{"entity": "researcher", "timestamp": "2026-06-17T03:29:00.890Z", "family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "affiliations": ["Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, 22362, Lund, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/1a556bc2e89c457fb1e45cfcd7b567e9.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/1a556bc2e89c457fb1e45cfcd7b567e9"}}, "publications": [{"entity": "publication", "iuid": "0a9eb063435d44b8b5aaa1d5222991bf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a9eb063435d44b8b5aaa1d5222991bf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a9eb063435d44b8b5aaa1d5222991bf"}}, "title": "The spatiotemporal distribution of human pathogens in ancient Eurasia.", "authors": [{"family": "Sikora", "given": "Martin", "initials": "M", "orcid": "0000-0003-2818-8319", "researcher": {"href": "https://publications.scilifelab.se/researcher/a55c0205eb8c4673b75ce6b3f5d8f061.json"}}, {"family": "Canteri", "given": "Elisabetta", "initials": "E", "orcid": "0000-0001-9867-8247", "researcher": {"href": "https://publications.scilifelab.se/researcher/6396a091e3434959ab086de16d7c2004.json"}}, {"family": "Fernandez-Guerra", "given": "Antonio", "initials": "A", "orcid": "0000-0002-8679-490X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9dae21b2abe4de6947cd132f9948819.json"}}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a556bc2e89c457fb1e45cfcd7b567e9.json"}}, {"family": "\u00c5gren", "given": "Rasmus", "initials": "R"}, {"family": "Hansson", "given": "Lena", "initials": "L"}, {"family": "Irving-Pease", "given": "Evan K", "initials": "EK", "orcid": "0000-0003-1940-2192", "researcher": {"href": "https://publications.scilifelab.se/researcher/02e144af5864412baa97c9fa5defbfd5.json"}}, {"family": "M\u00fchlemann", "given": "Barbara", "initials": "B", "orcid": "0000-0002-5314-8530", "researcher": {"href": "https://publications.scilifelab.se/researcher/50e4d63a643241dda76febe2c017ba17.json"}}, {"family": "Holtsmark Nielsen", "given": "Sofie", "initials": "S", "orcid": "0000-0001-7463-360X", "researcher": {"href": "https://publications.scilifelab.se/researcher/429c378d6a3c4701831cbe8f7de4d8c3.json"}}, {"family": "Scorrano", "given": "Gabriele", "initials": "G", "orcid": "0000-0002-0887-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce84de79eddb4dcfae112d976ac424d3.json"}}, {"family": "Allentoft", "given": "Morten E", "initials": "ME", "orcid": "0000-0003-4424-3568", "researcher": {"href": "https://publications.scilifelab.se/researcher/561280c38047471c9797eb18af77b701.json"}}, {"family": "Valeur Seersholm", "given": "Frederik", "initials": "F"}, {"family": "Schroeder", "given": "Hannes", "initials": "H", "orcid": "0000-0002-6743-0270", "researcher": {"href": "https://publications.scilifelab.se/researcher/42fd7d83095f4b849b4f3f774632581d.json"}}, {"family": "Gaunitz", "given": "Charleen", "initials": "C"}, {"family": "Stenderup", "given": "Jesper", "initials": "J", "orcid": "0000-0002-6916-106X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8dc81abfa4244623a43209c510a22f33.json"}}, {"family": "Vinner", "given": "Lasse", "initials": "L"}, {"family": "Jones", "given": "Terry C", "initials": "TC", "orcid": "0000-0003-1120-9531", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9b36b89964bf5a57076d0bf5f8f52.json"}}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Sj\u00f6gren", "given": "Karl-G\u00f6ran", "initials": "KG"}, {"family": "Parkhill", "given": "Julian", "initials": "J", "orcid": "0000-0002-7069-5958", "researcher": {"href": "https://publications.scilifelab.se/researcher/29c1551bb9e84080b2a0078966487128.json"}}, {"family": "Fugger", "given": "Lars", "initials": "L", "orcid": "0000-0003-2883-3226", "researcher": {"href": "https://publications.scilifelab.se/researcher/3fa5f367384c4e8a954a2a80510da69d.json"}}, {"family": "Racimo", "given": "Fernando", "initials": "F", "orcid": "0000-0002-5025-2607", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcd12137b4184a72a81c48d2926c5280.json"}}, {"family": "Kristiansen", "given": "Kristian", "initials": "K", "orcid": "0000-0003-2423-308X", "researcher": {"href": "https://publications.scilifelab.se/researcher/949ec2cfb14c4fae8d63de611b7456f7.json"}}, {"family": "Iversen", "given": "Astrid K