{"entity": "journal", "iuid": "f418080a521f4d66a28c176564411b41", "timestamp": "2026-08-13T19:06:26.637Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Cell%20Genomics.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Cell%20Genomics"}}, "title": "Cell Genomics", "issn": "2666-979X", "issn-l": null, "publications_count": 5, "publications": [{"entity": "publication", "iuid": "1435220b47f54e8daee499c4b6e628f4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1435220b47f54e8daee499c4b6e628f4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1435220b47f54e8daee499c4b6e628f4"}}, "title": "LINE-1 retrotransposons mediate cis-acting transcriptional control in human pluripotent stem cells and regulate early brain development.", "authors": [{"family": "Adami", "given": "Anita", "initials": "A"}, {"family": "Garza", "given": "Raquel", "initials": "R"}, {"family": "Gerdes", "given": "Patricia", "initials": "P"}, {"family": "Johansson", "given": "Pia A", "initials": "PA"}, {"family": "Dorazehi", "given": "Fereshteh", "initials": "F"}, {"family": "Koutounidou", "given": "Symela", "initials": "S"}, {"family": "Castilla-Vallmanya", "given": "Laura", "initials": "L"}, {"family": "Atacho", "given": "Diahann A M", "initials": "DAM"}, {"family": "Sharma", "given": "Yogita", "initials": "Y"}, {"family": "Johansson", "given": "Jenny G", "initials": "JG"}, {"family": "Tam", "given": "Oliver", "initials": "O"}, {"family": "Kirkeby", "given": "Agnete", "initials": "A"}, {"family": "Barker", "given": "Roger A", "initials": "RA"}, {"family": "Hammell", "given": "Molly Gale", "initials": "MG"}, {"family": "Douse", "given": "Christopher H", "initials": "CH"}, {"family": "Jakobsson", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2025-10-08", "journal": {"title": "Cell Genomics", "issn": "2666-979X", "volume": "5", "issue": "10", "pages": "100979", "issn-l": null}, "abstract": "Long interspersed nuclear element 1 (L1) retrotransposons represent a vast source of genetic variability. However, mechanistic analysis of whether and how L1s contribute to human developmental programs is lacking, in part due to the challenges associated with specific profiling and manipulation of human L1 expression. Here, we show that thousands of hominoid-specific L1 integrants are expressed in human induced pluripotent stem cells and cerebral organoids. The activity levels of individual L1 promoters vary widely and correlate with an active epigenetic state. Efficient on-target CRISPR interference (CRISPRi) silencing of L1s revealed nearly a hundred co-opted L1-derived chimeric transcripts, and L1 silencing resulted in changes in neural differentiation programs and reduced cerebral organoid size. Together, these data implicate L1s and L1-derived transcripts in hominoid-specific CNS developmental processes.", "doi": "10.1016/j.xgen.2025.100979", "pmid": "40848716", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Long read": "Service", "Clinical Genomics Lund": "Service"}, "xrefs": [{"db": "pii", "key": "S2666-979X(25)00235-6"}], "notes": [], "created": "2025-11-07T15:54:07.700Z", "modified": "2025-11-10T14:12:50.177Z"}, {"entity": "publication", "iuid": "dcfeee20dac44d149e7456edf098d297", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dcfeee20dac44d149e7456edf098d297.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dcfeee20dac44d149e7456edf098d297"}}, "title": "Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration.", "authors": [{"family": "Brown", "given": "Thomas", "initials": "T"}, {"family": "Mishra", "given": "Ketan", "initials": "K"}, {"family": "Elewa", "given": "Ahmed", "initials": "A"}, {"family": "Iarovenko", "given": "Svetlana", "initials": "S"}, {"family": "Subramanian", "given": "Elaiyaraja", "initials": "E"}, {"family": "Araus", "given": "Alberto Joven", "initials": "AJ"}, {"family": "Petzold", "given": "Andreas", "initials": "A"}, {"family": "Fromm", "given": "Bastian", "initials": "B", "orcid": "0000-0003-0352-3037", "researcher": {"href": "https://publications.scilifelab.se/researcher/f29dd3593b894c5e9d233da6049d59e8.