{"entity": "researcher", "timestamp": "2026-07-19T06:44:17.493Z", "family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "affiliations": ["Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d"}}, "publications": [{"entity": "publication", "iuid": "8878962be50c44d791a0589626c424a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8878962be50c44d791a0589626c424a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8878962be50c44d791a0589626c424a7"}}, "title": "Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images.", "authors": [{"family": "Wernersson", "given": "Erik", "initials": "E"}, {"family": "Gelali", "given": "Eleni", "initials": "E"}, {"family": "Girelli", "given": "Gabriele", "initials": "G", "orcid": "0000-0003-4264-6494", "researcher": {"href": "https://publications.scilifelab.se/researcher/a607510e88954d0980e1d4505ab27ee7.json"}}, {"family": "Wang", "given": "Su", "initials": "S"}, {"family": "Castillo", "given": "David", "initials": "D", "orcid": "0000-0003-0478-0828", "researcher": {"href": "https://publications.scilifelab.se/researcher/2430e6a8b8b341f18566cca62c27cc6d.json"}}, {"family": "Mattsson Langseth", "given": "Christoffer", "initials": "C"}, {"family": "Verron", "given": "Quentin", "initials": "Q"}, {"family": "Nguyen", "given": "Huy Q", "initials": "HQ"}, {"family": "Chattoraj", "given": "Shyamtanu", "initials": "S"}, {"family": "Martinez Casals", "given": "Anna", "initials": "A"}, {"family": "Blom", "given": "Hans", "initials": "H"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Marti-Renom", "given": "Marc A", "initials": "MA"}, {"family": "Wu", "given": "Chao-Ting", "initials": "C"}, {"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", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}], "type": "journal article", "published": "2024-06-06", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "issn-l": "1548-7091", "volume": null, "issue": null, "pages": null}, "abstract": "Microscopy-based spatially resolved omic methods are transforming the life sciences. However, these methods rely on high numerical aperture objectives and cannot resolve crowded molecular targets, limiting the amount of extractable biological information. To overcome these limitations, here we develop Deconwolf, an open-source, user-friendly software for high-performance deconvolution of widefield fluorescence microscopy images, which efficiently runs on laptop computers. Deconwolf enables accurate quantification of crowded diffraction limited fluorescence dots in DNA and RNA fluorescence in situ hybridization images and allows robust detection of individual transcripts in tissue sections imaged with \u00d720 air objectives. Deconvolution of in situ spatial transcriptomics images with Deconwolf increased the number of transcripts identified more than threefold, while the application of Deconwolf to images obtained by fluorescence in situ sequencing of barcoded Oligopaint probes drastically improved chromosome tracing. Deconwolf greatly facilitates the use of deconvolution in many bioimaging applications.", "doi": "10.1038/s41592-024-02294-7", "pmid": "38844629", "labels": {"Integrated Microscopy Technologies Stockholm": "Technology development", "Spatial Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41592-024-02294-7"}], "notes": [], "created": "2024-06-10T07:36:02.247Z", "modified": "2024-11-25T17:49:12.405Z"}, {"entity": "publication", "iuid": "8acfeb033c3c459a9cff10bf8bb576c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8acfeb033c3c459a9cff10bf8bb576c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8acfeb033c3c459a9cff10bf8bb576c9"}}, "title": "High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue.", "authors": [{"family": "Zhang", "given": "Ning", "initials": "N"}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Simonetti", "given": "Michele", "initials": "M", "orcid": "0000-0003-3322-1697", "researcher": {"href": "https://publications.scilifelab.se/researcher/839bf10741044782aecdc77b3f06fc88.json"}}, {"family": "Diekmann", "given": "Constantin", "initials": "C", "orcid": "0000-0002-4779-3541", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bc495c18087429f81dd51007ffe1582.json"}}, {"family": "Verron", "given": "Quentin", "initials": "Q"}, {"family": "Berrino", "given": "Enrico", "initials": "E", "orcid": "0000-0001-6728-5619", "researcher": {"href": "https://publications.scilifelab.se/researcher/d254d4e308064696b50b17806dec1a60.json"}}, {"family": "Bellomo", "given": "Sara E", "initials": "SE"}, {"family": "Longo", "given": "Gabriel