{"entity": "journal", "iuid": "4b1a5e2641b94b09bd8955e93907a2fb", "timestamp": "2026-06-15T20:53:25.607Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Sci%20Data.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Sci%20Data"}}, "title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "publications_count": 28, "publications": [{"entity": "publication", "iuid": "4a8447758bec4df191ec729e256f9f34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4a8447758bec4df191ec729e256f9f34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4a8447758bec4df191ec729e256f9f34"}}, "title": "De novo transcriptome assembly and annotation of the common freshwater amphipod (Gammarus pulex) a valuable resource for ecotoxicogenomics.", "authors": [{"family": "Escobar-Sierra", "given": "Camilo", "initials": "C", "orcid": "0000-0001-9105-4378", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed2b3eb0232f48d0ad3c685d72abd35a.json"}}, {"family": "Hassan", "given": "Sameer", "initials": "S"}, {"family": "Weichert", "given": "Fabian G", "initials": "FG"}, {"family": "Aronsson", "given": "Henrik", "initials": "H"}, {"family": "Lampert", "given": "Kathrin P", "initials": "KP"}, {"family": "Hollert", "given": "Henner", "initials": "H"}, {"family": "Backhaus", "given": "Thomas", "initials": "T"}, {"family": "Inostroza", "given": "Pedro A", "initials": "PA", "orcid": "0000-0001-7399-8308", "researcher": {"href": "https://publications.scilifelab.se/researcher/9cea8a42ffc2454d86f5f829b5dd7eff.json"}}], "type": "dataset", "published": "2025-08-28", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "12", "issue": "1", "pages": "1502", "issn-l": "2052-4463"}, "abstract": "This study presents de novo transcriptome assemblies for Gammarus pulex, a freshwater amphipod widely used in ecotoxicology due to its ecological importance and sensitivity to pollution. Specimens were collected from 13 river sites in Germany and Sweden, encompassing a gradient of micropollutant exposure. Using high-throughput RNA sequencing, we generated transcriptomes for German, Swedish, and combined populations. The assemblies yielded up to 170,000 transcripts with strong metrics, including N50 values over 1,500 base pairs and completeness scores approaching 89%. Functional annotation revealed over 123,000 unique protein hits, nearly 99,000 BLASTx matches, and approximately 30,000 annotated KEGG pathways. We also identified thousands of conserved domains, signal peptides, and transmembrane proteins. These comprehensive resources provide valuable molecular insight into the stress responses of Gammarus pulex and will facilitate the development of gene-based biomarkers for freshwater monitoring. By improving the molecular toolkit for this key sentinel species, our study supports broader applications of ecotoxicogenomics in environmental assessment and conservation.", "doi": "10.1038/s41597-025-05872-2", "pmid": "40877247", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12394684"}, {"db": "pii", "key": "10.1038/s41597-025-05872-2"}], "notes": [], "created": "2025-11-28T10:46:48.868Z", "modified": "2025-11-28T10:46:48.977Z"}, {"entity": "publication", "iuid": "14a490b69be949de8cbbefbdfbe5d0e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14a490b69be949de8cbbefbdfbe5d0e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14a490b69be949de8cbbefbdfbe5d0e5"}}, "title": "Data of the Insect Biome Atlas: a metabarcoding survey of the terrestrial arthropods of Sweden and Madagascar.", "authors": [{"family": "Miraldo", "given": "A", "initials": "A", "orcid": "0000-0001-6107-006X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b1de25c21dc4c5fb541f4e8766de4b7.json"}}, {"family": "Sundh", "given": "J", "initials": "J", "orcid": "0000-0003-3053-9392", "researcher": {"href": "https://publications.scilifelab.se/researcher/655b68ac26af42ad9fb4dfe0869e15ea.json"}}, {"family": "Iwaszkiewicz-Eggebrecht", "given": "E", "initials": "E"}, {"family": "Buczek", "given": "M", "initials": "M"}, {"family": "Goodsell", "given": "R", "initials": "R"}, {"family": "Johansson", "given": "H", "initials": "H"}, {"family": "Fisher", "given": "B L", "initials": "BL", "orcid": "0000-0002-4653-3270", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e4747cc54254e8181f595e6fe21b953.json"}}, {"family": "Raharinjanahary", "given": "D", "initials": "D"}, {"family": "Rajoelison", "given": "E T", "initials": "ET"}, {"family": "Ranaivo", "given": "C", "initials": "C"}, {"family": "Randrianandrasana", "given": "C", "initials": "C"}, {"family": "Rafanomezantsoa", "given": "J-J", "initials": "J"}, {"family": "Manoharan", "given": "L", "initials": "L"}, {"family": "Granqvist", "given": "E", "initials": "E", "orcid": "0000-0002-1513-1674", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b07f15f8724fdbbcdf34e6d6837147.json"}}, {"family": "van Dijk", "given": "L J A", "initials": "LJA"}, {"family": "Alberg", "given": "L", "initials": "L"}, {"family": "\u00c5hl\u00e9n", "given": "D", "initials": "D"}, {"family": "Aspebo", "given": "M", "initials": "M"}, {"family": "\u00c5str\u00f6m", "given": "S", "initials": "S"}, {"family": "Bellviken", "given": "A", "initials": "A"}, {"family": "Bergman", "given": "P-E", "initials": "P"}, {"family": "Bj\u00f6rklund", "given": "S", "initials": "S"}, {"family": "Bj\u00f6rkman", "given": "M P", "initials": "MP", "orcid": "0000-0001-5768-1976", "researcher": {"href": "https://publications.scilifelab.se/researcher/9821ee4a87c74dde82d9a6a4ebc2b1fc.json"}}, {"family": "Deng", "given": "J", "initials": "J"}, {"family": "Desborough", "given": "L", "initials": "L"}, {"family": "Dolff", "given": "E", "initials": "E"}, {"family": "Eliasson", "given": "A", "initials": "A"}, {"family": "Elmquist", "given": "H", "initials": "H"}, {"family": "Emanuelsson", "given": "H", "initials": "H"}, {"family": "Erixon", "given": "R", "initials": "R"}, {"family": "Fahlen", "given": "L", "initials": "L"}, {"family": "Frogner", "given": "C", "initials": "C"}, {"family": "F\u00fcrst", "given": "P", "initials": "P"}, {"family": "Grabs", "given": "A", "initials": "A"}, {"family": "Grudd", "given": "H", "initials": "H", "orcid": "0000-0002-9033-2505", "researcher": {"href": "https://publications.scilifelab.se/researcher/97348870e86e4c75ae6ce0be4cc99699.json"}}, {"family": "Guasconi", "given": "D", "initials": "D"}, {"family": "Gunnarsson", "given": "M", "initials": "M"}, {"family": "H\u00e4ggqvist", "given": "S", "initials": "S"}, {"family": "Hed", "given": "A", "initials": "A"}, {"family": "H\u00f6rnstr\u00f6m", "given": "E", "initials": "E"}, {"family": "J\u00f6nsson", "given": "A", "initials": "A"}, {"family": "Kanerot", "given": "S", "initials": "S"}, {"family": "Karlsson", "given": "A", "initials": "A"}, {"family": "Karlsson", "given": "D", "initials": "D", "orcid": "0000-0003-4639-823X", "researcher": {"href": "https://publications.scilifelab.se/researcher/09ecfa3c78df4076bce64c7eeb36ee4f.json"}}, {"family": "Klinth", "given": "M", "initials": "M"}, {"family": "Kraft", "given": "T", "initials": "T", "orcid": "0000-0002-1143-5494", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd6da126be9d48658afb96aac9532ead.json"}}, {"family": "Lahti", "given": "R", "initials": "R"}, {"family": "Larsson", "given": "M", "initials": "M"}, {"family": "Lernefalk", "given": "H", "initials": "H"}, {"family": "Lestander", "given": "Y", "initials": "Y"}, {"family": "Lindholm", "given": "L-T", "initials": "L"}, {"family": "Lindholm", "given": "M", "initials": "M"}, {"family": "Ljung", "given": "U", "initials": "U"}, {"family": "Ljung", "given": "K", "initials": "K"}, {"family": "Lundberg", "given": "J", "initials": "J", "orcid": "0000-0003-4316-9183", "researcher": {"href": "https://publications.scilifelab.se/researcher/86b74c200f2b402cad6b82cdf63259c9.json"}}, {"family": "Lundin", "given": "E", "initials": "E", "orcid": "0000-0002-3785-8305", "researcher": {"href": "https://publications.scilifelab.se/researcher/842e65aa96ef4dcaa8af13bf9e3f73f8.json"}}, {"family": "Malmenius", "given": "M", "initials": "M"}, {"family": "Marquina", "given": "D", "initials": "D"}, {"family": "Martinelli", "given": "J", "initials": "J"}, {"family": "Mertz", "given": "L", "initials": "L"}, {"family": "Nilsson", "given": "J", "initials": "J"}, {"family": "Patchett", "given": "A", "initials": "A"}, {"family": "Persson", "given": "N", "initials": "N"}, {"family": "Persson", "given": "J", "initials": "J"}, {"family": "Prus-Frankowska", "given": "M", "initials": "M"}, {"family": "Regazzoni", "given": "E", "initials": "E"}, {"family": "Rosander", "given": "K-G", "initials": "K"}, {"family": "Rydg\u00e5rd", "given": "M", "initials": "M"}, {"family": "Sandblom", "given": "C", "initials": "C"}, {"family": "Skord", "given": "J", "initials": "J"}, {"family": "St\u00e5lhandske", "given": "T", "initials": "T"}, {"family": "Svensson", "given": "F", "initials": "F"}, {"family": "Szpryngiel", "given": "S", "initials": "S", "orcid": "0000-0003-2965-2873", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec77cb9136184887b68a4ae8c4360927.json"}}, {"family": "Tajani", "given": "K", "initials": "K"}, {"family": "Tyboni", "given": "M", "initials": "M"}, {"family": "Ugarph", "given": "C", "initials": "C"}, {"family": "Vestermark", "given": "L", "initials": "L"}, {"family": "Vilhelmsson", "given": "J", "initials": "J"}, {"family": "Wahlgren", "given": "N", "initials": "N"}, {"family": "Wass", "given": "A", "initials": "A"}, {"family": "Wetterstrand", "given": "P", "initials": "P"}, {"family": "\u0141ukasik", "given": "P", "initials": "P", "orcid": "0000-0002-4164-6487", "researcher": {"href": "https://publications.scilifelab.se/researcher/71d69a579a304425b70249e7db42ad67.json"}}, {"family": "Tack", "given": "A J M", "initials": "AJM", "orcid": "0000-0002-3550-1070", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f9cf8fde705481281edab32bc9156e5.json"}}, {"family": "Andersson", "given": "A F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Roslin", "given": "T", "initials": "T", "orcid": "0000-0002-2957-4791", "researcher": {"href": "https://publications.scilifelab.se/researcher/04d92328b67e47ab82257567c07cf12f.json"}}, {"family": "Ronquist", "given": "F", "initials": "F"}], "type": "journal article", "published": "2025-05-21", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "12", "issue": "1", "pages": "835"}, "abstract": "We present the data from the Insect Biome Atlas project (IBA), characterizing the terrestrial arthropod faunas of Sweden and Madagascar. Over 12 months, Malaise trap samples were collected weekly (biweekly or monthly in the winter, when feasible) at 203 locations within 100 sites in Sweden and weekly at 50 locations within 33 sites in Madagascar; this was complemented by soil and litter samples from each site. The field samples comprise 4,749 Malaise trap, 192 soil and 192 litter samples from Sweden and 2,566 Malaise trap and 190 litter samples from Madagascar. Samples were processed using mild lysis or homogenization, followed by DNA metabarcoding of CO1 (418 bp). The data comprise 698,378 non-chimeric sequence variants from Sweden and 687,866 from Madagascar, representing 33,989 (33,046 Arthropoda) and 77,599 (77,380 Arthropoda) operational taxonomic units, respectively. These are the most comprehensive data presented on these faunas so far, allowing unique analyses of the size, composition, spatial turnover and seasonal dynamics of the sampled communities. They also provide an invaluable baseline against which to gauge future changes.", "doi": "10.1038/s41597-025-05151-0", "pmid": "40399316", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12095508"}, {"db": "pii", "key": "10.1038/s41597-025-05151-0"}], "notes": [], "created": "2025-11-19T08:51:31.233Z", "modified": "2025-11-21T12:26:09.639Z"}, {"entity": "publication", "iuid": "b9a52931d3d74346a7d1d9534c62ab91", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b9a52931d3d74346a7d1d9534c62ab91.