{"entity": "researcher", "timestamp": "2026-07-15T17:13:03.748Z", "family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "affiliations": ["Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden. marc.friedlander@scilifelab.se."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/744f7c6d0a884d9daa2e7303ed1779b8.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/744f7c6d0a884d9daa2e7303ed1779b8"}}, "publications": [{"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": "15068cccc8704f1789179c51b4f175eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15068cccc8704f1789179c51b4f175eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15068cccc8704f1789179c51b4f175eb"}}, "title": "Detection of transcriptome-wide microRNA-target interactions in single cells with agoTRIBE.", "authors": [{"family": "Sekar", "given": "Vaishnovi", "initials": "V"}, {"family": "M\u00e1rmol-S\u00e1nchez", "given": "Emilio", "initials": "E", "orcid": "0000-0002-4393-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d902a4dab4e48499f7e941ab4c6417f.json"}}, {"family": "Kalogeropoulos", "given": "Panagiotis", "initials": "P"}, {"family": "Stanicek", "given": "Laura", "initials": "L"}, {"family": "Sagredo", "given": "Eduardo A", "initials": "EA", "orcid": "0000-0001-9984-2985", "researcher": {"href": "https://publications.scilifelab.se/researcher/61dfefa432364269b33bbe8a4075de65.json"}}, {"family": "Widmark", "given": "Albin", "initials": "A"}, {"family": "Doukoumopoulos", "given": "Evangelos", "initials": "E"}, {"family": "Bonath", "given": "Franziska", "initials": "F"}, {"family": "Biryukova", "given": "Inna", "initials": "I", "orcid": "0000-0003-0701-2808", "researcher": {"href": "https://publications.scilifelab.se/researcher/47d787e9d8e14b8fa598d8c3e82e4058.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications.scilifelab.se/researcher/744f7c6d0a884d9daa2e7303ed1779b8.json"}}], "type": "journal article", "published": "2024-08-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "issn-l": "1087-0156", "volume": "42", "issue": "8", "pages": "1296-1302"}, "abstract": "MicroRNAs (miRNAs) exert their gene regulatory effects on numerous biological processes based on their selection of target transcripts. Current experimental methods available to identify miRNA targets are laborious and require millions of cells. Here we have overcome these limitations by fusing the miRNA effector protein Argonaute2 to the RNA editing domain of ADAR2, allowing the detection of miRNA targets transcriptome-wide in single cells. miRNAs guide the fusion protein to their natural target transcripts, causing them to undergo A>I editing, which can be detected by sensitive single-cell RNA sequencing. We show that agoTRIBE identifies functional miRNA targets, which are supported by evolutionary sequence conservation. In one application of the method we study microRNA interactions in single cells and identify substantial differential targeting across the cell cycle. AgoTRIBE also provides transcriptome-wide measurements of RNA abundance and allows the deconvolution of miRNA targeting in complex tissues at the single-cell level.", "doi": "10.1038/s41587-023-01951-0", "pmid": "37735263", "labels": {"National Genomics Infrastructure": "Service", "NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11324520"}, {"db": "pii", "key": "10.1038/s41587-023-01951-0"}], "notes": [], "created": "2023-10-19T13:55:15.412Z", "modified": "2024-11-25T10:19:39.688Z"}, {"entity": "publication", "iuid": "7a0719a5a1cc4cef963a4832ec073fd7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a0719a5a1cc4cef963a4832ec073fd7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a0719a5a1cc4cef963a4832ec073fd7"}}, "title": "Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity.", "authors": [{"family": "Edelbroek", "given": "Bart", "initials": "B", "orcid": "0000-0002-5184-0873", "researcher": {"href": "https://publications.scilifelab.se/researcher/164d0bef1b3e48668e136dbe0d2e8736.json"}}, {"family": "Kjellin", "given": "Jonas", "initials": "J", "orcid": "0000-0002-3830-7046", "researcher": {"href": "https://publications.scilifelab.se/researcher/daf9964b08fa498e9c0eb3540a0aa1fa.json"}}, {"family": "Biryukova", "given": "Inna", "initials": "I", "orcid": "0000-0003-0701-2808", "researcher": {"href": "https://publications.scilifelab.se/researcher/47d787e9d8e14b8fa598d8c3e82e4058.json"}}, {"family": "Liao", "given": "Zhen", "initials": "Z"}, {"family": "Lundberg", "given": "Torgny", "initials": "T"}, {"family": "Noegel", "given": "Angelika A", "initials": "AA"}, {"family": "Eichinger", "given": "Ludwig", "initials": "L", "orcid": "0000-0003-1594-6117", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2b977ccf8604c2a9a048b21878fc828.