{"entity": "journal", "iuid": "94566c2658084973af0ed69a94fb8095", "timestamp": "2026-09-12T08:19:39.369Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/journal/Sci%20Data.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/journal/Sci%20Data"}}, "title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "publications_count": 14, "publications": [{"entity": "publication", "iuid": "36212ac7310c4b549ce72c41f2cced1f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/36212ac7310c4b549ce72c41f2cced1f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/36212ac7310c4b549ce72c41f2cced1f"}}, "title": "A Multi-Stain Breast Cancer Histological Whole-Slide-Image Data Set from Routine Diagnostics.", "authors": [{"family": "Weitz", "given": "Philippe", "initials": "P", "orcid": "0000-0002-1788-0716", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a70939bc05a04f87b9a61e7d98448e09.json"}}, {"family": "Valkonen", "given": "Masi", "initials": "M", "orcid": "0000-0003-3091-2484", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ae4841e8a4124dc79c921b3af09096fe.json"}}, {"family": "Solorzano", "given": "Leslie", "initials": "L", "orcid": "0000-0001-8658-6417", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f5c33a5b8cef4cad8b9f57b4510fb0c2.json"}}, {"family": "Carr", "given": "Circe", "initials": "C"}, {"family": "Kartasalo", "given": "Kimmo", "initials": "K", "orcid": "0000-0002-9470-4783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c6fc97c06ed456c8bdd1f03db8a9b72.json"}}, {"family": "Boissin", "given": "Constance", "initials": "C"}, {"family": "Koivukoski", "given": "Sonja", "initials": "S", "orcid": "0000-0002-4909-3522", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1889b0f9c9f943609f51e8d8d15041f1.json"}}, {"family": "Kuusela", "given": "Aino", "initials": "A"}, {"family": "Rasic", "given": "Dusan", "initials": "D", "orcid": "0000-0003-4610-5265", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42ddfdb3b820417197cedfd1b96ab172.json"}}, {"family": "Feng", "given": "Yanbo", "initials": "Y"}, {"family": "Sinius Pouplier", "given": "Sandra", "initials": "S", "orcid": "0000-0002-2625-7440", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/190eef15655e4ea6b8eaa15ccddfb7a0.json"}}, {"family": "Sharma", "given": "Abhinav", "initials": "A"}, {"family": "Ledesma Eriksson", "given": "Kajsa", "initials": "K"}, {"family": "Latonen", "given": "Leena", "initials": "L", "orcid": "0000-0003-4502-2193", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f85efd5db6e74874acdb8d14237ae732.json"}}, {"family": "Laenkholm", "given": "Anne-Vibeke", "initials": "A"}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d62d622200d443b7b5be34ff3c0945be.json"}}, {"family": "Ruusuvuori", "given": "Pekka", "initials": "P", "orcid": "0000-0001-9086-9591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb947cd395e84612a53569f4a39abd19.json"}}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}], "type": "dataset", "published": "2023-08-24", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "10", "issue": "1", "pages": "562"}, "abstract": "The analysis of FFPE tissue sections stained with haematoxylin and eosin (H&E) or immunohistochemistry (IHC) is essential for the pathologic assessment of surgically resected breast cancer specimens. IHC staining has been broadly adopted into diagnostic guidelines and routine workflows to assess the status of several established biomarkers, including ER, PGR, HER2 and KI67. Biomarker assessment can also be facilitated by computational pathology image analysis methods, which have made numerous substantial advances recently, often based on publicly available whole slide image (WSI) data sets. However, the field is still considerably limited by the sparsity of public data sets. In particular, there are no large, high quality publicly available data sets with WSIs of matching IHC and H&E-stained tissue sections from the same tumour. Here, we publish the currently largest publicly available data set of WSIs of tissue sections from surgical resection specimens from female primary breast cancer patients with matched WSIs of corresponding H&E and IHC-stained tissue, consisting of 4,212 WSIs from 1,153 patients.", "doi": "10.1038/s41597-023-02422-6", "pmid": "37620357", "labels": {"Kimmo Kartasalo": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10449765"}, {"db": "pii", "key": "10.1038/s41597-023-02422-6"}], "notes": [], "created": "2024-11-05T16:10:24.038Z", "modified": "2024-11-29T09:28:40.734Z"}, {"entity": "publication", "iuid": "bd62e2d1b63f43cea0e1e651ebef6a19", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bd62e2d1b63f43cea0e1e651ebef6a19.