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b9a52931d3d74346a7d1d9534c62ab91"}}, "title": "A clinical prostate biopsy dataset with undetected cancer.", "authors": [{"family": "Chelebian", "given": "Eduard", "initials": "E", "orcid": "0000-0001-6852-6605", "researcher": {"href": "https://publications.scilifelab.se/researcher/278694af6d7e499f9432c6523da24f25.json"}}, {"family": "Avenel", "given": "Christophe", "initials": "C", "orcid": "0000-0002-1835-921X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5471168acdf94b63b1eab431fd1e8442.json"}}, {"family": "J\u00e4remo", "given": "Helena", "initials": "H"}, {"family": "Andersson", "given": "Pernilla", "initials": "P"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "Bergh", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2025-03-11", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "12", "issue": "1", "pages": "423", "issn-l": "2052-4463"}, "abstract": "Prostate cancer is a heterogeneous disease showing variability both among individuals and within a patient. While most cases are indolent, aggressive tumors require early intervention. Accurately predicting tumor behavior is challenging, contributing to overdiagnosis but also undertreatment. Current imaging methods may miss the most malignant areas, leading to biopsies often capturing non-malignant prostate tissue even if cancer is present elsewhere in the organ. This non-malignant tissue, however, holds potential as a source for novel diagnostic and prognostic markers. Our clinical dataset comprises men with raised prostate-specific antigen but whose initial prostate needle biopsies only contained benign tissue. Half of the paired patients remained cancer-free for over eight years, while the others were diagnosed with prostate cancer within 30 months of follow-up. We share these initial benign biopsies to enable the exploration of morphological changes in non-malignant tissue and the potential for improved diagnostic accuracy in the early identification of patients with prostate cancer.", "doi": "10.1038/s41597-025-04758-7", "pmid": "40069192", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11897396"}, {"db": "pii", "key": "10.1038/s41597-025-04758-7"}], "notes": [], "created": "2025-11-25T12:53:53.705Z", "modified": "2025-11-25T12:53:53.733Z"}, {"entity": "publication", "iuid": "97a9599da59641ebb05e5b7a8fe6ad45", "links": {"self": {"href": "https://publications.scilifelab.se/publication/97a9599da59641ebb05e5b7a8fe6ad45.json"}, "display": {"href": "https://publications.scilifelab.se/publication/97a9599da59641ebb05e5b7a8fe6ad45"}}, "title": "The expanded genome of Hexamita inflata, a free-living diplomonad.", "authors": [{"family": "Akdeniz", "given": "Zeynep", "initials": "Z", "orcid": "0000-0002-5279-6077", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b6a7222e2d3487db2b50842f74e173e.json"}}, {"family": "Havelka", "given": "Michal", "initials": "M"}, {"family": "Stoklasa", "given": "Michal", "initials": "M"}, {"family": "Jim\u00e9nez-Gonz\u00e1lez", "given": "Alejandro", "initials": "A", "orcid": "0000-0003-3493-4154", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c6b93b731741018637733969c308a6.json"}}, {"family": "\u017d\u00e1rsk\u00fd", "given": "Vojt\u011bch", "initials": "V"}, {"family": "Xu", "given": "Feifei", "initials": "F", "orcid": "0000-0003-1946-1520", "researcher": {"href": "https://publications.scilifelab.se/researcher/84c51ec60768479f851e29ebc804f547.json"}}, {"family": "Stairs", "given": "Courtney W", "initials": "CW", "orcid": "0000-0001-6650-0970", "researcher": {"href": "https://publications.scilifelab.se/researcher/618e83e896494c7bb6cbe06350baf0a5.json"}}, {"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J", "orcid": "0000-0002-7992-7970", "researcher": {"href": "https://publications.scilifelab.se/researcher/622d380bca244d738f5551cbed742b3e.json"}}, {"family": "Kol\u00edsko", "given": "Martin", "initials": "M"}, {"family": "Provazn\u00edk", "given": "Jan", "initials": "J"}, {"family": "Sv\u00e4rd", "given": "Staffan", "initials": "S", "orcid": "0000-0002-7392-1746", "researcher": {"href": "https://publications.scilifelab.se/researcher/b01942d70ef84a1db3aaccab65af9c57.json"}}, {"family": "Andersson", "given": "Jan O", "initials": "JO", "orcid": "0000-0002-3075-4896", "researcher": {"href": "https://publications.scilifelab.se/researcher/489ed7f61a7b49a3a7ebd9ee3c391f5b.json"}}, {"family": "Tachezy", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2025-02-01", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "12", "issue": "1", "pages": "192", "issn-l": "2052-4463"}, "abstract": "Diplomonads are anaerobic, flagellated protists, being part of the Metamonada group of Eukaryotes. Diplomonads either live as endobionts (parasites and commensals) of animals or free-living in low-oxygen environments. Genomic information is available for parasitic diplomonads like Giardia intestinalis and Spironucleus salmonicida, while little is known about the genomic arrangements of free-living diplomonads. We have generated the first reference genome of a free-living diplomonad, Hexamita inflata. The final version of the genome assembly is fragmented (1241 contigs) but substantially larger (142 Mbp) than the parasitic diplomonad genomes (9.8-14.7 Mbp). It encodes 79,341 proteins; 29,874 have functional annotations and 49,467 are hypothetical proteins. Interspersed repeats comprise 34% of the genome (9617 Retroelements, 2676 DNA transposons). The large expansion of protein-encoding capacity and the interspersed repeats are the major reasons for the large genome size. This genome from a free-living diplomonad will be the basis for further studies of the Diplomonadida lineage and the evolution of parasitism-free living style transitions.", "doi": "10.1038/s41597-025-04514-x", "pmid": "39893204", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11787283"}, {"db": "pii", "key": "10.1038/s41597-025-04514-x"}], "notes": [], "created": "2025-03-07T09:59:16.550Z", "modified": "2025-04-03T08:27:54.918Z"}, {"entity": "publication", "iuid": "728698aa891a4159a798b19be431232f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/728698aa891a4159a798b19be431232f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/728698aa891a4159a798b19be431232f"}}, "title": "Chromosome-level genome assembly of the morabine grasshopper Vandiemenella viatica19.", "authors": [{"family": "Li", "given": "Xuan", "initials": "X", "orcid": "0000-0003-0066-2373", "researcher": {"href": "https://publications.scilifelab.se/researcher/23234f8a3b2e4d299405be6a66008435.json"}}, {"family": "Jayaprasad", "given": "Suvratha", "initials": "S"}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3101-2285", "researcher": {"href": "https://publications.scilifelab.se/researcher/0db39539bdd94519a418e6dd7a287cc8.json"}}, {"family": "Cooper", "given": "Steven J B", "initials": "SJB", "orcid": "0000-0002-7843-8438", "researcher": {"href": "https://publications.scilifelab.se/researcher/8df76e7fede64a0294cf68a3ae20a07c.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Kawakami", "given": "Takeshi", "initials": "T"}, {"family": "Palacios-Gimenez", "given": "Octavio Manuel", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications.scilifelab.se/researcher/f90e29ecd5724ff19509983e65891915.json"}}], "type": "journal article", "published": "2024-09-12", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "11", "issue": "1", "pages": "997"}, "abstract": "Morabine grasshoppers in the Vandiemenella viatica species group, which show karyotype diversity, have been studied for their ecological distribution and speciation in relation to their genetic and chromosomal diversity. They are good models for studying sex chromosome evolution as \"old\" and newly emerged sex chromosomes co-exist within the group. Here we present a reference genome for the viatica19 chromosomal race, that possesses the ancestral karyotype within the group. Using PacBio HiFi and Hi-C sequencing, we generated a chromosome-level assembly of 4.09 Gb in span, scaffold N50 of 429 Mb, and complete BUSCO score of 98.1%, containing 10 pseudo-chromosomes. We provide Illumina datasets of males and females, used to identify the X chromosome. The assembly contains 19,034 predicted protein-coding genes, and a total of 75.21% of repetitive DNA sequences. By leveraging HiFi reads, we mapped the genome-wide distribution of methylated bases (5mC and 6 mA). This comprehensive assembly offers a robust reference for morabine grasshoppers and supports further research into speciation and sex chromosome diversification within the group and its related species.", "doi": "10.1038/s41597-024-03858-0", "pmid": "39266578", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Collaborative", "NGI Other": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11393057"}, {"db": "pii", "key": "10.1038/s41597-024-03858-0"}], "notes": [], "created": "2024-09-16T19:39:19.961Z", "modified": "2024-11-25T10:20:16.787Z"}, {"entity": "publication", "iuid": "c119e76b14514e52b934f2411b16aff8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c119e76b14514e52b934f2411b16aff8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c119e76b14514e52b934f2411b16aff8"}}, "title": "Chromosome-level genome assembly and annotation of the social amoeba Dictyostelium firmibasis.", "authors": [{"family": "Edelbroek", "given": "Bart", "initials": "B", "orcid": "0000-0002-5184-0873", "researcher": {"href": "https://publications.scilifelab.se/researcher/164d0bef1b3e48668e136dbe0d2e8736.json"}}, {"family": "Kjellin", "given": "Jonas", "initials": "J", "orcid": "0000-0002-3830-7046", "researcher": {"href": "https://publications.scilifelab.se/researcher/daf9964b08fa498e9c0eb3540a0aa1fa.json"}}, {"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J"}, {"family": "Koskiniemi", "given": "Sanna", "initials": "S"}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-3616-3509", "researcher": {"href": "https://publications.scilifelab.se/researcher/4952b493871a4970a089074117bb303f.json"}}], "type": "dataset", "published": "2024-06-22", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "11", "issue": "1", "pages": "678", "issn-l": "2052-4463"}, "abstract": "Dicytostelium