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"initials": "T", "orcid": "0000-0003-1829-0766", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5dd7a9e8e53349a495751970731ddab8.json"}}, {"family": "Andreassen", "given": "Ole A", "initials": "OA", "orcid": "0000-0002-4461-3568", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/43ded34fa6ff40ea9bd47d222d9df745.json"}}, {"family": "B\u00f8rglum", "given": "Anders D", "initials": "AD", "orcid": "0000-0001-8627-7219", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d018f8331d7344ae8d1b542f8c619f0a.json"}}, {"family": "Walitza", "given": "Susanne", "initials": "S", "orcid": "0000-0002-8161-8683", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e94bf203703240bebcc2b5ee7340043b.json"}}, {"family": "Hveem", "given": "Kristian", "initials": "K", "orcid": "0000-0001-8157-9744", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6565408abed545f2ba060b28b9932215.json"}}, {"family": "Hansen", "given": "Bjarne K", "initials": "BK", "orcid": "0000-0001-5659-1119", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ba271fb33bee4445bc5db73ddfc4a15f.json"}}, {"family": "R\u00fcck", "given": "Christian", "initials": "C", "orcid": "0000-0002-8742-0168", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9565fd9a92884bcd921f490c7a6c821b.json"}}, {"family": "Martin", "given": "Nicholas G", "initials": "NG", "orcid": "0000-0003-4069-8020", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5e77e96035ab425f93ef18778dfceb04.json"}}, {"family": "Milani", "given": "Lili", "initials": "L", "orcid": "0000-0002-5323-3102", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e92d1400307a42f3a8baffc008996d1b.json"}}, {"family": "Mors", "given": "Ole", "initials": "O", "orcid": "0000-0002-5660-0393", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07a21db389684e5a831f0e72c5554806.json"}}, {"family": "Reichborn-Kjennerud", "given": "Ted", "initials": "T", "orcid": "0000-0003-4653-0034", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18ef7309654e4257ae27a31ac7fb7405.json"}}, {"family": "Ribas\u00e9s", "given": "Marta", "initials": "M", "orcid": "0000-0003-1039-1116", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3b569893813a4a3f8eaaf394184962f6.json"}}, {"family": "Kvale", "given": "Gerd", "initials": "G", "orcid": "0000-0001-5449-2344", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9767b9d89894cb7ae48db54984a52cb.json"}}, {"family": "Mataix-Cols", "given": "David", "initials": "D", "orcid": "0000-0002-4545-0924", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e4e4cd9916d7420cb7ca20a9a107ff94.json"}}, {"family": "Domschke", "given": "Katharina", "initials": "K", "orcid": "0000-0002-2550-9132", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a43acde07c9404b80ed8f1178019581.json"}}, {"family": "Gr\u00fcnblatt", "given": "Edna", "initials": "E", "orcid": "0000-0001-8505-7265", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/00bc02aff3d141c29675261d9863b014.json"}}, {"family": "Wagner", "given": "Michael", "initials": "M", "orcid": "0000-0003-2589-6440", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6742dc7e5b8447c8ac0f3ca0848ac741.json"}}, {"family": "Zwart", "given": "John-Anker", "initials": "JA", "orcid": "0000-0001-5721-0154", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3bb8c5de231e4cfaabc31dc526a286e1.json"}}, {"family": "Breen", "given": "Gerome", "initials": "G", "orcid": "0000-0003-2053-1792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6153fda86a684873a1a6bd625a6a3483.json"}}, {"family": "Nestadt", "given": "Gerald", "initials": "G", "orcid": "0000-0001-9461-5249", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e5f34b9d60af458bbf37f90a0b606380.json"}}, {"family": "Kaprio", "given": "Jaakko", "initials": "J", "orcid": "0000-0002-3716-2455", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f7e6f19a0a7b4d5ba54d250fdecaee46.json"}}, {"family": "Arnold", "given": "Paul D", "initials": "PD", "orcid": "0000-0003-2496-4624", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e7b167a809ea4cd8956ca066d58e4c29.json"}}, {"family": "Grice", "given": "Dorothy E", "initials": "DE", "orcid": "0000-0002-8833-2549", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baf7b94523774b918bfd9bd7bacdb0b0.json"}}, {"family": "Knowles", "given": "James A", "initials": "JA", "orcid": "0000-0002-3307-5741", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/66d1c551ab074508ba442f0ce2168555.json"}}, {"family": "Ask", "given": "Helga", "initials": "H", "orcid": "0000-0003-0149-5319", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/69ada7e3440c4a399e67fb382ab13d28.json"}}, {"family": "Verweij", "given": "Karin J", "initials": "KJ", "orcid": "0000-0001-9868-7821", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/37c5146448f042dd84aca776c24de59e.json"}}, {"family": "Davis", "given": "Lea K", "initials": "LK", "orcid": "0000-0001-5143-2282", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7cd85392839d49e392ca9598f75f2e81.json"}}, {"family": "Smit", "given": "Dirk J", "initials": "DJ", "orcid": "0000-0001-8301-8860", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/72722d507e7447c5af1796829b4727e5.json"}}, {"family": "Crowley", "given": "James J", "initials": "JJ", "orcid": "0000-0001-9051-1557", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6a46d1ecc0e476bad9bbab566b4255a.json"}}, {"family": "Scharf", "given": "Jeremiah M", "initials": "JM", "orcid": "0000-0002-4742-5896", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9aa4f6673d74eeb90d62ec663421532.json"}}, {"family": "Stein", "given": "Murray B", "initials": "MB", "orcid": "0000-0001-9564-2871", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02defb98c7c442b8aa54a0d19816d949.json"}}, {"family": "Gelernter", "given": "Joel", "initials": "J", "orcid": "0000-0002-4067-1859", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/867b957d5ca7406ab3bd969db1f7daa0.json"}}, {"family": "Mathews", "given": "Carol A", "initials": "CA", "orcid": "0000-0003-2208-7058", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f3ca04cb775b44ec81c7d851f05d1e9c.json"}}, {"family": "Derks", "given": "Eske M", "initials": "EM", "orcid": "0000-0002-6292-6883", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ba4bce3f4c7d48b4990fdb6b34d64762.json"}}, {"family": "Mattheisen", "given": "Manuel", "initials": "M", "orcid": "0000-0002-8442-493X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc6a347bff244d59821f31a5aa0fd805.json"}}], "type": "journal article", "published": "2025-04-08", "journal": {"title": "medRxiv", "issn-l": null}, "abstract": "Obsessive-compulsive disorder (OCD) affects ~1% of children and adults and is partly caused by genetic factors. We conducted a genome-wide association study (GWAS) meta-analysis combining 53,660 OCD cases and 2,044,417 controls and identified 30 independent genome-wide significant loci. Gene-based approaches identified 249 potential effector genes for OCD, with 25 of these classified as the most likely causal candidates, including WDR6, DALRD3, CTNND1 and multiple genes in the MHC region. We estimated that ~11,500 genetic variants explained 90% of OCD genetic heritability. OCD genetic risk was associated with excitatory neurons in the hippocampus and cortex, along with D1- and D2-type dopamine receptor-containing medium spiny neurons. OCD genetic risk was shared with 65 of 112 additional phenotypes, including all of the psychiatric disorders we examined. In particular, OCD shared genetic risk with anxiety, depression, anorexia nervosa, and Tourette syndrome, and was negatively associated with inflammatory bowel diseases, educational attainment, and body mass index.", "doi": "10.1101/2024.03.13.24304161", "pmid": "38712091", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11071577"}, {"db": "pii", "key": "2024.03.13.24304161"}, {"db": "figshare", "key": "10.6084/m9.figshare.28451894"}], "notes": [], "created": "2026-08-20T10:52:45.924Z", "modified": "2026-08-20T10:52:50.588Z"}, {"entity": "publication", "iuid": "00e346ce54bf4f329ebeaf39f9b52aa7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/00e346ce54bf4f329ebeaf39f9b52aa7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/00e346ce54bf4f329ebeaf39f9b52aa7"}}, "title": "A burden of rare copy number variants in obsessive-compulsive disorder.", "authors": [{"family": "Halvorsen", "given": "Matthew W", "initials": "MW", "orcid": "0000-0002-6707-2418", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b3d072e2d5314d5abb6e07121e26e906.json"}}, {"family": "de Schipper", "given": "Elles", "initials": "E"}, {"family": "B\u00e4ckman", "given": "Julia", "initials": "J"}, {"family": "Strom", "given": "Nora I", "initials": "NI", "orcid": "0000-0002-5261-8852", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d805c34a1b224409bdaaba1ed7ae3137.json"}}, {"family": "Hagen", "given": "Kristen", "initials": "K", "orcid": "0000-0002-4286-1277", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e702371110c2474c849cd2c62fa35e83.json"}}, {"family": "Nordic OCD and Related Disorders Consortium (NORDiC)", "given": "", "initials": ""}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Wallert", "given": "John", "initials": "J"}, {"family": "Bulik", "given": "Cynthia M", "initials": "CM", "orcid": "0000-0001-7772-3264", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a787d2c77134fc4a20aa46b738881d0.json"}}, {"family": "Fund\u00edn", "given": "Bengt", "initials": "B"}, {"family": "Land\u00e9n", "given": "Mikael", "initials": "M", "orcid": "0000-0002-4496-6451", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e788f5999d644719a8c4816c88d7de3.json"}}, {"family": "Kvale", "given": "Gerd", "initials": "G"}, {"family": "Hansen", "given": "Bjarne", "initials": "B"}, {"family": "Haavik", "given": "Jan", "initials": "J", "orcid": "0000-0001-7865-2808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/19a75dabdfdb48338e8e6ceb8800347a.json"}}, {"family": "Mattheisen", "given": "Manuel", "initials": "M", "orcid": "0000-0002-8442-493X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc6a347bff244d59821f31a5aa0fd805.json"}}, {"family": "R\u00fcck", "given": "Christian", "initials": "C", "orcid": "0000-0002-8742-0168", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9565fd9a92884bcd921f490c7a6c821b.json"}}, {"family": "Mataix-Cols", "given": "David", "initials": "D", "orcid": "0000-0002-4545-0924", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e4e4cd9916d7420cb7ca20a9a107ff94.json"}}, {"family": "Crowley", "given": "James J", "initials": "JJ", "orcid": "0000-0001-9051-1557", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6a46d1ecc0e476bad9bbab566b4255a.