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications.scilifelab.se/researcher/744f7c6d0a884d9daa2e7303ed1779b8.json"}}, {"family": "Rikk", "given": "Lennart", "initials": "L"}, {"family": "Suzuki", "given": "Miyuki", "initials": "M"}, {"family": "Suzuki", "given": "Ken-Ichi T", "initials": "KT"}, {"family": "Hayashi", "given": "Toshinori", "initials": "T"}, {"family": "Toyoda", "given": "Atsushi", "initials": "A"}, {"family": "Oliveira", "given": "Catarina R", "initials": "CR"}, {"family": "Osipova", "given": "Ekaterina", "initials": "E", "orcid": "0000-0002-6769-7223", "researcher": {"href": "https://publications.scilifelab.se/researcher/f048ee0785094c2fa3e5b79eba6d1900.json"}}, {"family": "Leigh", "given": "Nicholas D", "initials": "ND", "orcid": "0000-0002-6978-6254", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7856432de344f3a2443bea13e157f8.json"}}, {"family": "Yun", "given": "Maximina H", "initials": "MH"}, {"family": "Simon", "given": "Andr\u00e1s", "initials": "A", "orcid": "0000-0002-1018-1891", "researcher": {"href": "https://publications.scilifelab.se/researcher/96bdae99574843959cede3393f727ee0.json"}}], "type": "journal article", "published": "2025-02-12", "journal": {"title": "Cell Genomics", "issn": "2666-979X", "issn-l": null, "volume": "5", "issue": "2", "pages": "100761"}, "abstract": "Newts have large genomes harboring many repeat elements. How these elements shape the genome and relate to newts' unique regeneration ability remains unknown. We present here the chromosome-scale assembly of the 20.3 Gb genome of the Iberian ribbed newt, Pleurodeles waltl, with a hitherto unprecedented contiguity and completeness among giant genomes. Utilizing this assembly, we demonstrate conserved synteny as well as genetic rearrangements, such as in the major histocompatibility complex locus. We provide evidence suggesting that intronic repeat elements drive newt-specific circular RNA (circRNA) biogenesis and show their regeneration-specific expression. We also present a comprehensive in-depth annotation and chromosomal mapping of microRNAs, highlighting genomic expansion profiles as well as a distinct regulatory pattern in the regenerating limb. These data reveal links between repeat elements, non-coding RNAs, and adult regeneration and provide key resources for addressing developmental, regenerative, and evolutionary principles.", "doi": "10.1016/j.xgen.2025.100761", "pmid": "39874962", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11872487"}, {"db": "pii", "key": "S2666-979X(25)00017-5"}], "notes": [], "created": "2025-01-30T10:51:47.306Z", "modified": "2025-11-14T11:06:23.898Z"}, {"entity": "publication", "iuid": "a7701b730ae64100a1a1c05e7d0ac0ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a7701b730ae64100a1a1c05e7d0ac0ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a7701b730ae64100a1a1c05e7d0ac0ac"}}, "title": "Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci.", "authors": [{"family": "Grochowski", "given": "Christopher M", "initials": "CM", "orcid": "0000-0002-3884-7720", "researcher": {"href": "https://publications.scilifelab.se/researcher/c94bd6d4a43e41f2990ae8b9426c0312.json"}}, {"family": "Bengtsson", "given": "Jesse D", "initials": "JD"}, {"family": "Du", "given": "Haowei", "initials": "H", "orcid": "0000-0001-9052-1587", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c66b32c1f0f497c8652ac2ec9a9cbe8.json"}}, {"family": "Gandhi", "given": "Mira", "initials": "M"}, {"family": "Lun", "given": "Ming Yin", "initials": "MY"}, {"family": "Mehaffey", "given": "Michele