N", "initials": "AKN", "orcid": "0000-0002-3507-5956", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7fb936cc43444d6a3d2d51fb6c5417a.json"}}, {"family": "Willerslev", "given": "Eske", "initials": "E", "orcid": "0000-0002-7081-6748", "researcher": {"href": "https://publications.scilifelab.se/researcher/da0055841300427e85d9af38b1863ef1.json"}}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "643", "issue": "8073", "pages": "1011-1019", "issn-l": "0028-0836"}, "abstract": "Infectious diseases have had devastating effects on human populations throughout history, but important questions about their origins and past dynamics remain1. To create an archaeogenetic-based spatiotemporal map of human pathogens, we screened shotgun-sequencing data from 1,313 ancient humans covering 37,000 years of Eurasian history. We demonstrate the widespread presence of ancient bacterial, viral and parasite DNA, identifying 5,486 individual hits against 492 species from 136 genera. Among those hits, 3,384 involve known human pathogens2, many of which had not previously been identified in ancient human remains. Grouping the ancient microbial species according to their likely reservoir and type of transmission, we find that most groups are identified throughout the entire sampling period. Zoonotic pathogens are only detected from around 6,500 years ago, peaking roughly 5,000 years ago, coinciding with the widespread domestication of livestock3. Our findings provide direct evidence that this lifestyle change resulted in an increased infectious disease burden. They also indicate that the spread of these pathogens increased substantially during subsequent millennia, coinciding with the pastoralist migrations from the Eurasian Steppe4,5.", "doi": "10.1038/s41586-025-09192-8", "pmid": "40634616", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12286840"}, {"db": "pii", "key": "10.1038/s41586-025-09192-8"}], "notes": [], "created": "2025-07-29T06:47:03.177Z", "modified": "2025-07-29T06:47:05.159Z"}, {"entity": "publication", "iuid": "a2b04350713c4675a839e6c03573f3d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2b04350713c4675a839e6c03573f3d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2b04350713c4675a839e6c03573f3d5"}}, "title": "Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes.", "authors": [{"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a556bc2e89c457fb1e45cfcd7b567e9.json"}}, {"family": "Jin", "given": "Chenyu", "initials": "C", "orcid": "0000-0002-2392-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/165a756337e8489f9621bbaa73fd4f7b.json"}}, {"family": "Clinton", "given": "Samantha L\u00f3pez", "initials": "SL", "orcid": "0000-0003-1364-9135", "researcher": {"href": "https://publications.scilifelab.se/researcher/46b97ad0ac8541dc807e570724e58c69.json"}}, {"family": "Guinet", "given": "Benjamin", "initials": "B", "orcid": "0000-0002-9922-2118", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca893ff5227f41a699fa68cca126600e.json"}}, {"family": "Wijnands", "given": "Flore", "initials": "F", "orcid": "0009-0009-6254-8964", "researcher": {"href": "https://publications.scilifelab.se/researcher/06418b4f9e90443d94452c87fb0b0588.json"}}, {"family": "Johnson", "given": "Ernst", "initials": "E", "orcid": "0009-0004-0745-2437", "researcher": {"href": "https://publications.scilifelab.se/researcher/891a915ffd054c57b7c0d107c4e1b7e1.json"}}, {"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f80fb4d234c4f2fa2179ad1e7c6a6db.json"}}, {"family": "Kinsella", "given": "Cormac M", "initials": "CM", "orcid": "0000-0001-9865-4608", "researcher": {"href": "https://publications.scilifelab.se/researcher/33c6e2a784b14b768416842ab8b0cbfd.json"}}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}], "type": "journal article", "published": "2025-01-06", "journal": {"title": "Gigascience", "issn": "2047-217X", "volume": "14", "issn-l": "2047-217X"}, "abstract": "Ancient environmental DNA is increasingly vital for reconstructing past ecosystems, particularly when paleontological and archaeological tissue remains are absent. Detecting ancient plant and animal DNA in environmental samples relies on using extensive eukaryotic reference genome databases for profiling metagenomics data. However, many eukaryotic genomes contain regions with high sequence similarity to microbial DNA, which can lead to the misclassification of bacterial and archaeal reads