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications.scilifelab.se/researcher/744f7c6d0a884d9daa2e7303ed1779b8.json"}}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-3616-3509", "researcher": {"href": "https://publications.scilifelab.se/researcher/4952b493871a4970a089074117bb303f.json"}}], "type": "journal article", "published": "2024-04-12", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "52", "issue": "6", "pages": "3121-3136", "issn-l": "0305-1048"}, "abstract": "MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in both plants and animals. They are thought to have evolved convergently in these lineages and hypothesized to have played a role in the evolution of multicellularity. In line with this hypothesis, miRNAs have so far only been described in few unicellular eukaryotes. Here, we investigate the presence and evolution of miRNAs in Amoebozoa, focusing on species belonging to Acanthamoeba, Physarum and dictyostelid taxonomic groups, representing a range of unicellular and multicellular lifestyles. miRNAs that adhere to both the stringent plant and animal miRNA criteria were identified in all examined amoebae, expanding the total number of protists harbouring miRNAs from 7 to 15. We found conserved miRNAs between closely related species, but the majority of species feature only unique miRNAs. This shows rapid gain and/or loss of miRNAs in Amoebozoa, further illustrated by a detailed comparison between two evolutionary closely related dictyostelids. Additionally, loss of miRNAs in the Dictyostelium discoideum drnB mutant did not seem to affect multicellular development and, hence, demonstrates that the presence of miRNAs does not appear to be a strict requirement for the transition from uni- to multicellular life.", "doi": "10.1093/nar/gkae109", "pmid": "38375870", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11014262"}, {"db": "pii", "key": "7611030"}], "notes": [], "created": "2024-10-22T07:38:55.161Z", "modified": "2024-11-25T10:25:30.684Z"}, {"entity": "publication", "iuid": "345d335f75d34a9c989df5d83cc38c93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/345d335f75d34a9c989df5d83cc38c93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/345d335f75d34a9c989df5d83cc38c93"}}, "title": "Historical RNA expression profiles from the extinct Tasmanian tiger.", "authors": [{"family": "M\u00e1rmol-S\u00e1nchez", "given": "Emilio", "initials": "E", "orcid": "0000-0002-4393-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d902a4dab4e48499f7e941ab4c6417f.json"}}, {"family": "Fromm", "given": "Bastian", "initials": "B", "orcid": "0000-0003-0352-3037", "researcher": {"href": "https://publications.scilifelab.se/researcher/f29dd3593b894c5e9d233da6049d59e8.json"}}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a556bc2e89c457fb1e45cfcd7b567e9.json"}}, {"family": "Pochon", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0001-7981-5795", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7355501dddb4508bf453c7c1ad9f107.json"}}, {"family": "Kalogeropoulos", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-6717-5011", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9e4e4366bb94239b2635da3f2a510de.json"}}, {"family": "Eriksson", "given": "Eli", "initials": "E", "orcid": "0000-0002-0340-3062", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb10331c72f24f2291455003f81a7a98.json"}}, {"family": "Biryukova", "given": "Inna", "initials": "I", "orcid": "0000-0003-0701-2808", "researcher": {"href": "https://publications.scilifelab.se/researcher/47d787e9d8e14b8fa598d8c3e82e4058.json"}}, {"family": "Sekar", "given": "Vaishnovi", "initials": "V", "orcid": "0000-0002-6810-1591", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8bb2f06511f4c3695c1e84dac62e6bb.json"}}, {"family": "Ersmark", "given": "Erik", "initials": "E", "orcid": "0000-0003-4186-7498", "researcher": {"href": "https://publications.scilifelab.se/researcher/7061c3d9591b40488954083d06ed2e17.json"}}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0003-2975-9400", "researcher": {"href": "https://publications.scilifelab.se/researcher/db755021d4474a7c836bdb418b5d12ca.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications.scilifelab.se/researcher/744f7c6d0a884d9daa2e7303ed1779b8.json"}}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Genome Res.", "issn": "1549-5469", "issn-l": "1088-9051", "volume": "33", "issue": "8", "pages": "1299-1316"}, "abstract": "Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost and historical skins from extant canids, but no attempts have been made so far on extinct species. We extract, sequence, and analyze historical RNA from muscle and skin tissue of a \u223c130-year-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA damage, tissue-specific RNA profiles, and expression hotspots genome-wide further confirm the thylacine origin of the sequences. RNA sequences are used to improve protein-coding and noncoding annotations, evidencing missing exonic loci and the location of ribosomal RNA genes while increasing the number of annotated thylacine microRNAs from 62 to 325. We discover a thylacine-specific microRNA isoform that could not have been confirmed without RNA evidence. Finally, we detect traces of RNA viruses, suggesting the possibility of profiling viral evolution. Our results represent the first successful attempt to obtain transcriptional profiles from an extinct animal species, providing thought-to-be-lost information on gene expression dynamics. These findings hold promising implications for the study of RNA molecules across the vast collections of natural history museums and from well-preserved permafrost remains.", "doi": "10.1101/gr.277663.123", "pmid": "37463752", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10552650"}, {"db": "pii", "key": "gr.277663.123"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2023-09-20T16:48:10.289Z", "modified": "2024-01-16T13:48:32.754Z"}, {"entity": "publication", "iuid": "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"}]}