G", "initials": "MG"}, {"family": "Park", "given": "KyungHee", "initials": "K"}, {"family": "H\u00f6ps", "given": "Wolfram", "initials": "W"}, {"family": "Benito", "given": "Eva", "initials": "E"}, {"family": "Hasenfeld", "given": "Patrick", "initials": "P"}, {"family": "Korbel", "given": "Jan O", "initials": "JO"}, {"family": "Mahmoud", "given": "Medhat", "initials": "M", "orcid": "0000-0002-2553-4231", "researcher": {"href": "https://publications.scilifelab.se/researcher/e05f2f3025d34f1e940334615a912e1e.json"}}, {"family": "Paulin", "given": "Luis F", "initials": "LF", "orcid": "0000-0003-2567-3773", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e25b0a91ea84c54af6407fead39e2e7.json"}}, {"family": "Jhangiani", "given": "Shalini N", "initials": "SN"}, {"family": "Hwang", "given": "James Paul", "initials": "JP"}, {"family": "Bhamidipati", "given": "Sravya V", "initials": "SV"}, {"family": "Muzny", "given": "Donna M", "initials": "DM"}, {"family": "Fatih", "given": "Jawid M", "initials": "JM"}, {"family": "Gibbs", "given": "Richard A", "initials": "RA", "orcid": "0000-0002-1356-5698", "researcher": {"href": "https://publications.scilifelab.se/researcher/b82176147e434163a72c946839708743.json"}}, {"family": "Pendleton", "given": "Matthew", "initials": "M", "orcid": "0000-0002-7465-4459", "researcher": {"href": "https://publications.scilifelab.se/researcher/eaf7bfd1f8b6492396f3354447413ea3.json"}}, {"family": "Harrington", "given": "Eoghan", "initials": "E"}, {"family": "Juul", "given": "Sissel", "initials": "S"}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}, {"family": "Sedlazeck", "given": "Fritz J", "initials": "FJ", "orcid": "0000-0001-6040-2691", "researcher": {"href": "https://publications.scilifelab.se/researcher/28f940f4fb8b47ec8acb7ba04ca3890b.json"}}, {"family": "Pehlivan", "given": "Davut", "initials": "D", "orcid": "0000-0001-5788-0270", "researcher": {"href": "https://publications.scilifelab.se/researcher/161dfab97b5b4438a16506714d94e751.json"}}, {"family": "Lupski", "given": "James R", "initials": "JR", "orcid": "0000-0001-9907-9246", "researcher": {"href": "https://publications.scilifelab.se/researcher/88dd1dee9767489aaf25865670feb7b7.json"}}, {"family": "Carvalho", "given": "Claudia M B", "initials": "CMB", "orcid": "0000-0002-2090-298X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1a6b6936aa442384c5aef0eff0715a.json"}}], "type": "journal article", "published": "2024-07-10", "journal": {"title": "Cell Genomics", "issn": "2666-979X", "volume": "4", "issue": "7", "pages": "100590", "issn-l": null}, "abstract": "The duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a complex genomic rearrangement (CGR). Although it has been identified as an important pathogenic DNA mutation signature in genomic disorders and cancer genomes, its architecture remains unresolved. Here, we studied the genomic architecture of DUP-TRP/INV-DUP by investigating the DNA of 24 patients identified by array comparative genomic hybridization (aCGH) on whom we found evidence for the existence of 4 out of 4 predicted structural variant (SV) haplotypes. Using a combination of short-read genome sequencing (GS), long-read GS, optical genome mapping, and single-cell DNA template strand sequencing (strand-seq), the haplotype structure was resolved in 18 samples. The point of template switching in 4 samples was shown to be a segment of \u223c2.2-5.5 kb of 100% nucleotide similarity within inverted repeat pairs. These data provide experimental evidence that inverted low-copy repeats act as recombinant substrates. This type of CGR can result in multiple conformers generating diverse SV haplotypes in susceptible dosage-sensitive loci.", "doi": "10.1016/j.xgen.2024.100590", "pmid": "38908378", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11293582"}, {"db": "pii", "key": "S2666-979X(24)00174-5"}], "notes": [], "created": "2024-08-15T12:10:53.870Z", "modified": "2024-11-27T09:00:48.437Z"}, {"entity": "publication", "iuid": "728cc0ed8d014a65b15817c2235987b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/728cc0ed8d014a65b15817c2235987b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/728cc0ed8d014a65b15817c2235987b9"}}, "title": "Genome-wide