{"entity": "researcher", "timestamp": "2026-08-20T20:26:21.738Z", "family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "affiliations": ["Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/1906700bcb724376ae84980b2f59c862.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/1906700bcb724376ae84980b2f59c862"}}, "publications": [{"entity": "publication", "iuid": "775edf1dec0941df90d9b4f9ac46e7b1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/775edf1dec0941df90d9b4f9ac46e7b1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/775edf1dec0941df90d9b4f9ac46e7b1"}}, "title": "READv2: Advanced and user-friendly detection of biological relatedness in archaeogenomics", "authors": [{"family": "Ala\u00e7aml\u0131", "given": "Erkin", "initials": "E"}, {"family": "Naidoo", "given": "Thijessen", "initials": "T"}, {"family": "Akt\u00fcrk", "given": "\u015eevval", "initials": "\u015e"}, {"family": "G\u00fcler", "given": "Merve N", "initials": "MN"}, {"family": "Mapelli", "given": "Igor", "initials": "I", "orcid": "0000-0001-9814-7884", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4fc1eff4bca4ba3979326d6992a19ab.json"}}, {"family": "Vural", "given": "K\u0131v\u0131lc\u0131m Ba\u015fak", "initials": "KB", "orcid": "0000-0003-3964-3065", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a6b3d270432423389db89905f0813f6.json"}}, {"family": "Somel", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-3138-1307", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/141c364779504facae706bd757e72580.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": 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"authors": [{"family": "Miranda", "given": "Pedro Morell", "initials": "PM", "orcid": "0000-0001-7678-9691", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/96ac4871605f46718b5ca7b0fb00a537.json"}}, {"family": "Soares", "given": "Andr\u00e9 ER", "initials": "AE", "orcid": "0000-0002-7768-2199", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9300e4d675645c0872ea209ce1e4fef.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1906700bcb724376ae84980b2f59c862.json"}}], "type": "posted-content", "published": "2023-06-18", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.06.16.545369", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:46:49.103Z", "modified": "2026-08-20T10:46:49.201Z"}, {"entity": "publication", "iuid": "f00276d2dd714500a034266db5996060", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f00276d2dd714500a034266db5996060.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f00276d2dd714500a034266db5996060"}}, "title": "Ancient DNA from a 2,700-year-old goitered gazelle ( Gazella subgutturosa ) confirms gazelle hunting in Iron Age Central Asia", "authors": [{"family": "Rodrigues Soares", "given": "Andr\u00e9 Elias", "initials": "AE", "orcid": "0000-0002-7768-2199", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9300e4d675645c0872ea209ce1e4fef.json"}}, {"family": "Boroffka", "given": "Nikolaus", "initials": "N", "orcid": "0000-0002-3437-1569", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5cfda51500324810952de7952c2d8651.json"}}, {"family": "Schr\u00f6der", "given": "Oskar", "initials": "O"}, {"family": "Sverchkov", "given": "Leonid", "initials": "L"}, {"family": "Benecke", "given": "Norbert", "initials": "N", "orcid": "0000-0003-2388-8594", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ca3d9a8d539429b843f120759699891.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1906700bcb724376ae84980b2f59c862.json"}}], "type": "posted-content", "published": "2021-12-10", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.12.08.471591", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:07:42.865Z", "modified": "2026-08-20T10:07:43.008Z"}, {"entity": "publication", "iuid": "cc8129c7431c4f4abe00e0d50be63b5f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cc8129c7431c4f4abe00e0d50be63b5f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cc8129c7431c4f4abe00e0d50be63b5f"}}, "title": "The presence and impact of reference bias on population genomic studies of prehistoric human populations.", "authors": [{"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1906700bcb724376ae84980b2f59c862.json"}}, {"family": "Nettelblad", "given": "Carl", "initials": "C", "orcid": "0000-0003-0458-6902", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da4567d9202441e29412c827729e7134.json"}}], "type": "journal article", "published": "2019-07-00", "journal": {"title": "PLoS Genet", "issn": "1553-7404", "volume": "15", "issue": "7", "pages": "e1008302", "issn-l": "1553-7390"}, "abstract": "Haploid