M C", "initials": "GMC", "orcid": "0000-0003-2028-1068", "researcher": {"href": "https://publications.scilifelab.se/researcher/2afe47a108d0451ebaf8269a0f18eb84.json"}}, {"family": "Ratz", "given": "Michael", "initials": "M", "orcid": "0000-0002-9795-8033", "researcher": {"href": "https://publications.scilifelab.se/researcher/a481899ca58a467499f56af4feb5457c.json"}}, {"family": "Schultz", "given": "Niklas", "initials": "N"}, {"family": "Tarish", "given": "Firas", "initials": "F"}, {"family": "Su", "given": "Peng", "initials": "P"}, {"family": "Han", "given": "Bo", "initials": "B"}, {"family": "Wang", "given": "Wanzhong", "initials": "W"}, {"family": "Onorato", "given": "Sofia", "initials": "S"}, {"family": "Grassini", "given": "Dora", "initials": "D"}, {"family": "Ballarino", "given": "Roberto", "initials": "R", "orcid": "0000-0001-7812-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb720f25876d45c39b9dad1b4b48a6fa.json"}}, {"family": "Giordano", "given": "Silvia", "initials": "S", "orcid": "0000-0003-1854-1086", "researcher": {"href": "https://publications.scilifelab.se/researcher/7072fc7ce1d44d0392b4ba3da82a16fb.json"}}, {"family": "Yang", "given": "Qifeng", "initials": "Q"}, {"family": "Sapino", "given": "Anna", "initials": "A", "orcid": "0000-0003-3542-9571", "researcher": {"href": "https://publications.scilifelab.se/researcher/b77045e1832b4267b330df154cbe80db.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23064ee2ac9b4c2fb1eb94e61f92148e.json"}}, {"family": "Alkass", "given": "Kanar", "initials": "K"}, {"family": "Druid", "given": "Henrik", "initials": "H", "orcid": "0000-0002-9198-023X", "researcher": {"href": "https://publications.scilifelab.se/researcher/14bb7f9c706b451f9813bae017e0fad7.json"}}, {"family": "Roukos", "given": "Vassilis", "initials": "V", "orcid": "0000-0002-5065-3937", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5da3165b15741ff967e77618bd96cc1.json"}}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Marchi\u00f2", "given": "Caterina", "initials": "C"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}], "type": "journal article", "published": "2024-04-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "3475", "issn-l": "2041-1723"}, "abstract": "Somatic copy number alterations (SCNAs) are pervasive in advanced human cancers, but their prevalence and spatial distribution in early-stage, localized tumors and their surrounding normal tissues are poorly characterized. Here, we perform multi-region, single-cell DNA sequencing to characterize the SCNA landscape across tumor-rich and normal tissue in two male patients with localized prostate cancer. We identify two distinct karyotypes: 'pseudo-diploid' cells harboring few SCNAs and highly aneuploid cells. Pseudo-diploid cells form numerous small-sized subclones ranging from highly spatially localized to broadly spread subclones. In contrast, aneuploid cells do not form subclones and are detected throughout the prostate, including normal tissue regions. Highly localized pseudo-diploid subclones are confined within tumor-rich regions and carry deletions in multiple tumor-suppressor genes. Our study reveals that SCNAs are widespread in normal and tumor regions across the prostate in localized prostate cancer patients and suggests that a subset of pseudo-diploid cells drive tumorigenesis in the aging prostate.", "doi": "10.1038/s41467-024-47664-z", "pmid": "38658552", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11043350"}, {"db": "pii", "key": "10.1038/s41467-024-47664-z"}], "notes": [], "created": "2024-05-17T09:16:39.558Z", "modified": "2024-11-25T10:16:43.449Z"}, {"entity": "publication", "iuid": "80c75635458e45f883e80acd6b1c4fc1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/80c75635458e45f883e80acd6b1c4fc1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/80c75635458e45f883e80acd6b1c4fc1"}}, "title": "scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells.", "authors": [{"family": "Chen", "given": "Jinxin Phaedo", "initials": "JP", "orcid": "0000-0002-0729-5214", "researcher": {"href": "https://publications.scilifelab.se/researcher/25fca568763f4476b53bdf7297689a2e.json"}}, {"family": "Diekmann", "given": "Constantin", "initials": "C", "orcid": "0000-0002-4779-3541", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bc495c18087429f81dd51007ffe1582.json"}}, {"family": "Wu", "given": "Honggui", "initials": "H", "orcid": "0000-0001-7880-0591", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd9697e391fe493ab4b26d2c40e7565f.json"}}, {"family": "Chen", "given": "Chong", "initials": "C", "orcid": "0000-0002-6787-0495", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8a6778068124d7cb3dd1aca6e7cc0ec.json"}}, {"family": "Della