{"entity": "researcher", "timestamp": "2026-10-05T20:39:03.446Z", "family": "Osipova", "given": "Ekaterina", "initials": "E", "orcid": "0000-0002-6769-7223", "affiliations": ["Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.", "Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany.", "Center for Systems Biology Dresden, 01307 Dresden, Germany.", "LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany.", "Senckenberg Research Institute, 60325 Frankfurt, Germany.", "Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/f048ee0785094c2fa3e5b79eba6d1900.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/f048ee0785094c2fa3e5b79eba6d1900"}}, "publications": [{"entity": "publication", "iuid": "4dd60a505f2b47d0aea28ccd3932c6d7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4dd60a505f2b47d0aea28ccd3932c6d7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4dd60a505f2b47d0aea28ccd3932c6d7"}}, "title": "Convergent and lineage-specific genomic changes shape adaptations in sugar-consuming birds", "authors": [{"family": "Osipova", "given": "Ekaterina", "initials": "E", "orcid": "0000-0002-6769-7223", "researcher": {"href": "https://publications.scilifelab.se/researcher/f048ee0785094c2fa3e5b79eba6d1900.json"}}, {"family": "Ko", "given": "Meng Ching", "initials": "MC", "orcid": "0000-0002-2234-9380", "researcher": {"href": "https://publications.scilifelab.se/researcher/176684b5bef346b9a53cbb7d2c847f6d.json"}}, {"family": "Petricek", "given": "Konstantin M", "initials": "KM", "orcid": "0000-0002-3352-093X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1b5a94d2bbc4232a9e51874f3dcbabd.json"}}, {"family": "Sin", "given": "Simon Yung Wa", "initials": "SYW", "orcid": "0000-0003-2484-2897", "researcher": {"href": "https://publications.scilifelab.se/researcher/99711b8610464003bacac1d9489b8edb.json"}}, {"family": "Brown", "given": "Thomas", "initials": "T", "orcid": "0000-0001-8293-4816", "researcher": {"href": "https://publications.scilifelab.se/researcher/7abb4018ee8a40b2929122db943d4ce9.json"}}, {"family": "Winkler", "given": "Sylke", "initials": "S", "orcid": "0000-0002-0915-3316", "researcher": {"href": "https://publications.scilifelab.se/researcher/f292bbf542f244278bef19506b21b031.json"}}, {"family": "Pippel", "given": "Martin", "initials": "M", "orcid": "0000-0002-8134-5929", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f59d0c98de64ac1a62234792258ee62.json"}}, {"family": "Jarrells", "given": "Julia", "initials": "J"}, {"family": "Weiche", "given": "Susanne", "initials": "S", "orcid": "0009-0001-8390-291X", "researcher": {"href": "https://publications.scilifelab.se/researcher/555d7a058151418ab45a539b24e8bfbf.json"}}, 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"Carolina", "initials": "C", "orcid": "0009-0000-2147-5863", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5154ca03c8b4092af4b3f8f193f4c4b.json"}}, {"family": "Kuhl", "given": "Heiner", "initials": "H", "orcid": "0000-0001-7623-9227", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3326add41974413be16c8a2bed157f8.json"}}, {"family": "Bakker", "given": "Antje", "initials": "A"}, {"family": "Gahr", "given": "Manfred", "initials": "M", "orcid": "0000-0002-6602-2291", "researcher": {"href": "https://publications.scilifelab.se/researcher/01bc4520860a42cd9d0adf7dde33e10b.json"}}, {"family": "Altshuler", "given": "Douglas L", "initials": "DL", "orcid": "0000-0002-1364-3617", "researcher": {"href": "https://publications.scilifelab.se/researcher/45030b418d1f4be1b1c47c2036de2acb.json"}}, {"family": "Buttemer", "given": "William A", "initials": "WA", "orcid": "0000-0003-3176-4452", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ee2ed6ecb9b42d282f799253a72c2c2.json"}}, {"family": "Schupp", "given": "Michael", "initials": "M", "orcid": "0000-0003-3720-1052", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0af2681468547dcbe7f2fed122128a0.json"}}, {"family": "Baldwin", "given": "Maude