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bd62e2d1b63f43cea0e1e651ebef6a19"}}, "title": "From biomedical cloud platforms to microservices: next steps in FAIR data and analysis.", "authors": [{"family": "Sheffield", "given": "Nathan C", "initials": "NC", "orcid": "0000-0001-5643-4068", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/23c4e57ecb2a444bae2f14867eeb0e39.json"}}, {"family": "Bonazzi", "given": "Vivien R", "initials": "VR"}, {"family": "Bourne", "given": "Philip E", "initials": "PE", "orcid": "0000-0002-7618-7292", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/08a8312b165045f890eeaaf913d8c65f.json"}}, {"family": "Burdett", "given": "Tony", "initials": "T"}, {"family": "Clark", "given": "Timothy", "initials": "T", "orcid": "0000-0003-4060-7360", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a68a020958404e1e872b4b00f949a21e.json"}}, {"family": "Grossman", "given": "Robert L", "initials": "RL", "orcid": "0000-0003-3741-5739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c9ff02b6d0f642209745de0466ad6daf.json"}}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c192389f99d4801b91f3350e07dfb9e.json"}}, {"family": "Yates", "given": "Andrew D", "initials": "AD"}], "type": "journal article", "published": "2022-09-08", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "9", "issue": "1", "pages": "553", "issn-l": "2052-4463"}, "abstract": "The biomedical research community is investing heavily in biomedical cloud platforms. Cloud computing holds great promise for addressing challenges with big data and ensuring reproducibility in biology. However, despite their advantages, cloud platforms in and of themselves do not automatically support FAIRness. The global push to develop biomedical cloud platforms has led to new challenges, including platform lock-in, difficulty integrating across platforms, and duplicated effort for both users and developers. Here, we argue that these difficulties are systemic and emerge from incentives that encourage development effort on self-sufficient platforms and data repositories instead of interoperable microservices. We argue that many of these issues would be alleviated by prioritizing microservices and access to modular data in smaller chunks or summarized form. We propose that emphasizing modularity and interoperability would lead to a more powerful Unix-like ecosystem of web services for biomedical analysis and data retrieval. We challenge funders, developers, and researchers to support a vision to improve interoperability through microservices as the next generation of cloud-based bioinformatics.", "doi": "10.1038/s41597-022-01619-5", "pmid": "36075919", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9458632"}, {"db": "pii", "key": "10.1038/s41597-022-01619-5"}], "notes": [], "created": "2026-08-20T09:04:15.513Z", "modified": "2026-08-20T09:04:15.726Z"}, {"entity": "publication", "iuid": "1d068e20fee34aeea758fca1f9bc453d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1d068e20fee34aeea758fca1f9bc453d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1d068e20fee34aeea758fca1f9bc453d"}}, "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-affiliated.scilifelab.se/researcher/7885bdf463cf41538ea08a35898c1cae.json"}}, {"family": "Bouwman", "given": "Britta A M", "initials": "BAM", "orcid": "0000-0002-9827-9497", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/26e2947dca1e4467aef5342387c5ca7d.json"}}, {"family": "Agostini", "given": "Federico", "initials": "F", "orcid": "0000-0002-5453-2737", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc126b42b76c456b828eb2d86c7619e4.json"}}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9967939c5d5494a85fac56173a49821.json"}}, {"family": "Diekmann", "given": "Constantin", "initials": "C", "orcid": "0000-0002-4779-3541", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0eeba08584234e5b8e585d2e85f0c4c5.json"}}, {"family": "Wernersson", "given": "Erik", "initials": "E", "orcid": "0000-0003-4778-1660", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5bac5fd9d38c4fd5bd13dc6c71fe77f1.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M"}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0b1cef698ae749749b4017dbacb9e3db.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": {"Magda Bienko": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9276747"}, {"db": "pii", "key": "10.1038/s41597-022-01508-x"}], "notes": [], "created": "2024-01-16T10:00:54.341Z", "modified": "2024-11-29T12:10:47.561Z"}, {"entity": "publication", "iuid": "232bb5bb7ebb4b7481d92385605210a6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/232bb5bb7ebb4b7481d92385605210a6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/232bb5bb7ebb4b7481d92385605210a6"}}, "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-affiliated.scilifelab.se/researcher/b6e11498cd3f493e8a980925f3dae5ca.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-affiliated.scilifelab.se/researcher/0b1cef698ae749749b4017dbacb9e3db.