firmibasis is a member of Dictyostelia, a group of social amoebae that upon starvation display aggregative multicellularity where the amoebae transition from uni- to multicellular life. The D. firmibasis genome assembly that is currently available is of limited use due to its low contiguity, large number of undetermined bases, and lack of annotations. Here we used Nanopore long read sequencing, complemented with Illumina sequencing, and developmental transcriptomics as well as small RNA-sequencing, to present a new, fully annotated, chromosome-level D. firmibasis genome assembly. The new assembly contains no undetermined bases, and consists mainly of six large contigs representing the chromosomes, as well as a complete mitochondrial genome. This new genome assembly will be a valuable tool, allowing comprehensive comparison to Dictyostelium discoideum, the dictyostelid genetically tractable model. Further, the new genome will be important for studies of evolutionary processes governing the transition from unicellular to multicellular organisms and will aid in the sequencing and annotation of other dictyostelids genomes, many of which are currently of poor quality.", "doi": "10.1038/s41597-024-03513-8", "pmid": "38909042", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11193728"}, {"db": "pii", "key": "10.1038/s41597-024-03513-8"}], "notes": [], "created": "2024-06-28T06:39:46.481Z", "modified": "2024-11-25T10:20:11.383Z"}, {"entity": "publication", "iuid": "caa37fd92a5c432fbea7349ddc016e59", "links": {"self": {"href": "https://publications.scilifelab.se/publication/caa37fd92a5c432fbea7349ddc016e59.json"}, "display": {"href": "https://publications.scilifelab.se/publication/caa37fd92a5c432fbea7349ddc016e59"}}, "title": "Integrative transcriptomic and proteomic profiling of the effects of cell confluency on gene expression.", "authors": [{"family": "Lobo", "given": "Vivian", "initials": "V"}, {"family": "Shcherbinina", "given": "Evgeniia", "initials": "E"}, {"family": "Westholm", "given": "Jakub O", "initials": "JO"}, {"family": "Nowak", "given": "Iwona", "initials": "I"}, {"family": "Huang", "given": "Hsiang-Chi", "initials": "HC"}, {"family": "Angeletti", "given": "Davide", "initials": "D", "orcid": "0000-0002-5256-1972", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae59c12bf82b4ad9a8d9ad8603d03d9c.json"}}, {"family": "Anastasakis", "given": "Dimitrios G", "initials": "DG"}, {"family": "Sarshad", "given": "Aishe A", "initials": "AA", "orcid": "0000-0001-7153-5959", "researcher": {"href": "https://publications.scilifelab.se/researcher/42c62bd8dbe34b5da39de17d6a2a06ab.json"}}], "type": "dataset", "published": "2024-06-12", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "11", "issue": "1", "pages": "617"}, "abstract": "In this study we examine the impact of cell confluency on gene expression. We focused on Argonaute (AGO) protein dynamics and associated gene and protein expression in HEK293, A375, and SHSY5Y cell lines. As a consequence of cell confluency, AGO2 protein translocates into the nucleus. Therefore, we generated transcriptomic data using RNA sequencing to compare gene expression in subconfluent versus confluent cells, which highlighted significant alterations in gene regulation patterns directly corresponding to changes in cell density. Our study also encompasses miRNA profiling data obtained through small RNA sequencing, revealing miRNA expressional changes dependent on cellular confluency, as well as cellular localization. Finally, we derived proteomic data from mass spectrometry analyses following AGO1-4 immunoprecipitation, providing a comprehensive view of AGO interactome in both nuclear and cytoplasmic compartments under varying confluency. These datasets offer a detailed exploration of the cellular and molecular dynamics, influenced by cell confluency, presenting a valuable resource for further research in cellular biology, particularly in understanding the basic mechanisms of cell density in cancer cells.", "doi": "10.1038/s41597-024-03465-z", "pmid": "38866801", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Glycoproteomics and MS Proteomics": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11169490"}, {"db": "pii", "key": "10.1038/s41597-024-03465-z"}], "notes": [], "created": "2024-06-14T17:35:54.427Z", "modified": "2024-11-27T15:37:51.552Z"}, {"entity": "publication", "iuid": "9362d0a9e2424b878878c0da9a3d7c67", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9362d0a9e2424b878878c0da9a3d7c67.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9362d0a9e2424b878878c0da9a3d7c67"}}, "title": "A comprehensive dataset on spatiotemporal variation of microbial plankton communities in the Baltic Sea.", "authors": [{"family": "Latz", "given": "Meike A C", "initials": "MAC", "orcid": "0000-0002-6583-9291", "researcher": {"href": "https://publications.scilifelab.se/researcher/664c30300eab4888a2e5562e077aab01.json"}}, {"family": "Andersson", "given": "Agneta", "initials": "A"}, {"family": "Brugel", "given": "Sonia", "initials": "S"}, {"family": "Hedblom", "given": "Mikael", "initials": "M"}, {"family": "Jurdzinski", "given": "Krzysztof T", "initials": "KT", "orcid": "0000-0001-9544-5755", "researcher": {"href": "https://publications.scilifelab.se/researcher/896a2f678e3143a2b855c1afa8e93499.json"}}, {"family": "Karlson", "given": "Bengt", "initials": "B"}, {"family": "Lindh", "given": "Markus", "initials": "M"}, {"family": "Lycken", "given": "Jenny", "initials": "J"}, {"family": "Torstensson", "given": "Anders", "initials": "A", "orcid": "0000-0002-8283-656X", "researcher": {"href": "https://publications.scilifelab.se/researcher/352fd53b3b584caa95ee5ff4405498cf.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "dataset", "published": "2024-01-02", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "11", "issue": "1", "pages": "18", "issn-l": "2052-4463"}, "abstract": "The Baltic Sea is one of the largest brackish water environments on earth and is characterised by pronounced physicochemical gradients and seasonal dynamics. Although the Baltic Sea has a long history of microscopy-based plankton monitoring, DNA-based metabarcoding has so far mainly been limited to individual transect cruises or time-series of single stations. Here we report a dataset covering spatiotemporal variation in prokaryotic and eukaryotic microbial communities and physicochemical parameters. Within 13-months between January 2019 and February 2020, 341 water samples were collected at 22 stations during monthly cruises along the salinity gradient. Both salinity and seasonality are strongly reflected in the data. Since the dataset was generated with both metabarcoding and microscopy-based methods, it provides unique opportunities for both technical and ecological analyses, and is a valuable biodiversity reference for future studies, in the prospect of climate change.", "doi": "10.1038/s41597-023-02825-5", "pmid": "38168085", "labels": {"Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10761891"}, {"db": "pii", "key": "10.1038/s41597-023-02825-5"}], "notes": [], "created": "2024-01-10T09:46:47.061Z", "modified": "2024-11-25T10:20:00.758Z"}, {"entity": "publication", "iuid": "eab4268374624f2ab14306ca0d1dd3b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eab4268374624f2ab14306ca0d1dd3b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eab4268374624f2ab14306ca0d1dd3b0"}}, "title": "Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta).", "authors": [{"family": "Landi", "given": "Michael", "initials": "M", "orcid": "0000-0001-5597-7802", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a48329b81f14ff191ed7a8c8cb562b8.json"}}, {"family": "Shah", "given": "Trushar", "initials": "T", "orcid": "0000-0002-0091-7981", "researcher": {"href": "https://publications.scilifelab.se/researcher/6db73454fcb34150bd72bcc5e850cb5e.json"}}, {"family": "Falquet", "given": "Laurent", "initials": "L", "orcid": "0000-0001-8102-7579", "researcher": {"href": "https://publications.scilifelab.se/researcher/bba0eeebd71e4f6ca50a2751f898fc6a.json"}}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Stavolone", "given": "Livia", "initials": "L"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E", "orcid": "0000-0002-1947-8288", "researcher": {"href": "https://publications.scilifelab.se/researcher/6970ca57259d498588ecf9e1ad28a9b0.json"}}, {"family": "Gisel", "given": "Andreas", "initials": "A", "orcid": "0000-0001-7218-9488", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2eb91acead14ec58845e9eda08742fa.json"}}], "type": "dataset", "published": "2023-12-09", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "10", "issue": "1", "pages": "887", "issn-l": "2052-4463"}, "abstract": "Cassava (Manihot esculenta Crantz) is a vital tropical root crop providing essential dietary energy to over 800 million people in tropical and subtropical regions. As a climate-resilient crop, its significance grows as the human population expands. However, yield improvement faces challenges from biotic and abiotic stress and limited breeding. Advanced sequencing and assembly techniques enabled the generation of a highly accurate, nearly complete, haplotype-resolved genome of the African cassava cultivar TMEB117. It is the most accurate cassava genome sequence to date with a base-level accuracy of QV > 64, N50 > 35 Mbp, and 98.9% BUSCO completeness. Over 60% of the genome comprises repetitive elements. We predicted over 45,000 gene models for both haplotypes. This achievement offers valuable insights into the heterozygosity genome organization of the cassava genome, with improved accuracy, completeness, and phased genomes. Due to its high susceptibility to African Cassava Mosaic Virus (ACMV) infections compared to other cassava varieties, TMEB117 provides an ideal reference for studying virus resistance mechanisms, including epigenetic variations and smallRNA expressions.", "doi": "10.1038/s41597-023-02800-0", "pmid": "38071206", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10710486"}, {"db": "pii", "key": "10.1038/s41597-023-02800-0"}], "notes": [], "created": "2023-12-11T06:42:02.155Z", "modified": "2024-01-05T16:18:41.036Z"}, {"entity": "publication", "iuid": "55a655ce643f48fa87e39fd46539cd1f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/55a655ce643f48fa87e39fd46539cd1f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/55a655ce643f48fa87e39fd46539cd1f"}}, "title": "Shotgun metagenomes from productive lakes in an urban region of Sweden.", "authors": [{"family": "Rodr\u00edguez-Gij\u00f3n", "given": "Alejandro", "initials": "A", "orcid": "0000-0002-1649-6894", "researcher": {"href": "https://publications.scilifelab.se/researcher/d25dfecc53e94af0b79799621f131631.json"}}, {"family": "Hampel", "given": "Justyna J", "initials": "JJ", "orcid": "0000-0002-2869-5807", "researcher": {"href": "https://publications.scilifelab.se/researcher/6400f81d7ac04606abe86b28400576dd.json"}}, {"family": "Dharamshi", "given": "Jennah", "initials": "J", "orcid": "0000-0003-4563-3939", "researcher": {"href": "https://publications.scilifelab.se/researcher/04c4fab7c00a48b29be068ac41016947.