spatial expression profiling in formalin-fixed tissues.", "authors": [{"family": "Gracia Villacampa", "given": "Eva", "initials": "E", "orcid": "0000-0003-0353-2101", "researcher": {"href": "https://publications.scilifelab.se/researcher/eaf72d81feea4b7899197c67131a85ba.json"}}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Mirzazadeh", "given": "Reza", "initials": "R"}, {"family": "Kvastad", "given": "Linda", "initials": "L", "orcid": "0000-0001-5869-3485", "researcher": {"href": "https://publications.scilifelab.se/researcher/22f1a6ef554a48a49733cc129f50d052.json"}}, {"family": "Andersson", "given": "Alma", "initials": "A"}, {"family": "Mollbrink", "given": "Annelie", "initials": "A"}, {"family": "Kokaraki", "given": "Georgia", "initials": "G"}, {"family": "Monteil", "given": "Vanessa", "initials": "V"}, {"family": "Schultz", "given": "Niklas", "initials": "N"}, {"family": "Appelberg", "given": "Karin Sofia", "initials": "KS"}, {"family": "Montserrat", "given": "Nuria", "initials": "N"}, {"family": "Zhang", "given": "Haibo", "initials": "H"}, {"family": "Penninger", "given": "Josef M", "initials": "JM"}, {"family": "Miesbach", "given": "Wolfgang", "initials": "W"}, {"family": "Mirazimi", "given": "Ali", "initials": "A"}, {"family": "Carlson", "given": "Joseph", "initials": "J", "orcid": "0000-0002-3006-4107", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb81cad4b24d4692bc21bda7305f21f1.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2021-12-08", "journal": {"title": "Cell Genomics", "issn": "2666-979X", "volume": "1", "issue": "3", "pages": "100065", "issn-l": null}, "abstract": "Formalin-fixed paraffin embedding (FFPE) is the most widespread long-term tissue preservation approach. Here, we report a procedure to perform genome-wide spatial analysis of mRNA in FFPE-fixed tissue sections, using well-established, commercially available methods for imaging and spatial barcoding using slides spotted with barcoded oligo(dT) probes to capture the 3' end of mRNA molecules in tissue sections. We applied this method for expression profiling and cell type mapping in coronal sections from the mouse brain to demonstrate the method's capability to delineate anatomical regions from a molecular perspective. We also profiled the spatial composition of transcriptomic signatures in two ovarian carcinosarcoma samples, exemplifying the method's potential to elucidate molecular mechanisms in heterogeneous clinical samples. Finally, we demonstrate the applicability of the assay to characterize human lung and kidney organoids and a human lung biopsy specimen infected with SARS-CoV-2. We anticipate that genome-wide spatial gene expression profiling in FFPE biospecimens will be used for retrospective analysis of biobank samples, which will facilitate longitudinal studies of biological processes and biomarker discovery.", "doi": "10.1016/j.xgen.2021.100065", "pmid": "36776149", "labels": {"NGI Spatial omics": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9903805"}, {"db": "pii", "key": "S2666-979X(21)00081-1"}], "notes": [], "created": "2023-01-03T14:49:59.765Z", "modified": "2023-06-02T10:33:04.298Z"}, {"entity": "publication", "iuid": "ee30e00b2af443009f454bd2fc3b373a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee30e00b2af443009f454bd2fc3b373a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee30e00b2af443009f454bd2fc3b373a"}}, "title": "Population genomics of the critically endangered k\u0101k\u0101p\u014d", "authors": [{"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Morales", "given": "Hern\u00e1n