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M"}], "type": "dataset", "published": "2022-02-10", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "9", "issue": "1", "pages": "47"}, "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": {"Magda Bienko": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8831585"}, {"db": "pii", "key": "10.1038/s41597-022-01139-2"}], "notes": [], "created": "2024-01-16T10:00:31.151Z", "modified": "2024-11-29T12:10:52.879Z"}, {"entity": "publication", "iuid": "7e4434caa19c49c0be320d4f43e61fa3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7e4434caa19c49c0be320d4f43e61fa3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7e4434caa19c49c0be320d4f43e61fa3"}}, "title": "Confocal imaging dataset to assess endothelial cell orientation during extreme glucose conditions.", "authors": [{"family": "Porras Hern\u00e1ndez", "given": "Ana Mar\u00eda", "initials": "AM", "orcid": "0000-0001-5952-2418", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b3c7742b33f8499baad542f0a2738a27.json"}}, {"family": "Barbe", "given": "Laurent", "initials": "L"}, {"family": "Pohlit", "given": "Hannah", "initials": "H", "orcid": "0000-0002-6366-7836", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/51f92fd9b801400d97400b78a937db6c.json"}}, {"family": "Tenje", "given": "Maria", "initials": "M", "orcid": "0000-0002-1264-1337", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bd13273274574923b354ca9c605efc8f.json"}}, {"family": "Antfolk", "given": "Maria", "initials": "M", "orcid": "0000-0003-0129-5640", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6d2f93e8ea8f4960801202f708186f84.json"}}], "type": "dataset", "published": "2022-01-27", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "9", "issue": "1", "pages": "26", "issn-l": "2052-4463"}, "abstract": "Confocal microscopy offers a mean to extract quantitative data on spatially confined subcellular structures. Here, we provide an imaging dataset of confocal z-stacks on endothelial cells spatially confined on lines with different widths, visualizing the nucleus, F-actin, and zonula occludens-1 (ZO-1), as well as the lines. This dataset also includes confocal images of spatially confined endothelial cells challenged with different glucose conditions. We have validated the image quality by established analytical means using the MeasureImageQuality module of the CellProfilerTM software. We envision that this dataset could be used to extract data on both a population and a single cell level, as well as a learning set for the development of new image analysis tools.", "doi": "10.1038/s41597-022-01130-x", "pmid": "35087120", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8795398"}, {"db": "pii", "key": "10.1038/s41597-022-01130-x"}], "notes": [], "created": "2026-08-20T09:04:13.297Z", "modified": "2026-08-20T09:04:13.391Z"}, {"entity": "publication", "iuid": "585a7d0b7c09481995b0c920691d6947", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/585a7d0b7c09481995b0c920691d6947.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/585a7d0b7c09481995b0c920691d6947"}}, "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-affiliated.scilifelab.se/researcher/df5f980a4dfb4b669961af28a1242f12.json"}}, {"family": "Fernandez", "given": "Leyden", "initials": "L"}, {"family": "Martin", "given": "Ga\u00ebtan", "initials": "G", "orcid": "0000-0002-5289-6131", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/12981562d398401388ce55692a75676e.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-affiliated.scilifelab.se/researcher/a28cdc7df4b647c683720acc145641b6.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4fd9423637a54230892379a5b50cf47f.json"}}, {"family": "Peura", "given": "Sari", "initials": "S", "orcid": "0000-0003-3892-8157", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be9a0edb050549978d1f489fb98017b3.json"}}], "type": "dataset", "published": "2021-05-14", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "8", "issue": "1", "pages": "131"}, "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": {"Sarahi Garcia": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41597-021-00910-1"}, {"db": "pmc", "key": "PMC8121793"}], "notes": [], "created": "2021-05-17T13:44:25.688Z", "modified": "2022-11-04T11:32:13.254Z"}, {"entity": "publication", "iuid": "67e8ebfe26e648568cf130f3a82dbd42", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/67e8ebfe26e648568cf130f3a82dbd42.