Chiara", "given": "Giulia", "initials": "G", "orcid": "0000-0001-5211-3814", "researcher": {"href": "https://publications.scilifelab.se/researcher/3410a95b5b674fa69d2c83b479d345a8.json"}}, {"family": "Berrino", "given": "Enrico", "initials": "E", "orcid": "0000-0001-6728-5619", "researcher": {"href": "https://publications.scilifelab.se/researcher/d254d4e308064696b50b17806dec1a60.json"}}, {"family": "Georgiadis", "given": "Konstantinos L", "initials": "KL"}, {"family": "Bouwman", "given": "Britta A M", "initials": "BAM"}, {"family": "Virdi", "given": "Mohit", "initials": "M"}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Bellomo", "given": "Sara Erika", "initials": "SE"}, {"family": "Marchi\u00f2", "given": "Caterina", "initials": "C"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}], "type": "journal article", "published": "2024-02-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "1768", "issn-l": "2041-1723"}, "abstract": "Extrachromosomal circular DNAs (eccDNAs) have emerged as important intra-cellular mobile genetic elements that affect gene copy number and exert in trans regulatory roles within the cell nucleus. Here, we describe scCircle-seq, a method for profiling eccDNAs and unraveling their diversity and complexity in single cells. We implement and validate scCircle-seq in normal and cancer cell lines, demonstrating that most eccDNAs vary largely between cells and are stochastically inherited during cell division, although their genomic landscape is cell type-specific and can be used to accurately cluster cells of the same origin. eccDNAs are preferentially produced from chromatin regions enriched in H3K9me3 and H3K27me3 histone marks and are induced during replication stress conditions. Concomitant sequencing of eccDNAs and RNA from the same cell uncovers the absence of correlation between eccDNA copy number and gene expression levels, except for a few oncogenes, including MYC, contained within a large eccDNA in colorectal cancer cells. Lastly, we apply scCircle-seq to one prostate cancer and two breast cancer specimens, revealing cancer-specific eccDNA landscapes and a higher propensity of eccDNAs to form in amplified genomic regions. scCircle-seq is a scalable tool that can be used to dissect the complexity of eccDNAs across different cell and tissue types, and further expands the potential of eccDNAs for cancer diagnostics.", "doi": "10.1038/s41467-024-45972-y", "pmid": "38409079", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10897160"}, {"db": "pii", "key": "10.1038/s41467-024-45972-y"}], "notes": [], "created": "2024-03-14T11:05:03.191Z", "modified": "2024-04-26T09:08:57.780Z"}, {"entity": "publication", "iuid": "34c38b3d3f564542956074b47323ddb5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34c38b3d3f564542956074b47323ddb5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34c38b3d3f564542956074b47323ddb5"}}, "title": "Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis.", "authors": [{"family": "Mastropasqua", "given": "Francesca", "initials": "F", "orcid": "0000-0003-4237-2446", "researcher": {"href": "https://publications.scilifelab.se/researcher/30aece0009c94ace82728640c71682f7.json"}}, {"family": "Oksanen", "given": "Marika", "initials": "M", "orcid": "0000-0003-4140-4282", "researcher": {"href": "https://publications.scilifelab.se/researcher/76a8727638dc49fe88b15052d5741fd5.json"}}, {"family": "Soldini", "given": "Cristina", "initials": "C"}, {"family": "Alatar", "given": "Shemim", "initials": "S", "orcid": "0009-0009-0738-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/0500cee4755b46479d0818314e5c05a7.json"}}, {"family": "Arora", "given": "Abishek", "initials": "A", "orcid": "0000-0002-6149-4417", "researcher": {"href": "https://publications.scilifelab.se/researcher/384ef4f8d6eb49d6873c87556843a7a2.json"}}, {"family": "Ballarino", "given": "Roberto", "initials": "R", "orcid": "0000-0001-7812-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb720f25876d45c39b9dad1b4b48a6fa.json"}}, {"family": "Molinari", "given": "Maya", "initials": "M"}, {"family": "Agostini", "given": "Federico", "initials": "F", "orcid": "0000-0002-5453-2737", "researcher": {"href": "https://publications.scilifelab.se/researcher/a21ea8b7e9a5427eb0e48a822c840b8b.json"}}, {"family": "Poulet", "given": "Axel", "initials": "A", "orcid": "0000-0002-3415-8960", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4dfc191bbfd4ed6922008f10531835c.json"}}, {"family": "Watts", "given": "Michelle", "initials": "M", "orcid": "0000-0002-3178-3429", "researcher": {"href": "https://publications.scilifelab.se/researcher/28a00d3b8c3e40e1b68fc333a7aa4fb7.json"}}, {"family": "Rabkina", "given": "Ielyzaveta", "initials": "I", "orcid": "0000-0001-5890-4115", "researcher": {"href": "https://publications.scilifelab.se/researcher/509d3fdbf53b45acbae3ddea4903a0ba.json"}}, {"family": "Becker", "given": "Martin", "initials": "M", "orcid": "0000-0001-8442-4246", "researcher": {"href": "https://publications.scilifelab.se/researcher/85eaa4173364473d83506125206a7193.json"}}, {"family": "Li", "given": "Danyang", "initials": "D", "orcid": "0000-0001-7470-6645", "researcher": {"href": "https://publications.scilifelab.se/researcher/01900295a1904ac886960b3eea5915f0.json"}}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "BM", "orcid": "0000-0002-2488-6024", "researcher": {"href": "https://publications.scilifelab.se/researcher/73c8590243874a0a9f18b9e7138ce9a9.json"}}, {"family": "Isaksson", "given": "Johan", "initials": "J", "orcid": "0000-0003-1033-2618", "researcher": {"href": "https://publications.scilifelab.se/researcher/af22620f762a4a5e80dca3f546223caa.json"}}, {"family": "Lundin Remnelius", "given": "Karl", "initials": "K"}, {"family": "Moslem", "given": "Mohsen", "initials": "M"}, {"family": "Jacob", "given": "Yannick", "initials": "Y", "orcid": "0000-0003-4741-0755", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f553bc5034e4768bad65bf8b1236e6a.json"}}, {"family": "Falk", "given": "Anna", "initials": "A", "orcid": "0000-0003-1634-8610", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b708dfb7f0548589bdee53d6e6b536e.json"}}, {"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", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Santini", "given": "Emanuela", "initials": "E", "orcid": "0000-0002-8948-9652", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d176892d0f14922bab782fe4cd69e90.json"}}, {"family": "Borgkvist", "given": "Anders", "initials": "A", "orcid": "0000-0003-1698-0288", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c0f5180d7a74249bcfeb59386a7c65d.json"}}, {"family": "B\u00f6lte", "given": "Sven", "initials": "S", "orcid": "0000-0002-4579-4970", "researcher": {"href": "https://publications.scilifelab.se/researcher/bead50319cae447f90bcf7658d9edf56.json"}}, {"family": "Tammimies", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-8324-4697", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba19ec07147743c6942ea10c9a92482a.json"}}], "type": "journal article", "published": "2023-10-15", "journal": {"title": "Biol Open", "issn": "2046-6390", "volume": "12", "issue": "10", "issn-l": "2046-6390"}, "abstract": "Genetic variants affecting Heterogeneous Nuclear Ribonucleoprotein U (HNRNPU) have been identified in several neurodevelopmental disorders (NDDs). HNRNPU is widely expressed in the human brain and shows the highest postnatal expression in the cerebellum. Recent studies have investigated the role of HNRNPU in cerebral cortical development, but the effects of HNRNPU deficiency on cerebellar development remain unknown. Here, we describe the molecular and cellular outcomes of HNRNPU locus deficiency during in vitro neural differentiation of patient-derived and isogenic neuroepithelial stem cells with a hindbrain profile. We demonstrate that HNRNPU deficiency leads to chromatin remodeling of A/B compartments, and transcriptional rewiring, partly by impacting exon inclusion during mRNA processing. Genomic regions affected by the chromatin restructuring and host genes of exon usage differences show a strong enrichment for genes implicated in epilepsies, intellectual disability, and autism. Lastly, we show that at the cellular level HNRNPU downregulation leads to an increased fraction of neural progenitors in the maturing neuronal population. We conclude that the HNRNPU locus is involved in delayed commitment of neural progenitors to differentiate in cell types with hindbrain profile.", "doi": "10.1242/bio.060113", "pmid": "37815090", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10581386"}, {"db": "pii", "key": "330791"}], "notes": [], "created": "2023-11-16T12:03:03.393Z", "modified": "2024-01-16T13:48:31.943Z"}, {"entity": "publication", "iuid": "6448eef2b2ba45f08ede2ebd059ea9d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6448eef2b2ba45f08ede2ebd059ea9d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6448eef2b2ba45f08ede2ebd059ea9d8"}}, "title": "FRET-FISH