as eukaryotic. This issue is especially problematic in ancient eDNA datasets, where plant and animal DNA is typically present at very low abundance. In this study, we present a method for identifying bacterial- and archaeal-like sequences in eukaryotic genomes and apply it to nearly 3,000 reference genomes from NCBI RefSeq and GenBank (vertebrates, invertebrates, plants) as well as the 1,323 PhyloNorway plant genome assemblies from herbarium material from northern high-latitude regions. We find that microbial-like regions are widespread across eukaryotic genomes and provide a comprehensive resource of their genomic coordinates and taxonomic annotations. This resource enables the masking of microbial-like regions during profiling analyses, thereby improving the reliability of ancient environmental metagenomic datasets for downstream analyses.", "doi": "10.1093/gigascience/giaf108", "pmid": "41041810", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12491943"}, {"db": "pii", "key": "8271467"}], "notes": [], "created": "2025-10-30T13:19:17.629Z", "modified": "2025-11-28T10:49:20.910Z"}, {"entity": "publication", "iuid": "b2cb8fa709924974859cd7b23995e51b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b2cb8fa709924974859cd7b23995e51b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b2cb8fa709924974859cd7b23995e51b"}}, "title": "Epigenetic modulators link mitochondrial redox homeostasis to cardiac function in a sex-dependent manner.", "authors": [{"family": "ElBeck", "given": "Zaher", "initials": "Z", "orcid": "0000-0002-2073-7988", "researcher": {"href": "https://publications.scilifelab.se/researcher/9abd18865bda4f53a1521974e6f9e46b.json"}}, {"family": "Hossain", "given": "Mohammad Bakhtiar", "initials": "MB", "orcid": "0000-0002-4251-1912", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7e91850afd945dfb91a396d843194f4.json"}}, {"family": "Siga", "given": "Humam", "initials": "H", "orcid": "0000-0003-1842-0882", "researcher": {"href": "https://publications.scilifelab.se/researcher/058b6ec6390a41929dc1288f71de63d4.json"}}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a556bc2e89c457fb1e45cfcd7b567e9.json"}}, {"family": "Karlsson", "given": "Fredrik", "initials": "F"}, {"family": "Lindgren", "given": "Julia", "initials": "J", "orcid": "0000-0002-3566-2069", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3c465ab67924de69b7248e3acff0978.json"}}, {"family": "Walentinsson", "given": "Anna", "initials": "A", "orcid": "0000-0001-8100-6866", "researcher": {"href": "https://publications.scilifelab.se/researcher/991f835d5cb84de6ad619c50d81d5dd1.json"}}, {"family": "Koppenh\u00f6fer", "given": "Dominique", "initials": "D", "orcid": "0000-0001-5807-9645", "researcher": {"href": "https://publications.scilifelab.se/researcher/24ab61b179f940a8853619f5a817e06a.json"}}, {"family": "Jarvis", "given": "Rebecca", "initials": "R", "orcid": "0000-0001-7583-6548", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bfea4b88ef64bebbcdf8839e4428864.json"}}, {"family": "B\u00fcrli", "given": "Roland", "initials": "R"}, {"family": "Jamier", "given": "Tanguy", "initials": "T", "orcid": "0000-0003-3014-3662", "researcher": {"href": "https://publications.scilifelab.se/researcher/eab91541aeb24d9face573899b25b19c.json"}}, {"family": "Franssen", "given": "Elske", "initials": "E"}, {"family": "Firth", "given": "Mike", "initials": "M"}, {"family": "Degasperi", "given": "Andrea", "initials": "A", "orcid": "0000-0001-6879-0596", "researcher": {"href": "https://publications.scilifelab.se/researcher/c074b0dc07bb4b779a4c20e190854594.json"}}, {"family": "Bendtsen", "given": "Claus", "initials": "C", "orcid": "0000-0002-8338-987X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a21acfbf749d4f1ca0a8be226d4696ce.json"}}, {"family": "Menzies", "given": "Robert I", "initials": "RI"}, {"family": "Streckfuss-B\u00f6meke", "given": "Katrin", "initials": "K"}, {"family": "Kohlhaas", "given": "Michael", "initials": "M"}, {"family": "Nickel", "given": "Alexander G", "initials": "AG"}, {"family": "Lund", "given": "Lars H", "initials": "LH"}, {"family": "Maack", "given": "Christoph", "initials": "C", "orcid": "0000-0003-3694-4559", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee3dedbf152c4f24847d6d83b15ed1c3.