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL", "orcid": "0000-0002-8622-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/8aabc8c17d5b4ad7872c7380301d4562.json"}}], "type": "dataset", "published": "2023-11-17", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "10", "issue": "1", "pages": "810", "issn-l": "2052-4463"}, "abstract": "Urban lakes provide multiple benefits to society while influencing life quality. Moreover, lakes and their microbiomes are sentinels of anthropogenic impact and can be used for natural resource management and planning. Here, we release original metagenomic data from several well-characterized and anthropogenically impacted eutrophic lakes in the vicinity of Stockholm (Sweden). Our goal was to collect representative microbial community samples and use shotgun sequencing to provide a broad view on microbial diversity of productive urban lakes. Our dataset has an emphasis on Lake M\u00e4laren as a major drinking water reservoir under anthropogenic impact. This dataset includes short-read sequence data and metagenome assemblies from each of 17 samples collected from eutrophic lakes near the greater Stockholm area. We used genome-resolved metagenomics and obtained 2378 metagenome assembled genomes that de-replicated into 514 species representative genomes. This dataset adds new datapoints to previously sequenced lakes and it includes the first sequenced set of metagenomes from Lake M\u00e4laren. Our dataset serves as a baseline for future monitoring of drinking water reservoirs and urban lakes.", "doi": "10.1038/s41597-023-02722-x", "pmid": "37978200", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10656542"}, {"db": "pii", "key": "10.1038/s41597-023-02722-x"}], "notes": [], "created": "2024-01-02T13:30:18.895Z", "modified": "2024-11-25T10:19:55.700Z"}, {"entity": "publication", "iuid": "5eab650a5a5a402b8a354be7de674cb0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5eab650a5a5a402b8a354be7de674cb0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5eab650a5a5a402b8a354be7de674cb0"}}, "title": "Mountain- and brown hare genetic polymorphisms to survey local adaptations and conservation status of the heath hare (Lepus timidus sylvaticus, Nilsson 1831).", "authors": [{"family": "Michell", "given": "Craig T", "initials": "CT"}, {"family": "Pohjoism\u00e4ki", "given": "Jaakko L O", "initials": "JLO", "orcid": "0000-0002-1185-3610", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3dec32b253440eab477911e81ec3c1f.json"}}, {"family": "Spong", "given": "G\u00f6ran", "initials": "G"}, {"family": "Thulin", "given": "Carl-Gustaf", "initials": "CG"}], "type": "dataset", "published": "2022-11-03", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "9", "issue": "1", "pages": "667"}, "abstract": "We provide the first whole genome sequences from three specimens of the mountain hare subspecies the heath hare (Lepus timidus sylvaticus), along with samples from two mountain hares (Lepus timidus timidus) and two brown hares (Lepus europaeus) from Sweden. The heath hare has a unique grey winter pelage as compared to other mountain hares (white) and brown hares (mostly brown), and face regional extinction, likely due to competitive exclusion from the non-native brown hare. Whole genome resequencing from the seven hare specimens were mapped to the Lepus timidus pseudoreference genome and used for detection of 11,363,883 polymorphic nucleotide positions. The data presented here could be useful for addressing local adaptations and conservation status of mountain hares and brown hares in Sweden, including unique subspecies.", "doi": "10.1038/s41597-022-01794-5", "pmid": "36329035", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9633808"}, {"db": "pii", "key": "10.1038/s41597-022-01794-5"}], "notes": [], "created": "2022-12-19T10:39:22.701Z", "modified": "2023-10-16T12:44:10.504Z"}, {"entity": "publication", "iuid": "8a75948c51be42018169ce7fe05133b1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a75948c51be42018169ce7fe05133b1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a75948c51be42018169ce7fe05133b1"}}, "title": "A chromosome-scale reference genome for Spironucleus salmonicida.", "authors": [{"family": "Xu", "given": "Feifei", "initials": "F", "orcid": "0000-0003-1946-1520", "researcher": {"href": "https://publications.scilifelab.se/researcher/84c51ec60768479f851e29ebc804f547.json"}}, {"family": "Jim\u00e9nez-Gonz\u00e1lez", "given": "Alejandro", "initials": "A", "orcid": "0000-0003-3493-4154", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c6b93b731741018637733969c308a6.json"}}, {"family": "Kurt", "given": "Zeynep", "initials": "Z"}, {"family": "\u00c1stvaldsson", "given": "\u00c1sgeir", "initials": "\u00c1", "orcid": "0000-0002-0320-6974", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a3d973dc6d246b48426d2063eef8934.json"}}, {"family": "Andersson", "given": "Jan O", "initials": "JO", "orcid": "0000-0002-3075-4896", "researcher": {"href": "https://publications.scilifelab.se/researcher/489ed7f61a7b49a3a7ebd9ee3c391f5b.json"}}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG"}], "type": "dataset", "published": "2022-09-24", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "9", "issue": "1", "pages": "585", "issn-l": "2052-4463"}, "abstract": "Spironucleus salmonicida is a diplomonad causing systemic infection in salmon. The first S. salmonicida genome assembly was published 2014 and has been a valuable reference genome in protist research. However, the genome assembly is fragmented without assignment of the sequences to chromosomes. In our previous Giardia genome study, we have shown how a fragmented genome assembly can be improved with long-read sequencing technology complemented with optical maps. Combining Pacbio long-read sequencing technology and optical maps, we are presenting here this new S. salmonicida genome assembly in nine near-complete chromosomes with only three internal gaps at long repeats. This new genome assembly is not only more complete sequence-wise but also more complete at annotation level, providing more details into gene families, gene organizations and chromosomal structure. This near-complete reference genome will aid comparative genomics at chromosomal level, and serve as a valuable resource for the diplomonad community and protist research.", "doi": "10.1038/s41597-022-01703-w", "pmid": "36153341", "labels": {"NGI Long read": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9509377"}, {"db": "pii", "key": "10.1038/s41597-022-01703-w"}], "notes": [], "created": "2022-11-28T10:42:49.061Z", "modified": "2022-11-28T10:42:49.118Z"}, {"entity": "publication", "iuid": "c6cacf53d4f344af86090e590b32f848", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6cacf53d4f344af86090e590b32f848.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6cacf53d4f344af86090e590b32f848"}}, "title": "Inflation of test accuracy due to data leakage in deep learning-based classification of OCT images.", "authors": [{"family": "Tampu", "given": "Iulian Emil", "initials": "IE", "orcid": "0000-0002-7582-1706", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f3497ed6c634acca2acca14a37d098c.json"}}, {"family": "Eklund", "given": "Anders", "initials": "A", "orcid": "0000-0001-7061-7995", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dd215e5257a41e4866e3cfb15dce4db.json"}}, {"family": "Haj-Hosseini", "given": "Neda", "initials": "N", "orcid": "0000-0002-0555-8877", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c00390b63594e7ea150a3ec742a812c.json"}}], "type": "journal article", "published": "2022-09-22", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "9", "issue": "1", "pages": "580", "issn-l": "2052-4463"}, "abstract": "In the application of deep learning on optical coherence tomography (OCT) data, it is common to train classification networks using 2D images originating from volumetric data. Given the micrometer resolution of OCT systems, consecutive images are often very similar in both visible structures and noise. Thus, an inappropriate data split can result in overlap between the training and testing sets, with a large portion of the literature overlooking this aspect. In this study, the effect of improper dataset splitting on model evaluation is demonstrated for three classification tasks using three OCT open-access datasets extensively used, Kermany's and Srinivasan's ophthalmology datasets, and AIIMS breast tissue dataset. Results show that the classification performance is inflated by 0.07 up to 0.43 in terms of Matthews Correlation Coefficient (accuracy: 5% to 30%) for models tested on datasets with improper splitting, highlighting the considerable effect of dataset handling on model evaluation. This study intends to raise awareness on the importance of dataset splitting given the increased research interest in implementing deep learning on OCT data.", "doi": "10.1038/s41597-022-01618-6", "pmid": "36138025", "labels": {"AIDA Data Hub": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9500039"}, {"db": "pii", "key": "10.1038/s41597-022-01618-6"}], "notes": [], "created": "2023-05-25T15:53:47.993Z", "modified": "2023-05-25T16:03:38.140Z"}, {"entity": "publication", "iuid": "26b36e84d7ee4479848b114b7c51ba21", "links": {"self": {"href": "https://publications.scilifelab.se/publication/26b36e84d7ee4479848b114b7c51ba21.json"}, "display": {"href": "https://publications.scilifelab.se/publication/26b36e84d7ee4479848b114b7c51ba21"}}, "title": "An atlas of endogenous DNA double-strand breaks arising during human neural cell fate determination.", "authors": [{"family": "Ballarino", "given": "Roberto", "initials": "R", "orcid": "0000-0001-7812-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb720f25876d45c39b9dad1b4b48a6fa.json"}}, {"family": "Bouwman", "given": "Britta A M", "initials": "BAM", "orcid": "0000-0002-9827-9497", "researcher": {"href": "https://publications.scilifelab.se/researcher/7933c49c5e6448408159ddb654286127.json"}}, {"family": "Agostini", "given": "Federico", "initials": "F", "orcid": "0000-0002-5453-2737", "researcher": {"href": "https://publications.scilifelab.se/researcher/a21ea8b7e9a5427eb0e48a822c840b8b.json"}}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Diekmann", "given": "Constantin", "initials": "C", "orcid": "0000-0002-4779-3541", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bc495c18087429f81dd51007ffe1582.json"}}, {"family": "Wernersson", "given": "Erik", "initials": "E", "orcid": "0000-0003-4778-1660", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae0de6d4af244cec84bbe8c1240d89ae.