probes chromatin compaction at individual genomic loci in single cells.", "authors": [{"family": "Mota", "given": "Ana", "initials": "A", "orcid": "0000-0001-8592-9764", "researcher": {"href": "https://publications.scilifelab.se/researcher/508960cbe03d4490a6e4594fc76e3510.json"}}, {"family": "Berezicki", "given": "Szymon", "initials": "S", "orcid": "0000-0003-3980-6290", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8794ceeb3bf405a8125545b49f7ebc7.json"}}, {"family": "Wernersson", "given": "Erik", "initials": "E", "orcid": "0000-0003-4778-1660", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae0de6d4af244cec84bbe8c1240d89ae.json"}}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Li-Wang", "given": "Xiaoze", "initials": "X"}, {"family": "Gradin", "given": "Katarina", "initials": "K"}, {"family": "Peuckert", "given": "Christiane", "initials": "C"}, {"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", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}], "type": "journal article", "published": "2022-11-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "6680"}, "abstract": "Chromatin compaction is a key biophysical property that influences multiple DNA transactions. Lack of chromatin accessibility is frequently used as proxy for chromatin compaction. However, we currently lack tools for directly probing chromatin compaction at individual genomic loci. To fill this gap, here we present FRET-FISH, a method combining fluorescence resonance energy transfer (FRET) with DNA fluorescence in situ hybridization (FISH) to probe chromatin compaction at select loci in single cells. We first validate FRET-FISH by comparing it with ATAC-seq, demonstrating that local compaction and accessibility are strongly correlated. FRET-FISH also detects expected differences in compaction upon treatment with drugs perturbing global chromatin condensation. We then leverage FRET-FISH to study local chromatin compaction on the active and inactive X chromosome, along the nuclear radius, in different cell cycle phases, and during increasing passage number. FRET-FISH is a robust tool for probing local chromatin compaction in single cells.", "doi": "10.1038/s41467-022-34183-y", "pmid": "36335096", "labels": {"Spatial Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9637210"}, {"db": "pii", "key": "10.1038/s41467-022-34183-y"}], "notes": [], "created": "2023-06-26T12:49:38.233Z", "modified": "2023-11-29T16:29:33.698Z"}, {"entity": "publication", "iuid": "e18b31942e41465999c590cac3365408", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e18b31942e41465999c590cac3365408.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e18b31942e41465999c590cac3365408"}}, "title": "COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance.", "authors": [{"family": "Simonetti", "given": "Michele", "initials": "M", "orcid": "0000-0003-3322-1697", "researcher": {"href": "https://publications.scilifelab.se/researcher/839bf10741044782aecdc77b3f06fc88.json"}}, {"family": "Zhang", "given": "Ning", "initials": "N", "orcid": "0000-0002-6430-4236", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3fdde99294d422694c7a8a00c9811ed.json"}}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Milia", "given": "Maria Grazia", "initials": "MG"}, {"family": "Brossa", "given": "Silvia", "initials": "S"}, {"family": "Huong Nguyen", "given": "Thi Thu", "initials": "TT", "orcid": "0000-0002-9089-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/57451410c8ac4547a4b09111a020e396.json"}}, {"family": "Cerutti", "given": "Francesco", "initials": "F", "orcid": "0000-0003-0480-8296", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a243dc846624a8a8292dde5416fa402.json"}}, {"family": "Berrino", "given": "Enrico", "initials": "E"}, {"family": "Sapino", "given": "Anna", "initials": "A"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Sottile", "given": "Antonino", "initials": "A"}, {"family": "Ghisetti", "given": "Valeria", "initials": "V", "orcid": "0000-0002-4698-598X", "researcher": {"href": "https://publications.scilifelab.se/researcher/75237266d0b1496f909cb0c53ff87920.