{"entity": "researcher", "timestamp": "2026-08-11T14:51:44.232Z", "family": "Simon", "given": "Andr\u00e1s", "initials": "A", "orcid": "0000-0002-1018-1891", "affiliations": ["Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden. andras.simon@ki.se."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/96bdae99574843959cede3393f727ee0.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/96bdae99574843959cede3393f727ee0"}}, "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": "953e70aba81b4127939f42ea17f61c21", "links": {"self": {"href": "https://publications.scilifelab.se/publication/953e70aba81b4127939f42ea17f61c21.json"}, "display": {"href": "https://publications.scilifelab.se/publication/953e70aba81b4127939f42ea17f61c21"}}, "title": "Evaluation of genetic demultiplexing of single-cell sequencing data from model species.", "authors": [{"family": "Cardiello", "given": "Joseph F", "initials": "JF", "orcid": "0000-0001-7212-6508", "researcher": {"href": "https://publications.scilifelab.se/researcher/f66dfd07566947b68638630de5b8e807.json"}}, {"family": "Joven Araus", "given": "Alberto", "initials": "A", "orcid": "0000-0002-0926-4665", "researcher": {"href": "https://publications.scilifelab.se/researcher/11c7df4727464e1c95bdaa9372ce7409.json"}}, {"family": "Giatrellis", "given": "Sarantis", "initials": "S"}, {"family": "Helsens", "given": "Clement", "initials": "C", "orcid": "0000-0002-9243-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c293306f5704b2eb524f1e195dc6113.json"}}, {"family": "Simon", "given": "Andr\u00e1s", "initials": "A", "orcid": "0000-0002-1018-1891", "researcher": {"href": "https://publications.scilifelab.se/researcher/96bdae99574843959cede3393f727ee0.json"}}, {"family": "Leigh", "given": "Nicholas D", "initials": "ND", "orcid": "0000-0002-6978-6254", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7856432de344f3a2443bea13e157f8.json"}}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "issn-l": "2575-1077", "volume": "6", "issue": "8", "pages": "e202301979"}, "abstract": "Single-cell sequencing (sc-seq) provides a species agnostic tool to study cellular processes. However, these technologies are expensive and require sufficient cell quantities and biological replicates to avoid artifactual results. An option to address these problems is pooling cells from multiple individuals into one sc-seq library. In humans, genotype-based computational separation (i.e., demultiplexing) of pooled sc-seq samples is common. This approach would be instrumental for studying non-isogenic model organisms. We set out to determine whether genotype-based demultiplexing could be more broadly applied among species ranging from zebrafish to non-human primates. Using such non-isogenic species, we benchmark genotype-based demultiplexing of pooled sc-seq datasets against various ground truths. We demonstrate that genotype-based demultiplexing of pooled sc-seq samples can be used with confidence in several non-isogenic model organisms and uncover limitations of this method. Importantly, the only genomic resource required for this approach is sc-seq data and a de novo transcriptome. The incorporation of pooling into sc-seq study designs will decrease cost while simultaneously increasing the reproducibility and experimental options in non-isogenic model organisms.", "doi": "10.26508/lsa.202301979", "pmid": "37197983", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Single cell": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10192724"}, {"db": "pii", "key": "6/8/e202301979"}], "notes": [], "created": "2022-12-01T13:53:09.953Z", "modified": "2024-10-16T13:17:03.038Z"}, {"entity": "publication", "iuid": "a956d64b6ab24e9d965b0f87d4ee55f3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a956d64b6ab24e9d965b0f87d4ee55f3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a956d64b6ab24e9d965b0f87d4ee55f3"}}, "title": "Epicardium-derived cells organize through