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M"}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}], "type": "dataset", "published": "2022-07-12", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "9", "issue": "1", "pages": "400"}, "abstract": "Endogenous DNA double-strand breaks (DSBs) occurring in neural cells have been implicated in the pathogenesis of neurodevelopmental disorders (NDDs). Currently, a genomic map of endogenous DSBs arising during human neurogenesis is missing. Here, we applied in-suspension Breaks Labeling In Situ and Sequencing (sBLISS), RNA-Seq, and Hi-C to chart the genomic landscape of DSBs and relate it to gene expression and genome architecture in 2D cultures of human neuroepithelial stem cells (NES), neural progenitor cells (NPC), and post-mitotic neural cells (NEU). Endogenous DSBs were enriched at the promoter and along the gene body of transcriptionally active genes, at the borders of topologically associating domains (TADs), and around chromatin loop anchors. NDD risk genes harbored significantly more DSBs in comparison to other protein-coding genes, especially in NEU cells. We provide sBLISS, RNA-Seq, and Hi-C datasets for each differentiation stage, and all the scripts needed to reproduce our analyses. Our datasets and tools represent a unique resource that can be harnessed to investigate the role of genome fragility in the pathogenesis of NDDs.", "doi": "10.1038/s41597-022-01508-x", "pmid": "35821502", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9276747"}, {"db": "pii", "key": "10.1038/s41597-022-01508-x"}], "notes": [], "created": "2022-08-19T08:38:43.514Z", "modified": "2023-10-16T11:44:09.152Z"}, {"entity": "publication", "iuid": "05430c40833b4be3b4985f41f27377d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/05430c40833b4be3b4985f41f27377d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/05430c40833b4be3b4985f41f27377d6"}}, "title": "Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH.", "authors": [{"family": "Mota", "given": "Ana", "initials": "A", "orcid": "0000-0001-8592-9764", "researcher": {"href": "https://publications.scilifelab.se/researcher/508960cbe03d4490a6e4594fc76e3510.json"}}, {"family": "Schweitzer", "given": "Maud", "initials": "M"}, {"family": "Wernersson", "given": "Erik", "initials": "E"}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M"}], "type": "dataset", "published": "2022-02-10", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "9", "issue": "1", "pages": "47", "issn-l": "2052-4463"}, "abstract": "Single-molecule DNA fluorescence in situ hybridization (FISH) techniques enable studying the three-dimensional (3D) organization of the genome at the single cell level. However, there is a major unmet need for open access, high quality, curated and reproducible DNA FISH datasets. Here, we describe a dataset obtained by applying our recently developed iFISH method to simultaneously visualize 16 small (size range: 62-73 kilobases, kb) DNA loci evenly spaced on chromosome 2 in human cells, in a single round of hybridization. We show how combinatorial color coding can be used to precisely localize multiple loci in 3D within single cells, and how inter-locus distances scale inversely with chromosome contact frequencies determined by high-throughput chromosome conformation capture (Hi-C). We provide raw images and 3D coordinates for nearly 10,000 FISH dots. Our dataset provides a free resource that can facilitate studies of 3D genome organization in single cells and can be used to develop automatic FISH analysis algorithms.", "doi": "10.1038/s41597-022-01139-2", "pmid": "35145120", "labels": {"Spatial Proteomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC8831585"}, {"db": "pii", "key": "10.1038/s41597-022-01139-2"}], "notes": [], "created": "2023-06-26T12:49:04.953Z", "modified": "2023-06-26T12:49:05.083Z"}, {"entity": "publication", "iuid": "1d95029adc794903bf11503ddeab9127", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d95029adc794903bf11503ddeab9127.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d95029adc794903bf11503ddeab9127"}}, "title": "Insights into the changes in the proteome of Alzheimer disease elucidated by a meta-analysis.", "authors": [{"family": "Haytural", "given": "Hazal", "initials": "H", "orcid": "0000-0002-6805-6989", "researcher": {"href": "https://publications.scilifelab.se/researcher/863ccd2db6794dff8e36a313075e4ea2.json"}}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "Schedin-Weiss", "given": "Sophia", "initials": "S"}, {"family": "Bereczki", "given": "Erika", "initials": "E"}, {"family": "Rezeli", "given": "Melinda", "initials": "M"}, {"family": "Unwin", "given": "Richard D", "initials": "RD"}, {"family": "Wang", "given": "Xusheng", "initials": "X"}, {"family": "Dammer", "given": "Eric B", "initials": "EB", "orcid": "0000-0003-2947-7606", "researcher": {"href": "https://publications.scilifelab.se/researcher/026547f280c8451586bf92ab028090f7.json"}}, {"family": "Johnson", "given": "Erik C B", "initials": "ECB"}, {"family": "Seyfried", "given": "Nicholas T", "initials": "NT", "orcid": "0000-0002-4507-624X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c940f8678724c38b1c6e98ea1b335e4.json"}}, {"family": "Winblad", "given": "Bengt", "initials": "B", "orcid": "0000-0002-0011-1179", "researcher": {"href": "https://publications.scilifelab.se/researcher/73185a13ca474153b66415e6a2dfff0f.json"}}, {"family": "Tijms", "given": "Betty M", "initials": "BM", "orcid": "0000-0002-2612-1797", "researcher": {"href": "https://publications.scilifelab.se/researcher/74734f1c78e840b0aaadd74cc2c1ae9f.json"}}, {"family": "Visser", "given": "Pieter Jelle", "initials": "PJ"}, {"family": "Frykman", "given": "Susanne", "initials": "S"}, {"family": "Tjernberg", "given": "Lars O", "initials": "LO", "orcid": "0000-0001-6889-4950", "researcher": {"href": "https://publications.scilifelab.se/researcher/35d7bd25361f4e08a7223926311b399a.json"}}], "type": "journal article", "published": "2021-12-03", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "8", "issue": "1", "pages": "312", "issn-l": "2052-4463"}, "abstract": "Mass spectrometry (MS)-based proteomics is a powerful tool to explore pathogenic changes of a disease in an unbiased manner and has been used extensively in Alzheimer disease (AD) research. Here, by performing a meta-analysis of high-quality proteomic studies, we address which pathological changes are observed consistently and therefore most likely are of great importance for AD pathogenesis. We retrieved datasets, comprising a total of 21,588 distinct proteins identified across 857 postmortem human samples, from ten studies using labeled or label-free MS approaches. Our meta-analysis findings showed significant alterations of 757 and 1,195 proteins in AD in the labeled and label-free datasets, respectively. Only 33 proteins, some of which were associated with synaptic signaling, had the same directional change across the individual studies. However, despite alterations in individual proteins being different between the labeled and the label-free datasets, several pathways related to synaptic signaling, oxidative phosphorylation, immune response and extracellular matrix were commonly dysregulated in AD. These pathways represent robust changes in the human AD brain and warrant further investigation.", "doi": "10.1038/s41597-021-01090-8", "pmid": "34862388", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41597-021-01090-8"}, {"db": "pmc", "key": "PMC8642431"}], "notes": [], "created": "2021-12-06T08:17:14.664Z", "modified": "2024-01-16T13:48:38.002Z"}, {"entity": "publication", "iuid": "34a48de26bb1448da0afb5d96f1a811d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34a48de26bb1448da0afb5d96f1a811d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34a48de26bb1448da0afb5d96f1a811d"}}, "title": "Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study.", "authors": [{"family": "Zhao", "given": "Yongmei", "initials": "Y", "orcid": "0000-0003-0800-4658", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a5a787c429e416da061067ec701a3b1.json"}}, {"family": "Fang", "given": "Li Tai", "initials": "LT", "orcid": "0000-0003-3201-5162", "researcher": {"href": "https://publications.scilifelab.se/researcher/b580a1ef08e04613adc5824605d9d442.json"}}, {"family": "Shen", "given": "Tsai-Wei", "initials": "T"}, {"family": "Choudhari", "given": "Sulbha", "initials": "S"}, {"family": "Talsania", "given": "Keyur", "initials": "K"}, {"family": "Chen", "given": "Xiongfong", "initials": "X"}, {"family": "Shetty", "given": "Jyoti", "initials": "J"}, {"family": "Kriga", "given": "Yuliya", "initials": "Y"}, {"family": "Tran", "given": "Bao", "initials": "B"}, {"family": "Zhu", "given": "Bin", "initials": "B", "orcid": "0000-0003-0172-5516", "researcher": {"href": "https://publications.scilifelab.se/researcher/67eaeee64f3741c58132c76ba8d33d2b.json"}}, {"family": "Chen", "given": "Zhong", "initials": "Z"}, {"family": "Chen", "given": "Wanqiu", "initials": "W", "orcid": "0000-0003-3706-7834", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff236616beef483ea11661874e91b7d1.json"}}, {"family": "Wang", "given": "Charles", "initials": "C", "orcid": "0000-0001-8861-2121", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f245b91838442ef859874ad23d0aae8.json"}}, {"family": "Jaeger", "given": "Erich", "initials": "E"}, {"family": "Meerzaman", "given": "Daoud", "initials": "D"}, {"family": "Lu", "given": "Charles", "initials": "C"}, {"family": "Idler", "given": "Kenneth", "initials": "K"}, {"family": "Ren", "given": "Luyao", "initials": "L"}, {"family": "Zheng", "given": "Yuanting", "initials": "Y"}, {"family": "Shi", "given": "Leming", "initials": "L"}, {"family": "Petitjean", "given": "Virginie", "initials": "V"}, {"family": "Sultan", "given": "Marc", "initials": "M"}, {"family": "Hung", "given": "Tiffany", "initials": "T"}, {"family": "Peters", "given": "Eric", "initials": "E"}, {"family": "Drabek", "given": "Jiri", "initials": "J"}, {"family": "Vojta", "given": "Petr", "initials": "P"}, {"family": "Maestro", "given": "Roberta", "initials": "R"}, {"family": "Gasparotto", "given": "Daniela", "initials": "D"}, {"family": "K\u00f5ks", "given": "Sulev", "initials": "S", "orcid": "0000-0001-6087-6643", "researcher": {"href": "https://publications.scilifelab.se/researcher/dea893f45b1b45a5a92890878fa044e5.json"}}, {"family": "Reimann", "given": "Ene", "initials": "E", "orcid": "0000-0002-5410-4433", "researcher": {"href": "https://publications.scilifelab.se/researcher/25325fa20b3940a6acd1ebd0a58629ef.json"}}, {"family": "Scherer", "given": "Andreas", "initials": "A"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U"}, {"family": "Foox", "given": "Jonathan", "initials": "J"}, {"family": "Mason", "given": "Christopher