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}], "type": "journal article", "published": "2021-06-23", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "3903", "issn-l": "2041-1723"}, "abstract": "While mass-scale vaccination campaigns are ongoing worldwide, genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to monitor the emergence and global spread of viral variants of concern (VOC). Here, we present a streamlined workflow-COVseq-which can be used to generate highly multiplexed sequencing libraries compatible with Illumina platforms from hundreds of SARS-CoV-2 samples in parallel, in a rapid and cost-effective manner. We benchmark COVseq against a standard library preparation method (NEBNext) on 29 SARS-CoV-2 positive samples, reaching 95.4% of concordance between single-nucleotide variants detected by both methods. Application of COVseq to 245 additional SARS-CoV-2 positive samples demonstrates the ability of the method to reliably detect emergent VOC as well as its compatibility with downstream phylogenetic analyses. A cost analysis shows that COVseq could be used to sequence thousands of samples at less than 15 USD per sample, including library preparation and sequencing costs. We conclude that COVseq is a versatile and scalable method that is immediately applicable for SARS-CoV-2 genomic surveillance and easily adaptable to other pathogens such as influenza viruses.", "doi": "10.1038/s41467-021-24078-9", "pmid": "34162869", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-24078-9"}, {"db": "pmc", "key": "PMC8222401"}], "notes": [], "created": "2021-10-01T09:02:30.491Z", "modified": "2024-01-16T13:48:39.472Z"}, {"entity": "publication", "iuid": "7799f6442abe4a21905074224e018909", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7799f6442abe4a21905074224e018909.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7799f6442abe4a21905074224e018909"}}, "title": "Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells.", "authors": [{"family": "Tarbier", "given": "Marcel", "initials": "M", "orcid": "0000-0003-0556-2531", "researcher": {"href": "https://publications.scilifelab.se/researcher/662e96c24ee6442898ec2caab1eec25d.json"}}, {"family": "Mackowiak", "given": "Sebastian D", "initials": "SD"}, {"family": "Frade", "given": "Jo\u00e3o", "initials": "J", "orcid": "0000-0003-3961-7641", "researcher": {"href": "https://publications.scilifelab.se/researcher/92f0e07be91a4e858100b84a287e133a.json"}}, {"family": "Catuara-Solarz", "given": "Silvina", "initials": "S"}, {"family": "Biryukova", "given": "Inna", "initials": "I", "orcid": "0000-0003-0701-2808", "researcher": {"href": "https://publications.scilifelab.se/researcher/47d787e9d8e14b8fa598d8c3e82e4058.json"}}, {"family": "Gelali", "given": "Eleni", "initials": "E", "orcid": "0000-0003-0067-5473", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1a4d90932dd45509d71a672ec5a12af.json"}}, {"family": "Men\u00e9ndez", "given": "Diego B\u00e1rcena", "initials": "DB"}, {"family": "Zapata", "given": "Luis", "initials": "L", "orcid": "0000-0002-1386-2019", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1e6b01d1d074ce78a9cf40a9560e7fc.json"}}, {"family": "Ossowski", "given": "Stephan", "initials": "S"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Gallant", "given": "Caroline J", "initials": "CJ"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications.scilifelab.se/researcher/744f7c6d0a884d9daa2e7303ed1779b8.json"}}], "type": "journal article", "published": "2020-10-28", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "5445"}, "abstract": "Single-cell RNA sequencing studies on gene co-expression patterns could yield important regulatory and functional insights, but have so far been limited by the confounding effects of differentiation and cell cycle. We apply a tailored experimental design that eliminates these confounders, and report thousands of intrinsically covarying gene pairs in mouse embryonic stem cells. These covariations form a network with biological properties, outlining known and novel gene interactions. We provide the first evidence that miRNAs naturally induce transcriptome-wide covariations and compare the relative importance of nuclear organization, transcriptional and post-transcriptional regulation in defining covariations. We find that nuclear organization has the greatest impact, and that genes encoding for physically interacting proteins specifically tend to covary, suggesting importance for protein complex formation. Our results lend support to the concept of post-transcriptional RNA operons, but we further present evidence that nuclear proximity of genes may provide substantial functional regulation in mammalian single cells.", "doi": "10.1038/s41467-020-19011-5", "pmid": "33116115", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-19011-5"}, {"db": "pmc", "key": "PMC7595044"}], "notes": [], "created": "2021-01-11T11:38:53.729Z", "modified": "2024-01-16T13:48:41.524Z"}, {"entity": "publication", "iuid": "d71873c329c7421db086762eddcf7cb7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d71873c329c7421db086762eddcf7cb7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d71873c329c7421db086762eddcf7cb7"}}, "title": "GPSeq