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/67e8ebfe26e648568cf130f3a82dbd42"}}, "title": "The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe.", "authors": [{"family": "Mart\u00ednez-Sancho", "given": "Elisabet", "initials": "E"}, {"family": "Sl\u00e1mov\u00e1", "given": "Lenka", "initials": "L"}, {"family": "Morganti", "given": "Sandro", "initials": "S"}, {"family": "Grefen", "given": "Claudio", "initials": "C"}, {"family": "Carvalho", "given": "Barbara", "initials": "B", "orcid": "0000-0002-4129-2746", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f6a8b99f289a4865b0d5900627dc5011.json"}}, {"family": "Dauphin", "given": "Benjamin", "initials": "B"}, {"family": "Rellstab", "given": "Christian", "initials": "C"}, {"family": "Gugerli", "given": "Felix", "initials": "F", "orcid": "0000-0003-3878-1845", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e601c3d99064e3e9fa70374957a9fea.json"}}, {"family": "Opgenoorth", "given": "Lars", "initials": "L"}, {"family": "Heer", "given": "Katrin", "initials": "K", "orcid": "0000-0002-1036-599X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0c4f4c014a624537b95cc753e793f92a.json"}}, {"family": "Knutzen", "given": "Florian", "initials": "F"}, {"family": "von Arx", "given": "Georg", "initials": "G"}, {"family": "Valladares", "given": "Fernando", "initials": "F"}, {"family": "Cavers", "given": "Stephen", "initials": "S"}, {"family": "Fady", "given": "Bruno", "initials": "B", "orcid": "0000-0003-2379-7617", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246053db155d4170a149ebc4afa9fc11.json"}}, {"family": "Al\u00eda", "given": "Ricardo", "initials": "R"}, {"family": "Aravanopoulos", "given": "Filippos", "initials": "F"}, {"family": "Avanzi", "given": "Camilla", "initials": "C", "orcid": "0000-0003-1632-5304", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/216f8a371a274476a43c44115c51dab6.json"}}, {"family": "Bagnoli", "given": "Francesca", "initials": "F"}, {"family": "Barbas", "given": "Evangelos", "initials": "E"}, {"family": "Bastien", "given": "Catherine", "initials": "C"}, {"family": "Benavides", "given": "Raquel", "initials": "R"}, {"family": "Bernier", "given": "Fr\u00e9d\u00e9ric", "initials": "F"}, {"family": "Bodineau", "given": "Guillaume", "initials": "G"}, {"family": "Bastias", "given": "Cristina C", "initials": "CC"}, {"family": "Charpentier", "given": "Jean-Paul", "initials": "JP"}, {"family": "Climent", "given": "Jos\u00e9 M", "initials": "JM"}, {"family": "Corr\u00e9ard", "given": "Marianne", "initials": "M"}, {"family": "Courdier", "given": "Florence", "initials": "F"}, {"family": "Danusevicius", "given": "Darius", "initials": "D"}, {"family": "Farsakoglou", "given": "Anna-Maria", "initials": "AM", "orcid": "0000-0002-1906-2813", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a2edf3be5614211aaa65dda8e426fa4.json"}}, {"family": "Del Barrio", "given": "Jos\u00e9 M Garc\u00eda", "initials": "JMG"}, {"family": "Gilg", "given": "Olivier", "initials": "O"}, {"family": "Gonz\u00e1lez-Mart\u00ednez", "given": "Santiago C", "initials": "SC"}, {"family": "Gray", "given": "Alan", "initials": "A"}, {"family": "Hartleitner", "given": "Christoph", "initials": "C"}, {"family": "Hurel", "given": "Agathe", "initials": "A"}, {"family": "Jouineau", "given": "Arnaud", "initials": "A"}, {"family": "K\u00e4rkk\u00e4inen", "given": "Katri", "initials": "K"}, {"family": "Kujala", "given": "Sonja T", "initials": "ST"}, {"family": "Labriola", "given": "Mariaceleste", "initials": "M"}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0730d0f9c2524eb19383640612924701.json"}}, {"family": "Lefebvre", "given": "Marl\u00e8ne", "initials": "M"}, {"family": "Lejeune", "given": "Vincent", "initials": "V"}, {"family": "Le-Provost", "given": "Gr\u00e9goire", "initials": "G"}, {"family": "Liesebach", "given": "Mirko", "initials": "M"}, {"family": "Malliarou", "given": "Ermioni", "initials": "E"}, {"family": "Mariotte", "given": "Nicolas", "initials": "N"}, {"family": "Matesanz", "given": "Silvia", "initials": "S"}, {"family": "Michotey", "given": "C\u00e9lia", "initials": "C"}, {"family": "Milesi", "given": "Pascal", "initials": "P"}, {"family": "Myking", "given": "Tor", "initials": "T"}, {"family": "Notivol", "given": "Eduardo", "initials": "E", "orcid": "0000-0003-4272-4536", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a164ab1dee0940c9bb0998cdb891a046.json"}}, {"family": "Pakull", "given": "Birte", "initials": "B"}, {"family": "Piotti", "given": "Andrea", "initials": "A"}, {"family": "Plomion", "given": "Christophe", "initials": "C"}, {"family": "Pringarbe", "given": "Mehdi", "initials": "M"}, {"family": "Pyh\u00e4j\u00e4rvi", "given": "Tanja", "initials": "T"}, {"family": "Raffin", "given": "Annie", "initials": "A"}, {"family": "Ram\u00edrez-Valiente", "given": "Jos\u00e9 A", "initials": "JA"}, {"family": "Ramskogler", "given": "Kurt", "initials": "K"}, {"family": "Robledo-Arnuncio", "given": "Juan J", "initials": "JJ"}, {"family": "Savolainen", "given": "Outi", "initials": "O"}, {"family": "Schueler", "given": "Silvio", "initials": "S"}, {"family": "Semerikov", "given": "Vladimir", "initials": "V"}, {"family": "Spanu", "given": "Ilaria", "initials": "I"}, {"family": "Th\u00e9venet", "given": "Jean", "initials": "J"}, {"family": "Mette