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Betsholtz", "given": "Christer", "initials": "C", "orcid": "0000-0002-8494-971X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a00cfe9d521047f280978d84d7dcf1b3.json"}}], "type": "journal article", "published": "2024-03-20", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "15", "issue": "1", "pages": "2358"}, "abstract": "While excessive production of reactive oxygen species (ROS) is a characteristic hallmark of numerous diseases, clinical approaches that ameliorate oxidative stress have been unsuccessful. Here, utilizing multi-omics, we demonstrate that in cardiomyocytes, mitochondrial isocitrate dehydrogenase (IDH2) constitutes a major antioxidative defense mechanism. Paradoxically reduced expression of IDH2 associated with ventricular eccentric hypertrophy is counterbalanced by an increase in the enzyme activity. We unveil redox-dependent sex dimorphism, and extensive mutual regulation of the antioxidative activities of IDH2 and NRF2 by a feedforward network that involves 2-oxoglutarate and L-2-hydroxyglutarate and mediated in part through unconventional hydroxy-methylation of cytosine residues present in introns. Consequently, conditional targeting of ROS in a murine model of heart failure improves cardiac function in sex- and phenotype-dependent manners. Together, these insights may explain why previous attempts to treat heart failure with antioxidants have been unsuccessful and open new approaches to personalizing and, thereby, improving such treatment.", "doi": "10.1038/s41467-024-46384-8", "pmid": "38509128", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "BioImage Informatics": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10954618"}, {"db": "pii", "key": "10.1038/s41467-024-46384-8"}], "notes": [], "created": "2024-03-21T08:13:07.086Z", "modified": "2024-11-13T10:25:41.474Z"}, {"entity": "publication", "iuid": "9c923275b471491eb5b481510293b1cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9c923275b471491eb5b481510293b1cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9c923275b471491eb5b481510293b1cf"}}, "title": "aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow.", "authors": [{"family": "Pochon", "given": "Zo\u00e9", "initials": "Z"}, {"family": "Bergfeldt", "given": "Nora", "initials": "N"}, {"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E"}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Naidoo", "given": "Thijessen", "initials": "T"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Alt\u0131n\u0131\u015f\u0131k", "given": "N Ezgi", "initials": "NE"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Mirabello", "given": "Claudio", "initials": "C"}, {"family": "Unneberg", "given": "Per", "initials": "P"}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a556bc2e89c457fb1e45cfcd7b567e9.json"}}], "type": "journal article", "published": "2023-10-23", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "24", "issue": "1", "pages": "242", "issn-l": "1474-7596"}, "abstract": "Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge in ancient metagenomics, and the availability of computational frameworks that meet the demands of the field is limited. Here, we propose aMeta, an accurate metagenomic profiling workflow for ancient DNA designed to minimize the amount of false discoveries and computer memory requirements. Using simulated data, we benchmark aMeta against a current state-of-the-art workflow and demonstrate its superiority in microbial detection and authentication, as well as substantially lower usage of computer memory.", "doi": "10.1186/s13059-023-03083-9", "pmid": "37872569", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Ancient DNA": "Technology development", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10591440"}, {"db": "pii", "key": "10.1186/s13059-023-03083-9"}], "notes": [], "created": "2023-11-22T08:11:22.492Z", "modified": "2023-12-01T12:50:34.089Z"}, {"entity": "publication", "iuid": "e4efffe1a3fe4bafa6f2e4b256ee3a7d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e4efffe1a3fe4bafa6f2e4b256ee3a7d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e4efffe1a3fe4bafa6f2e4b256ee3a7d"}}, "title": "Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT", "authors": [{"family": "Borry", "given": "Maxime", "initials": "M", "orcid": "0000-0001-9140-7559", "researcher": {"href": "https://publications.scilifelab.se/researcher/f37c9a36c2c34d4ea4f8756e4a16dba0.json"}}, {"family": "Forsythe", "given": "Adrian", "initials": "A"}, {"family": "Andrades