{"entity": "researcher", "timestamp": "2026-08-20T21:22:58.170Z", "family": "Genereux", "given": "Diane P", "initials": "DP", "orcid": "0000-0001-5770-0989", "affiliations": ["Broad Institute of MIT and Harvard, Cambridge, MA 02142."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/352ee25047c544aaa486a69e7e3333fc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/352ee25047c544aaa486a69e7e3333fc"}}, "publications": [{"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": "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": "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"}]}