W", "initials": "MW", "orcid": "0000-0002-7601-8894", "researcher": {"href": "https://publications.scilifelab.se/researcher/39f6d099da8e4dcaaab8e63e6ffc9d97.json"}}, {"family": "Hiller", "given": "Michael", "initials": "M", "orcid": "0000-0003-3024-1449", "researcher": {"href": "https://publications.scilifelab.se/researcher/c304600adfb24d45a7bd0c94f55d1f5b.json"}}, {"family": "Sackton", "given": "Timothy B", "initials": "TB", "orcid": "0000-0003-1673-9216", "researcher": {"href": "https://publications.scilifelab.se/researcher/52cecad2238440ae815708ce70b3bafc.json"}}], "type": "journal-article", "published": "2026-02-26", "journal": {"title": "Science", "issn": "0036-8075", "volume": "391", "issue": "6788", "issn-l": null}, "abstract": null, "doi": "10.1126/science.adt1522", "pmid": null, "labels": {"NGI Long read": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative"}, "xrefs": [], "notes": [], "created": "2026-08-12T15:29:44.930Z", "modified": "2026-08-12T15:29:45.439Z"}, {"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": "048080e8a4d44a78bbecf7078f9d6901", "links": {"self": {"href": "https://publications.scilifelab.se/publication/048080e8a4d44a78bbecf7078f9d6901.json"}, "display": {"href": "https://publications.scilifelab.se/publication/048080e8a4d44a78bbecf7078f9d6901"}}, "title": "Integrating gene annotation with orthology inference at scale.", "authors": [{"family": "Kirilenko", "given": "Bogdan M", "initials": "BM", "orcid": "0000-0002-9394-4275", "researcher": {"href": "https://publications.scilifelab.se/researcher/104f94382f604235ac8edd862204924e.json"}}, {"family": "Munegowda", "given": "Chetan", "initials": "C", "orcid": "0000-0002-3790-2185", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ffdf84352a347a790277d9a7debbe28.json"}}, {"family": "Osipova", "given": "Ekaterina", "initials": "E", "orcid": "0000-0002-6769-7223", "researcher": {"href": "https://publications.scilifelab.se/researcher/f048ee0785094c2fa3e5b79eba6d1900.json"}}, {"family": "Jebb", "given": "David", "initials": "D"}, {"family": "Sharma", "given": "Virag", "initials": "V", "orcid": "0000-0003-4086-4105", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bfd936285cc49c6b40d3c3d0ee4ed26.json"}}, {"family": "Blumer", "given": "Moritz", "initials": "M", "orcid": "0000-0002-5775-1767", "researcher": {"href": "https://publications.scilifelab.se/researcher/58505e8b013b4428bb69b52b1d2f5cf1.json"}}, {"family": "Morales", "given": "Ariadna E", "initials": "AE", "orcid": "0000-0002-0637-7349", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d82eb099b284f068e85ba556ef1cbf5.json"}}, {"family": "Ahmed", "given": "Alexis-Walid", "initials": "A"}, {"family": "Kontopoulos", "given": "Dimitrios-Georgios", "initials": "D"}, {"family": "Hilgers", "given": "Leon", "initials": "L", "orcid": "0000-0002-3539-2513", "researcher": {"href": "https://publications.scilifelab.se/researcher/819689e4085e481b931f20d96a395a27.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Zoonomia Consortium\u2021", "given": "", "initials": ""}, {"family": "Hiller", "given": "Michael", "initials": "M", "orcid": "0000-0003-3024-1449", "researcher": {"href": "https://publications.scilifelab.se/researcher/c304600adfb24d45a7bd0c94f55d1f5b.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn3107"}, "abstract": "Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method that integrates structural gene annotation and orthology inference. TOGA implements a different paradigm to infer orthologous loci, improves ortholog detection and annotation of conserved genes compared with state-of-the-art methods, and handles even highly fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 501 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. TOGA is a powerful and scalable method to annotate and compare genes in the genomic era.", "doi": "10.1126/science.abn3107", "pmid": "37104600", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1898035"}, {"db": "pmc", "key": "PMC10193443"}], "notes": [], "created": "2023-12-01T09:07:33.771Z", "modified": "2024-01-16T13:48:33.629Z"}]}