E", "initials": "CE", "orcid": "0000-0002-1850-1642", "researcher": {"href": "https://publications.scilifelab.se/researcher/2af4cb8577d34907b22b030f9e79e90e.json"}}, {"family": "Xiao", "given": "Chunlin", "initials": "C", "orcid": "0000-0001-8702-4889", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b1a63c56506470cba459c6e60378ba2.json"}}, {"family": "Hong", "given": "Huixiao", "initials": "H", "orcid": "0000-0001-8087-3968", "researcher": {"href": "https://publications.scilifelab.se/researcher/158916b8a0cc4a28b2dceb12514d4a88.json"}}, {"family": "Xiao", "given": "Wenming", "initials": "W", "orcid": "0000-0003-4096-9724", "researcher": {"href": "https://publications.scilifelab.se/researcher/633df103f81f4142ace7a3763b56af54.json"}}], "type": "dataset", "published": "2021-11-09", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "8", "issue": "1", "pages": "296"}, "abstract": "With the rapid advancement of sequencing technologies, next generation sequencing (NGS) analysis has been widely applied in cancer genomics research. More recently, NGS has been adopted in clinical oncology to advance personalized medicine. Clinical applications of precision oncology require accurate tests that can distinguish tumor-specific mutations from artifacts introduced during NGS processes or data analysis. Therefore, there is an urgent need to develop best practices in cancer mutation detection using NGS and the need for standard reference data sets for systematically measuring accuracy and reproducibility across platforms and methods. Within the SEQC2 consortium context, we established paired tumor-normal reference samples and generated whole-genome (WGS) and whole-exome sequencing (WES) data using sixteen library protocols, seven sequencing platforms at six different centers. We systematically interrogated somatic mutations in the reference samples to identify factors affecting detection reproducibility and accuracy in cancer genomes. These large cross-platform/site WGS and WES datasets using well-characterized reference samples will represent a powerful resource for benchmarking NGS technologies, bioinformatics pipelines, and for the cancer genomics studies.", "doi": "10.1038/s41597-021-01077-5", "pmid": "34753956", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41597-021-01077-5"}, {"db": "pmc", "key": "PMC8578599"}], "notes": [], "created": "2022-02-22T16:04:58.400Z", "modified": "2022-03-31T15:20:05.415Z"}, {"entity": "publication", "iuid": "54e8c2df71e24922b03fbbba056478b2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/54e8c2df71e24922b03fbbba056478b2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/54e8c2df71e24922b03fbbba056478b2"}}, "title": "Community composition of aquatic fungi across the thawing Arctic.", "authors": [{"family": "Kluge", "given": "Mariana", "initials": "M", "orcid": "0000-0001-7500-2041", "researcher": {"href": "https://publications.scilifelab.se/researcher/f89b91331601447bb8302fc376ab05f2.json"}}, {"family": "Wurzbacher", "given": "Christian", "initials": "C"}, {"family": "Wauthy", "given": "Maxime", "initials": "M", "orcid": "0000-0002-7768-7133", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e16ef79cd75436e8fb7b2f490b16b74.json"}}, {"family": "Clemmensen", "given": "Karina Engelbrecht", "initials": "KE", "orcid": "0000-0002-9627-6428", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a4e19bdfc1431c9dd1c3f1cd58c766.json"}}, {"family": "Hawkes", "given": "Jeffrey Alistair", "initials": "JA"}, {"family": "Einarsdottir", "given": "Karolina", "initials": "K"}, {"family": "Stenlid", "given": "Jan", "initials": "J", "orcid": "0000-0002-5344-2094", "researcher": {"href": "https://publications.scilifelab.se/researcher/eac6fc31e38c4552a986310015fcb1b4.json"}}, {"family": "Peura", "given": "Sari", "initials": "S"}], "type": "dataset", "published": "2021-08-19", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "8", "issue": "1", "pages": "221", "issn-l": "2052-4463"}, "abstract": "Thermokarst activity at permafrost sites releases considerable amounts of ancient carbon to the atmosphere. A large part of this carbon is released via thermokarst ponds, and fungi could be an important organismal group enabling its recycling. However, our knowledge about aquatic fungi in thermokarstic systems is extremely limited. In this study, we collected samples from five permafrost sites distributed across circumpolar Arctic and representing different stages of permafrost integrity. Surface water samples were taken from the ponds and, additionally, for most of the ponds also the detritus and sediment samples were taken. All the samples were extracted for total DNA, which was then amplified for the fungal ITS2 region of the ribosomal genes. These amplicons were sequenced using PacBio technology. Water samples were also collected to analyze the chemical conditions in the ponds, including nutrient status and the quality and quantity of dissolved organic carbon. This dataset gives a unique overview of the impact of the thawing permafrost on fungal communities and their potential role on carbon recycling.", "doi": "10.1038/s41597-021-01005-7", "pmid": "34413318", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41597-021-01005-7"}, {"db": "pmc", "key": "PMC8377128"}], "notes": [], "created": "2021-10-18T19:54:16.212Z", "modified": "2024-01-16T13:48:38.697Z"}, {"entity": "publication", "iuid": "eac7874ed8294cfabb98f904d734dc74", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eac7874ed8294cfabb98f904d734dc74.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eac7874ed8294cfabb98f904d734dc74"}}, "title": "Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds.", "authors": [{"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL", "orcid": "0000-0002-8622-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/8aabc8c17d5b4ad7872c7380301d4562.json"}}, {"family": "Fernandez", "given": "Leyden", "initials": "L"}, {"family": "Martin", "given": "Ga\u00ebtan", "initials": "G", "orcid": "0000-0002-5289-6131", "researcher": {"href": "https://publications.scilifelab.se/researcher/3fa7c61072034af188ed3685ce83ca3c.json"}}, {"family": "Martinez-Rodriguez", "given": "Gustavo A", "initials": "GA"}, {"family": "Saarenheimo", "given": "Jatta", "initials": "J"}, {"family": "Zopfi", "given": "Jakob", "initials": "J", "orcid": "0000-0002-8437-7344", "researcher": {"href": "https://publications.scilifelab.se/researcher/fea1eab419af4e60b1455c0221a5b6e7.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Peura", "given": "Sari", "initials": "S", "orcid": "0000-0003-3892-8157", "researcher": {"href": "https://publications.scilifelab.se/researcher/c430ad5c3bd14387b768c588a9b12ce0.json"}}], "type": "dataset", "published": "2021-05-14", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "8", "issue": "1", "pages": "131", "issn-l": "2052-4463"}, "abstract": "Stratified lakes and ponds featuring steep oxygen gradients are significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the microbial communities, especially in the oxygen depleted compartments, are poorly known. Here, we present a comprehensive dataset including 267 shotgun metagenomes from 41 stratified lakes and ponds mainly located in the boreal and subarctic regions, but also including one tropical reservoir and one temperate lake. For most lakes and ponds, the data includes a vertical sample set spanning from the oxic surface to the anoxic bottom layer. The majority of the samples were collected during the open water period, but also a total of 29 samples were collected from under the ice. In addition to the metagenomic sequences, the dataset includes environmental variables for the samples, such as oxygen, nutrient and organic carbon concentrations. The dataset is ideal for further exploring the microbial taxonomic and functional diversity in freshwater environments and potential climate change impacts on the functioning of these ecosystems.", "doi": "10.1038/s41597-021-00910-1", "pmid": "33990618", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41597-021-00910-1"}, {"db": "pmc", "key": "PMC8121793"}], "notes": [], "created": "2021-06-01T20:55:20.891Z", "modified": "2024-01-16T13:48:39.756Z"}, {"entity": "publication", "iuid": "fb4bbf803de54b088cfb068d05fc005b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fb4bbf803de54b088cfb068d05fc005b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fb4bbf803de54b088cfb068d05fc005b"}}, "title": "Key insights in the AIDA community policy on sharing of clinical imaging data for research in Sweden.", "authors": [{"family": "Hedlund", "given": "Joel", "initials": "J", "orcid": "0000-0001-6443-3604", "researcher": {"href": "https://publications.scilifelab.se/researcher/241552a1caee487298f4eef04daa3023.json"}}, {"family": "Eklund", "given": "Anders", "initials": "A", "orcid": "0000-0001-7061-7995", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dd215e5257a41e4866e3cfb15dce4db.json"}}, {"family": "Lundstr\u00f6m", "given": "Claes", "initials": "C", "orcid": "0000-0002-9368-0177", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dbd78a0aa02482c9587af4c9e6331a5.json"}}], "type": "journal article", "published": "2020-10-06", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "7", "issue": "1", "pages": "331"}, "abstract": "Development of world-class artificial intelligence (AI) for medical imaging requires access to massive amounts of training data from clinical sources, but effective data sharing is often hindered by uncertainty regarding data protection. We describe an initiative to reduce this uncertainty through a policy describing a national community consensus on sound data sharing practices.", "doi": "10.1038/s41597-020-00674-0", "pmid": "33024103", "labels": {"AIDA Data Hub": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7538928"}, {"db": "pii", "key": "10.1038/s41597-020-00674-0"}], "notes": [], "created": "2021-11-10T16:53:56.042Z", "modified": "2023-05-25T16:01:47.054Z"}, {"entity": "publication", "iuid": "92f8202f59a04becbbbcac6a1abbc60d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92f8202f59a04becbbbcac6a1abbc60d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92f8202f59a04becbbbcac6a1abbc60d"}}, "title": "Systems biology of acidophile biofilms for efficient metal extraction.", "authors": [{"family": "Buetti-Dinh", "given": "Antoine", "initials": "A"}, {"family": "Herold", "given": "Malte", "initials": "M"}, {"family": "Christel", "given": "Stephan", "initials": "S"}, {"family": "Hajjami", "given": "Mohamed El", "initials": "ME"}, {"family": "Bellenberg", "given": "S\u00f6ren", "initials": "S"}, {"family": "Ilie", "given": "Olga", "initials": "O"}, {"family": "Wilmes", "given": "Paul", "initials": "P"}, {"family": "Poetsch", "given": "Ansgar", "initials": "A"}, {"family": "Sand", "given": "Wolfgang", "initials": "W"}, {"family": "Vera", "given": "Mario", "initials": "M"}, {"family": "Pivkin", "given": "Igor V", "initials": "IV"}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "dataset", "published": "2020-07-07", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "7", "issue": "1", "pages": "215", "issn-l": "2052-4463"}, "abstract": "Society's