Valtue\u00f1a", "given": "Aida", "initials": "A"}, {"family": "H\u00fcbner", "given": "Alexander", "initials": "A"}, {"family": "Ibrahim", "given": "Anan", "initials": "A", "orcid": "0000-0003-3719-901X", "researcher": {"href": "https://publications.scilifelab.se/researcher/686fb778845345b9aac5b1527cbc9276.json"}}, {"family": "Quagliariello", "given": "Andrea", "initials": "A"}, {"family": "White", "given": "Anna E", "initials": "AE", "orcid": "0000-0001-6922-7885", "researcher": {"href": "https://publications.scilifelab.se/researcher/affa464cff694825a20a6a8fcfee2787.json"}}, {"family": "Kocher", "given": "Arthur", "initials": "A"}, {"family": "V\u00e5gene\u202c", "given": "\u00c5shild J", "initials": "\u00c5J"}, {"family": "Bartholdy", "given": "Bj\u00f8rn Peare", "initials": "BP"}, {"family": "Spur\u012bte", "given": "Di\u0101na", "initials": "D"}, {"family": "Ponce-Soto", "given": "Gabriel Yaxal", "initials": "GY"}, {"family": "Neumann", "given": "Gunnar", "initials": "G"}, {"family": "Huang", "given": "I Ting", "initials": "IT"}, {"family": "Light", "given": "Ian", "initials": "I"}, {"family": "Velsko", "given": "Irina M", "initials": "IM"}, {"family": "Jackson", "given": "Iseult", "initials": "I", "orcid": "0000-0001-6572-8244", "researcher": {"href": "https://publications.scilifelab.se/researcher/5796a1b209134dbaa3684e6c818946c5.json"}}, {"family": "Frangenberg", "given": "Jasmin", "initials": "J", "orcid": "0009-0004-5961-4709", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5c33d573584490cb13929c3e76b6353.json"}}, {"family": "Serrano", "given": "Javier G", "initials": "JG"}, {"family": "Fumey", "given": "Julien", "initials": "J", "orcid": "0000-0002-6272-5619", "researcher": {"href": "https://publications.scilifelab.se/researcher/29a3d4a77a6c4df593493d28a0377f8e.json"}}, {"family": "\u00d6zdo\u011fan", "given": "Kadir T", "initials": "KT"}, {"family": "Blevins", "given": "Kelly E", "initials": "KE"}, {"family": "Daly", "given": "Kevin G", "initials": "KG"}, {"family": "Lopopolo", "given": "Maria", "initials": "M"}, {"family": "Moraitou", "given": "Markella", "initials": "M"}, {"family": "Michel", "given": "Megan", "initials": "M"}, {"family": "van Os", "given": "Meriam", "initials": "M"}, {"family": "Bravo-Lopez", "given": "Miriam J", "initials": "MJ"}, {"family": "Sarhan", "given": "Mohamed S", "initials": "MS", "orcid": "0000-0003-0904-976X", "researcher": {"href": "https://publications.scilifelab.se/researcher/16a94ba6ed8c40588d340809cdf48e8f.json"}}, {"family": "Dagtas", "given": "Nihan D", "initials": "ND"}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a556bc2e89c457fb1e45cfcd7b567e9.json"}}, {"family": "Smith", "given": "Olivia S", "initials": "OS"}, {"family": "Lebrasseur", "given": "Oph\u00e9lie", "initials": "O"}, {"family": "Rozwalak", "given": "Piotr", "initials": "P"}, {"family": "Eisenhofer", "given": "Raphael", "initials": "R"}, {"family": "Wasef", "given": "Sally", "initials": "S", "orcid": "0000-0002-7207-7395", "researcher": {"href": "https://publications.scilifelab.se/researcher/7097f4b5f9c841908470d2a541dfc0da.json"}}, {"family": "Ramachandran", "given": "Shreya L", "initials": "SL", "orcid": "0000-0001-6760-5053", "researcher": {"href": "https://publications.scilifelab.se/researcher/c95b50b3942e4ac0b2caf2dc30d9db70.json"}}, {"family": "Vanghi", "given": "Valentina", "initials": "V"}, {"family": "Warinner", "given": "Christina", "initials": "C"}, {"family": "Fellows Yates", "given": "James A", "initials": "JA", "orcid": "0000-0001-5585-6277", "researcher": {"href": "https://publications.scilifelab.se/researcher/d9dfb63e40db44e8a1a3ea85028fda09.json"}}], "type": "journal-article", "published": "2023-08-02", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "12", "pages": "926", "issn-l": "2046-1402"}, "abstract": null, "doi": "10.12688/f1000research.134798.1", "pmid": null, "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2023-11-22T08:12:52.987Z", "modified": "2025-12-01T07:48:29.014Z"}, {"entity": "publication", "iuid": "345d335f75d34a9c989df5d83cc38c93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/345d335f75d34a9c989df5d83cc38c93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/345d335f75d34a9c989df5d83cc38c93"}}, "title": "Historical