E", "initials": "HE"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW", "orcid": "0000-0003-1863-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e498f04977a48c89ffcd0bae890d4cb.json"}}, {"family": "D\u00edez-del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}, {"family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/caeaa61758c4474ebd104ec232041341.json"}}, {"family": "Foster", "given": "Yasmin", "initials": "Y"}, {"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f80fb4d234c4f2fa2179ad1e7c6a6db.json"}}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications.scilifelab.se/researcher/84b8b0757f02429b9bd419acb42ab6a3.json"}}, {"family": "Rhie", "given": "Arang", "initials": "A", "orcid": "0000-0002-9809-8127", "researcher": {"href": "https://publications.scilifelab.se/researcher/17dfb02e5b09465ea5b24d4a45652799.json"}}, {"family": "Phillippy", "given": "Adam M", "initials": "AM", "orcid": "0000-0003-2983-8934", "researcher": {"href": "https://publications.scilifelab.se/researcher/eadfad6b448a4438abee6a1b2f842b35.json"}}, {"family": "Korlach", "given": "Jonas", "initials": "J"}, {"family": "Howe", "given": "Kerstin", "initials": "K", "orcid": "0000-0003-2237-513X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee1dac1c74d3497aa987c5a615f2d6c4.json"}}, {"family": "Chow", "given": "William", "initials": "W"}, {"family": "Pelan", "given": "Sarah", "initials": "S"}, {"family": "Mendes Damas", "given": "Joanna D", "initials": "JD"}, {"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2f6f17d3e4b4b7e8f47349bda4c1bb0.json"}}, {"family": "Hastie", "given": "Alex R", "initials": "AR"}, {"family": "Formenti", "given": "Giulio", "initials": "G", "orcid": "0000-0002-7554-5991", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdf78195993a481483d7cbbf1a6d64ed.json"}}, {"family": "Fedrigo", "given": "Olivier", "initials": "O", "orcid": "0000-0002-6450-7551", "researcher": {"href": "https://publications.scilifelab.se/researcher/fae69dfab7d841d4850da7349714cd9c.json"}}, {"family": "Guhlin", "given": "Joseph", "initials": "J"}, {"family": "Harrop", "given": "Thomas W R", "initials": "TWR"}, {"family": "Le Lec", "given": "Marissa F", "initials": "MF"}, {"family": "Dearden", "given": "Peter K", "initials": "PK"}, {"family": "Haggerty", "given": "Leanne", "initials": "L"}, {"family": "Martin", "given": "Fergal J", "initials": "FJ"}, {"family": "Kodali", "given": "Vamsi", "initials": "V"}, {"family": "Thibaud-Nissen", "given": "Fran\u00e7oise", "initials": "F"}, {"family": "Iorns", "given": "David", "initials": "D"}, {"family": "Knapp", "given": "Michael", "initials": "M"}, {"family": "Gemmell", "given": "Neil J", "initials": "NJ", "orcid": "0000-0003-0671-3637", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ca2b0a676d84b878b3f9faa8748e148.json"}}, {"family": "Robertson", "given": "Fiona", "initials": "F"}, {"family": "Moorhouse", "given": "Ron", "initials": "R"}, {"family": "Digby", "given": "Andrew", "initials": "A"}, {"family": "Eason", "given": "Daryl", "initials": "D"}, {"family": "Vercoe", "given": "Deidre", "initials": "D"}, {"family": "Howard", "given": "Jason", "initials": "J"}, {"family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "researcher": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}}, {"family": "Robertson", "given": "Bruce C", "initials": "BC", "orcid": "0000-0002-5348-2731", "researcher": {"href": "https://publications.scilifelab.se/researcher/765ee347a5f04b29b28a17f14f707231.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal-article", "published": "2021-10-00", "journal": {"title": "Cell Genomics", "issn": "2666-979X", "volume": "1", "issue": "1", "pages": "100002", "issn-l": null}, "abstract": null, "doi": "10.1016/j.xgen.2021.100002", "pmid": "36777713", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2022-04-28T06:50:35.104Z", "modified": "2023-06-19T12:48:03.795Z"}], "created": "2022-04-28T06:50:35.123Z", "modified": "2022-04-28T06:50:35.123Z"}