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Mol. Psychiatry", "issn": "1476-5578", "volume": "30", "issue": "4", "pages": "1510-1517", "issn-l": "1359-4184"}, "abstract": "Current genetic research on obsessive-compulsive disorder (OCD) supports contributions to risk specifically from common single nucleotide variants (SNVs), along with rare coding SNVs and small insertion-deletions (indels). The contribution to OCD risk from rare copy number variants (CNVs), however, has not been formally assessed at a similar scale. Here we describe an analysis of rare CNVs called from genotype array data in 2248 deeply phenotyped OCD cases and 3608 unaffected controls from Sweden and Norway. Cases carry an elevated burden of CNVs \u226530 kb in size (OR = 1.12, P = 1.77 \u00d7 10-3). The excess rate of these CNVs in cases versus controls was around 0.07 (95% CI 0.02-0.11, P = 2.58 \u00d7 10-3). This signal was largely driven by CNVs overlapping protein-coding regions (OR = 1.19, P = 3.08 \u00d7 10-4), particularly deletions impacting loss-of-function intolerant genes (pLI >0.995, OR = 4.12, P = 2.54 \u00d7 10-5). We did not identify any specific locus where CNV burden was associated with OCD case status at genome-wide significance, but we noted non-random recurrence of CNV deletions in cases (permutation P = 2.60 \u00d7 10-3). In cases where sufficient clinical data were available (n = 1612) we found that carriers of neurodevelopmental duplications were more likely to have comorbid autism (P < 0.001), and that carriers of deletions overlapping neurodevelopmental genes had lower treatment response (P = 0.02). The results demonstrate a contribution of rare CNVs to OCD risk, and suggest that studies of rare coding variation in OCD would have increased power to identify risk genes if this class of variation were incorporated into formal tests.", "doi": "10.1038/s41380-024-02763-7", "pmid": "39463448", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11919692"}, {"db": "pii", "key": "10.1038/s41380-024-02763-7"}], "notes": [], "created": "2026-08-20T08:48:07.296Z", "modified": "2026-08-20T08:48:07.839Z"}, {"entity": "publication", "iuid": "423e19a9f50f4ce787723017cade475a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/423e19a9f50f4ce787723017cade475a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/423e19a9f50f4ce787723017cade475a"}}, "title": "Using evolutionary constraint to define novel candidate driver genes in medulloblastoma.", "authors": [{"family": "Roy", "given": "Ananya", "initials": "A"}, {"family": "Sakthikumar", "given": "Sharadha", "initials": "S"}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV"}, {"family": "Nordin", "given": "Jessika", "initials": "J", "orcid": "0000-0002-8414-2190", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a285875862f24b6fa0b378550da371fa.json"}}, {"family": "Pensch", "given": "Raphaela", "initials": "R", "orcid": "0000-0002-0313-8369", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca3190f9abf5474fae557aa4c8bbea3d.json"}}, {"family": "M\u00e4kel\u00e4inen", "given": "Suvi", "initials": "S"}, {"family": "Pettersson", "given": "Mats", "initials": "M", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a2310759fe6e4fd0b4a48ba9c35d3f84.json"}}, {"family": "Zoonomia Consortium", "given": "", "initials": ""}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2023-08-15", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "120", "issue": "33", "pages": "e2300984120", "issn-l": "0027-8424"}, "abstract": "Current knowledge of cancer genomics remains biased against noncoding mutations. To systematically search for regulatory noncoding mutations, we assessed mutations in conserved positions in the genome under the assumption that these are more likely to be functional than mutations in positions with low conservation. To this end, we use whole-genome sequencing data from the International Cancer Genome Consortium and combined it with evolutionary constraint inferred from 240 mammals, to identify genes enriched in noncoding constraint mutations (NCCMs), mutations likely to be regulatory in nature. We compare medulloblastoma (MB), which is malignant, to pilocytic astrocytoma (PA), a primarily benign tumor, and find highly different NCCM frequencies between the two, in agreement with the fact that malignant cancers tend to have more mutations. In PA, a high NCCM frequency only affects the BRAF locus, which is the most commonly mutated gene in PA. In contrast, in MB, >500 genes have high levels of NCCMs. Intriguingly, several loci with NCCMs in MB are associated with different ages of onset, such as the HOXB cluster in young MB patients. In adult patients, NCCMs occurred in, e.g., the WASF-2/AHDC1/FGR locus. One of these NCCMs led to increased expression of the SRC kinase FGR and augmented responsiveness of MB cells to dasatinib, a SRC kinase inhibitor. Our analysis thus points to different molecular pathways in different patient groups. These newly identified putative candidate driver mutations may aid in patient stratification in MB and could be valuable for future selection of personalized treatment options.", "doi": "10.1073/pnas.2300984120", "pmid": "37549291", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10438395"}], "notes": [], "created": "2026-08-20T09:31:26.073Z", "modified": "2026-08-20T09:31:26.234Z"}, {"entity": "publication", "iuid": "7aa5056b58e3462f93a00ad80578b6ec", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7aa5056b58e3462f93a00ad80578b6ec.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7aa5056b58e3462f93a00ad80578b6ec"}}, "title": "Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia.", "authors": [{"family": "Paulat", "given": "Nicole S", "initials": "NS"}, {"family": "Storer", "given": "Jessica M", "initials": "JM"}, {"family": "Moreno-Santill\u00e1n", "given": "Diana D", "initials": "DD"}, {"family": "Osmanski", "given": "Austin B", "initials": "AB"}, {"family": "Sullivan", "given": "Kevin A M", "initials": "KAM"}, {"family": "Grimshaw", "given": "Jenna R", "initials": "JR", "orcid": "0000-0001-7673-5167", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47c81a9b846f488d9b140dcfcb28edaf.json"}}, {"family": "Korstian", "given": "Jennifer", "initials": "J"}, {"family": "Halsey", "given": "Michaela", "initials": "M"}, {"family": "Garcia", "given": "Carlos J", "initials": "CJ"}, {"family": "Crookshanks", "given": "Claudia", "initials": "C"}, {"family": "Roberts", "given": "Jaquelyn", "initials": "J"}, {"family": "Smit", "given": "Arian F A", "initials": "AFA"}, {"family": "Hubley", "given": "Robert", "initials": "R"}, {"family": "Rosen", "given": "Jeb", "initials": "J"}, {"family": "Teeling", "given": "Emma C", "initials": "EC"}, {"family": "Vernes", "given": "Sonja C", "initials": "SC"}, {"family": "Myers", "given": "Eugene", "initials": "E"}, {"family": "Pippel", "given": "Martin", "initials": "M"}, {"family": "Brown", "given": "Thomas", "initials": "T"}, {"family": "Hiller", "given": "Michael", "initials": "M", "orcid": "0000-0003-3024-1449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1005d0d1f4264b46b1cfe214c7aca246.json"}}, {"family": "Zoonomia Consortium\n", "given": "", "initials": ""}, {"family": "Rojas", "given": "Danny", "initials": "D"}, {"family": "D\u00e1valos", "given": "Liliana M", "initials": "LM", "orcid": "0000-0002-4327-7697", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7d8a875eb2704b75ac10564ffb83c3b0.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Ray", "given": "David A", "initials": "DA", "orcid": "0000-0002-3340-3987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6392a5497414b98999823cbafd67d4b.json"}}], "type": "journal article", "published": "2023-05-02", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "40", "issue": "5", "issn-l": "0737-4038"}, "abstract": "Horizontal transfer of transposable elements (TEs) is an important mechanism contributing to genetic diversity and innovation. Bats (order Chiroptera) have repeatedly been shown to experience horizontal transfer of TEs at what appears to be a high rate compared with other mammals. We investigated the occurrence of horizontally transferred (HT) DNA transposons involving bats. We found over 200 putative HT elements within bats; 16 transposons were shared across distantly related mammalian clades, and 2 other elements were shared with a fish and two lizard species. Our results indicate that bats are a hotspot for horizontal transfer of DNA transposons. These events broadly coincide with the diversification of several bat clades, supporting the hypothesis that DNA transposon invasions have contributed to genetic diversification of bats.", "doi": "10.1093/molbev/msad092", "pmid": "37071810", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10162687"}, {"db": "pii", "key": "7128099"}], "notes": [], "created": "2026-08-20T09:42:31.229Z", "modified": "2026-08-20T09:42:31.404Z"}, {"entity": "publication", "iuid": "9b6c299c3be9475c925b30a7b62e0588", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9b6c299c3be9475c925b30a7b62e0588.