Tollefsrud", "given": "Mari", "initials": "M"}, {"family": "Turion", "given": "Norbert", "initials": "N"}, {"family": "Veisse", "given": "Dominique", "initials": "D"}, {"family": "Vendramin", "given": "Giovanni Giuseppe", "initials": "GG"}, {"family": "Villar", "given": "Marc", "initials": "M"}, {"family": "Westin", "given": "Johan", "initials": "J"}, {"family": "Fonti", "given": "Patrick", "initials": "P", "orcid": "0000-0002-7070-3292", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/deed1937dbed41b6a0abfc4e47ced628.json"}}], "type": "dataset", "published": "2020-01-02", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "7", "issue": "1", "pages": "1"}, "abstract": "The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios.", "doi": "10.1038/s41597-019-0340-y", "pmid": "31896794", "labels": {"Pascal Milesi": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41597-019-0340-y"}, {"db": "pmc", "key": "PMC6940356"}], "notes": [], "created": "2020-11-30T09:18:28.360Z", "modified": "2022-11-04T11:32:15.557Z"}, {"entity": "publication", "iuid": "39cc477dba754b6e95adde7a8b8d1f59", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/39cc477dba754b6e95adde7a8b8d1f59.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/39cc477dba754b6e95adde7a8b8d1f59"}}, "title": "STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse.", "authors": [{"family": "Gomez-Cabrero", "given": "David", "initials": "D"}, {"family": "Tarazona", "given": "Sonia", "initials": "S"}, {"family": "Ferreir\u00f3s-Vidal", "given": "Isabel", "initials": "I"}, {"family": "Ramirez", "given": "Ricardo N", "initials": "RN"}, {"family": "Company", "given": "Carlos", "initials": "C"}, {"family": "Schmidt", "given": "Andreas", "initials": "A"}, {"family": "Reijmers", "given": "Theo", "initials": "T"}, {"family": "Paul", "given": "Veronica von Saint", "initials": "VVS"}, {"family": "Marabita", "given": "Francesco", "initials": "F", "orcid": "0000-0001-6180-0106", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1a4d3f450acf42eeadf9eff163be6730.json"}}, {"family": "Rodr\u00edguez-Ubreva", "given": "Javier", "initials": "J"}, {"family": "Garcia-Gomez", "given": "Antonio", "initials": "A"}, {"family": "Carroll", "given": "Thomas", "initials": "T"}, {"family": "Cooper", "given": "Lee", "initials": "L", "orcid": "0000-0002-4425-1843", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eca3a82a14ff49909032a707c66d6bb8.json"}}, {"family": "Liang", "given": "Ziwei", "initials": "Z"}, {"family": "Dharmalingam", "given": "Gopuraja", "initials": "G"}, {"family": "van der Kloet", "given": "Frans", "initials": "F"}, {"family": "Harms", "given": "Amy C", "initials": "AC", "orcid": "0000-0002-2931-4295", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2426aeec0ffc4d9eb934370fd155aa90.json"}}, {"family": "Balzano-Nogueira", "given": "Leandro", "initials": "L"}, {"family": "Lagani", "given": "Vincenzo", "initials": "V"}, {"family": "Tsamardinos", "given": "Ioannis", "initials": "I"}, {"family": "Lappe", "given": "Michael", "initials": "M"}, {"family": "Maier", "given": "Dieter", "initials": "D"}, {"family": "Westerhuis", "given": "Johan A", "initials": "JA", "orcid": "0000-0002-6747-9779", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1415efd18a4483a94285335c62a214b.json"}}, {"family": "Hankemeier", "given": "Thomas", "initials": "T"}, {"family": "Imhof", "given": "Axel", "initials": "A", "orcid": "0000-0003-2993-8249", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b955f71cbbc3409e8d172cbf38b48154.json"}}, {"family": "Ballestar", "given": "Esteban", "initials": "E"}, {"family": "Mortazavi", "given": "Ali", "initials": "A"}, {"family": "Merkenschlager", "given": "Matthias", "initials": "M"}, {"family": "Tegner", "given": "Jesper", "initials": "J", "orcid": "0000-0002-9568-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b115e5faf68a4acbb6f947c711fd37ec.json"}}, {"family": "Conesa", "given": "Ana", "initials": "A"}], "type": "dataset", "published": "2019-10-31", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "6", "issue": "1", "pages": "256", "issn-l": "2052-4463"}, "abstract": "Multi-omics approaches use a diversity of high-throughput technologies to profile the different molecular layers of living cells. Ideally, the integration of this information should result in comprehensive systems models of cellular physiology and regulation. However, most multi-omics projects still include a limited number of molecular assays and there have been very few multi-omic studies that evaluate dynamic processes such as cellular growth, development and adaptation. Hence, we lack formal analysis methods and comprehensive multi-omics datasets that can be leveraged to develop true multi-layered models for dynamic cellular systems. Here we present the STATegra multi-omics dataset that combines measurements