{"entity": "researcher", "timestamp": "2026-07-14T03:38:28.774Z", "family": "M\u00e1rmol-S\u00e1nchez", "given": "Emilio", "initials": "E", "orcid": "0000-0002-4393-1740", "affiliations": ["Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden; marc.friedlander@scilifelab.se love.dalen@zoologi.su.se emilio.marmol.sanchez@gmail.com.", "Centre for Palaeogenetics, 106 91 Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/7d902a4dab4e48499f7e941ab4c6417f.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/7d902a4dab4e48499f7e941ab4c6417f"}}, "publications": [{"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": "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"}]}