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9b6c299c3be9475c925b30a7b62e0588"}}, "title": "Data from Genomically Complex Human Angiosarcoma and Canine Hemangiosarcoma Establish Convergent Angiogenic Transcriptional Programs Driven by Novel Gene Fusions", "authors": [{"family": "Kim", "given": "Jong Hyuk", "initials": "JH", "orcid": "0000-0002-1645-0036", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3553b69d2420463ca6a24d52696a7da7.json"}}, {"family": "Megquier", "given": "Kate", "initials": "K", "orcid": "0000-0002-1458-0865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d84d6a467fac40d5a926885732eca967.json"}}, {"family": "Thomas", "given": "Rachael", "initials": "R", "orcid": "0000-0002-3029-8798", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d7613e07c9b242748a912e2ab73a5542.json"}}, {"family": "Sarver", "given": "Aaron L", "initials": "AL"}, {"family": "Song", "given": "Jung Min", "initials": "JM"}, {"family": "Kim", "given": "Yoon Tae", "initials": "YT"}, {"family": "Cheng", "given": "Nuojin", "initials": "N"}, {"family": "Schulte", "given": "Ashley J", "initials": "AJ"}, {"family": "Linden", "given": "Michael A", "initials": "MA"}, {"family": "Murugan", "given": "Paari", "initials": "P", "orcid": "0000-0003-4706-213X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6bf0a99d52e4f5abed4fad7da3c8e02.json"}}, {"family": "Oseth", "given": "LeAnn", "initials": "L"}, {"family": "Forster", "given": "Colleen L", "initials": "CL"}, {"family": "Elvers", "given": "Ingegerd", "initials": "I"}, {"family": "Swofford", "given": "Ross", "initials": "R", "orcid": "0000-0003-3676-8479", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85b0174c633b417b933092763175bb1c.json"}}, {"family": "Turner-Maier", "given": "Jason", "initials": "J"}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Breen", "given": "Matthew", "initials": "M"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Modiano", "given": "Jaime F", "initials": "JF", "orcid": "0000-0001-6398-7648", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ba4bb579a21472dab716ebf61874801.json"}}], "type": "posted-content", "published": "2023-04-03", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1158/1541-7786.c.6545168.v1", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T12:14:04.142Z", "modified": "2026-08-20T12:14:04.329Z"}, {"entity": "publication", "iuid": "9ab47c1d66844d9991ae6934f6e185ef", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9ab47c1d66844d9991ae6934f6e185ef.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9ab47c1d66844d9991ae6934f6e185ef"}}, "title": "Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia", "authors": [{"family": "Paulat", "given": "Nicole S", "initials": "NS"}, {"family": "Storer", "given": "Jessica M", "initials": "JM"}, {"family": "Moreno-Santill\u00e1n", "given": "Diana D", "initials": "DD"}, {"family": "Osmanski", "given": "Austin B", "initials": "AB", "orcid": "0000-0002-1485-6446", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9dda01496474b11a018f3c629f18d1b.json"}}, {"family": "Sullivan", "given": "Kevin AM", "initials": "KA"}, {"family": "Grimshaw", "given": "Jenna R", "initials": "JR"}, {"family": "Korstian", "given": "Jennifer", "initials": "J"}, {"family": "Halsey", "given": "Michaela", "initials": "M"}, {"family": "Garcia", "given": "Carlos J", "initials": "CJ"}, {"family": "Crookshanks", "given": "Claudia", "initials": "C"}, {"family": "Roberts", "given": "Jaquelyn", "initials": "J"}, {"family": "Smit", "given": "Arian FA", "initials": "AF"}, {"family": "Hubley", "given": "Robert", "initials": "R"}, {"family": "Rosen", "given": "Jeb", "initials": "J"}, {"family": "Teeling", "given": "Emma C", "initials": "EC"}, {"family": "Vernes", "given": "Sonja C", "initials": "SC"}, {"family": "Myers", "given": "Eugene", "initials": "E"}, {"family": "Pippel", "given": "Martin", "initials": "M", "orcid": "0000-0002-8134-5929", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ba8b75f9bf1244a9a2ec5d07229aa153.json"}}, {"family": "Brown", "given": "Thomas", "initials": "T"}, {"family": "Hiller", "given": "Michael", "initials": "M"}, {"family": "Rojas", "given": "Danny", "initials": "D"}, {"family": "D\u00e1valos", "given": "Liliana M", "initials": "LM"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Ray", "given": "David A", "initials": "DA", "orcid": "0000-0002-3340-3987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6392a5497414b98999823cbafd67d4b.json"}}], "type": "posted-content", "published": "2023-03-23", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.03.23.533946", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:44:44.121Z", "modified": "2026-08-20T10:44:44.216Z"}, {"entity": "publication", "iuid": "8b9b4c80163b4b61b0bff465ae4bb6ae", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8b9b4c80163b4b61b0bff465ae4bb6ae.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8b9b4c80163b4b61b0bff465ae4bb6ae"}}, "title": "Insights into mammalian TE diversity via the curation of 248 mammalian genome assemblies", "authors": [{"family": "Osmanski", "given": "Austin B", "initials": "AB", "orcid": "0000-0002-1485-6446", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9dda01496474b11a018f3c629f18d1b.json"}}, {"family": "Paulat", "given": "Nicole S", "initials": "NS", "orcid": "0000-0002-6881-2588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4ca5ca8c8acd4c65b5836fecb4b443a0.json"}}, {"family": "Korstian", "given": "Jenny", "initials": "J", "orcid": "0000-0003-3872-8948", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8f961ea9153345278a8acd0586608b41.json"}}, {"family": "Grimshaw", "given": "Jenna R", "initials": "JR", "orcid": "0000-0001-7673-5167", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47c81a9b846f488d9b140dcfcb28edaf.json"}}, {"family": "Halsey", "given": "Michaela", "initials": "M"}, {"family": "Sullivan", "given": "Kevin A M", "initials": "KAM"}, {"family": "Moreno-Santill\u00e1n", "given": "Diana D", "initials": "DD", "orcid": "0000-0003-2153-0732", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80c929d82dfe4c969e2b68bd20b99263.json"}}, {"family": "Crookshanks", "given": "Claudia", "initials": "C"}, {"family": "Roberts", "given": "Jacquelyn", "initials": "J"}, {"family": "Garcia", "given": "Carlos", "initials": "C"}, {"family": "Johnson", "given": "Matthew G", "initials": "MG", "orcid": "0000-0002-1958-6334", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6507717463ae46e3ad96fb00d4544a11.json"}}, {"family": "Densmore", "given": "Llewellyn D", "initials": "LD"}, {"family": "Stevens", "given": "Richard D", "initials": "RD"}, {"family": "Rosen", "given": "Jeb", "initials": "J", "orcid": "0000-0002-8832-1276", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7405a278ed5f428c9ba38968182d409f.json"}}, {"family": "Storer", "given": "Jessica M", "initials": "JM"}, {"family": "Hubley", "given": "Robert", "initials": "R", "orcid": "0000-0001-9261-3821", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/86b6fe3c9be54bc58dd8c750dda51aa3.json"}}, {"family": "Smit", "given": "Arian F A", "initials": "AFA", "orcid": "0000-0003-2088-3165", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ddf0080c6ee44cbe830114f0ab126884.json"}}, {"family": "D\u00e1valos", "given": "Liliana M", "initials": "LM", "orcid": "0000-0002-4327-7697", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7d8a875eb2704b75ac10564ffb83c3b0.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Ray", "given": "David A", "initials": "DA", "orcid": "0000-0002-3340-3987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6392a5497414b98999823cbafd67d4b.json"}}], "type": "posted-content", "published": "2022-12-30", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.12.28.522108", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:43:12.222Z", "modified": "2026-08-20T10:43:12.564Z"}, {"entity": "publication", "iuid": "aad4619ecdcc4770ae68236724ac91a1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/aad4619ecdcc4770ae68236724ac91a1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/aad4619ecdcc4770ae68236724ac91a1"}}, "title": "Three-dimensional genome re-wiring in loci with Human Accelerated Regions", "authors": [{"family": "Keough", "given": "Kathleen C", "initials": "KC", "orcid": "0000-0002-7481-0511", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27ba6707b77e4d0eb914e71063dab333.json"}}, {"family": "Whalen", "given": "Sean", "initials": "S", "orcid": "0000-0002-6648-3610", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d06b9f8ca8ea41c4acba0e438ea0d373.json"}}, {"family": "Inoue", "given": "Fumitaka", "initials": "F", "orcid": "0000-0003-0657-434X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/edd281f2f6b44ff1b562e0d25ccc9847.json"}}, {"family": "Przytycki", "given": "Pawel F", "initials": "PF", "orcid": "0000-0002-3360-6936", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3670767ba35043cea5f52291ebdd1c95.json"}}, {"family": "Fair", "given": "Tyler", "initials": "T"}, {"family": "Deng", "given": "Chengyu", "initials": "C", "orcid": "0000-0003-3595-9935", "researcher": {"href": 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"https://publications-affiliated.scilifelab.se/researcher/86098b2cd2ed490c8366e5ccc292e915.json"}}, {"family": "Pollen", "given": "Alex", "initials": "A", "orcid": "0000-0003-3263-8634", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e4e6cdef8fb466d8f1c600aeefd2c44.json"}}, {"family": "Pollard", "given": "Katherine S", "initials": "KS", "orcid": "0000-0002-9870-6196", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d080bc9bff548958f0c161612cdc4cf.json"}}], "type": "posted-content", "published": "2022-10-05", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.10.04.510859", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:41:21.778Z", "modified": "2026-08-20T10:41:22.106Z"}, {"entity": "publication", "iuid": "b09c06812d9246c6941dc437ba05b1e1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b09c06812d9246c6941dc437ba05b1e1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b09c06812d9246c6941dc437ba05b1e1"}}, "title": "Evolution of the ancestral mammalian karyotype and syntenic regions.", "authors": [{"family": "Damas", "given": "Joana", "initials": "J", "orcid": "0000-0003-4857-2510", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f60eb6afeabc435ea1e6378786162fa8.json"}}, {"family": "Corbo", "given": "Marco", "initials": "M"}, {"family": "Kim", "given": "Jaebum", "initials": "J"}, {"family": "Turner-Maier", "given": "Jason", "initials": "J"}, {"family": "Farr\u00e9", "given": "Marta", "initials": "M"}, {"family": "Larkin", "given": "Denis