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"https://publications-affiliated.scilifelab.se/researcher/75d7f80346a54b03b6a979d706df7aa7.json"}}, {"family": "Liti", "given": "Gianni", "initials": "G"}, {"family": "Rudbeck", "given": "Emilio", "initials": "E"}, {"family": "Golicz", "given": "Agnieszka A", "initials": "AA", "orcid": "0000-0002-9711-4826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/00e6ce757691402eab951b2d4f3456af.json"}}, {"family": "Nahnsen", "given": "Sven", "initials": "S", "orcid": "0000-0002-4375-0691", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/822afa4ff0b041bcb7743d15d23b0c22.json"}}, {"family": "Yang", "given": "Zuyu", "initials": "Z", "orcid": "0000-0002-0651-848X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ff490cb664cb423a9df6e73fd4d0af3c.json"}}, {"family": "Mwaniki", "given": "Moses Njagi", "initials": "MN"}, {"family": "Nobrega", "given": "Franklin L", "initials": "FL", "orcid": "0000-0002-8238-1083", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e0e4489785ca4c789e5c3b026f7cf4d1.json"}}, {"family": "Wu", "given": "Yi", "initials": "Y"}, {"family": "Chen", "given": "Hao", "initials": "H"}, {"family": "de Ligt", "given": "Joep", "initials": "J", "orcid": "0000-0002-0348-419X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/119cc9aa12a44667a5bbdf2a711c3a63.json"}}, {"family": "Sudmant", "given": "Peter H", "initials": "PH", "orcid": "0000-0002-9573-8248", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/51dce83846184d3697a56d8d6bb06db7.json"}}, {"family": "Huang", "given": "Sanwen", "initials": "S", "orcid": "0000-0002-8547-5309", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3234328fbd4741638d4464e2de00f72a.json"}}, {"family": "Weigel", "given": "Detlef", "initials": "D", "orcid": "0000-0002-2114-7963", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/869682094103499d9e61cb48d8fda862.json"}}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Colonna", "given": "Vincenza", "initials": "V", "orcid": "0000-0002-3966-0474", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/817771f5031644c3b995c37be8c112ac.json"}}, {"family": "Williams", "given": "Robert W", "initials": "RW"}, {"family": "Prins", "given": "Pjotr", "initials": "P", "orcid": "0000-0002-8021-9162", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be784d1883984d6bbf587a060417c1ed.json"}}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "issn-l": "1548-7091", "volume": "21", "issue": "11", "pages": "2008-2012"}, "abstract": "Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference. In response, we developed the PanGenome Graph Builder, a pipeline for constructing pangenome graphs without bias or exclusion. The PanGenome Graph Builder uses all-to-all alignments to build a variation graph in which we can identify variation, measure conservation, detect recombination events and infer phylogenetic relationships.", "doi": "10.1038/s41592-024-02430-3", "pmid": "39433878", "labels": {"Kaisa Thorell": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41592-024-02430-3"}], "notes": [], "created": "2025-03-19T17:07:47.110Z", "modified": "2025-03-21T13:34:53.012Z"}, {"entity": "publication", "iuid": "3e55948203104658ab74310562478c6d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3e55948203104658ab74310562478c6d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3e55948203104658ab74310562478c6d"}}, "title": "An ancient ecospecies of Helicobacter pylori.", "authors": [{"family": "Tourrette", "given": "Elise", "initials": "E", "orcid": "0000-0002-0822-5330", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a2633bd0cd04e9981429f449e3d3248.json"}}, {"family": "Torres", "given": "Roberto C", "initials": "RC", "orcid": "0000-0001-6990-9114", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ba4620c612a481989a81983eb9f405a.json"}}, {"family": "Svensson", "given": "Sarah L", "initials": "SL", "orcid": "0000-0002-3183-6084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2b41514d94c442c98e9e8b4e4ce98242.json"}}, {"family": "Matsumoto", "given": "Takashi", "initials": "T", "orcid": "0000-0002-6899-1686", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f06a8462b1034c5ab2114555cc6ccae0.json"}}, {"family": "Miftahussurur", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-1415-6033", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0cd1c83607a44aa786bb746860e24c0f.json"}}, {"family": "Fauzia", "given": "Kartika Afrida", "initials": "KA"}, {"family": "Alfaray", "given": "Ricky Indra", "initials": "RI", "orcid": "0000-0001-7721-9455", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e1b6b6e420d40f4b386f23f36733514.json"}}, {"family": "Vilaichone", "given": "Ratha-Korn", "initials": "R"}, {"family": "Tuan", "given": "Vo Phuoc", "initials": "VP"}, {"family": "Helicobacter Genomics Consortium", "given": "", "initials": ""}, {"family": "Wang", "given": "Difei", "initials": "D", "orcid": "0000-0003-4088-3859", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47af1e6daf8641d089d6def9b137e677.json"}}, {"family": "Yadegar", "given": "Abbas", "initials": "A", "orcid": "0000-0002-2135-7581", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ef1ab6bffbb64bdd828d0491d9f16136.json"}}, {"family": "Olsson", "given": "Lisa M", "initials": "LM", "orcid": "0000-0001-9730-1915", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ebc33ee3a5840c8b3c71ce912057c39.json"}}, {"family": "Zhou", "given": "Zhemin", "initials": "Z", "orcid": "0000-0001-9783-0366", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2659842e6f74c4187b1d6a032d7b6d8.json"}}, {"family": "Yamaoka", "given": "Yoshio", "initials": "Y", "orcid": "0000-0002-1222-5819", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a710e567386a47d283402e7f05d8a500.json"}}, {"family": "Thorell", "given": "Kaisa", "initials": "K", "orcid": "0000-0002-4447-8968", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/789d4029a5c14d3c83df7c47b3b514c7.json"}}, {"family": "Falush", "given": "Daniel", "initials": "D", "orcid": "0000-0002-2956-0795", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eb315b1088084cf59f2a0ab3767f03b2.json"}}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": "635", "issue": "8037", "pages": "178-185"}, "abstract": "Helicobacter pylori disturbs the stomach lining during long-term colonization of its human host, with sequelae including ulcers and gastric cancer1,2. Numerous H. pylori virulence factors have been identified, showing extensive geographic variation1. Here we identify a 'Hardy' ecospecies of H. pylori that shares the ancestry of 'Ubiquitous' H. pylori from the same region in most of the genome but has nearly fixed single-nucleotide polymorphism differences in 100 genes, many of which encode outer membrane proteins and host interaction factors. Most Hardy strains have a second urease, which uses iron as a cofactor rather than nickel3, and two additional copies of the vacuolating cytotoxin VacA. Hardy strains currently have a limited distribution, including in Indigenous populations in Siberia and the Americas and in lineages that have jumped from humans to other mammals. Analysis of polymorphism data implies that Hardy and Ubiquitous coexisted in the stomachs of modern humans since before we left Africa and that both were dispersed around the world by our migrations. Our results also show that highly distinct adaptive strategies can arise and be maintained stably within bacterial populations, even in the presence of continuous genetic exchange between strains.", "doi": "10.1038/s41586-024-07991-z", "pmid": "39415013", "labels": {"Kaisa Thorell": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11541087"}, {"db": "pii", "key": "10.1038/s41586-024-07991-z"}], "notes": [], "created": "2025-03-19T17:07:43.934Z", "modified": "2025-03-21T13:35:08.471Z"}]}