RNA expression profiles from the extinct Tasmanian tiger.", "authors": [{"family": "M\u00e1rmol-S\u00e1nchez", "given": "Emilio", "initials": "E", "orcid": "0000-0002-4393-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d902a4dab4e48499f7e941ab4c6417f.json"}}, {"family": "Fromm", "given": "Bastian", "initials": "B", "orcid": "0000-0003-0352-3037", "researcher": {"href": "https://publications.scilifelab.se/researcher/f29dd3593b894c5e9d233da6049d59e8.json"}}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a556bc2e89c457fb1e45cfcd7b567e9.json"}}, {"family": "Pochon", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0001-7981-5795", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7355501dddb4508bf453c7c1ad9f107.json"}}, {"family": "Kalogeropoulos", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-6717-5011", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9e4e4366bb94239b2635da3f2a510de.json"}}, {"family": "Eriksson", "given": "Eli", "initials": "E", "orcid": "0000-0002-0340-3062", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb10331c72f24f2291455003f81a7a98.json"}}, {"family": "Biryukova", "given": "Inna", "initials": "I", "orcid": "0000-0003-0701-2808", "researcher": {"href": "https://publications.scilifelab.se/researcher/47d787e9d8e14b8fa598d8c3e82e4058.json"}}, {"family": "Sekar", "given": "Vaishnovi", "initials": "V", "orcid": "0000-0002-6810-1591", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8bb2f06511f4c3695c1e84dac62e6bb.json"}}, {"family": "Ersmark", "given": "Erik", "initials": "E", "orcid": "0000-0003-4186-7498", "researcher": {"href": "https://publications.scilifelab.se/researcher/7061c3d9591b40488954083d06ed2e17.json"}}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0003-2975-9400", "researcher": {"href": "https://publications.scilifelab.se/researcher/db755021d4474a7c836bdb418b5d12ca.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications.scilifelab.se/researcher/744f7c6d0a884d9daa2e7303ed1779b8.json"}}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Genome Res.", "issn": "1549-5469", "issn-l": "1088-9051", "volume": "33", "issue": "8", "pages": "1299-1316"}, "abstract": "Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost and historical skins from extant canids, but no attempts have been made so far on extinct species. We extract, sequence, and analyze historical RNA from muscle and skin tissue of a \u223c130-year-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA damage, tissue-specific RNA profiles, and expression hotspots genome-wide further confirm the thylacine origin of the sequences. RNA sequences are used to improve protein-coding and noncoding annotations, evidencing missing exonic loci and the location of ribosomal RNA genes while increasing the number of annotated thylacine microRNAs from 62 to 325. We discover a thylacine-specific microRNA isoform that could not have been confirmed without RNA evidence. Finally, we detect traces of RNA viruses, suggesting the possibility of profiling viral evolution. Our results represent the first successful attempt to obtain transcriptional profiles from an extinct animal species, providing thought-to-be-lost information on gene expression dynamics. These findings hold promising implications for the study of RNA molecules across the vast collections of natural history museums and from well-preserved permafrost remains.", "doi": "10.1101/gr.277663.123", "pmid": "37463752", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10552650"}, {"db": "pii", "key": "gr.277663.123"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2023-09-20T16:48:10.289Z", "modified": "2024-01-16T13:48:32.754Z"}, {"entity": "publication", "iuid": "1cc7c4b78f2047019f3e222063dffbaf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1cc7c4b78f2047019f3e222063dffbaf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1cc7c4b78f2047019f3e222063dffbaf"}}, "title": "Mercury\u2013Selenium Accumulation Patterns in Muscle Tissue of Two Freshwater Fish Species, Eurasian Perch (Perca fluviatilis) and Vendace (Coregonus albula)", "authors": [{"family": "Regnell", "given": "Olof", "initials": "O", "orcid": "0000-0002-1801-5695", "researcher": {"href": "https://publications.scilifelab.se/researcher/89e012b5507445c5a19e9b8fd096a5d7.json"}}, {"family": "Tesson", "given": "Sylvie