M", "initials": "DM"}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d18635ed6fa42d4bbcfddadae70e308.json"}}, {"family": "Steiner", "given": "Cynthia", "initials": "C"}, {"family": "Houck", "given": "Marlys L", "initials": "ML"}, {"family": "Hall", "given": "Shaune", "initials": "S"}, {"family": "Shiue", "given": "Lily", "initials": "L"}, {"family": "Thomas", "given": "Stephen", "initials": "S"}, {"family": "Swale", "given": "Thomas", "initials": "T"}, {"family": "Daly", "given": "Mark", "initials": "M"}, {"family": "Korlach", "given": "Jonas", "initials": "J"}, {"family": "Uliano-Silva", "given": "Marcela", "initials": "M"}, {"family": "Mazzoni", "given": "Camila J", "initials": "CJ"}, {"family": "Birren", "given": "Bruce W", "initials": "BW"}, {"family": "Genereux", "given": "Diane P", "initials": "DP", "orcid": "0000-0001-5770-0989", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/352ee25047c544aaa486a69e7e3333fc.json"}}, {"family": "Johnson", "given": "Jeremy", "initials": "J"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Nweeia", "given": "Martin T", "initials": "MT", "orcid": "0000-0001-7079-4123", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4846b6d146a4a7288db1543583a0158.json"}}, {"family": "Johnson", "given": "Rebecca N", "initials": "RN", "orcid": "0000-0003-3035-2827", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5486418f837c4e9199e31f61b20887cd.json"}}, {"family": "Zoonomia Consortium", "given": "", "initials": ""}, {"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5059da24204049c696aec45b62526759.json"}}], "type": "journal article", "published": "2022-10-04", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "119", "issue": "40", "pages": "e2209139119", "issn-l": "0027-8424"}, "abstract": "Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes and syntenic relationships at 16 nodes along the mammalian phylogeny. Three different reference genomes (human, sloth, and cattle) representing phylogenetically distinct mammalian superorders were used to assess reference bias in the reconstructed ancestral karyotypes and to expand the number of clades with reconstructed genomes. The mammalian ancestor likely had 19 pairs of autosomes, with nine of the smallest chromosomes shared with the common ancestor of all amniotes (three still conserved in extant mammals), demonstrating a striking conservation of synteny for \u223c320 My of vertebrate evolution. The numbers and types of chromosome rearrangements were classified for transitions between the ancestral mammalian karyotype, descendent ancestors, and extant species. For example, 94 inversions, 16 fissions, and 14 fusions that occurred over 53 My differentiated the therian from the descendent eutherian ancestor. The highest breakpoint rate was observed between the mammalian and therian ancestors (3.9 breakpoints/My). Reconstructed mammalian ancestor chromosomes were found to have distinct evolutionary histories reflected in their rates and types of rearrangements. The distributions of genes, repetitive elements, topologically associating domains, and actively transcribed regions in multispecies homologous synteny blocks and evolutionary breakpoint regions indicate that purifying selection acted over millions of years of vertebrate evolution to maintain syntenic relationships of developmentally important genes and regulatory landscapes of gene-dense chromosomes.", "doi": "10.1073/pnas.2209139119", "pmid": "36161960", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9550189"}], "notes": [], "created": "2026-08-20T09:31:15.877Z", "modified": "2026-08-20T09:31:15.982Z"}, {"entity": "publication", "iuid": "5747b955d1ce4f45ab8564863b6011a9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5747b955d1ce4f45ab8564863b6011a9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5747b955d1ce4f45ab8564863b6011a9"}}, "title": "The Antarctic Weddell seal genome reveals evidence of selection on cardiovascular phenotype and lipid handling.", "authors": [{"family": "Noh", "given": "Hyun Ji", "initials": "HJ"}, {"family": "Turner-Maier", "given": "Jason", "initials": "J"}, {"family": "Schulberg", "given": "S Anne", "initials": "SA"}, {"family": "Fitzgerald", "given": "Michael L", "initials": "ML"}, {"family": "Johnson", "given": "Jeremy", "initials": "J"}, {"family": "Allen", "given": "Kaitlin N", "initials": "KN", "orcid": "0000-0001-8036-1110", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee49cf351f0c4f0583cf4fbbc9bf6062.json"}}, {"family": "H\u00fcckst\u00e4dt", "given": "Luis A", "initials": "LA"}, {"family": "Batten", "given": "Annabelle J", "initials": "AJ"}, {"family": "Alfoldi", "given": "Jessica", "initials": "J", "orcid": "0000-0001-9713-6200", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0fdea3b614934331a6398fb24feb54c6.json"}}, {"family": "Costa", "given": "Daniel P", "initials": "DP"}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Zapol", "given": "Warren M", "initials": "WM"}, {"family": "Buys", "given": "Emmanuel S", "initials": "ES"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Hindle", "given": "Allyson G", "initials": "AG", "orcid": "0000-0002-1983-9573", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/49459b37810943aca91c847060596160.json"}}], "type": "journal article", "published": "2022-02-17", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "5", "issue": "1", "pages": "140", "issn-l": "2399-3642"}, "abstract": "The Weddell seal (Leptonychotes weddellii) thrives in its extreme Antarctic environment. We generated the Weddell seal genome assembly and a high-quality annotation to investigate genome-wide evolutionary pressures that underlie its phenotype and to study genes implicated in hypoxia tolerance and a lipid-based metabolism. Genome-wide analyses included gene family expansion/contraction, positive selection, and diverged sequence (acceleration) compared to other placental mammals, identifying selection in coding and non-coding sequence in five pathways that may shape cardiovascular phenotype. Lipid metabolism as well as hypoxia genes contained more accelerated regions in the Weddell seal compared to genomic background. Top-significant genes were SUMO2 and EP300; both regulate hypoxia inducible factor signaling. Liver expression of four genes with the strongest acceleration signals differ between Weddell seals and a terrestrial mammal, sheep. We also report a high-density lipoprotein-like particle in Weddell seal serum not present in other mammals, including the shallow-diving harbor seal.", "doi": "10.1038/s42003-022-03089-2", "pmid": "35177770", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8854659"}, {"db": "pii", "key": "10.1038/s42003-022-03089-2"}], "notes": [], "created": "2026-08-20T09:25:05.912Z", "modified": "2026-08-20T09:25:06.076Z"}, {"entity": "publication", "iuid": "3841603fbf9e43e6a1460db8f686ef9e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3841603fbf9e43e6a1460db8f686ef9e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3841603fbf9e43e6a1460db8f686ef9e"}}, "title": "Why sequence all eukaryotes?", "authors": [{"family": "Blaxter", "given": "Mark", "initials": "M", "orcid": "0000-0003-2861-949X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9b785bc131a241c4815ab5ef1576709b.json"}}, {"family": "Archibald", "given": "John M", "initials": "JM", "orcid": "0000-0001-7255-780X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9381e61c33164dca82411b18b9fcc0d3.json"}}, {"family": "Childers", "given": "Anna K", "initials": "AK", "orcid": "0000-0002-0747-8539", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b04257eed5dd48a7b631d8c8e78c2df1.json"}}, {"family": "Coddington", "given": "Jonathan A", "initials": "JA", "orcid": "0000-0001-6004-7730", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/efae0bfdf0c64e86a175c8921b1af0b4.json"}}, {"family": "Crandall", "given": "Keith A", "initials": "KA", "orcid": "0000-0002-0836-3389", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/853c5da68a5a4c96bd2248b21bd15ba7.json"}}, {"family": "Di Palma", "given": "Federica", "initials": "F", "orcid": "0000-0002-4394-0102", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3cf0785a103c45368f4e1cca6e5cb5f7.json"}}, {"family": "Durbin", "given": "Richard", "initials": "R", "orcid": "0000-0002-9130-1006", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a8972546b724b0d9c6ed69a766cc41b.json"}}, {"family": "Edwards", "given": "Scott V", "initials": "SV", "orcid": "0000-0003-2535-6217", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/249a83cc8fb240609cd7bd76c6c79e2c.json"}}, {"family": "Graves", "given": "Jennifer A M", "initials": "JAM", "orcid": "0000-0001-6480-7856", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48044e7f378c41e28b58ae92e1102efb.json"}}, {"family": "Hackett", "given": "Kevin J", "initials": "KJ", "orcid": "0000-0002-7459-7175", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc72dad2a31b443db715bf82966f44f4.json"}}, {"family": "Hall", "given": "Neil", "initials": "N", "orcid": "0000-0003-2808-0009", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc8087425525426994b690f1ae2637e0.json"}}, {"family": "Jarvis", "given": "Erich D", "initials": "ED"}, {"family": "Johnson", "given": "Rebecca N", "initials": "RN", "orcid": "0000-0003-3035-2827", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5486418f837c4e9199e31f61b20887cd.