{"entity": "researcher", "timestamp": "2026-07-20T22:51:04.422Z", "family": "Lohi", "given": "Hannes", "initials": "H", "orcid": "0000-0003-1087-5532", "affiliations": ["Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkh\u00e4lsan Research Center, 02900, Helsinki, Finland."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/903f658d43ea414fb37ef530df3e15e4.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/903f658d43ea414fb37ef530df3e15e4"}}, "publications": [{"entity": "publication", "iuid": "af16f7f2a5004801bdd004545bd190b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af16f7f2a5004801bdd004545bd190b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af16f7f2a5004801bdd004545bd190b9"}}, "title": "The DoGA consortium expression atlas of promoters and genes in 100 canine tissues.", "authors": [{"family": "H\u00f6rtenhuber", "given": "Matthias", "initials": "M", "orcid": "0000-0002-5599-5565", "researcher": {"href": "https://publications.scilifelab.se/researcher/a02296c8f90742c6a9de21e12359560c.json"}}, {"family": "Hyt\u00f6nen", "given": "Marjo K", "initials": "MK", "orcid": "0000-0003-1976-5874", "researcher": {"href": "https://publications.scilifelab.se/researcher/89e3788ab09f415f918f0bf9ed441fac.json"}}, {"family": "Mukarram", "given": "Abdul Kadir", "initials": "AK"}, {"family": "Arumilli", "given": "Meharji", "initials": "M"}, {"family": "Araujo", "given": "C\u00e9sar L", "initials": "CL"}, {"family": "Quintero", "given": "Ileana", "initials": "I", "orcid": "0000-0001-7040-1289", "researcher": {"href": "https://publications.scilifelab.se/researcher/208e9727fc004f10acca1e3ed3244366.json"}}, {"family": "Syrj\u00e4", "given": "Pernilla", "initials": "P"}, {"family": "Airas", "given": "Niina", "initials": "N"}, {"family": "Kaukonen", "given": "Maria", "initials": "M", "orcid": "0000-0002-2146-4694", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4e0e0816a714e72976563c625549785.json"}}, {"family": "Ky\u00f6stil\u00e4", "given": "Kaisa", "initials": "K"}, {"family": "Niskanen", "given": "Julia", "initials": "J", "orcid": "0000-0002-2871-6890", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c9070b3a4bb4b9f93f85caf587b2b98.json"}}, {"family": "Jokinen", "given": "Tarja S", "initials": "TS", "orcid": "0000-0001-6389-0109", "researcher": {"href": "https://publications.scilifelab.se/researcher/435d360e63f94f48831777352c2e1d9a.json"}}, {"family": "Mottaghitalab", "given": "Faezeh", "initials": "F", "orcid": "0000-0001-6495-6667", "researcher": {"href": "https://publications.scilifelab.se/researcher/faed0b7f48c144de81c6720b9866b50f.json"}}, {"family": "Takan", "given": "I\u015f\u0131l", "initials": "I", "orcid": "0000-0002-0269-6625", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7c6daf8dc524e21a2d44de764146965.json"}}, {"family": "Salokorpi", "given": "Noora", "initials": "N"}, {"family": "Raman", "given": "Amitha", "initials": "A"}, {"family": "Stevens", "given": "Irene", "initials": "I", "orcid": "0000-0003-3823-1499", "researcher": {"href": "https://publications.scilifelab.se/researcher/90f6fa81197146ae946e2f68630c1238.json"}}, {"family": "Iivanainen", "given": "Antti", "initials": "A", "orcid": "0000-0003-1002-3225", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f39943341f5457986553f672841ae04.json"}}, {"family": "Yoshihara", "given": "Masahito", "initials": "M", "orcid": "0000-0002-8915-9282", "researcher": {"href": "https://publications.scilifelab.se/researcher/4303ab7a18254bb59f8e2386a7f7fb0a.json"}}, {"family": "Gusev", "given": "Oleg", "initials": "O", "orcid": "0000-0002-6203-9758", "researcher": {"href": "https://publications.scilifelab.se/researcher/31d4a1b245d449428a6fe219c91cde24.json"}}, {"family": "Bannasch", "given": "Danika", "initials": "D", "orcid": "0000-0002-7614-7207", "researcher": {"href": "https://publications.scilifelab.se/researcher/828a952f3be54507bedcb950fbafaf12.json"}}, {"family": "Sukura", "given": "Antti", "initials": "A", "orcid": "0000-0002-8992-1695", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea53fec228424344bd642575de25aec3.json"}}, {"family": "Schoenebeck", "given": "Jeffrey