tight junctions to replenish cardiac muscle in salamanders.", "authors": [{"family": "Eroglu", "given": "Elif", "initials": "E", "orcid": "0000-0003-3952-3178", "researcher": {"href": "https://publications.scilifelab.se/researcher/56f528128b8d46d4b6773c78f74d2f27.json"}}, {"family": "Yen", "given": "Christopher Y T", "initials": "CYT", "orcid": "0000-0001-5999-6306", "researcher": {"href": "https://publications.scilifelab.se/researcher/16c21e09bed648d09277181129eac844.json"}}, {"family": "Tsoi", "given": "Yat-Long", "initials": "YL", "orcid": "0000-0002-8890-3989", "researcher": {"href": "https://publications.scilifelab.se/researcher/c58e997420f2443dab668d9aad863006.json"}}, {"family": "Witman", "given": "Nevin", "initials": "N", "orcid": "0000-0002-1109-778X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b19cd00ecdc47838411d6ab8fe58498.json"}}, {"family": "Elewa", "given": "Ahmed", "initials": "A"}, {"family": "Joven Araus", "given": "Alberto", "initials": "A", "orcid": "0000-0002-0926-4665", "researcher": {"href": "https://publications.scilifelab.se/researcher/11c7df4727464e1c95bdaa9372ce7409.json"}}, {"family": "Wang", "given": "Heng", "initials": "H", "orcid": "0000-0002-1727-9226", "researcher": {"href": "https://publications.scilifelab.se/researcher/1861054d4a744bc885fa876e97591208.json"}}, {"family": "Szattler", "given": "Tamara", "initials": "T", "orcid": "0000-0002-1562-1278", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa689c60e4dc4a79b082369bbf25b46b.json"}}, {"family": "Umeano", "given": "Chimezie H", "initials": "CH"}, {"family": "Sohlm\u00e9r", "given": "Jesper", "initials": "J", "orcid": "0000-0003-2607-7500", "researcher": {"href": "https://publications.scilifelab.se/researcher/579e770e2f774bb68ed8059bc6aa2aef.json"}}, {"family": "Goedel", "given": "Alexander", "initials": "A", "orcid": "0000-0002-5980-2257", "researcher": {"href": "https://publications.scilifelab.se/researcher/866e8580c3d8462da0f3ee3b8909ea6f.json"}}, {"family": "Simon", "given": "Andr\u00e1s", "initials": "A", "orcid": "0000-0002-1018-1891", "researcher": {"href": "https://publications.scilifelab.se/researcher/96bdae99574843959cede3393f727ee0.json"}}, {"family": "Chien", "given": "Kenneth R", "initials": "KR", "orcid": "0000-0002-2759-8378", "researcher": {"href": "https://publications.scilifelab.se/researcher/971382878b474966bbe58acaa1585999.json"}}], "type": "journal article", "published": "2022-05-00", "journal": {"title": "Nat Cell Biol", "issn": "1476-4679", "issn-l": null, "volume": "24", "issue": "5", "pages": "645-658"}, "abstract": "The contribution of the epicardium, the outermost layer of the heart, to cardiac regeneration has remained controversial due to a lack of suitable analytical tools. By combining genetic marker-independent lineage-tracing strategies with transcriptional profiling and loss-of-function methods, we report here that the epicardium of the highly regenerative salamander species Pleurodeles waltl has an intrinsic capacity to differentiate into cardiomyocytes. Following cryoinjury, CLDN6+ epicardium-derived cells appear at the lesion site, organize into honeycomb-like structures connected via focal tight junctions and undergo transcriptional reprogramming that results in concomitant differentiation into de novo cardiomyocytes. Ablation of CLDN6+ differentiation intermediates as well as disruption of their tight junctions impairs cardiac regeneration. Salamanders constitute the evolutionarily closest species to mammals with an extensive ability to regenerate heart muscle and our results highlight the epicardium and tight junctions as key targets in efforts to promote cardiac regeneration.", "doi": "10.1038/s41556-022-00902-2", "pmid": "35550612", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9106584"}, {"db": "pii", "key": "10.1038/s41556-022-00902-2"}], "notes": [], "created": "2022-08-19T08:37:51.908Z", "modified": "2024-01-16T13:48:36.843Z"}]}