{"entity": "researcher", "timestamp": "2026-08-15T07:19:56.271Z", "family": "Sabeti", "given": "Pardis C", "initials": "PC", "orcid": "0000-0002-9843-1890", "affiliations": ["Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.", "Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.", "Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/7a05c59f83114ac68c7bd1a0930fa0c9.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/7a05c59f83114ac68c7bd1a0930fa0c9"}}, "publications": [{"entity": "publication", "iuid": "0c70433579774cc297a55baabec049ea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0c70433579774cc297a55baabec049ea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0c70433579774cc297a55baabec049ea"}}, "title": "The functional and evolutionary impacts of human-specific deletions in conserved elements.", "authors": [{"family": "Xue", "given": "James R", "initials": "JR", "orcid": "0000-0002-3332-5747", "researcher": {"href": "https://publications.scilifelab.se/researcher/c910e64598674d5da576b3b5057afb43.json"}}, {"family": "Mackay-Smith", "given": "Ava", "initials": "A", "orcid": "0000-0003-0404-0563", "researcher": {"href": "https://publications.scilifelab.se/researcher/a60ce7b39d8c4b25bfddc8b8cd460970.json"}}, {"family": "Mouri", "given": "Kousuke", "initials": "K", "orcid": "0000-0003-1712-6833", "researcher": {"href": "https://publications.scilifelab.se/researcher/66c28c463e194c4395f03776335db2f1.json"}}, {"family": "Garcia", "given": "Meilin Fernandez", "initials": "MF", "orcid": "0000-0002-8745-9775", "researcher": {"href": "https://publications.scilifelab.se/researcher/c28f08d4f61f4c07ae57f56d220ab158.json"}}, {"family": "Dong", "given": "Michael X", "initials": "MX", "orcid": "0000-0003-4084-3099", "researcher": {"href": "https://publications.scilifelab.se/researcher/d44d219b319346c481c82d69d5055cd8.json"}}, {"family": "Akers", "given": "Jared F", "initials": "JF", "orcid": "0000-0002-9270-0017", "researcher": {"href": "https://publications.scilifelab.se/researcher/11555b05f1914cd8b1a63a07335d9f70.json"}}, {"family": "Noble", "given": "Mark", "initials": "M", "orcid": "0000-0002-9618-120X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d35842f19164723979bd2e19ae4c470.json"}}, {"family": "Li", "given": "Xue", "initials": "X", "orcid": "0000-0002-9126-2692", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfa777bbc9d34c0e9f4920decc7cdcb3.json"}}, {"family": "Zoonomia Consortium\u2020", "given": "", "initials": ""}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Noonan", "given": "James P", "initials": "JP", "orcid": "0000-0001-9632-5835", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e35cb8e4ed64e5a8c5583b81c29bb65.json"}}, {"family": "Capellini", "given": "Terence D", "initials": "TD", "orcid": "0000-0003-3842-8478", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ca4d388b3314861afe8593858bac9ab.json"}}, {"family": "Brennand", "given": "Kristen J", "initials": "KJ", "orcid": "0000-0003-0993-5956", "researcher": {"href": "https://publications.scilifelab.se/researcher/79ac89080d28492ab5fb4012939b0994.json"}}, {"family": "Tewhey", "given": "Ryan", "initials": "R", "orcid": "0000-0002-4607-8001", "researcher": {"href": "https://publications.scilifelab.se/researcher/08c06e4a031147ec8e0a4692b86a8198.json"}}, {"family": "Sabeti", "given": "Pardis C", "initials": "PC", "orcid": "0000-0002-9843-1890", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a05c59f83114ac68c7bd1a0930fa0c9.json"}}, {"family": "Reilly", "given": "Steven K", "initials": "SK", "orcid": "0000-0003-3140-1483", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c12bcf707394bb5b9c34075aba19f13.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn2253"}, "abstract": "Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) deletions are enriched for human brain functions across genetic, epigenomic, and transcriptomic datasets. Using massively parallel reporter assays in six cell types, we discovered 800 hCONDELs conferring significant differences in regulatory activity, half of which enhance rather than disrupt regulatory function. We highlight several hCONDELs with putative human-specific effects on brain development, including HDAC5, CPEB4, and PPP2CA. Reverting an hCONDEL to the ancestral sequence alters the expression of LOXL2 and developmental genes involved in myelination and synaptic function. Our data provide a rich resource to investigate the evolutionary mechanisms driving new traits in humans and other species.", "doi": "10.1126/science.abn2253", "pmid": "37104592", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1897409"}, {"db": "pmc", "key": "PMC10202372"}], "notes": [], "created": "2023-12-01T09:07:31.011Z", "modified": "2024-01-16T13:48:33.587Z"}, {"entity": "publication", "iuid": "d7e4da3ff4c54966b53e2e1210128441", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7e4da3ff4c54966b53e2e1210128441.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7e4da3ff4c54966b53e2e1210128441"}}, "title": "Evolutionary constraint and innovation across hundreds of placental mammals.", "authors": [{"family": "Christmas", "given": 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"type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn3943"}, "abstract": "Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.", "doi": "10.1126/science.abn3943", "pmid": "37104599", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1896905"}, {"db": "pmc", "key": "PMC10250106"}], "notes": [], "created": "2023-12-01T08:40:50.036Z", "modified": "2024-01-16T13:48:33.655Z"}]}