reveals the radial organization of chromatin in the cell nucleus.", "authors": [{"family": "Girelli", "given": "Gabriele", "initials": "G", "orcid": "0000-0003-4264-6494", "researcher": {"href": "https://publications.scilifelab.se/researcher/a607510e88954d0980e1d4505ab27ee7.json"}}, {"family": "Custodio", "given": "Joaquin", "initials": "J"}, {"family": "Kallas", "given": "Tomasz", "initials": "T"}, {"family": "Agostini", "given": "Federico", "initials": "F", "orcid": "0000-0002-5453-2737", "researcher": {"href": "https://publications.scilifelab.se/researcher/a21ea8b7e9a5427eb0e48a822c840b8b.json"}}, {"family": "Wernersson", "given": "Erik", "initials": "E", "orcid": "0000-0003-4778-1660", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae0de6d4af244cec84bbe8c1240d89ae.json"}}, {"family": "Spanjaard", "given": "Bastiaan", "initials": "B"}, {"family": "Mota", "given": "Ana", "initials": "A"}, {"family": "Kolbeinsdottir", "given": "Solrun", "initials": "S"}, {"family": "Gelali", "given": "Eleni", "initials": "E", "orcid": "0000-0003-0067-5473", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1a4d90932dd45509d71a672ec5a12af.json"}}, {"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", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}], "type": "journal article", "published": "2020-10-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "volume": "38", "issue": "10", "pages": "1184-1193", "issn-l": "1087-0156"}, "abstract": "With the exception of lamina-associated domains, the radial organization of chromatin in mammalian cells remains largely unexplored. Here we describe genomic loci positioning by sequencing (GPSeq), a genome-wide method for inferring distances to the nuclear lamina all along the nuclear radius. GPSeq relies on gradual restriction digestion of chromatin from the nuclear lamina toward the nucleus center, followed by sequencing of the generated cut sites. Using GPSeq, we mapped the radial organization of the human genome at 100-kb resolution, which revealed radial patterns of genomic and epigenomic features and gene expression, as well as A and B subcompartments. By combining radial information with chromosome contact frequencies measured by Hi-C, we substantially improved the accuracy of whole-genome structure modeling. Finally, we charted the radial topography of DNA double-strand breaks, germline variants and cancer mutations and found that they have distinctive radial arrangements in A and B subcompartments. We conclude that GPSeq can reveal fundamental aspects of genome architecture.", "doi": "10.1038/s41587-020-0519-y", "pmid": "32451505", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41587-020-0519-y"}, {"db": "pmc", "key": "PMC7610410"}, {"db": "mid", "key": "EMS118404"}], "notes": [], "created": "2020-05-26T07:12:39.312Z", "modified": "2021-11-10T12:46:51.496Z"}, {"entity": "publication", "iuid": "f110ed0f92844e4cbd068a8671f9fee9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f110ed0f92844e4cbd068a8671f9fee9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f110ed0f92844e4cbd068a8671f9fee9"}}, "title": "A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.", "authors": [{"family": "Asp", "given": "Michaela", "initials": "M", "orcid": "0000-0001-5941-7220", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf1751a54e274e60b77290464b4d9733.json"}}, {"family": "Giacomello", "given": "Stefania", "initials": "S", "orcid": "0000-0003-0738-1574", "researcher": {"href": "https://publications.scilifelab.se/researcher/8499e792cc394c42b4240ef5fb3fd06c.json"}}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Wu", "given": "Chenglin", "initials": "C"}, {"family": "F\u00fcrth", "given": "Daniel", "initials": "D"}, {"family": "Qian", "given": "Xiaoyan", "initials": "X"}, {"family": "W\u00e4rdell", "given": "Eva", "initials": "E"}, {"family": "Custodio", "given": "Joaquin", "initials": "J"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "\u00d6sterholm", "given": "Cecilia", "initials": "C"}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL", "orcid": "0000-0002-2207-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ea50cf03c6748c086846c3a28882979.json"}}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "\u00c5kesson", "given": "Elisabet", "initials": "E"}, {"family": "Bergmann", "given": "Olaf", "initials": "O"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "M\u00e5nsson-Broberg", "given": "Agneta", "initials": "A"}, {"family": "Nilsson", "given": "Mats", "initials": "M"}, {"family": "Sylv\u00e9n", "given": "Christer", "initials": "C"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2019-12-12", "journal": {"title": "Cell", "issn": "1097-4172", "issn-l": "0092-8674", "volume": "179", "issue": "7", "pages": "1647-1660.e19"}, "abstract": "The