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Kress", "given": "W John", "initials": "WJ", "orcid": "0000-0002-0140-5267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25477498e7dd41e7891088988a40713e.json"}}, {"family": "Kuraku", "given": "Shigehiro", "initials": "S", "orcid": "0000-0003-1464-8388", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be2fb1e4a3e548498f5590365dedc81e.json"}}, {"family": "Lawniczak", "given": "Mara K N", "initials": "MKN"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Lopez", "given": "Jose V", "initials": "JV", "orcid": "0000-0002-1637-4125", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d60d31a72bb64d6894367a3ffc1785e7.json"}}, {"family": "Moran", "given": "Nancy A", "initials": "NA", "orcid": "0000-0003-2983-9769", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74c685964435471096e5dbc580505cb8.json"}}, {"family": "Robinson", "given": "Gene E", "initials": "GE", "orcid": "0000-0003-4828-4068", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/86d1dc6e76694345ba735e5612bff820.json"}}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d18635ed6fa42d4bbcfddadae70e308.json"}}, {"family": "Shapiro", "given": "Beth", "initials": "B"}, {"family": "Soltis", "given": "Pamela S", "initials": "PS", "orcid": "0000-0001-9310-8659", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c4308f7e0e84bbfaad58eac840db765.json"}}, {"family": "Warnow", "given": "Tandy", "initials": "T", "orcid": "0000-0001-7717-3514", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/072c8f6823984406aedb974d6a97f7dc.json"}}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ec2e418a32c4161abc876171467f5ea.json"}}, {"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5059da24204049c696aec45b62526759.json"}}], "type": "journal article", "published": "2022-01-25", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "119", "issue": "4", "issn-l": "0027-8424"}, "abstract": "Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes-about 2 million species-should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing divergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine.", "doi": "10.1073/pnas.2115636118", "pmid": "35042801", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8795522"}, {"db": "pii", "key": "2115636118"}], "notes": [], "created": "2026-08-20T09:31:06.931Z", "modified": "2026-08-20T09:31:07.517Z"}, {"entity": "publication", "iuid": "626310cbddb14ff48c80c0f9372c585b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/626310cbddb14ff48c80c0f9372c585b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/626310cbddb14ff48c80c0f9372c585b"}}, "title": "The Earth BioGenome Project 2020: Starting the clock.", "authors": [{"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5059da24204049c696aec45b62526759.json"}}, {"family": "Richards", "given": "Stephen", "initials": "S", "orcid": "0000-0001-8959-5466", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8005cf3b343461388e2b82a2c61c293.json"}}, {"family": "Lieberman Aiden", "given": "Erez", "initials": "E"}, {"family": "Allende", "given": "Miguel L", "initials": "ML", "orcid": "0000-0002-2783-2152", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27d6fdda2e7b4487b651c852c3f3cd11.json"}}, {"family": "Archibald", "given": "John M", "initials": "JM"}, {"family": "B\u00e1lint", "given": "Mikl\u00f3s", "initials": "M"}, {"family": "Barker", "given": "Katharine B", "initials": "KB"}, {"family": "Baumgartner", "given": "Bridget", "initials": "B"}, {"family": "Belov", "given": "Katherine", "initials": "K"}, {"family": "Bertorelle", "given": "Giorgio", "initials": "G"}, {"family": "Blaxter", "given": "Mark L", "initials": "ML", "orcid": "0000-0003-2861-949X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9b785bc131a241c4815ab5ef1576709b.json"}}, {"family": "Cai", "given": "Jing", "initials": "J"}, {"family": "Caperello", "given": "Nicolette D", "initials": "ND"}, {"family": "Carlson", "given": "Keith", "initials": "K"}, {"family": "Castilla-Rubio", "given": "Juan Carlos", "initials": "JC"}, {"family": "Chaw", "given": "Shu-Miaw", "initials": "SM"}, {"family": "Chen", "given": "Lei", "initials": "L"}, {"family": "Childers", "given": "Anna K", "initials": "AK"}, {"family": "Coddington", "given": "Jonathan A", "initials": "JA", "orcid": "0000-0001-6004-7730", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/efae0bfdf0c64e86a175c8921b1af0b4.json"}}, {"family": "Conde", "given": "Dalia A", "initials": "DA", "orcid": "0000-0002-7923-8163", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5b73243e2df04c5a8d771456b262a4bf.json"}}, {"family": "Corominas", "given": "Montserrat", "initials": "M", "orcid": "0000-0002-0724-8346", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0805b84e0e824c93a51262f4fdc8f8e2.json"}}, {"family": "Crandall", "given": "Keith A", "initials": "KA", "orcid": "0000-0002-0836-3389", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/853c5da68a5a4c96bd2248b21bd15ba7.json"}}, {"family": "Crawford", "given": "Andrew J", "initials": "AJ"}, {"family": "DiPalma", "given": "Federica", "initials": "F"}, {"family": "Durbin", "given": "Richard", "initials": "R", "orcid": "0000-0002-9130-1006", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a8972546b724b0d9c6ed69a766cc41b.json"}}, {"family": "Ebenezer", "given": "ThankGod E", "initials": "TE"}, {"family": "Edwards", "given": "Scott V", "initials": "SV", "orcid": "0000-0003-2535-6217", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/249a83cc8fb240609cd7bd76c6c79e2c.json"}}, {"family": "Fedrigo", "given": "Olivier", "initials": "O"}, {"family": "Flicek", "given": "Paul", "initials": "P"}, {"family": "Formenti", "given": "Giulio", "initials": "G"}, {"family": "Gibbs", "given": "Richard A", "initials": "RA"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/93cbe282154844588f63bc7cc6983b30.json"}}, {"family": "Goldstein", "given": "Melissa M", "initials": "MM"}, {"family": "Graves", "given": "Jennifer Marshall", "initials": "JM", "orcid": "0000-0001-6480-7856", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48044e7f378c41e28b58ae92e1102efb.json"}}, {"family": "Greely", "given": "Henry T", "initials": "HT", "orcid": "0000-0002-1105-6734", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ea9e4bfb13764d13b4418be1ecc2d27d.json"}}, {"family": "Grigoriev", "given": "Igor V", "initials": "IV", "orcid": "0000-0002-3136-8903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5cb43708257842149fbbeed91293d400.json"}}, {"family": "Hackett", "given": "Kevin J", "initials": "KJ"}, {"family": "Hall", "given": "Neil", "initials": "N"}, {"family": "Haussler", "given": "David", "initials": "D"}, {"family": "Helgen", "given": "Kristofer M", "initials": "KM"}, {"family": "Hogg", "given": "Carolyn J", "initials": "CJ", "orcid": "0000-0002-6328-398X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/faf4b7a234c84bdbac97cf9b0e8f5531.json"}}, {"family": "Isobe", "given": "Sachiko", "initials": "S"}, {"family": "Jakobsen", "given": "Kjetill Sigurd", "initials": "KS", "orcid": "0000-0002-8861-5397", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2fe02e097b342508301397260ef7cc3.json"}}, {"family": "Janke", "given": "Axel", "initials": "A", "orcid": "0000-0002-9394-1904", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ef0f0bab20e45cca4e726c84b8645f2.json"}}, {"family": "Jarvis", "given": "Erich D", "initials": "ED"}, {"family": "Johnson", "given": "Warren E", "initials": "WE", "orcid": "0000-0002-5954-186X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa69a0b1643541b0b490e0c1186c8307.json"}}, {"family": "Jones", "given": "Steven J M", "initials": "SJM"}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Kersey", "given": "Paul J", "initials": "PJ"}, {"family": "Kim", "given": "Jin-Hyoung", "initials": "JH"}, {"family": "Kress", "given": "W John", "initials": "WJ", "orcid": "0000-0002-0140-5267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25477498e7dd41e7891088988a40713e.json"}}, {"family": "Kuraku", "given": "Shigehiro", "initials": "S"}, {"family": "Lawniczak", "given": "Mara K N", "initials": "MKN"}, {"family": "Leebens-Mack", "given": "James H", "initials": "JH", "orcid": "0000-0003-4811-2231", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b52ac9ce6dba4bee8dae7b594242c49b.json"}}, {"family": "Li", "given": "Xueyan", "initials": "X"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Liu", "given": "Xin", "initials": "X"}, {"family": "Lopez", "given": "Jose V", "initials": "JV"}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T", "orcid": "0000-0002-5597-3075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1091cb5bfe394d459969d24bb1c22c66.json"}}, {"family": "Mazard", "given": "Sophie", "initials": "S"}, {"family": "Mazet", "given": "Jonna A K", "initials": "JAK", "orcid": "0000-0002-8712-5951", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9daa6d747c704145a06420aa76ce3426.json"}}, {"family": "Mazzoni", "given": "Camila J", "initials": "CJ"}, {"family": "Myers", "given": "Eugene W", "initials": "EW", "orcid": "0000-0002-6580-7839", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bf74ba4bae3546eca812b29793341604.json"}}, {"family": "O'Neill", "given": "Rachel J", "initials": "RJ"}, {"family": "Paez", "given": "Sadye", "initials": "S"}, {"family": "Park", "given": "Hyun", "initials": "H"}, {"family": "Robinson", "given": "Gene E", "initials": "GE", "orcid": "0000-0003-4828-4068", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/86d1dc6e76694345ba735e5612bff820.json"}}, {"family": "Roquet", "given": "Cristina", "initials": "C", "orcid": "0000-0001-8748-3743", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/82e0bb00dab543318861f81cb3569541.json"}}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d18635ed6fa42d4bbcfddadae70e308.json"}}, {"family": "Sabir", "given": "Jamal S M", "initials": "JSM", "orcid": "0000-0003-4785-9894", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b644127a1d8740bba24dc2fef3c23c81.json"}}, {"family": "Shaffer", "given": "H Bradley", "initials": "HB", "orcid": "0000-0002-5795-9242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/910008f9a77840e5ada4302460516dec.json"}}, {"family": "Shank", "given": "Timothy M", "initials": "TM"}, {"family": "Sherkow", "given": "Jacob S", "initials": "JS", "orcid": "0000-0002-9724-9261", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4ac5a78ced4f490499d8ea3358a73741.json"}}, {"family": "Soltis", "given": "Pamela S", "initials": "PS", "orcid": "0000-0001-9310-8659", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c4308f7e0e84bbfaad58eac840db765.json"}}, {"family": "Tang", "given": "Boping", "initials": "B", "orcid": "0000-0002-3241-7914", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab99aedf62e948c5839d1912180fc2b9.json"}}, {"family": "Tedersoo", "given": "Leho", "initials": "L"}, {"family": "Uliano-Silva", "given": "Marcela", "initials": "M"}, {"family": "Wang", "given": "Kun", "initials": "K"}, {"family": "Wei", "given": "Xiaofeng", "initials": "X"}, {"family": "Wetzer", "given": "Regina", "initials": "R"}, {"family": "Wilson", "given": "Julia