J", "initials": "JJ", "orcid": "0000-0003-4964-2138", "researcher": {"href": "https://publications.scilifelab.se/researcher/674777750c7144d783483e2c8f130b8b.json"}}, {"family": "DoGA Consortium", "given": "", "initials": ""}, {"family": "Ezer", "given": "Sini", "initials": "S"}, {"family": "Katayama", "given": "Shintaro", "initials": "S", "orcid": "0000-0001-7581-5157", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7765acd351b40c091615258c3d751b4.json"}}, {"family": "Daub", "given": "Carsten O", "initials": "CO", "orcid": "0000-0002-3295-8729", "researcher": {"href": "https://publications.scilifelab.se/researcher/eda6a90f9d9046ada163d9843d169393.json"}}, {"family": "Kere", "given": "Juha", "initials": "J", "orcid": "0000-0003-1974-0271", "researcher": {"href": "https://publications.scilifelab.se/researcher/102085fb1c3147ceaf8dcb7651df1303.json"}}, {"family": "Lohi", "given": "Hannes", "initials": "H", "orcid": "0000-0003-1087-5532", "researcher": {"href": "https://publications.scilifelab.se/researcher/903f658d43ea414fb37ef530df3e15e4.json"}}], "type": "journal article", "published": "2024-10-21", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "9082", "issn-l": "2041-1723"}, "abstract": "The dog, Canis lupus familiaris, is an important model for studying human diseases. Unlike many model organisms, the dog genome has a comparatively poor functional annotation, which hampers gene discovery for development, morphology, disease, and behavior. To fill this gap, we established a comprehensive tissue biobank for both the dog and wolf samples. The biobank consists of 5485 samples representing 132 tissues from 13 dogs, 12 dog embryos, and 24 wolves. In a subset of 100 tissues from nine dogs and 12 embryos, we characterized gene expression activity for each promoter, including alternative and novel, i.e., previously not annotated, promoter regions, using the 5' targeting RNA sequencing technology STRT2-seq. We identified over 100,000 promoter region candidates in the recent canine genome assembly, CanFam4, including over 45,000 highly reproducible sites with gene expression and respective tissue enrichment levels. We provide a promoter and gene expression atlas with interactive, open data resources, including a data coordination center and genome browser track hubs. We demonstrated the applicability of Dog Genome Annotation (DoGA) data and resources using multiple examples spanning canine embryonic development, morphology and behavior, and diseases across species.", "doi": "10.1038/s41467-024-52798-1", "pmid": "39433728", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11494170"}, {"db": "pii", "key": "10.1038/s41467-024-52798-1"}], "notes": [], "created": "2025-02-28T14:14:28.582Z", "modified": "2025-02-28T14:14:29.644Z"}, {"entity": "publication", "iuid": "a6e01a3cb4e94b1f8abee9bf3a1dcada", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a6e01a3cb4e94b1f8abee9bf3a1dcada.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a6e01a3cb4e94b1f8abee9bf3a1dcada"}}, "title": "Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture.", "authors": [{"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications.scilifelab.se/researcher/86acdca0104c4552880d5a7cb5ac6565.json"}}, {"family": "Kidd", "given": "Jeffrey M", "initials": "JM", "orcid": "0000-0002-9631-1465", "researcher": {"href": "https://publications.scilifelab.se/researcher/443559b87cc54118873bf603b40a2859.json"}}, {"family": "Wang", "given": "Guo-Dong", "initials": "G"}, {"family": "Parker", "given": "Heidi G", "initials": "HG", "orcid": "0000-0002-9707-6380", "researcher": {"href": "https://publications.scilifelab.se/researcher/51a8621269234efba8a9db6e56198d34.json"}}, {"family": "Schall", "given": "Peter