V M", "initials": "SVM", "orcid": "0000-0002-0751-6953", "researcher": {"href": "https://publications.scilifelab.se/researcher/476c32dd6ce5422b94f393477d1e568b.json"}}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a556bc2e89c457fb1e45cfcd7b567e9.json"}}, {"family": "Nerentorp", "given": "Michelle", "initials": "M", "orcid": "0000-0002-8162-7205", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d6d53eb179747898aa346b59dce2f88.json"}}], "type": "journal-article", "published": "2022-07-00", "journal": {"title": "Water Air Soil Pollut", "issn": "0049-6979", "volume": "233", "issue": "7", "issn-l": null}, "abstract": null, "doi": "10.1007/s11270-022-05709-3", "pmid": null, "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2022-11-18T09:54:25.264Z", "modified": "2023-06-02T10:31:56.810Z"}, {"entity": "publication", "iuid": "0501e4e6d44c4a8c947ef756d0262288", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0501e4e6d44c4a8c947ef756d0262288.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0501e4e6d44c4a8c947ef756d0262288"}}, "title": "Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia.", "authors": [{"family": "Halvorsen", "given": "Matthew", "initials": "M"}, {"family": "Huh", "given": "Ruth", "initials": "R"}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a556bc2e89c457fb1e45cfcd7b567e9.json"}}, {"family": "Wen", "given": "Jia", "initials": "J", "orcid": "0000-0003-3273-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/872570fb0f94464d988fd5b2d3a8b7e7.json"}}, {"family": "Netotea", "given": "Sergiu", "initials": "S"}, {"family": "Giusti-Rodriguez", "given": "Paola", "initials": "P", "orcid": "0000-0002-1921-1305", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6594f03c6c344d69b08234fd751ab23.json"}}, {"family": "Karlsson", "given": "Robert", "initials": "R", "orcid": "0000-0002-8949-2587", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df14bf33f3342408d624caa70d45b7c.json"}}, {"family": "Bryois", "given": "Julien", "initials": "J"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "K\u00e4hler", "given": "Anna K", "initials": "AK"}, {"family": "Ancalade", "given": "NaEshia", "initials": "N"}, {"family": "Farrell", "given": "Martilias", "initials": "M", "orcid": "0000-0002-9520-6209", "researcher": {"href": "https://publications.scilifelab.se/researcher/20be04f56c474537ad8fa07cb17241cf.json"}}, {"family": "Crowley", "given": "James J", "initials": "JJ"}, {"family": "Li", "given": "Yun", "initials": "Y"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Hultman", "given": "Christina M", "initials": "CM"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "Szatkiewicz", "given": "Jin P", "initials": "JP", "orcid": "0000-0002-4898-7401", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb39edd3c6c14938a47f1e22ecfea080.json"}}], "type": "journal article", "published": "2020-04-15", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "1842"}, "abstract": "Despite considerable progress in schizophrenia genetics, most findings have been for large rare structural variants and common variants in well-imputed regions with few genes implicated from exome sequencing. Whole genome sequencing (WGS) can potentially provide a more complete enumeration of etiological genetic variation apart from the exome and regions of high linkage disequilibrium. We analyze high-coverage WGS data from 1162 Swedish schizophrenia cases and 936 ancestry-matched population controls. Our main objective is to evaluate the contribution to schizophrenia etiology from a variety of genetic variants accessible to WGS but not by previous technologies. Our results suggest that ultra-rare structural variants that affect the boundaries of topologically associated domains (TADs) increase risk for schizophrenia. Alterations in TAD boundaries may lead to dysregulation of gene expression. Future mechanistic studies will be needed to determine the precise functional effects of these variants on biology.", "doi": "10.1038/s41467-020-15707-w", "pmid": "32296054", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Systems Biology": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-15707-w"}, {"db": "pmc", "key": "PMC7160146"}], "notes": [], "created": "2020-04-20T06:46:04.706Z", "modified": "2024-01-16T13:48:42.613Z"}]}