L", "initials": "JL"}, {"family": "Xu", "given": "Xun", "initials": "X"}, {"family": "Yang", "given": "Huanming", "initials": "H"}, {"family": "Yoder", "given": "Anne D", "initials": "AD", "orcid": "0000-0002-1781-9552", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f4e827f5db545de84e8ae91e7603fc1.json"}}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ec2e418a32c4161abc876171467f5ea.json"}}], "type": "introductory journal article", "published": "2022-01-25", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "119", "issue": "4", "issn-l": "0027-8424"}, "abstract": null, "doi": "10.1073/pnas.2115635118", "pmid": "35042800", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8795548"}, {"db": "pii", "key": "2115635118"}], "notes": [], "created": "2026-08-20T09:31:03.855Z", "modified": "2026-08-20T09:31:05.035Z"}, {"entity": "publication", "iuid": "d05f4aeea1d543a6818bf3faaf86357e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d05f4aeea1d543a6818bf3faaf86357e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d05f4aeea1d543a6818bf3faaf86357e"}}, "title": "Genomically Complex Human Angiosarcoma and Canine Hemangiosarcoma Establish Convergent Angiogenic Transcriptional Programs Driven by Novel Gene Fusions.", "authors": [{"family": "Kim", "given": "Jong Hyuk", "initials": "JH", "orcid": "0000-0002-1645-0036", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3553b69d2420463ca6a24d52696a7da7.json"}}, {"family": "Megquier", "given": "Kate", "initials": "K", "orcid": "0000-0002-1458-0865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d84d6a467fac40d5a926885732eca967.json"}}, {"family": "Thomas", "given": "Rachael", "initials": "R", "orcid": "0000-0002-3029-8798", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d7613e07c9b242748a912e2ab73a5542.json"}}, {"family": "Sarver", "given": "Aaron L", "initials": "AL"}, {"family": "Song", "given": "Jung Min", "initials": "JM"}, {"family": "Kim", "given": "Yoon Tae", "initials": "YT"}, {"family": "Cheng", "given": "Nuojin", "initials": "N"}, {"family": "Schulte", "given": "Ashley J", "initials": "AJ"}, {"family": "Linden", "given": "Michael A", "initials": "MA"}, {"family": "Murugan", "given": "Paari", "initials": "P", "orcid": "0000-0003-4706-213X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6bf0a99d52e4f5abed4fad7da3c8e02.json"}}, {"family": "Oseth", "given": "LeAnn", "initials": "L"}, {"family": "Forster", "given": "Colleen L", "initials": "CL"}, {"family": "Elvers", "given": "Ingegerd", "initials": "I"}, {"family": "Swofford", "given": "Ross", "initials": "R", "orcid": "0000-0003-3676-8479", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85b0174c633b417b933092763175bb1c.json"}}, {"family": "Turner-Maier", "given": "Jason", "initials": "J"}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Breen", "given": "Matthew", "initials": "M"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Modiano", "given": "Jaime F", "initials": "JF", "orcid": "0000-0001-6398-7648", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ba4bb579a21472dab716ebf61874801.json"}}], "type": "journal article", "published": "2021-05-00", "journal": {"title": "Mol. Cancer Res.", "issn": "1557-3125", "volume": "19", "issue": "5", "pages": "847-861", "issn-l": "1541-7786"}, "abstract": "Sporadic angiosarcomas are aggressive vascular sarcomas whose rarity and genomic complexity present significant obstacles in deciphering the pathogenic significance of individual genetic alterations. Numerous fusion genes have been identified across multiple types of cancers, but their existence and significance remain unclear in sporadic angiosarcomas. In this study, we leveraged RNA-sequencing data from 13 human angiosarcomas and 76 spontaneous canine hemangiosarcomas to identify fusion genes associated with spontaneous vascular malignancies. Ten novel protein-coding fusion genes, including TEX2-PECAM1 and ATP8A2-FLT1, were identified in seven of the 13 human tumors, with two tumors showing mutations of TP53. HRAS and NRAS mutations were found in angiosarcomas without fusions or TP53 mutations. We found 15 novel protein-coding fusion genes including MYO16-PTK2, GABRA3-FLT1, and AKT3-XPNPEP1 in 11 of the 76 canine hemangiosarcomas; these fusion genes were seen exclusively in tumors of the angiogenic molecular subtype that contained recurrent mutations in TP53, PIK3CA, PIK3R1, and NRAS. In particular, fusion genes and mutations of TP53 cooccurred in tumors with higher frequency than expected by random chance, and they enriched gene signatures predicting activation of angiogenic pathways. Comparative transcriptomic analysis of human angiosarcomas and canine hemangiosarcomas identified shared molecular signatures associated with activation of PI3K/AKT/mTOR pathways. Our data suggest that genome instability induced by TP53 mutations might create a predisposition for fusion events that may contribute to tumor progression by promoting selection and/or enhancing fitness through activation of convergent angiogenic pathways in this vascular malignancy. IMPLICATIONS: This study shows that, while drive events of malignant vasoformative tumors of humans and dogs include diverse mutations and stochastic rearrangements that create novel fusion genes, convergent transcriptional programs govern the highly conserved morphologic organization and biological behavior of these tumors in both species.", "doi": "10.1158/1541-7786.MCR-20-0937", "pmid": "33649193", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1675846"}, {"db": "pmc", "key": "PMC8137578"}, {"db": "pii", "key": "1541-7786.MCR-20-0937"}], "notes": [], "created": "2026-08-20T12:14:23.333Z", "modified": "2026-08-20T12:14:23.423Z"}, {"entity": "publication", "iuid": "ed19a0d3a6a54e6286ae3864d7b22467", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ed19a0d3a6a54e6286ae3864d7b22467.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ed19a0d3a6a54e6286ae3864d7b22467"}}, "title": "The meadow jumping mouse genome and transcriptome suggest mechanisms of hibernation", "authors": [{"family": "Cong", "given": "Qian", "initials": "Q", "orcid": "0000-0002-8909-0414", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e13afd7052d342379141b61efcda4092.json"}}, {"family": "Brem", "given": "Ethan A", "initials": "EA"}, {"family": "Zhang", "given": "Jing", "initials": "J", "orcid": "0000-0003-4190-3065", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/adaf1f6e41474f9f95539a4516af0651.json"}}, {"family": "Alf\u00f6ldi", "given": "Jessica", "initials": "J"}, {"family": "Johnson", "given": "Jeremy", "initials": "J"}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Malaney", "given": "Jason L", "initials": "JL", "orcid": "0000-0002-3187-7652", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21ee9ce35e7c4e2caa19aa4af70edd43.json"}}, {"family": "Israelsen", "given": "William J", "initials": "WJ", "orcid": "0000-0002-3653-9353", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c2d5796dc2a44163b7ff1c88fb16eb48.json"}}], "type": "posted-content", "published": "2020-11-03", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.11.02.365791", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T09:59:40.561Z", "modified": "2026-08-20T09:59:59.923Z"}, {"entity": "publication", "iuid": "1eefcae7314541e0a3860a83a1c16d84", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1eefcae7314541e0a3860a83a1c16d84.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1eefcae7314541e0a3860a83a1c16d84"}}, "title": "Progressive Cactus is a multiple-genome aligner for the thousand-genome era.", "authors": [{"family": "Armstrong", "given": "Joel", "initials": "J", "orcid": "0000-0003-2077-4671", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e05c7c5e78e448cdb7d94bae26e7bcb1.json"}}, {"family": "Hickey", "given": "Glenn", "initials": "G"}, {"family": "Diekhans", "given": "Mark", "initials": "M", "orcid": "0000-0002-0430-0989", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7999277bf08b4dbdbcc7d5e78cafcb00.json"}}, {"family": "Fiddes", "given": "Ian T", "initials": "IT"}, {"family": "Novak", "given": "Adam M", "initials": "AM", "orcid": "0000-0001-5828-047X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0cc29a94bc2347e0a4d64bdb105b29c0.json"}}, {"family": "Deran", "given": "Alden", "initials": "A"}, {"family": "Fang", "given": "Qi", "initials": "Q", "orcid": "0000-0002-9181-8689", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a04a244840c248c4a7515c427ffdc5de.json"}}, {"family": "Xie", "given": "Duo", "initials": "D", "orcid": "0000-0001-7010-3601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0bee104c168a4a2994257ccca5a835ca.json"}}, {"family": "Feng", "given": "Shaohong", "initials": "S", "orcid": "0000-0002-2462-7348", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/458d41da2844484a82fb7b21231a567e.json"}}, {"family": "Stiller", "given": "Josefin", "initials": "J", "orcid": "0000-0001-6009-9581", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c58298dbc8ef46a086a0f74bdded4a6b.json"}}, {"family": "Genereux", "given": "Diane", "initials": "D"}, {"family": "Johnson", "given": "Jeremy", "initials": "J"}, {"family": "Marinescu", "given": "Voichita Dana", "initials": "VD"}, {"family": "Alf\u00f6ldi", "given": "Jessica", "initials": "J"}, {"family": "Harris", "given": "Robert S", "initials": "RS"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Haussler", "given": "David", "initials": "D", "orcid": "0000-0003-1533-4575", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4b918ad2e1c4544a4a52dfd64f6ebba.json"}}, {"family": "Karlsson", "given": "Elinor", "initials": "E", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Jarvis", "given": "Erich D", "initials": "ED"}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ec2e418a32c4161abc876171467f5ea.json"}}, {"family": "Paten", "given": "Benedict", "initials": "B", "orcid": "0000-0001-8863-3539", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c916e24b35f2459480cf87e27bb21ee1.json"}}], "type": "comparative