{"entity": "researcher", "timestamp": "2026-04-16T17:50:59.895Z", "family": "Paulat", "given": "Nicole S", "initials": "NS", "orcid": "0000-0002-6881-2588", "affiliations": ["Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/58778de33da041ceba1481ae528dbb0c.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/58778de33da041ceba1481ae528dbb0c"}}, "publications": [{"entity": "publication", "iuid": "1b55f000e45e48569ce691e5f288112a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b55f000e45e48569ce691e5f288112a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b55f000e45e48569ce691e5f288112a"}}, "title": "Insights into mammalian TE diversity through the curation of 248 genome assemblies.", "authors": [{"family": "Osmanski", "given": "Austin B", "initials": "AB", "orcid": "0000-0002-1485-6446", "researcher": {"href": "https://publications.scilifelab.se/researcher/861bdbbf0e72446795a267d6d0a4cb81.json"}}, {"family": "Paulat", "given": "Nicole S", "initials": "NS", "orcid": "0000-0002-6881-2588", "researcher": {"href": "https://publications.scilifelab.se/researcher/58778de33da041ceba1481ae528dbb0c.json"}}, {"family": "Korstian", "given": "Jenny", "initials": "J", "orcid": "0000-0003-3872-8948", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3541cf73dab433cace7f4e670155278.json"}}, {"family": "Grimshaw", "given": "Jenna R", "initials": "JR", "orcid": "0000-0001-7673-5167", "researcher": {"href": "https://publications.scilifelab.se/researcher/1658aea21a524780b67bfdca293ab1d0.json"}}, {"family": "Halsey", "given": "Michaela", "initials": "M"}, {"family": "Sullivan", "given": "Kevin A M", "initials": "KAM", "orcid": "0000-0001-8499-0491", "researcher": {"href": "https://publications.scilifelab.se/researcher/13f0fe7f177c4422bd5ab25dd2a070c6.json"}}, {"family": "Moreno-Santill\u00e1n", "given": "Diana D", "initials": "DD", "orcid": "0000-0003-2153-0732", "researcher": {"href": "https://publications.scilifelab.se/researcher/460f9988264e4be58157b65c376561b0.json"}}, {"family": "Crookshanks", "given": "Claudia", "initials": "C"}, {"family": "Roberts", "given": "Jacquelyn", "initials": "J"}, {"family": "Garcia", "given": "Carlos", "initials": "C", "orcid": "0000-0001-9194-4514", "researcher": {"href": "https://publications.scilifelab.se/researcher/f836e2eaf97a4f09837704347f112324.json"}}, {"family": "Johnson", "given": "Matthew G", "initials": "MG", "orcid": "0000-0002-1958-6334", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e75a950635a403eb0e34a15cdf0fef2.json"}}, {"family": "Densmore", "given": "Llewellyn D", "initials": "LD", "orcid": "0000-0002-6681-5507", "researcher": {"href": "https://publications.scilifelab.se/researcher/941b0334a8374ec79bfaf95881b370ff.json"}}, {"family": "Stevens", "given": "Richard D", "initials": "RD"}, {"family": "Zoonomia Consortium\u2020", "given": "", "initials": ""}, {"family": "Rosen", "given": "Jeb", "initials": "J", "orcid": "0000-0002-8832-1276", "researcher": {"href": "https://publications.scilifelab.se/researcher/39406330ee844bdbb9476ee472ff44a8.json"}}, {"family": "Storer", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-9619-5265", "researcher": {"href": "https://publications.scilifelab.se/researcher/17dbab57213847a8b685d1fd7d0885d8.json"}}, {"family": "Hubley", "given": "Robert", "initials": "R", "orcid": "0000-0001-9261-3821", "researcher": {"href": "https://publications.scilifelab.se/researcher/76c6f83d0eb34efc9e50811d6af5a0b1.json"}}, {"family": "Smit", "given": "Arian F A", "initials": "AFA", "orcid": "0000-0003-2088-3165", "researcher": {"href": "https://publications.scilifelab.se/researcher/34068300dba84e9f80ffde962a8ca49b.json"}}, {"family": "D\u00e1valos", "given": "Liliana M", "initials": "LM", "orcid": "0000-0002-4327-7697", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c73133e743c4560a2660c7ab5b036cd.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Ray", "given": "David A", "initials": "DA", "orcid": "0000-0002-3340-3987", "researcher": {"href": "https://publications.scilifelab.se/researcher/1637808586b2454190e734d575cf0140.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn1430"}, "abstract": "We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion and quiescence events across the mammalian tree. Young TEs, particularly long interspersed elements, drive increases in genome size, whereas DNA transposons are associated with smaller genomes. Mammals tend to accumulate only a few types of TEs at any given time, with one TE type dominating. We also found association between dietary habit and the presence of DNA transposon invasions. These detailed annotations will serve as a benchmark for future comparative TE analyses among placental mammals.", "doi": "10.1126/science.abn1430", "pmid": "37104570", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-12-01T08:54:16.075Z", "modified": "2024-01-16T13:48:33.640Z"}, {"entity": "publication", "iuid": "d7e4da3ff4c54966b53e2e1210128441", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7e4da3ff4c54966b53e2e1210128441.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7e4da3ff4c54966b53e2e1210128441"}}, "title": "Evolutionary constraint and innovation across hundreds of placental mammals.", "authors": [{"family": "Christmas", "given": "Matthew J", "initials": "MJ", "orcid": "0000-0002-6355-7581", "researcher": {"href": 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"researcher": {"href": "https://publications.scilifelab.se/researcher/bedfc4bc5b6e421da56cfe2bebfa21f3.json"}}, {"family": "Navarro", "given": "Arcadi", "initials": "A", "orcid": "0000-0003-2162-8246", "researcher": {"href": "https://publications.scilifelab.se/researcher/c541642111d94cb8a682b1ff8bea41ac.json"}}, {"family": "Paten", "given": "Benedict", "initials": "B", "orcid": "0000-0001-8863-3539", "researcher": {"href": "https://publications.scilifelab.se/researcher/956ebe9c0b6e43d7ac2a568519f43431.json"}}, {"family": "Pollard", "given": "Katherine S", "initials": "KS", "orcid": "0000-0002-9870-6196", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb2a865a28524f55bb5d9df3db79563f.json"}}, {"family": "Ray", "given": "David A", "initials": "DA", "orcid": "0000-0002-3340-3987", "researcher": {"href": "https://publications.scilifelab.se/researcher/1637808586b2454190e734d575cf0140.json"}}, {"family": "Ruf", "given": "Irina", "initials": "I", "orcid": "0000-0002-9728-1210", "researcher": {"href": "https://publications.scilifelab.se/researcher/838b4e91f9484f26a6dcc1404051a38a.json"}}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a55f8ea442f4168a8426ae4a2c43a46.json"}}, {"family": "Pfenning", "given": "Andreas R", "initials": "AR", "orcid": "0000-0002-3447-9801", "researcher": {"href": "https://publications.scilifelab.se/researcher/579e32fe57da4d738b7fbf0a57fb6faf.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"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn3943"}, "abstract": "Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.", "doi": "10.1126/science.abn3943", "pmid": "37104599", "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": "NIHMS1896905"}, {"db": "pmc", "key": "PMC10250106"}], "notes": [], "created": "2023-12-01T08:40:50.036Z", "modified": "2024-01-16T13:48:33.655Z"}]}