "Y"}, {"family": "Vu", "given": "Trung Nghia", "initials": "TN", "orcid": "0000-0001-7945-5750", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c68ab75cfd4458aaa0cff82a637a24b.json"}}], "type": "posted-content", "published": "2024-06-08", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.06.05.597583", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:55:06.724Z", "modified": "2026-08-20T10:55:06.811Z"}, {"entity": "publication", "iuid": "b14473323e934321b8443c64c0102100", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b14473323e934321b8443c64c0102100.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b14473323e934321b8443c64c0102100"}}, "title": "Delineating functional and molecular impact of ex vivo sample handling in precision medicine.", "authors": [{"family": "Struyf", "given": "Nona", "initials": "N", "orcid": "0000-0002-6975-0753", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be1087023d40465ca8133ea9845cd968.json"}}, {"family": "\u00d6sterroos", "given": "Albin", "initials": "A", "orcid": "0000-0001-8749-7299", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aafab8cd17e94d52a3cdeaf86d3acfa6.json"}}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e443cdb01cc44a7fa786941b5c0b62d6.json"}}, {"family": "Arnroth", "given": "Cornelia", "initials": "C"}, {"family": "James", "given": "Tojo", "initials": "T"}, {"family": "Sunandar", "given": "Stephanie", "initials": "S"}, {"family": "Mermelekas", "given": "Georgios", "initials": "G"}, {"family": "Bohlin", "given": "Anna", "initials": "A"}, {"family": "Hamberg Levedahl", "given": "Kerstin", "initials": "K"}, {"family": "Bengtz\u00e9n", "given": "Sofia", "initials": "S"}, {"family": "Jafari", "given": "Rozbeh", "initials": "R", "orcid": "0000-0002-3396-4709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/95546f158dde40709fbfbb822a8f89c5.json"}}, {"family": "Orre", "given": "Lukas M", "initials": "LM", "orcid": "0000-0002-0384-1003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e290f7cb5dfd49eb93e63cb704459516.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B", "orcid": "0000-0001-8658-5967", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a8ea4c3fdb14de1b651d0367b0a70a4.json"}}, {"family": "Erkers", "given": "Tom", "initials": "T", "orcid": "0000-0002-2754-6287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a1539d1d6a944eb882fdb80eb450706.json"}}], "type": "journal article", "published": "2024-02-19", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "volume": "8", "issue": "1", "pages": "38", "issn-l": null}, "abstract": "Consistent handling of samples is crucial for achieving reproducible molecular and functional testing results in translational research. Here, we used 229 acute myeloid leukemia (AML) patient samples to assess the impact of sample handling on high-throughput functional drug testing, mass spectrometry-based proteomics, and flow cytometry. Our data revealed novel and previously described changes in cell phenotype and drug response dependent on sample biobanking. Specifically, myeloid cells with a CD117 (c-KIT) positive phenotype decreased after biobanking, potentially distorting cell population representations and affecting drugs targeting these cells. Additionally, highly granular AML cell numbers decreased after freezing. Secondly, protein expression levels, as well as sensitivity to drugs targeting cell proliferation, metabolism, tyrosine kinases (e.g., JAK, KIT, FLT3), and BH3 mimetics were notably affected by biobanking. Moreover, drug response profiles of paired fresh and frozen samples showed that freezing samples can lead to systematic errors in drug sensitivity scores. While a high correlation between fresh and frozen for the entire drug library was observed, freezing cells had a considerable impact at an individual level, which could influence outcomes in translational studies. Our study highlights conditions where standardization is needed to improve reproducibility, and where validation of data generated from biobanked cohorts may be particularly important.", "doi": "10.1038/s41698-024-00528-7", "pmid": "38374206", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10876937"}, {"db": "pii", "key": "10.1038/s41698-024-00528-7"}], "notes": [], "created": "2026-08-20T09:24:34.463Z", "modified": "2026-08-20T09:24:34.644Z"}, {"entity": "publication", "iuid": "292b6c1981dd454a9db47e7dd46315f2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/292b6c1981dd454a9db47e7dd46315f2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/292b6c1981dd454a9db47e7dd46315f2"}}, "title": "Deep thermal profiling for