Z", "initials": "PZ", "orcid": "0000-0003-1016-6998", "researcher": {"href": "https://publications.scilifelab.se/researcher/769dfe26fcfc49ceb8178ef7ae55b304.json"}}, {"family": "Bianchi", "given": "Matteo", "initials": "M", "orcid": "0000-0003-3394-6495", "researcher": {"href": "https://publications.scilifelab.se/researcher/d645ef0e04a245f0ac9e7d7498b2bd69.json"}}, {"family": "Christmas", "given": "Matthew J", "initials": "MJ", "orcid": "0000-0002-6355-7581", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e069a0271e4a1fbc31fd3cb440366f.json"}}, {"family": "Bougiouri", "given": "Katia", "initials": "K", "orcid": "0000-0002-7890-2755", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f3e12cdbe6e4dd5acfc609275595f8b.json"}}, {"family": "Buckley", "given": "Reuben M", "initials": "RM", "orcid": "0000-0001-6334-3906", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f83f4dbc5a847e1aff7e5d0f55971ce.json"}}, {"family": "Hitte", "given": "Christophe", "initials": "C", "orcid": "0000-0003-1714-437X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d3a7672564d4111a42bcb497355b8c1.json"}}, {"family": "Nguyen", "given": "Anthony K", "initials": "AK", "orcid": "0000-0002-9634-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6352471c5cb492d9ebf3db25d29af47.json"}}, {"family": "Wang", "given": "Chao", "initials": "C", "orcid": "0000-0003-3936-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/202a8fd115e14824809a362a7cfc5a41.json"}}, {"family": "Jagannathan", "given": "Vidhya", "initials": "V", "orcid": "0000-0002-8155-0041", "researcher": {"href": "https://publications.scilifelab.se/researcher/b49072ce24044ccc8bbb3425be609ec5.json"}}, {"family": "Niskanen", "given": "Julia E", "initials": "JE", "orcid": "0000-0002-2871-6890", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c9070b3a4bb4b9f93f85caf587b2b98.json"}}, {"family": "Frantz", "given": "Laurent A F", "initials": "LAF", "orcid": "0000-0001-8030-3885", "researcher": {"href": "https://publications.scilifelab.se/researcher/76b1179f8ee34ebbbdd466fb977f3ce7.json"}}, {"family": "Arumilli", "given": "Meharji", "initials": "M"}, {"family": "Hundi", "given": "Sruthi", "initials": "S", "orcid": "0000-0002-5803-1841", "researcher": {"href": "https://publications.scilifelab.se/researcher/6874df319b014e4384fb593f2bbeb560.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Ginja", "given": "Catarina", "initials": "C", "orcid": "0000-0003-2278-7089", "researcher": {"href": "https://publications.scilifelab.se/researcher/56dfd5da6c504f16bb79196f54f8e833.json"}}, {"family": "Agustina", "given": "Kadek Karang", "initials": "KK", "orcid": "0000-0002-7128-0914", "researcher": {"href": "https://publications.scilifelab.se/researcher/88728c8a24db4794b2b44bc2affc64fe.json"}}, {"family": "Andr\u00e9", "given": "Catherine", "initials": "C"}, {"family": "Boyko", "given": "Adam R", "initials": "AR", "orcid": "0000-0002-9125-6874", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b0d17b0c37c427781065fe542810589.json"}}, {"family": "Davis", "given": "Brian W", "initials": "BW", "orcid": "0000-0002-6121-135X", "researcher": {"href": "https://publications.scilifelab.se/researcher/63981f53ab2e4dc09a4a2a62ae0b7a84.json"}}, {"family": "Dr\u00f6gem\u00fcller", "given": "Michaela", "initials": "M", "orcid": "0000-0001-9378-7903", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f0a8a9e9cd34fa3a633a808bcdad3b4.json"}}, {"family": "Feng", "given": "Xin-Yao", "initials": "X"}, {"family": "Gkagkavouzis", "given": "Konstantinos", "initials": "K"}, {"family": "Iliopoulos", "given": "Giorgos", "initials": "G"}, {"family": "Harris", "given": "Alexander C", "initials": "AC", "orcid": "0000-0002-6868-5363", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c2fbbbe8ed149528f5481f93e867d36.json"}}, {"family": "Hyt\u00f6nen", "given": "Marjo