from up to 10 different omics technologies applied to the same biological system, namely the well-studied mouse pre-B-cell differentiation. STATegra includes high-throughput measurements of chromatin structure, gene expression, proteomics and metabolomics, and it is complemented with single-cell data. To our knowledge, the STATegra collection is the most diverse multi-omics dataset describing a dynamic biological system.", "doi": "10.1038/s41597-019-0202-7", "pmid": "31672995", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6823427"}, {"db": "pii", "key": "10.1038/s41597-019-0202-7"}], "notes": [], "created": "2026-08-21T11:52:33.321Z", "modified": "2026-08-21T11:52:33.495Z"}, {"entity": "publication", "iuid": "5dd8f5d2161c4ddb977e8f1435199277", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5dd8f5d2161c4ddb977e8f1435199277.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5dd8f5d2161c4ddb977e8f1435199277"}}, "title": "Addendum: 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": "Jan Aalbersberg", "given": "Ijsbrand", "initials": "I"}, {"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": "AJG"}, {"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": "Hoen", "given": "Peter A C 't", "initials": "PAC'"}, {"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"}, {"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": "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": "2019-03-19", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "6", "issue": "1", "pages": "6", "issn-l": "2052-4463"}, "abstract": null, "doi": "10.1038/s41597-019-0009-6", "pmid": "30890711", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6427092"}, {"db": "pii", "key": "10.1038/s41597-019-0009-6"}], "notes": [], "created": "2026-08-20T09:04:11.385Z", "modified": "2026-08-20T09:04:11.425Z"}, {"entity": "publication", "iuid": "d7dfb2dc45294753ace4915621c9d0af", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d7dfb2dc45294753ace4915621c9d0af.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d7dfb2dc45294753ace4915621c9d0af"}}, "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", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28b77762086343048e74046a6486caff.json"}}, {"family": "Kisand", "given": "Veljo", "initials": "V"}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a666f6ec1a584756ab4c725b7ace3d3a.json"}}, {"family": "J\u00fcrgens", "given": "Klaus", "initials": "K"}, {"family": "Labrenz", "given": "Matthias", "initials": "M"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc9be99ec6ca47ed8a805ebb4db7c168.json"}}], "type": "dataset", "published": "2018-07-31", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "5", "pages": "180146", "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": {"Luisa Hugerth": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6067050"}, {"db": "pii", "key": "sdata2018146"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.3831631"}], "notes": [], "created": "2022-11-08T07:01:14.252Z", "modified": "2023-10-27T09:33:57.663Z"}, {"entity": "publication", "iuid": "016ebb3d28ab472dbf8d949ad3391346", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/016ebb3d28ab472dbf8d949ad3391346.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/016ebb3d28ab472dbf8d949ad3391346"}}, "title": "The Alexandria library, a quantum-chemical database of molecular properties for force field development.", "authors": [{"family": "Ghahremanpour", "given": "Mohammad M", "initials": "MM"}, {"family": "van Maaren", "given": "Paul J", "initials": "PJ"}, {"family": "van der Spoel", "given": "David", "initials": "D", "orcid": "0000-0002-7659-8526", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5e69bc348284be9936c3f4ac9c6cb35.json"}}], "type": "dataset", "published": "2018-04-10", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "5", "pages": "180062", "issn-l": "2052-4463"}, "abstract": "Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.", "doi": "10.1038/sdata.2018.62", "pmid": "29633987", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC5892371"}, {"db": "pii", "key": "sdata201862"}], "notes": [], "created": "2026-08-21T11:55:08.582Z", "modified": "2026-08-21T11:55:08.616Z"}, {"entity": "publication", "iuid": "8fd0370dd27241dfaeb90c51aa701cec", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8fd0370dd27241dfaeb90c51aa701cec.