detection of functional proteoform groups.", "authors": [{"family": "Kurzawa", "given": "Nils", "initials": "N", "orcid": "0000-0002-7846-2817", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/082e8989ae6e4d61bea479a19a0f0de3.json"}}, {"family": "Leo", "given": "Isabelle Rose", "initials": "IR"}, {"family": "Stahl", "given": "Matthias", "initials": "M"}, {"family": "Kunold", "given": "Elena", "initials": "E"}, {"family": "Becher", "given": "Isabelle", "initials": "I"}, {"family": "Audrey", "given": "Anastasia", "initials": "A", "orcid": "0000-0002-8172-8575", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/436d3f91960447c384d04bf8535b35a9.json"}}, {"family": "Mermelekas", "given": "Georgios", "initials": "G"}, {"family": "Huber", "given": "Wolfgang", "initials": "W", "orcid": "0000-0002-0474-2218", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/138102f5e406446a8b5f9c421ea1e595.json"}}, {"family": "Mateus", "given": "Andr\u00e9", "initials": "A", "orcid": "0000-0001-6870-0677", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ebf0d242aa894a66b60828456bbc22aa.json"}}, {"family": "Savitski", "given": "Mikhail M", "initials": "MM", "orcid": "0000-0003-2011-9247", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/374222bd4bce42f282690629b9679628.json"}}, {"family": "Jafari", "given": "Rozbeh", "initials": "R", "orcid": "0000-0002-3396-4709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/95546f158dde40709fbfbb822a8f89c5.json"}}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Nat. Chem. Biol.", "issn": "1552-4469", "volume": "19", "issue": "8", "pages": "962-971", "issn-l": "1552-4450"}, "abstract": "The complexity of the functional proteome extends considerably beyond the coding genome, resulting in millions of proteoforms. Investigation of proteoforms and their functional roles is important to understand cellular physiology and its deregulation in diseases but challenging to perform systematically. Here we applied thermal proteome profiling with deep peptide coverage to detect functional proteoform groups in acute lymphoblastic leukemia cell lines with different cytogenetic aberrations. We detected 15,846 proteoforms, capturing differently spliced, cleaved and post-translationally modified proteins expressed from 9,290 genes. We identified differential co-aggregation of proteoform pairs and established links to disease biology. Moreover, we systematically made use of measured biophysical proteoform states to find specific biomarkers of drug sensitivity. Our approach, thus, provides a powerful and unique tool for systematic detection and functional annotation of proteoform groups.", "doi": "10.1038/s41589-023-01284-8", "pmid": "36941476", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10374440"}, {"db": "pii", "key": "10.1038/s41589-023-01284-8"}], "notes": [], "created": "2026-08-20T09:01:33.664Z", "modified": "2026-08-20T09:01:33.770Z"}, {"entity": "publication", "iuid": "e18900613386411ca6ad306c75d7d436", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e18900613386411ca6ad306c75d7d436.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e18900613386411ca6ad306c75d7d436"}}, "title": "Delineating functional and molecular impact of ex vivo sample handling in precision medicine", "authors": [{"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "Struyf", "given": "Nona", "initials": "N"}, {"family": "Arnroth", "given": "Cornelia", "initials": "C"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e443cdb01cc44a7fa786941b5c0b62d6.json"}}, {"family": "James", "given": "Tojo", "initials": "T"}, {"family": "Sunandar", "given": "Stephanie", "initials": "S"}, {"family": "Bohlin", "given": "Anna", "initials": "A"}, {"family": "Hamberg-Levedahl", "given": "Kerstin", "initials": "K"}, {"family": "Bengtz\u00e9n", "given": "Sofia", "initials": "S"}, {"family": "Jafari", "given": "Rozbeh", "initials": "R", "orcid": "0000-0002-3396-4709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/95546f158dde40709fbfbb822a8f89c5.json"}}, {"family": "Orre", "given": "Lukas", "initials": "L"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}, {"family": "Ostling", "given": "Paivi", "initials": "P"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B", "orcid": "0000-0001-8658-5967", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a8ea4c3fdb14de1b651d0367b0a70a4.json"}}], "type": "posted-content", "published": "2023-07-26", "journal": {"issn-l": null}, "abstract": null, "doi": "10.21203/rs.3.rs-3072667/v1", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T12:59:12.192Z", "modified": "2026-08-20T12:59:12.224Z"}]}