demand for metals is ever increasing while stocks of high-grade minerals are being depleted. Biomining, for example of chalcopyrite for copper recovery, is a more sustainable biotechnological process that exploits the capacity of acidophilic microbes to catalyze solid metal sulfide dissolution to soluble metal sulfates. A key early stage in biomining is cell attachment and biofilm formation on the mineral surface that results in elevated mineral oxidation rates. Industrial biomining of chalcopyrite is typically carried out in large scale heaps that suffer from the downsides of slow and poor metal recoveries. In an effort to mitigate these drawbacks, this study investigated planktonic and biofilm cells of acidophilic (optimal growth pH < 3) biomining bacteria. RNA and proteins were extracted, and high throughput \"omics\" performed from a total of 80 biomining experiments. In addition, micrographs of biofilm formation on the chalcopyrite mineral surface over time were generated from eight separate experiments. The dataset generated in this project will be of great use to microbiologists, biotechnologists, and industrial researchers.", "doi": "10.1038/s41597-020-0519-2", "pmid": "32636389", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41597-020-0519-2"}, {"db": "pmc", "key": "PMC7340779"}], "notes": [], "created": "2020-12-07T16:29:57.828Z", "modified": "2024-01-16T13:48:42.188Z"}, {"entity": "publication", "iuid": "67b440a208864ecea283f09dd7ca7f80", "links": {"self": {"href": "https://publications.scilifelab.se/publication/67b440a208864ecea283f09dd7ca7f80.json"}, "display": {"href": "https://publications.scilifelab.se/publication/67b440a208864ecea283f09dd7ca7f80"}}, "title": "Transcriptomic resources for evolutionary studies in flat periwinkles and related species.", "authors": [{"family": "Marques", "given": "Jo\u00e3o P", "initials": "JP", "orcid": "0000-0001-9834-1361", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bb0a67732e44e108fe1f58f86ce4ef2.json"}}, {"family": "Sotelo", "given": "Graciela", "initials": "G"}, {"family": "Galindo", "given": "Juan", "initials": "J"}, {"family": "Chaube", "given": "Pragya", "initials": "P"}, {"family": "Costa", "given": "Diana", "initials": "D"}, {"family": "Afonso", "given": "Sandra", "initials": "S"}, {"family": "Panova", "given": "Marina", "initials": "M"}, {"family": "Nowick", "given": "Katja", "initials": "K"}, {"family": "Butlin", "given": "Roger", "initials": "R", "orcid": "0000-0003-4736-0954", "researcher": {"href": "https://publications.scilifelab.se/researcher/e510a963ebeb4e8c8af68b10a001a326.json"}}, {"family": "Hollander", "given": "Johan", "initials": "J"}, {"family": "Faria", "given": "Rui", "initials": "R"}], "type": "dataset", "published": "2020-03-03", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "7", "issue": "1", "pages": "73", "issn-l": "2052-4463"}, "abstract": "The flat periwinkles, Littorina fabalis and L. obtusata, comprise two sister gastropod species that have an enormous potential to elucidate the mechanisms involved in ecological speciation in the marine realm. However, the molecular resources currently available for these species are still scarce. In order to circumvent this limitation, we used RNA-seq data to characterize the transcriptome of four individuals from each species sampled in different locations across the Iberian Peninsula. Four de novo transcriptome assemblies were generated, as well as a pseudo-reference using the L. saxatilis reference transcriptome as backbone. After transcripts' annotation, variant calling resulted in the identification of 19,072 to 45,340 putatively species-diagnostic SNPs. The discriminatory power of a subset of these SNPs was validated by implementing an independent genotyping assay to characterize reference populations, resulting in an accurate classification of individuals into each species and in the identification of hybrids between the two. These data comprise valuable genomic resources for a wide range of evolutionary and conservation studies in flat periwinkles and related taxa.", "doi": "10.1038/s41597-020-0408-8", "pmid": "32127542", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41597-020-0408-8"}, {"db": "pmc", "key": "PMC7054417"}], "notes": [], "created": "2020-03-16T09:47:51.783Z", "modified": "2021-11-10T12:53:19.043Z"}, {"entity": "publication", "iuid": "53fc32e0ae72487f9138a071ec3fdaba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/53fc32e0ae72487f9138a071ec3fdaba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/53fc32e0ae72487f9138a071ec3fdaba"}}, "title": "A chromosome-scale reference genome for Giardia intestinalis WB.", "authors": [{"family": "Xu", "given": "Feifei", "initials": "F", "orcid": "0000-0003-1946-1520", "researcher": {"href": "https://publications.scilifelab.se/researcher/84c51ec60768479f851e29ebc804f547.json"}}, {"family": "Jex", "given": "Aaron", "initials": "A"}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG"}], "type": "dataset", "published": "2020-02-04", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "7", "issue": "1", "pages": "38", "issn-l": "2052-4463"}, "abstract": "Giardia intestinalis is a protist causing diarrhea in humans. The first G. intestinalis genome, from the WB isolate, was published more than ten years ago, and has been widely used as the reference genome for Giardia research. However, the genome is fragmented, thus hindering research at the chromosomal level. We re-sequenced the Giardia genome with Pacbio long-read sequencing technology and obtained a new reference genome, which was assembled into near-complete chromosomes with only four internal gaps at long repeats. This new genome is not only more complete but also better annotated at both structural and functional levels, providing more details about gene families, gene organizations and chromosomal structure. This near-complete reference genome will be a valuable resource for the Giardia community and protist research. It also showcases how a fragmented genome can be improved with long-read sequencing technology completed with optical maps.", "doi": "10.1038/s41597-020-0377-y", "pmid": "32019935", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41597-020-0377-y"}, {"db": "pmc", "key": "PMC7000408"}], "notes": [], "created": "2020-02-11T18:48:52.944Z", "modified": "2021-11-10T12:54:10.933Z"}, {"entity": "publication", "iuid": "03a8b4f010b64f98b90e3af194d3c9ff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/03a8b4f010b64f98b90e3af194d3c9ff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/03a8b4f010b64f98b90e3af194d3c9ff"}}, "title": "Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials.", "authors": [{"family": "H\u00f6gfors-R\u00f6nnholm", "given": "Eva", "initials": "E"}, {"family": "Lopez-Fernandez", "given": "Margarita", "initials": "M"}, {"family": "Christel", "given": "Stephan", "initials": "S"}, {"family": "Brambilla", "given": "Diego", "initials": "D"}, {"family": "Huntemann", "given": "Marcel", "initials": "M"}, {"family": "Clum", "given": "Alicia", "initials": "A"}, {"family": "Foster", "given": "Brian", "initials": "B"}, {"family": "Foster", "given": "Bryce", "initials": "B"}, {"family": "Roux", "given": "Simon", "initials": "S"}, {"family": "Palaniappan", "given": "Krishnaveni", "initials": "K"}, {"family": "Varghese", "given": "Neha", "initials": "N"}, {"family": "Mukherjee", "given": "Supratim", "initials": "S"}, {"family": "Reddy", "given": "T B K", "initials": "TBK"}, {"family": "Daum", "given": "Chris", "initials": "C"}, {"family": "Copeland", "given": "Alex", "initials": "A"}, {"family": "Chen", "given": "I-Min A", "initials": "IA"}, {"family": "Ivanova", "given": "Natalia N", "initials": "NN"}, {"family": "Kyrpides", "given": "Nikos C", "initials": "NC"}, {"family": "Harmon-Smith", "given": "Miranda", "initials": "M"}, {"family": "Eloe-Fadrosh", "given": "Emiley A", "initials": "EA"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Engblom", "given": "Sten", "initials": "S"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2019-10-16", "journal": {"volume": "6", "issn": "2052-4463", "issue": "1", "pages": "207", "title": "Sci Data", "issn-l": "2052-4463"}, "abstract": "Natural sulfide rich deposits are common in coastal areas worldwide, including along the Baltic Sea coast. When artificial drainage exposes these deposits to atmospheric oxygen, iron sulfide minerals in the soils are rapidly oxidized. This process turns the potential acid sulfate soils into actual acid sulfate soils and mobilizes large quantities of acidity and leachable toxic metals that cause severe environmental problems. It is known that acidophilic microorganisms living in acid sulfate soils catalyze iron sulfide mineral oxidation. However, only a few studies regarding these communities have been published. In this study, we sampled the oxidized actual acid sulfate soil, the transition zone where oxidation is actively taking place, and the deepest un-oxidized potential acid sulfate soil. Nucleic acids were extracted and 16S rRNA gene amplicons, metagenomes, and metatranscriptomes generated to gain a detailed insight into the communities and their activities. The project will be of great use to microbiologists, environmental biologists, geochemists, and geologists as there is hydrological and geochemical monitoring from the site stretching back for many years.", "doi": "10.1038/s41597-019-0222-3", "pmid": "31619684", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41597-019-0222-3"}, {"db": "pmc", "key": "PMC6795848"}], "notes": [], "created": "2020-01-08T16:48:16.453Z", "modified": "2020-01-21T13:56:16.447Z"}, {"entity": "publication", "iuid": "0e6079a517d040d69e5a52d2fd623ff9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e6079a517d040d69e5a52d2fd623ff9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e6079a517d040d69e5a52d2fd623ff9"}}, "title": "Single-cell RNA sequencing of mouse brain and lung vascular and vessel-associated cell types.", "authors": [{"family": "He", "given": "Liqun", "initials": "L"}, {"family": "Vanlandewijck", "given": "Michael", "initials": "M"}, {"family": "M\u00e4e", "given": "Maarja Andaloussi", "initials": "MA"}, {"family": "Andrae", "given": "Johanna", "initials": "J"}, {"family": "Ando", "given": "Koji", "initials": "K"}, {"family": "Del Gaudio", "given": "Francesca", "initials": "F"}, {"family": "Nahar", "given": "Khayrun", "initials": "K"}, {"family": "Lebouvier", "given": "Thibaud", "initials": "T"}, {"family": "Lavi\u00f1a", "given": "B\u00e0rbara", "initials": "B"}, {"family": "Gouveia", "given": "Leonor", "initials": "L"}, {"family": "Sun", "given": "Ying", "initials": "Y"}, {"family": "Raschperger", "given": "Elisabeth", "initials": "E"}, {"family": "Segerstolpe", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Liu", "given": "Jianping", "initials": "J"}, {"family": "Gustafsson", "given": "Sonja", "initials": "S"}, {"family": "R\u00e4s\u00e4nen", "given": "Markus", "initials": "M"}, {"family": "Zarb", "given": "Yvette", "initials": "Y"}, {"family": "Mochizuki", "given": "Naoki", "initials": "N"}, {"family": "Keller", "given": "Annika", "initials": "A"}, {"family": "Lendahl", "given": "Urban", "initials": "U"}, {"family": "Betsholtz", "given": "Christer", "initials": "C"}], "type": "journal