process of cardiac morphogenesis in humans is incompletely understood. Its full characterization requires a deep exploration of the organ-wide orchestration of gene expression with a single-cell spatial resolution. Here, we present a molecular approach that reveals the comprehensive transcriptional landscape of cell types populating the embryonic heart at three developmental stages and that maps cell-type-specific gene expression to specific anatomical domains. Spatial transcriptomics identified unique gene profiles that correspond to distinct anatomical regions in each developmental stage. Human embryonic cardiac cell types identified by single-cell RNA sequencing confirmed and enriched the spatial annotation of embryonic cardiac gene expression. In situ sequencing was then used to refine these results and create a spatial subcellular map for the three developmental phases. Finally, we generated a publicly available web resource of the human developing heart to facilitate future studies on human cardiogenesis.", "doi": "10.1016/j.cell.2019.11.025", "pmid": "31835037", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Advanced FISH Technologies": null, "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "In Situ Sequencing": "Technology development"}, "xrefs": [{"db": "pii", "key": "S0092-8674(19)31282-6"}], "notes": [], "created": "2019-12-16T15:05:37.917Z", "modified": "2025-10-17T13:02:18.291Z"}, {"entity": "publication", "iuid": "c7414fa518d74fd0a11e89491b445b95", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7414fa518d74fd0a11e89491b445b95.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7414fa518d74fd0a11e89491b445b95"}}, "title": "RollFISH achieves robust quantification of single-molecule RNA biomarkers in paraffin-embedded tumor tissue samples.", "authors": [{"family": "Wu", "given": "Chenglin", "initials": "C"}, {"family": "Simonetti", "given": "Michele", "initials": "M"}, {"family": "Rossell", "given": "Carla", "initials": "C"}, {"family": "Mignardi", "given": "Marco", "initials": "M"}, {"family": "Mirzazadeh", "given": "Reza", "initials": "R"}, {"family": "Annaratone", "given": "Laura", "initials": "L", "orcid": "0000-0001-5750-1445", "researcher": {"href": "https://publications.scilifelab.se/researcher/d341ea28491445688116796fc15f53ae.json"}}, {"family": "Marchi\u00f2", "given": "Caterina", "initials": "C"}, {"family": "Sapino", "given": "Anna", "initials": "A"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}], "type": "journal article", "published": "2018-11-28", "journal": {"volume": "1", "issn": "2399-3642", "issue": null, "pages": "209", "title": "Commun Biol", "issn-l": "2399-3642"}, "abstract": "Single-molecule RNA fluorescence in situ hybridization (smFISH) represents a promising approach to quantify the expression of clinically useful biomarkers in tumor samples. However, routine application of smFISH to formalin-fixed, paraffin-embedded (FFPE) samples is challenging due to the low signal intensity and high background noise. Here we present RollFISH, a method combining the specificity of smFISH with the signal boosting of rolling circle amplification. We apply RollFISH to quantify widely used breast cancer biomarkers in cell lines and FFPE samples. Thanks to the high signal-to-noise ratio, we can visualize selected biomarkers at low magnification (20 \u00d7 ) across entire tissue sections, and thus assess their spatial heterogeneity. Lastly, we apply RollFISH to quantify HER2 mRNA in 150 samples on a single tissue microarray, achieving a sensitivity and specificity of detection of HER2-positive samples of ~90%. RollFISH is a robust method for quantifying the expression and intratumor heterogeneity of biomarkers in FFPE tissues.", "doi": "10.1038/s42003-018-0218-0", "pmid": "30511022", "labels": {"Advanced FISH Technologies": "Technology development", "In Situ Sequencing": "Technology development"}, "xrefs": [{"db": "pii", "key": "218"}, {"db": "pmc", "key": "PMC6262000"}], "notes": [], "created": "2020-01-21T12:30:17.817Z", "modified": "2025-10-17T13:02:18.566Z"}]}