high quality reference genomes are an important resource in genomic research projects. A consequence is that DNA fragments carrying the reference allele will be more likely to map successfully, or receive higher quality scores. This reference bias can have effects on downstream population genomic analysis when heterozygous sites are falsely considered homozygous for the reference allele. In palaeogenomic studies of human populations, mapping against the human reference genome is used to identify endogenous human sequences. Ancient DNA studies usually operate with low sequencing coverages and fragmentation of DNA molecules causes a large proportion of the sequenced fragments to be shorter than 50 bp-reducing the amount of accepted mismatches, and increasing the probability of multiple matching sites in the genome. These ancient DNA specific properties are potentially exacerbating the impact of reference bias on downstream analyses, especially since most studies of ancient human populations use pseudo-haploid data, i.e. they randomly sample only one sequencing read per site. We show that reference bias is pervasive in published ancient DNA sequence data of prehistoric humans with some differences between individual genomic regions. We illustrate that the strength of reference bias is negatively correlated with fragment length. Most genomic regions we investigated show little to no mapping bias but even a small proportion of sites with bias can impact analyses of those particular loci or slightly skew genome-wide estimates. Therefore, reference bias has the potential to cause minor but significant differences in the results of downstream analyses such as population allele sharing, heterozygosity estimates and estimates of archaic ancestry. These spurious results highlight how important it is to be aware of these technical artifacts and that we need strategies to mitigate the effect. Therefore, we suggest some post-mapping filtering strategies to resolve reference bias which help to reduce its impact substantially.", "doi": "10.1371/journal.pgen.1008302", "pmid": "31348818", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6685638"}, {"db": "pii", "key": "PGENETICS-D-19-00061"}], "notes": [], "created": "2026-08-20T12:43:40.040Z", "modified": "2026-08-20T12:43:40.126Z"}, {"entity": "publication", "iuid": "5ecd8803519d425c958b5f6b859bcb3e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5ecd8803519d425c958b5f6b859bcb3e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5ecd8803519d425c958b5f6b859bcb3e"}}, "title": "The presence and impact of reference bias on population genomic studies of prehistoric human populations", "authors": [{"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1906700bcb724376ae84980b2f59c862.json"}}, {"family": "Nettelblad", "given": "Carl", "initials": "C", "orcid": "0000-0003-0458-6902", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da4567d9202441e29412c827729e7134.json"}}], "type": "posted-content", "published": "2018-12-06", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/487983", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:11:43.455Z", "modified": "2026-08-20T11:11:43.478Z"}, {"entity": "publication", "iuid": "1ba9a649d6ac4850ae38fc295b54210b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1ba9a649d6ac4850ae38fc295b54210b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1ba9a649d6ac4850ae38fc295b54210b"}}, "title": "Genomics of Mesolithic Scandinavia reveal colonization routes and high-latitude adaptation", "authors": [{"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1906700bcb724376ae84980b2f59c862.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f7b3d882fb140a0b48c90752747e82f.json"}}, {"family": "Svensson", "given": "Emma M", "initials": "EM", "orcid": "0000-0002-4349-849X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/32ad3c6846e5406d8cc57926c65114ca.json"}}, {"family": "Omrak", "given": "Ay\u00e7a", "initials": "A"}, {"family": "S\u00e1nchez-Quinto", "given": "Federico", "initials": "F", "orcid": "0000-0002-0201-6204", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af937184fa2b42adabcc9e1b74d55b84.json"}}, {"family": "K\u0131l\u0131n\u00e7", "given": 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"G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ff87fd5aabe4a38954dd96d8e6c261d.