study", "published": "2020-11-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "587", "issue": "7833", "pages": "246-251", "issn-l": "0028-0836"}, "abstract": "New genome assemblies have been arriving at a rapidly increasing pace, thanks to decreases in sequencing costs and improvements in third-generation sequencing technologies1-3. For example, the number of vertebrate genome assemblies currently in the NCBI (National Center for Biotechnology Information) database4 increased by more than 50% to 1,485 assemblies in the year from July 2018 to July 2019. In addition to this influx of assemblies from different species, new human de novo assemblies5 are being produced, which enable the analysis of not only small polymorphisms, but also complex, large-scale structural differences between human individuals and haplotypes. This coming era and its unprecedented amount of data offer the opportunity to uncover many insights into genome evolution but also present challenges in how to adapt current analysis methods to meet the increased scale. Cactus6, a reference-free multiple genome alignment program, has been shown to be highly accurate, but the existing implementation scales poorly with increasing numbers of genomes, and struggles in regions of highly duplicated sequences. Here we describe progressive extensions to Cactus to create Progressive Cactus, which enables the reference-free alignment of tens to thousands of large vertebrate genomes while maintaining high alignment quality. We describe results from an alignment of more than 600 amniote genomes, which is to our knowledge the largest multiple vertebrate genome alignment created so far.", "doi": "10.1038/s41586-020-2871-y", "pmid": "33177663", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1615919"}, {"db": "pmc", "key": "PMC7673649"}, {"db": "pii", "key": "10.1038/s41586-020-2871-y"}], "notes": [], "created": "2026-08-20T08:56:20.261Z", "modified": "2026-08-20T08:56:56.935Z"}, {"entity": "publication", "iuid": "b8f68b45bcd643d784b9cf62a589160d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b8f68b45bcd643d784b9cf62a589160d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b8f68b45bcd643d784b9cf62a589160d"}}, "title": "Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates.", "authors": [{"family": "Damas", "given": "Joana", "initials": "J", "orcid": "0000-0003-4857-2510", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f60eb6afeabc435ea1e6378786162fa8.json"}}, {"family": "Hughes", "given": "Graham M", "initials": "GM", "orcid": "0000-0003-3088-345X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9785e94b95a3466dbb70ad8eb9b34ccd.json"}}, {"family": "Keough", "given": "Kathleen C", "initials": "KC", "orcid": "0000-0002-7481-0511", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27ba6707b77e4d0eb914e71063dab333.json"}}, {"family": "Painter", "given": "Corrie A", "initials": "CA", "orcid": "0000-0001-6174-1548", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d8344bb3d42144f98f550aa8f83e42d7.json"}}, {"family": "Persky", "given": "Nicole S", "initials": "NS", "orcid": "0000-0002-9948-2761", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ed0fc24668b242f1ab1c772856f17d24.json"}}, {"family": "Corbo", "given": "Marco", "initials": "M", "orcid": "0000-0002-4566-2724", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8133d835c1ec4fe4937748d71a6794e8.json"}}, {"family": "Hiller", "given": "Michael", "initials": "M", "orcid": "0000-0003-3024-1449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1005d0d1f4264b46b1cfe214c7aca246.json"}}, {"family": "Koepfli", "given": "Klaus-Peter", "initials": "KP", "orcid": "0000-0001-7281-0676", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/90e8966ff0e04ca391070664d52cdf04.json"}}, {"family": "Pfenning", "given": "Andreas R", "initials": "AR", "orcid": "0000-0002-3447-9801", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f7c2be6e32147d19f03c7ff88fb3f80.json"}}, {"family": "Zhao", "given": "Huabin", "initials": "H", "orcid": "0000-0002-7848-6392", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce72657ddbab4665991d934bf3ccfdbe.json"}}, {"family": "Genereux", "given": "Diane P", "initials": "DP", "orcid": "0000-0001-5770-0989", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/352ee25047c544aaa486a69e7e3333fc.json"}}, {"family": "Swofford", "given": "Ross", "initials": "R", "orcid": "0000-0003-3676-8479", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85b0174c633b417b933092763175bb1c.json"}}, {"family": "Pollard", "given": "Katherine S", "initials": "KS", "orcid": "0000-0002-9870-6196", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d080bc9bff548958f0c161612cdc4cf.json"}}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d18635ed6fa42d4bbcfddadae70e308.json"}}, {"family": "Nweeia", "given": "Martin T", "initials": "MT", "orcid": "0000-0001-7079-4123", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4846b6d146a4a7288db1543583a0158.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Teeling", "given": "Emma C", "initials": "EC", "orcid": "0000-0002-3309-1346", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28069443db794cb596e58aea060d9dea.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5059da24204049c696aec45b62526759.json"}}], "type": "comparative study", "published": "2020-09-08", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "117", "issue": "36", "pages": "22311-22322", "issn-l": "0027-8424"}, "abstract": "The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19. The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of ACE2 sequences from 410 vertebrate species, including 252 mammals, to study the conservation of ACE2 and its potential to be used as a receptor by SARS-CoV-2. We designed a five-category binding score based on the conservation properties of 25 amino acids important for the binding between ACE2 and the SARS-CoV-2 spike protein. Only mammals fell into the medium to very high categories and only catarrhine primates into the very high category, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 spike protein binding and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (frequency <0.001) variants in 10/25 binding sites. In addition, we found significant signals of selection and accelerated evolution in the ACE2 coding sequence across all mammals, and specific to the bat lineage. Our results, if confirmed by additional experimental data, may lead to the identification of intermediate host species for SARS-CoV-2, guide the selection of animal models of COVID-19, and assist the conservation of animals both in native habitats and in human care.", "doi": "10.1073/pnas.2010146117", "pmid": "32826334", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7486773"}, {"db": "pii", "key": "2010146117"}], "notes": [], "created": "2026-08-20T09:30:48.684Z", "modified": "2026-08-20T09:30:49.333Z"}, {"entity": "publication", "iuid": "8624d906d1e24618a40cccf883d5bb4d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8624d906d1e24618a40cccf883d5bb4d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8624d906d1e24618a40cccf883d5bb4d"}}, "title": "Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals.", "authors": [{"family": "Casewell", "given": "Nicholas R", "initials": "NR", "orcid": "0000-0002-8035-4719", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55a396fc6b444511831b3fab0301fab6.json"}}, {"family": "Petras", "given": "Daniel", "initials": "D", "orcid": "0000-0002-6561-3022", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f150f02896549d4a761b566a35ad324.json"}}, {"family": "Card", "given": "Daren C", "initials": "DC"}, {"family": "Suranse", "given": "Vivek", "initials": "V"}, {"family": "Mychajliw", "given": "Alexis M", "initials": "AM"}, {"family": "Richards", "given": "David", "initials": "D"}, {"family": "Koludarov", "given": "Ivan", "initials": "I"}, {"family": "Albulescu", "given": "Laura-Oana", "initials": "LO"}, {"family": "Slagboom", "given": "Julien", "initials": "J"}, {"family": "Hempel", "given": "Benjamin-Florian", "initials": "BF"}, {"family": "Ngum", "given": "Neville M", "initials": "NM"}, {"family": "Kennerley", "given": "Rosalind J", "initials": "RJ"}, {"family": "Brocca", "given": "Jorge L", "initials": "JL"}, {"family": "Whiteley", "given": "Gareth", "initials": "G"}, {"family": "Harrison", "given": "Robert A", "initials": "RA"}, {"family": "Bolton", "given": "Fiona M S", "initials": "FMS"}, {"family": "Debono", "given": "Jordan", "initials": "J"}, {"family": "Vonk", "given": "Freek J", "initials": "FJ"}, {"family": "Alf\u00f6ldi", "given": "Jessica", "initials": "J"}, {"family": "Johnson", "given": "Jeremy", "initials": "J"}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Mellor", "given": "Ian R", "initials": "IR"}, {"family": "S\u00fcssmuth", "given": "Roderich D", "initials": "RD"}, {"family": "Fry", "given": "Bryan G", "initials": "BG", "orcid": "0000-0001-6661-1283", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/87705340b9f543afb27fe96c7525d0fd.json"}}, {"family": "Kuruppu", "given": "Sanjaya", "initials": "S"}, {"family": "Hodgson", "given": "Wayne C", "initials": "WC"}, {"family": "Kool", "given": "Jeroen", "initials": "J"}, {"family": "Castoe", "given": "Todd A", "initials": "TA"}, {"family": "Barnes", "given": "Ian", "initials": "I", "orcid": "0000-0001-8322-6918", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e706d69898324d919e97ec1899a2f0c8.json"}}, {"family": "Sunagar", "given": "Kartik", "initials": "K", "orcid": "0000-0003-0998-1581", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/19962794263d411b96425e2b99024a47.json"}}, {"family": "Undheim", "given": "Eivind A B", "initials": "EAB", "orcid": "0000-0002-8667-3999", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c0af2f7915b14b8e8b062ab7b72c7987.json"}}, {"family": "Turvey", "given": "Samuel T", "initials": "ST"}], "type": "journal article", "published": "2019-12-17", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "116", "issue": "51", "pages": "25745-25755", "issn-l": "0027-8424"}, "abstract": "Venom systems are key