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8fd0370dd27241dfaeb90c51aa701cec"}}, "title": "Sequence data and association statistics from 12,940 type 2 diabetes cases and controls.", "authors": [{"family": "Flannick", "given": "Jason", "initials": "J"}, {"family": "Fuchsberger", "given": "Christian", "initials": "C"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Teslovich", 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"journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "4", "issue": null, "pages": "170179", "issn-l": "2052-4463"}, "abstract": "To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (>80% of low-frequency coding variants in ~82\u2009K Europeans via the exome chip, and ~90% of low-frequency non-coding variants in ~44\u2009K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.", "doi": "10.1038/sdata.2017.179", "pmid": "29257133", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "sdata2017179"}, {"db": "pmc", "key": "PMC5735917"}], "notes": [], "created": "2018-12-05T12:07:44.419Z", "modified": "2018-12-05T12:07:44.438Z"}, {"entity": "publication", "iuid": "661b65b435de4b19b76bb481d62361bb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/661b65b435de4b19b76bb481d62361bb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/661b65b435de4b19b76bb481d62361bb"}}, "title": "Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source.", "authors": [{"family": "Reddy", "given": "Hemanth K N", "initials": "HKN"}, {"family": "Yoon", "given": "Chun Hong", "initials": "CH"}, {"family": "Aquila", "given": "Andrew", "initials": "A"}, {"family": "Awel", "given": "Salah", "initials": "S"}, {"family": "Ayyer", "given": "Kartik", "initials": "K"}, {"family": "Barty", "given": "Anton", "initials": "A"}, {"family": "Berntsen", "given": "Peter", "initials": "P"}, {"family": "Bielecki", "given": "Johan", "initials": "J"}, {"family": "Bobkov", "given": "Sergey", "initials": "S"}, {"family": "Bucher", "given": "Maximilian", "initials": "M"}, {"family": "Carini", "given": "Gabriella A", "initials": "GA"}, {"family": "Carron", "given": "Sebastian", "initials": "S"}, {"family": "Chapman", "given": "Henry", "initials": "H"}, {"family": "Daurer", "given": "Benedikt", "initials": "B"}, {"family": "DeMirci", "given": "Hasan", "initials": "H"}, {"family": "Ekeberg", "given": "Tomas", "initials": "T"}, {"family": "Fromme", "given": "Petra", "initials": "P"}, {"family": "Hajdu", "given": "Janos", "initials": "J"}, {"family": "Hanke", "given": "Max Felix", "initials": "MF"}, {"family": "Hart", "given": "Philip", "initials": "P"}, {"family": "Hogue", "given": "Brenda G", "initials": "BG"}, {"family": "Hosseinizadeh", "given": "Ahmad", "initials": "A"}, {"family": "Kim", "given": "Yoonhee", "initials": "Y"}, {"family": "Kirian", "given": "Richard A", "initials": "RA"}, {"family": "Kurta", "given": "Ruslan P", "initials": "RP"}, {"family": "Larsson", "given": "Daniel S D", "initials": "DSD"}, {"family": "Duane Loh", "given": "N", "initials": "N"}, {"family": "Maia", "given": "Filipe R N C", "initials": "FRNC"}, {"family": "Mancuso", "given": "Adrian P", "initials": "AP"}, {"family": "M\u00fchlig", "given": "Kerstin", "initials": "K"}, {"family": "Munke", "given": "Anna", "initials": "A"}, {"family": "Nam", "given": "Daewoong", "initials": "D"}, {"family": "Nettelblad", "given": "Carl", "initials": "C"}, {"family": "Ourmazd", "given": "Abbas", "initials": "A"}, {"family": "Rose", "given": "Max", "initials": "M"}, {"family": "Schwander", "given": "Peter", "initials": "P"}, {"family": "Seibert", "given": "Marvin", "initials": "M"}, {"family": "Sellberg", "given": "Jonas A", "initials": "JA"}, {"family": "Song", "given": "Changyong", "initials": "C"}, {"family": "Spence", "given": "John C H", "initials": "JCH"}, {"family": "Svenda", "given": "Martin", "initials": "M"}, {"family": "Van der Schot", "given": "Gijs", "initials": "G"}, {"family": "Vartanyants", "given": "Ivan A", "initials": "IA"}, {"family": "Williams", "given": "Garth J", "initials": "GJ"}, {"family": "Xavier", "given": "P Lourdu", "initials": "PL"}], "type": "dataset", "published": "2017-06-27", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "4", "issue": null, "pages": "170079", "issn-l": "2052-4463"}, "abstract": "Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65-70\u2009nm, which is considerably smaller than the previously reported ~600\u2009nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.", "doi": "10.1038/sdata.2017.79", "pmid": "28654088", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "sdata201779"}, {"db": "pmc", "key": "PMC5501160"}], "notes": [], "created": "2018-12-05T11:57:31.083Z", "modified": "2018-12-05T11:57:31.111Z"}, {"entity": "publication", "iuid": "e6c0d332d61f4640843ff4931598477e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e6c0d332d61f4640843ff4931598477e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e6c0d332d61f4640843ff4931598477e"}}, "title": "Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source.", "authors": [{"family": "Munke", "given": "Anna", "initials": "A", "orcid": "0000-0002-5510-2245", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e3b83fcda1004315a30e61c7c2c678f7.json"}}, {"family": "Andreasson", "given": "Jakob", "initials": "J"}, {"family": "Aquila", "given": "Andrew", "initials": "A"}, {"family": "Awel", "given": "Salah", "initials": "S"}, {"family": "Ayyer", "given": "Kartik", "initials": "K"}, {"family": "Barty", "given": "Anton", "initials": "A"}, {"family": "Bean", "given": "Richard