{"entity": "researcher", "timestamp": "2026-09-23T22:14:59.071Z", "family": "Jeggari", "given": "Ashwini", "initials": "A", "orcid": "0000-0002-7155-9050", "affiliations": ["Department of Cell and Molecular Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/b323a794f5054c77b32cc4452f45df32.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/b323a794f5054c77b32cc4452f45df32"}}, "publications": [{"entity": "publication", "iuid": "c49d024a51654ae79653a603c99a7379", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c49d024a51654ae79653a603c99a7379.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c49d024a51654ae79653a603c99a7379"}}, "title": "Sensitive Detection of Cell-Free Tumour DNA Using Optimised Targeted Sequencing Can Predict Prognosis in Gastro-Oesophageal Cancer.", "authors": [{"family": "Wallander", "given": "Karin", "initials": "K", "orcid": "0000-0001-8166-9678", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d3f581341864b9696eb87f2eb139335.json"}}, {"family": "Haider", "given": "Zahra", "initials": "Z", "orcid": "0000-0002-0759-3932", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ef882ad3a8d74e1787677446c20045ae.json"}}, {"family": "Jeggari", "given": "Ashwini", "initials": "A", "orcid": "0000-0002-7155-9050", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b323a794f5054c77b32cc4452f45df32.json"}}, {"family": "Foroughi-Asl", "given": "Hassan", "initials": "H"}, {"family": "Gellerbring", "given": "Anna", "initials": "A"}, {"family": "Lyander", "given": "Anna", "initials": "A"}, {"family": "Chozhan", "given": "Athithyan", "initials": "A"}, {"family": "Cuba Gyllensten", "given": "Ollanta", "initials": "O"}, {"family": "H\u00e4gglund", "given": "Moa", "initials": "M", "orcid": "0000-0003-3765-4342", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c2a00a2a4fb94d278b2c71e1c5160469.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a4f538e838c483eb968174f2df89165.json"}}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Lindblad", "given": "Mats", "initials": "M"}, {"family": "Tham", "given": "Emma", "initials": "E", "orcid": "0000-0001-6079-164X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e5a7c4ae89f441ca0fa14238aa9511b.json"}}], "type": "journal article", "published": "2023-02-11", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "15", "issue": "4", "issn-l": "2072-6694"}, "abstract": "In this longitudinal study, cell-free tumour DNA (a liquid biopsy) from plasma was explored as a prognostic biomarker for gastro-oesophageal cancer. Both tumour-informed and tumour-agnostic approaches for plasma variant filtering were evaluated in 47 participants. This was possible through sequencing of DNA from tissue biopsies from all participants and cell-free DNA from plasma sampled before and after surgery (n = 42), as well as DNA from white blood cells (n = 21) using a custom gene panel with and without unique molecular identifiers (UMIs). A subset of the plasma samples (n = 12) was also assayed with targeted droplet digital PCR (ddPCR). In 17/31 (55%) diagnostic plasma samples, tissue-verified cancer-associated variants could be detected by the gene panel. In the tumour-agnostic approach, 26 participants (59%) had cancer-associated variants, and UMIs were necessary to filter the true variants from the technical artefacts. Additionally, clonal haematopoietic variants could be excluded using the matched white blood cells or follow-up plasma samples. ddPCR detected its targets in 10/12 (83%) and provided an ultra-sensitive method for follow-up. Detectable cancer-associated variants in plasma correlated to a shorter overall survival and shorter time to progression, with a significant correlation for the tumour-informed approaches. In summary, liquid biopsy gene panel sequencing using a tumour-agnostic approach can be applied to all patients regardless of the presence of a tissue biopsy, although this requires UMIs and the exclusion of clonal haematopoietic variants. However, if sequencing data from tumour biopsies are available, a tumour-informed approach improves the value of cell-free tumour DNA as a negative prognostic biomarker in gastro-oesophageal cancer patients.", "doi": "10.3390/cancers15041160", "pmid": "36831507", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9954085"}, {"db": "pii", "key": "cancers15041160"}], "notes": [], "created": "2026-09-23T12:15:49.447Z", "modified": "2026-09-23T12:15:49.595Z"}, {"entity": "publication", "iuid": "6b6e8a7e8697435baaa36054b1576495", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6b6e8a7e8697435baaa36054b1576495.