adaptations that have evolved throughout the tree of life and typically facilitate predation or defense. Despite venoms being model systems for studying a variety of evolutionary and physiological processes, many taxonomic groups remain understudied, including venomous mammals. Within the order Eulipotyphla, multiple shrew species and solenodons have oral venom systems. Despite morphological variation of their delivery systems, it remains unclear whether venom represents the ancestral state in this group or is the result of multiple independent origins. We investigated the origin and evolution of venom in eulipotyphlans by characterizing the venom system of the endangered Hispaniolan solenodon (Solenodon paradoxus). We constructed a genome to underpin proteomic identifications of solenodon venom toxins, before undertaking evolutionary analyses of those constituents, and functional assessments of the secreted venom. Our findings show that solenodon venom consists of multiple paralogous kallikrein 1 (KLK1) serine proteases, which cause hypotensive effects in vivo, and seem likely to have evolved to facilitate vertebrate prey capture. Comparative analyses provide convincing evidence that the oral venom systems of solenodons and shrews have evolved convergently, with the 4 independent origins of venom in eulipotyphlans outnumbering all other venom origins in mammals. We find that KLK1s have been independently coopted into the venom of shrews and solenodons following their divergence during the late Cretaceous, suggesting that evolutionary constraints may be acting on these genes. Consequently, our findings represent a striking example of convergent molecular evolution and demonstrate that distinct structural backgrounds can yield equivalent functions.", "doi": "10.1073/pnas.1906117116", "pmid": "31772017", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6926037"}, {"db": "pii", "key": "1906117116"}, {"db": "figshare", "key": "10.6084/m9.figshare.7640456"}], "notes": [], "created": "2026-08-20T09:30:29.471Z", "modified": "2026-08-20T09:30:29.766Z"}, {"entity": "publication", "iuid": "d365ac0a2fe941bbb47a27b146d888b1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d365ac0a2fe941bbb47a27b146d888b1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d365ac0a2fe941bbb47a27b146d888b1"}}, "title": "Comparative Genomics Reveals Shared Mutational Landscape in Canine Hemangiosarcoma and Human Angiosarcoma.", "authors": [{"family": "Megquier", "given": "Kate", "initials": "K", "orcid": "0000-0002-1458-0865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d84d6a467fac40d5a926885732eca967.json"}}, {"family": "Turner-Maier", "given": "Jason", "initials": "J"}, {"family": "Swofford", "given": "Ross", "initials": "R"}, {"family": "Kim", "given": "Jong-Hyuk", "initials": "JH", "orcid": "0000-0002-1645-0036", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3553b69d2420463ca6a24d52696a7da7.json"}}, {"family": "Sarver", "given": "Aaron L", "initials": "AL"}, {"family": "Wang", "given": "Chao", "initials": "C"}, {"family": "Sakthikumar", "given": "Sharadha", "initials": "S", "orcid": "0000-0002-7746-8264", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/38967e663cdc4351ae2c0c090ab8c39e.json"}}, {"family": "Johnson", "given": "Jeremy", "initials": "J"}, {"family": "Koltookian", "given": "Michele", "initials": "M"}, {"family": "Lewellen", "given": "Mitzi", "initials": "M"}, {"family": "Scott", "given": "Milcah C", "initials": "MC"}, {"family": "Schulte", "given": "Ashley J", "initials": "AJ"}, {"family": "Borst", "given": "Luke", "initials": "L"}, {"family": "Tonomura", "given": "Noriko", "initials": "N"}, {"family": "Alfoldi", "given": "Jessica", "initials": "J"}, {"family": "Painter", "given": "Corrie", "initials": "C"}, {"family": "Thomas", "given": "Rachael", "initials": "R", "orcid": "0000-0002-3029-8798", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d7613e07c9b242748a912e2ab73a5542.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Breen", "given": "Matthew", "initials": "M"}, {"family": "Modiano", "given": "Jaime F", "initials": "JF", "orcid": "0000-0001-6398-7648", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ba4bb579a21472dab716ebf61874801.json"}}, {"family": "Elvers", "given": "Ingegerd", "initials": "I"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}], "type": "journal article", "published": "2019-12-00", "journal": {"title": "Mol. Cancer Res.", "issn": "1557-3125", "volume": "17", "issue": "12", "pages": "2410-2421", "issn-l": "1541-7786"}, "abstract": "Angiosarcoma is a highly aggressive cancer of blood vessel-forming cells with few effective treatment options and high patient mortality. It is both rare and heterogenous, making large, well-powered genomic studies nearly impossible. Dogs commonly suffer from a similar cancer, called hemangiosarcoma, with breeds like the golden retriever carrying heritable genetic factors that put them at high risk. If the clinical similarity of canine hemangiosarcoma and human angiosarcoma reflects shared genomic etiology, dogs could be a critically needed model for advancing angiosarcoma research. We assessed the genomic landscape of canine hemangiosarcoma via whole-exome sequencing (47 golden retriever hemangiosarcomas) and RNA sequencing (74 hemangiosarcomas from multiple breeds). Somatic coding mutations occurred most frequently in the tumor suppressor TP53 (59.6% of cases) as well as two genes in the PI3K pathway: the oncogene PIK3CA (29.8%) and its regulatory subunit PIK3R1 (8.5%). The predominant mutational signature was the age-associated deamination of cytosine to thymine. As reported in human angiosarcoma, CDKN2A/B was recurrently deleted and VEGFA, KDR, and KIT recurrently gained. We compared the canine data to human data recently released by The Angiosarcoma Project, and found many of the same genes and pathways significantly enriched for somatic mutations, particularly in breast and visceral angiosarcomas. Canine hemangiosarcoma closely models the genomic landscape of human angiosarcoma of the breast and viscera, and is a powerful tool for investigating the pathogenesis of this devastating disease. IMPLICATIONS: We characterize the genomic landscape of canine hemangiosarcoma and demonstrate its similarity to human angiosarcoma.", "doi": "10.1158/1541-7786.MCR-19-0221", "pmid": "31570656", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1540746"}, {"db": "pmc", "key": "PMC7067513"}, {"db": "pii", "key": "1541-7786.MCR-19-0221"}], "notes": [], "created": "2026-08-20T12:14:09.684Z", "modified": "2026-08-20T12:14:09.813Z"}, {"entity": "publication", "iuid": "8955a5a719694fbea4af383469a1bf34", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8955a5a719694fbea4af383469a1bf34.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8955a5a719694fbea4af383469a1bf34"}}, "title": "BarkBase: Epigenomic Annotation of Canine Genomes.", "authors": [{"family": "Megquier", "given": "Kate", "initials": "K"}, {"family": "Genereux", "given": "Diane P", "initials": "DP", "orcid": "0000-0001-5770-0989", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/352ee25047c544aaa486a69e7e3333fc.json"}}, {"family": "Hekman", "given": "Jessica", "initials": "J", "orcid": "0000-0002-7296-8307", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f3ef16c6ca1145a3b6f2481005c1c137.json"}}, {"family": "Swofford", "given": "Ross", "initials": "R"}, {"family": "Turner-Maier", "given": "Jason", "initials": "J"}, {"family": "Johnson", "given": "Jeremy", "initials": "J"}, {"family": "Alonso", "given": "Jacob", "initials": "J"}, {"family": "Li", "given": "Xue", "initials": "X"}, {"family": "Morrill", "given": "Kathleen", "initials": "K"}, {"family": "Anguish", "given": "Lynne J", "initials": "LJ"}, {"family": "Koltookian", "given": "Michele", "initials": "M"}, {"family": "Logan", "given": "Brittney", "initials": "B"}, {"family": "Sharp", "given": "Claire R", "initials": "CR", "orcid": "0000-0002-1797-9783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cae69274b2f445dbb4fb184d783fee58.json"}}, {"family": "Ferrer", "given": "Lluis", "initials": "L"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Meyers-Wallen", "given": "Vicki N", "initials": "VN"}, {"family": "Hoffman", "given": "Andrew", "initials": "A"}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}], "type": "journal article", "published": "2019-06-07", "journal": {"title": "Genes (Basel)", "issn": "2073-4425", "volume": "10", "issue": "6", "issn-l": "2073-4425"}, "abstract": "Dogs are an unparalleled natural model for investigating the genetics of health and disease, particularly for complex diseases like cancer. Comprehensive genomic annotation of regulatory elements active in healthy canine tissues is crucial both for identifying candidate causal variants and for designing functional studies needed to translate genetic associations into disease insight. Currently, canine geneticists rely primarily on annotations of the human or mouse genome that have been remapped to dog, an approach that misses dog-specific features. Here, we describe BarkBase, a canine epigenomic resource available at barkbase.org. BarkBase hosts data for 27 adult tissue types, with biological replicates, and for one sample of up to five tissues sampled at each of four carefully staged embryonic time points. RNA sequencing is complemented with whole genome sequencing and with assay for transposase-accessible chromatin using sequencing (ATAC-seq), which identifies open chromatin regions. By including replicates, we can more confidently discern tissue-specific transcripts and assess differential gene expression between tissues and timepoints. By offering data in easy-to-use file formats, through a visual browser modeled on similar genomic resources for human, BarkBase introduces a powerful new resource to support comparative studies in dogs and humans.", "doi": "10.3390/genes10060433", "pmid": "31181663", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6627511"}, {"db": "pii", "key": "genes10060433"}], "notes": [], "created": "2026-08-20T13:40:36.288Z", "modified": "2026-08-20T13:40:36.465Z"}]}