J", "initials": "RJ"}, {"family": "Berntsen", "given": "Peter", "initials": "P"}, {"family": "Bielecki", "given": "Johan", "initials": "J"}, {"family": "Boutet", "given": "S\u00e9bastien", "initials": "S"}, {"family": "Bucher", "given": "Maximilian", "initials": "M", "orcid": "0000-0001-7896-473X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bff3b3f3e7504b5fba4e5ead46fc22be.json"}}, {"family": "Chapman", "given": "Henry N", "initials": "HN"}, {"family": "Daurer", "given": "Benedikt J", "initials": "BJ", "orcid": "0000-0002-1887-7551", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22e1c4b4b7fc427f9069efa4b1486d47.json"}}, {"family": "DeMirci", "given": "Hasan", "initials": "H", "orcid": "0000-0002-9135-5397", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e0493a130604cea86ba6e3bc188df8c.json"}}, {"family": "Elser", "given": "Veit", "initials": "V"}, {"family": "Fromme", "given": "Petra", "initials": "P"}, {"family": "Hajdu", "given": "Janos", "initials": "J"}, {"family": "Hantke", "given": "Max F", "initials": "MF"}, {"family": "Higashiura", "given": "Akifumi", "initials": "A"}, {"family": "Hogue", "given": "Brenda G", "initials": "BG"}, {"family": "Hosseinizadeh", "given": "Ahmad", "initials": "A"}, {"family": "Kim", "given": "Yoonhee", "initials": "Y"}, {"family": "Kirian", "given": "Richard A", "initials": "RA"}, {"family": "Reddy", "given": "Hemanth K N", "initials": "HK"}, {"family": "Lan", "given": "Ti-Yen", "initials": "TY"}, {"family": "Larsson", "given": "Daniel S D", "initials": "DS"}, {"family": "Liu", "given": "Haiguang", "initials": "H", "orcid": "0000-0001-7324-6632", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6fcf493cacb4132b34d2400965a34b4.json"}}, {"family": "Loh", "given": "N Duane", "initials": "ND"}, {"family": "Maia", "given": "Filipe R N C", "initials": "FR", "orcid": "0000-0002-2141-438X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a305c750241840a19612dc53e34beacc.json"}}, {"family": "Mancuso", "given": "Adrian P", "initials": "AP"}, {"family": "M\u00fchlig", "given": "Kerstin", "initials": "K"}, {"family": "Nakagawa", "given": "Atsushi", "initials": "A", "orcid": "0000-0002-1700-7861", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d332e49a07cc479abdde79e160b888f9.json"}}, {"family": "Nam", "given": "Daewoong", "initials": "D"}, {"family": "Nelson", "given": "Garrett", "initials": "G"}, {"family": "Nettelblad", "given": "Carl", "initials": "C"}, {"family": "Okamoto", "given": "Kenta", "initials": "K"}, {"family": "Ourmazd", "given": "Abbas", "initials": "A", "orcid": "0000-0001-9946-3889", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/75dd2011254b4b908c484f74284c3388.json"}}, {"family": "Rose", "given": "Max", "initials": "M"}, {"family": "van der Schot", "given": "Gijs", "initials": "G"}, {"family": "Schwander", "given": "Peter", "initials": "P"}, {"family": "Seibert", "given": "M Marvin", "initials": "MM"}, {"family": "Sellberg", "given": "Jonas A", "initials": "JA", "orcid": "0000-0003-2793-5052", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/86c7efd806b5436296298d6243778574.json"}}, {"family": "Sierra", "given": "Raymond G", "initials": "RG"}, {"family": "Song", "given": "Changyong", "initials": "C"}, {"family": "Svenda", "given": "Martin", "initials": "M"}, {"family": "Timneanu", "given": "Nicusor", "initials": "N", "orcid": "0000-0001-7328-0400", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c2a9165954da4b14b334d1d7151efb9e.json"}}, {"family": "Vartanyants", "given": "Ivan A", "initials": "IA"}, {"family": "Westphal", "given": "Daniel", "initials": "D"}, {"family": "Wiedorn", "given": "Max O", "initials": "MO"}, {"family": "Williams", "given": "Garth J", "initials": "GJ"}, {"family": "Xavier", "given": "Paulraj Lourdu", "initials": "PL"}, {"family": "Yoon", "given": "Chun Hong", "initials": "CH"}, {"family": "Zook", "given": "James", "initials": "J"}], "type": "dataset", "published": "2016-08-01", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "3", "pages": "160064", "issn-l": "2052-4463"}, "abstract": "Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 \u03bcm diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 \u00c5ngstr\u00f6m were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.", "doi": "10.1038/sdata.2016.64", "pmid": "27478984", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC4968191"}, {"db": "pii", "key": "sdata201664"}, {"db": "figshare", "key": "10.6084/M9.FIGSHARE.C.2342581"}], "notes": [], "created": "2026-08-20T09:27:01.495Z", "modified": "2026-08-20T09:27:01.848Z"}], "created": "2018-12-05T11:57:31.095Z", "modified": "2020-11-27T13:12:58.912Z"}