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/377f1b52aa8d4bf394f82148a2b23d40.json"}}], "type": "posted-content", "published": "2017-07-17", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/164400", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T09:54:46.404Z", "modified": "2026-08-20T09:54:46.695Z"}, {"entity": "publication", "iuid": "66ed8e296fb04da184158d9f7d9ec004", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/66ed8e296fb04da184158d9f7d9ec004.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/66ed8e296fb04da184158d9f7d9ec004"}}, "title": "Ancient genomes from southern Africa pushes modern human divergence beyond 260,000 years ago", "authors": [{"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c3c5882a2df9403a8756665cc3ae6b76.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f7b3d882fb140a0b48c90752747e82f.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1906700bcb724376ae84980b2f59c862.json"}}, {"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "Coutinho", "given": "Alexandra", "initials": "A"}, {"family": "Edlund", "given": "Hanna", "initials": "H", "orcid": "0000-0003-3784-4285", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2157545203ca4da1b755fd2765b1938f.json"}}, {"family": "Munters", "given": "Arielle R", "initials": "AR"}, {"family": "Steyn", "given": "Maryna", "initials": "M"}, {"family": "Soodyall", "given": "Himla", "initials": "H", "orcid": "0000-0003-2488-9185", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bf2d1df317a44617bc2bd8fa1b1c642a.json"}}, {"family": "Lombard", "given": "Marlize", "initials": "M", "orcid": "0000-0002-0675-0414", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f8f297c6ace476a968d8102657c47dc.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/377f1b52aa8d4bf394f82148a2b23d40.json"}}], "type": "posted-content", "published": "2017-06-05", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/145409", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T09:54:34.407Z", "modified": "2026-08-20T09:54:34.614Z"}, {"entity": "publication", "iuid": "873ba90e2c5546c0964021f3bb85db6f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/873ba90e2c5546c0964021f3bb85db6f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/873ba90e2c5546c0964021f3bb85db6f"}}, "title": "Reply to Lazaridis and Reich: Robust model-based inference of male-biased admixture during Bronze Age migration from the Pontic-Caspian Steppe.", "authors": [{"family": "Goldberg", "given": "Amy", "initials": "A", "orcid": "0000-0001-9306-1539", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6658a193179a43b8817ec59eac105f0b.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1906700bcb724376ae84980b2f59c862.json"}}, {"family": "Rosenberg", "given": "Noah A", "initials": "NA"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M"}], "type": "letter", "published": "2017-05-16", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "114", "issue": "20", "pages": "E3875-E3877", "issn-l": "0027-8424"}, "abstract": null, "doi": "10.1073/pnas.1704442114", "pmid": "28476765", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC5441823"}, {"db": "pii", "key": "1704442114"}], "notes": [], "created": "2026-08-20T09:29:44.212Z", "modified": "2026-08-20T09:29:44.303Z"}, {"entity": "publication", "iuid": "80c7ecb916af447b8825de34b657d73f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/80c7ecb916af447b8825de34b657d73f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/80c7ecb916af447b8825de34b657d73f"}}, "title": "Estimating Genetic Kin Relationships in Prehistoric Populations", "authors": [{"family": "Kuhn", "given": "Jose Manuel Monroy", "initials": "JMM"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/377f1b52aa8d4bf394f82148a2b23d40.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1906700bcb724376ae84980b2f59c862.json"}}], "type": "posted-content", "published": "2017-01-13", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/100297", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T09:53:57.838Z", "modified": "2026-08-20T09:53:57.896Z"}, {"entity": "publication", "iuid": "5978f88e1eee4b8eb8938c3ea8a08852", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5978f88e1eee4b8eb8938c3ea8a08852.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5978f88e1eee4b8eb8938c3ea8a08852"}}, "title": "Genes mirror migrations and cultures in prehistoric Europe \u2013 a population genomic perspective", "authors": [{"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1906700bcb724376ae84980b2f59c862.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M"}], "type": "posted-content", "published": "2016-09-01", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/072926", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T09:53:37.397Z", "modified": "2026-08-20T09:53:37.459Z"}]}