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6b6e8a7e8697435baaa36054b1576495"}}, "title": "A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells.", "authors": [{"family": "Dias", "given": "Jos\u00e9 M", "initials": "JM", "orcid": "0000-0002-1402-0323", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa189d497af4380b7db4c1aba55ae80.json"}}, {"family": "Alekseenko", "given": "Zhanna", "initials": "Z", "orcid": "0000-0002-6560-9699", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/445652e37bbe48729174f49e389b79b2.json"}}, {"family": "Jeggari", "given": "Ashwini", "initials": "A", "orcid": "0000-0002-7155-9050", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b323a794f5054c77b32cc4452f45df32.json"}}, {"family": "Boareto", "given": "Marcelo", "initials": "M", "orcid": "0000-0002-9915-6376", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b4fc8d2ae534ff3aa7ee88457346a16.json"}}, {"family": "Vollmer", "given": "Jannik", "initials": "J", "orcid": "0000-0001-8341-7730", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2613649376a74ff1b465b1876298b6f6.json"}}, {"family": "Kozhevnikova", "given": "Mariya", "initials": "M", "orcid": "0000-0001-9177-6303", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ad46be6158194a729e4286901403c2e7.json"}}, {"family": "Wang", "given": "Hui", "initials": "H", "orcid": "0000-0002-5444-1579", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8f37c92155e4494390f02d6f59e821ac.json"}}, {"family": "Matise", "given": "Michael P", "initials": "MP", "orcid": "0000-0003-2998-9927", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b141693f76654b30be9ab0324f43df86.json"}}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A", "orcid": "0000-0001-8812-6481", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8078f1505d9747e1ac76cf2f6d4ee606.json"}}, {"family": "Iber", "given": "Dagmar", "initials": "D", "orcid": "0000-0001-8051-1035", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/634585a0768c4149ac5287d0bed67c30.json"}}, {"family": "Ericson", "given": "Johan", "initials": "J", "orcid": "0000-0002-8019-7127", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2963ca6a73bb409baea88ca67eeca936.json"}}], "type": "journal article", "published": "2020-09-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "6", "issue": "38", "issn-l": "2375-2548"}, "abstract": "How time is measured by neural stem cells during temporal neurogenesis has remained unresolved. By combining experiments and computational modeling, we define a Shh/Gli-driven three-node timer underlying the sequential generation of motor neurons (MNs) and serotonergic neurons in the brainstem. The timer is founded on temporal decline of Gli-activator and Gli-repressor activities established through down-regulation of Gli transcription. The circuitry conforms an incoherent feed-forward loop, whereby Gli proteins not only promote expression of Phox2b and thereby MN-fate but also account for a delayed activation of a self-promoting transforming growth factor-\u03b2 (Tgf\u03b2) node triggering a fate switch by repressing Phox2b. Hysteresis and spatial averaging by diffusion of Tgf\u03b2 counteract noise and increase temporal accuracy at the population level, providing a functional rationale for the intrinsically programmed activation of extrinsic switch signals in temporal patterning. Our study defines how time is reliably encoded during the sequential specification of neurons.", "doi": "10.1126/sciadv.aba8196", "pmid": "32938678", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7494341"}, {"db": "pii", "key": "6/38/eaba8196"}], "notes": [], "created": "2026-09-23T12:02:37.544Z", "modified": "2026-09-23T12:02:37.826Z"}, {"entity": "publication", "iuid": "b0d815ccfad3407a96c595bb20f1148d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b0d815ccfad3407a96c595bb20f1148d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b0d815ccfad3407a96c595bb20f1148d"}}, "title": "A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells", "authors": [{"family": "Dias", "given": "Jos\u00e9 M", "initials": "JM"}, {"family": "Alekseenko", "given": "Zhanna", "initials": "Z", "orcid": "0000-0002-6560-9699", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/445652e37bbe48729174f49e389b79b2.json"}}, {"family": "Jeggari", "given": "Ashwini", "initials": "A", "orcid": "0000-0002-7155-9050", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b323a794f5054c77b32cc4452f45df32.json"}}, {"family": "Boareto", "given": "Marcelo", "initials": "M", "orcid": "0000-0002-9915-6376", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b4fc8d2ae534ff3aa7ee88457346a16.json"}}, {"family": "Vollmer", "given": "Jannik", "initials": "J"}, {"family": "Kozhevnikova", "given": "Mariya", "initials": "M", "orcid": "0000-0001-9177-6303", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ad46be6158194a729e4286901403c2e7.json"}}, {"family": "Wang", "given": "Hui", "initials": "H"}, {"family": "Matise", "given": "Michael P", "initials": "MP"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A", "orcid": "0000-0001-8812-6481", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8078f1505d9747e1ac76cf2f6d4ee606.json"}}, {"family": "Iber", "given": "Dagmar", "initials": "D", "orcid": "0000-0001-8051-1035", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/634585a0768c4149ac5287d0bed67c30.json"}}, {"family": "Ericson", "given": "Johan", "initials": "J", "orcid": "0000-0003-0135-3871", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/297463631cb34278a96a50aba9a849a3.json"}}], "type": "posted-content", "published": "2019-10-17", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/809418", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-09-23T15:01:12.393Z", "modified": "2026-09-23T15:01:12.478Z"}]}