K", "initials": "MK", "orcid": "0000-0003-1976-5874", "researcher": {"href": "https://publications.scilifelab.se/researcher/89e3788ab09f415f918f0bf9ed441fac.json"}}, {"family": "Kalthoff", "given": "Daniela C", "initials": "DC", "orcid": "0000-0003-2439-5484", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c18227dc17f428daca466f6fc7d3888.json"}}, {"family": "Liu", "given": "Yan-Hu", "initials": "Y"}, {"family": "Lymberakis", "given": "Petros", "initials": "P"}, {"family": "Poulakakis", "given": "Nikolaos", "initials": "N"}, {"family": "Pires", "given": "Ana Elisabete", "initials": "AE", "orcid": "0000-0002-1118-8569", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8856555c77443eb8038f5e6c9cead89.json"}}, {"family": "Racimo", "given": "Fernando", "initials": "F", "orcid": "0000-0002-5025-2607", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcd12137b4184a72a81c48d2926c5280.json"}}, {"family": "Ramos-Almodovar", "given": "Fabian", "initials": "F", "orcid": "0000-0001-9094-7895", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ead8fce39844a2d8f9415780d2acdd1.json"}}, {"family": "Savolainen", "given": "Peter", "initials": "P", "orcid": "0000-0002-1495-8338", "researcher": {"href": "https://publications.scilifelab.se/researcher/af5298b9990946b080ac61188cb2b2af.json"}}, {"family": "Venetsani", "given": "Semina", "initials": "S"}, {"family": "Tammen", "given": "Imke", "initials": "I", "orcid": "0000-0002-5520-6597", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5d3f973dfae4a1a914ff8d023e1c5ad.json"}}, {"family": "Triantafyllidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0003-0469-011X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8323f04a414e405380d92113f3628ab8.json"}}, {"family": "vonHoldt", "given": "Bridgett", "initials": "B", "orcid": "0000-0001-6908-1687", "researcher": {"href": "https://publications.scilifelab.se/researcher/b49c5a042db049778ec2d777b985238e.json"}}, {"family": "Wayne", "given": "Robert K", "initials": "RK", "orcid": "0000-0003-3537-2245", "researcher": {"href": "https://publications.scilifelab.se/researcher/641654eaf0d14a2899ce760fda55bc52.json"}}, {"family": "Larson", "given": "Greger", "initials": "G", "orcid": "0000-0002-4092-0392", "researcher": {"href": "https://publications.scilifelab.se/researcher/8313c5d2d5a148349ad14e51deca8ab5.json"}}, {"family": "Nicholas", "given": "Frank W", "initials": "FW", "orcid": "0000-0002-9178-3965", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e6a880495ec4d8da0922ebc94f207db.json"}}, {"family": "Lohi", "given": "Hannes", "initials": "H", "orcid": "0000-0003-1087-5532", "researcher": {"href": "https://publications.scilifelab.se/researcher/903f658d43ea414fb37ef530df3e15e4.json"}}, {"family": "Leeb", "given": "Tosso", "initials": "T", "orcid": "0000-0003-0553-4880", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f3aab15785e4875a06b659c9ded0ddd.json"}}, {"family": "Zhang", "given": "Ya-Ping", "initials": "Y"}, {"family": "Ostrander", "given": "Elaine A", "initials": "EA", "orcid": "0000-0001-6075-9738", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d531414c37d46e987e06cca25f2f9de.json"}}], "type": "journal article", "published": "2023-08-15", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "issn-l": "1474-7596", "volume": "24", "issue": "1", "pages": "187"}, "abstract": "The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 \u00d7 data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function.\r\n\r\nWe report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection.\r\n\r\nWe have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.", "doi": "10.1186/s13059-023-03023-7", "pmid": "37582787", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10426128"}, {"db": "pii", "key": "10.1186/s13059-023-03023-7"}], "notes": [], "created": "2023-11-27T21:59:43.116Z", "modified": "2024-01-16T13:48:32.480Z"}]}