article", "published": "2018-08-21", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "5", "issue": "1", "pages": "180160"}, "abstract": "Vascular diseases are major causes of death, yet our understanding of the cellular constituents of blood vessels, including how differences in their gene expression profiles create diversity in vascular structure and function, is limited. In this paper, we describe a single-cell RNA sequencing (scRNA-seq) dataset that defines vascular and vessel-associated cell types and subtypes in mouse brain and lung. The dataset contains 3,436 single cell transcriptomes from mouse brain, which formed 15 distinct clusters corresponding to cell (sub)types, and another 1,504 single cell transcriptomes from mouse lung, which formed 17 cell clusters. In order to allow user-friendly access to our data, we constructed a searchable database (http://betsholtzlab.org/VascularSingleCells/database.html). Our dataset constitutes a comprehensive molecular atlas of vascular and vessel-associated cell types in the mouse brain and lung, and as such provides a strong foundation for future studies of vascular development and diseases.", "doi": "10.1038/sdata.2018.160", "pmid": "30129931", "labels": {"National Genomics Infrastructure": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "sdata2018160"}, {"db": "pmc", "key": "PMC6103262"}, {"db": "GEO", "description": "Single cell RNA-seq of mouse brain vascular transcriptomes", "key": "GSE98816"}, {"db": "GEO", "description": "Single cell RNA-seq of mouse lung vascular transcriptomes", "key": "GSE99235"}, {"db": "GEO", "description": "Single cell RNA-seq of mouse brain astrocyte transcriptomes", "key": "GSE99058"}, {"db": "figshare", "description": "Single cell RNAseq of mouse brain and lung vascular and vessel-associated cell types", "key": "https://doi.org/10.6084/m9.figshare.c.4077260)."}], "notes": [], "created": "2018-10-31T13:12:57.513Z", "modified": "2024-01-16T13:48:45.720Z"}, {"entity": "publication", "iuid": "1fe9214171b24f35bfca0414c1502c7f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1fe9214171b24f35bfca0414c1502c7f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1fe9214171b24f35bfca0414c1502c7f"}}, "title": "BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea.", "authors": [{"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Bennke", "given": "Christin", "initials": "C"}, {"family": "Beier", "given": "Sara", "initials": "S"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Kisand", "given": "Veljo", "initials": "V"}, {"family": "Riemann", "given": "Lasse", "initials": "L"}, {"family": "J\u00fcrgens", "given": "Klaus", "initials": "K"}, {"family": "Labrenz", "given": "Matthias", "initials": "M"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}], "type": "journal article", "published": "2018-07-31", "journal": {"volume": "5", "issn": "2052-4463", "issue": null, "pages": "180146", "title": "Sci Data", "issn-l": "2052-4463"}, "abstract": "The Baltic Sea is one of the world's largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset.", "doi": "10.1038/sdata.2018.146", "pmid": "30063227", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "sdata2018146"}, {"db": "pmc", "key": "PMC6067050"}, {"db": "European Nucleotide Archive", "description": "https://www.ebi.ac.uk/ena/data/view/PRJEB22997", "key": "PRJEB22997"}, {"db": "SRA", "description": "https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP058493", "key": "SRP058493"}, {"db": "figshare", "description": "BARM Annotation and Quantification Data", "key": "https://doi.org/10.6084/m9.figshare.c.3831631"}, {"db": "SRA", "description": "https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP077551", "key": "SRP077551"}], "notes": [], "created": "2018-10-31T19:45:28.762Z", "modified": "2024-01-16T13:48:45.935Z"}, {"entity": "publication", "iuid": "e9badd25eb314fd19db593e64594aecf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e9badd25eb314fd19db593e64594aecf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e9badd25eb314fd19db593e64594aecf"}}, "title": "A microarray whole-genome gene expression dataset in a rat model of inflammatory corneal angiogenesis.", "authors": [{"family": "Mukwaya", "given": "Anthony", "initials": "A"}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Xeroudaki", "given": "Maria", "initials": "M"}, {"family": "Peebo", "given": "Beatrice", "initials": "B"}, {"family": "Ali", "given": "Zaheer", "initials": "Z"}, {"family": "Lennikov", "given": "Anton", "initials": "A"}, {"family": "Jensen", "given": "Lasse Dahl Ejby", "initials": "LD"}, {"family": "Lagali", "given": "Neil", "initials": "N"}], "type": "journal article", "published": "2016-11-22", "journal": {"volume": "3", "issn": "2052-4463", "issue": null, "pages": "160103", "title": "Sci Data", "issn-l": "2052-4463"}, "abstract": "In angiogenesis with concurrent inflammation, many pathways are activated, some linked to VEGF and others largely VEGF-independent. Pathways involving inflammatory mediators, chemokines, and micro-RNAs may play important roles in maintaining a pro-angiogenic environment or mediating angiogenic regression. Here, we describe a gene expression dataset to facilitate exploration of pro-angiogenic, pro-inflammatory, and remodelling/normalization-associated genes during both an active capillary sprouting phase, and in the restoration of an avascular phenotype. The dataset was generated by microarray analysis of the whole transcriptome in a rat model of suture-induced inflammatory corneal neovascularisation. Regions of active capillary sprout growth or regression in the cornea were harvested and total RNA extracted from four biological replicates per group. High quality RNA was obtained for gene expression analysis using microarrays. Fold change of selected genes was validated by qPCR, and protein expression was evaluated by immunohistochemistry. We provide a gene expression dataset that may be re-used to investigate corneal neovascularisation, and may also have implications in other contexts of inflammation-mediated angiogenesis.", "doi": "10.1038/sdata.2016.103", "pmid": "27874850", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "sdata2016103"}, {"db": "pmc", "key": "PMC5119432"}], "notes": [], "created": "2017-05-03T13:00:41.157Z", "modified": "2021-07-05T12:48:16.053Z"}, {"entity": "publication", "iuid": "61db8ba720fb47f987a590d2723035c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61db8ba720fb47f987a590d2723035c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61db8ba720fb47f987a590d2723035c5"}}, "title": "The FAIR Guiding Principles for scientific data management and stewardship.", "authors": [{"family": "Wilkinson", "given": "Mark D", "initials": "MD"}, {"family": "Dumontier", "given": "Michel", "initials": "M"}, {"family": "Aalbersberg", "given": "I Jsbrand Jan", "initials": "IJ"}, {"family": "Appleton", "given": "Gabrielle", "initials": "G"}, {"family": "Axton", "given": "Myles", "initials": "M"}, {"family": "Baak", "given": "Arie", "initials": "A"}, {"family": "Blomberg", "given": "Niklas", "initials": "N"}, {"family": "Boiten", "given": "Jan-Willem", "initials": "JW"}, {"family": "da Silva Santos", "given": "Luiz Bonino", "initials": "LB"}, {"family": "Bourne", "given": "Philip E", "initials": "PE"}, {"family": "Bouwman", "given": "Jildau", "initials": "J"}, {"family": "Brookes", "given": "Anthony J", "initials": "AJ"}, {"family": "Clark", "given": "Tim", "initials": "T"}, {"family": "Crosas", "given": "Merc\u00e8", "initials": "M"}, {"family": "Dillo", "given": "Ingrid", "initials": "I"}, {"family": "Dumon", "given": "Olivier", "initials": "O"}, {"family": "Edmunds", "given": "Scott", "initials": "S"}, {"family": "Evelo", "given": "Chris T", "initials": "CT"}, {"family": "Finkers", "given": "Richard", "initials": "R"}, {"family": "Gonzalez-Beltran", "given": "Alejandra", "initials": "A"}, {"family": "Gray", "given": "Alasdair J G", "initials": "AJ"}, {"family": "Groth", "given": "Paul", "initials": "P"}, {"family": "Goble", "given": "Carole", "initials": "C"}, {"family": "Grethe", "given": "Jeffrey S", "initials": "JS"}, {"family": "Heringa", "given": "Jaap", "initials": "J"}, {"family": "'t Hoen", "given": "Peter A C", "initials": "PA"}, {"family": "Hooft", "given": "Rob", "initials": "R"}, {"family": "Kuhn", "given": "Tobias", "initials": "T"}, {"family": "Kok", "given": "Ruben", "initials": "R"}, {"family": "Kok", "given": "Joost", "initials": "J"}, {"family": "Lusher", "given": "Scott J", "initials": "SJ"}, {"family": "Martone", "given": "Maryann E", "initials": "ME"}, {"family": "Mons", "given": "Albert", "initials": "A"}, {"family": "Packer", "given": "Abel L", "initials": "AL"}, {"family": "Persson", "given": "Bengt", "initials": "B", "orcid": "0000-0003-3165-5344", "researcher": {"href": "https://publications.scilifelab.se/researcher/38f116ef0ed146419cb18e742c270c4a.json"}}, {"family": "Rocca-Serra", "given": "Philippe", "initials": "P"}, {"family": "Roos", "given": "Marco", "initials": "M"}, {"family": "van Schaik", "given": "Rene", "initials": "R"}, {"family": "Sansone", "given": "Susanna-Assunta", "initials": "SA"}, {"family": "Schultes", "given": "Erik", "initials": "E"}, {"family": "Sengstag", "given": "Thierry", "initials": "T"}, {"family": "Slater", "given": "Ted", "initials": "T"}, {"family": "Strawn", "given": "George", "initials": "G"}, {"family": "Swertz", "given": "Morris A", "initials": "MA"}, {"family": "Thompson", "given": "Mark", "initials": "M"}, {"family": "van der Lei", "given": "Johan", "initials": "J"}, {"family": "van Mulligen", "given": "Erik", "initials": "E"}, {"family": "Velterop", "given": "Jan", "initials": "J"}, {"family": "Waagmeester", "given": "Andra", "initials": "A"}, {"family": "Wittenburg", "given": "Peter", "initials": "P"}, {"family": "Wolstencroft", "given": "Katherine", "initials": "K"}, {"family": "Zhao", "given": "Jun", "initials": "J"}, {"family": "Mons", "given": "Barend", "initials": "B"}], "type": "journal article", "published": "2016-03-15", "journal": {"volume": "3", "issn": "2052-4463", "issue": null, "pages": "160018", "title": "Sci Data", "issn-l": "2052-4463"}, "abstract": "There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.", "doi": "10.1038/sdata.2016.18", "pmid": "26978244", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "sdata201618"}, {"db": "pmc", "key": "PMC4792175"}], "notes": [], "created": "2017-05-03T13:00:41.473Z", "modified": "2021-07-05T12:34:46.011Z"}], "created": "2017-05-09T09:12:49.641Z", "modified": "2020-11-27T13:14:08.930Z"}