{"entity": "researcher", "timestamp": "2026-06-08T05:06:58.981Z", "family": "Kaplow", "given": "Irene M", "initials": "IM", "orcid": "0000-0002-8924-8269", "affiliations": ["Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.", "Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/9bbc94842b1f4195b678beee7cc8cf6e.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/9bbc94842b1f4195b678beee7cc8cf6e"}}, "publications": [{"entity": "publication", "iuid": "bfb6fdc7339947a692119410b04c42a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bfb6fdc7339947a692119410b04c42a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bfb6fdc7339947a692119410b04c42a1"}}, "title": "Relating enhancer genetic variation across mammals to complex phenotypes using machine learning.", "authors": [{"family": "Kaplow", "given": "Irene M", "initials": "IM", "orcid": "0000-0002-8924-8269", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bbc94842b1f4195b678beee7cc8cf6e.json"}}, {"family": "Lawler", "given": "Alyssa J", "initials": "AJ", "orcid": "0000-0002-2151-5164", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ac870df8d074925b9956e82fba828eb.json"}}, {"family": "Sch\u00e4ffer", "given": "Daniel E", "initials": "DE", "orcid": "0000-0003-3608-152X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0be4ccbb9fd247eaa3320c4f1a8d64dc.json"}}, {"family": "Srinivasan", "given": "Chaitanya", "initials": "C", "orcid": "0000-0002-1487-541X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1f3803c67844809b8d460e321034287.json"}}, {"family": "Sestili", "given": "Heather H", "initials": "HH", "orcid": "0000-0002-3944-3429", "researcher": {"href": "https://publications.scilifelab.se/researcher/247a3b572c934443a8b06bf1eeab2e06.json"}}, {"family": "Wirthlin", "given": "Morgan E", "initials": "ME", "orcid": "0000-0001-7967-7070", "researcher": {"href": "https://publications.scilifelab.se/researcher/d37d43eda07f49fa8f44adf0d1f41b5a.json"}}, {"family": "Phan", "given": "BaDoi N", "initials": "BN", "orcid": "0000-0001-6331-5980", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9e37df4e5c54204a19ea394e1f7651e.json"}}, {"family": "Prasad", "given": "Kavya", "initials": "K", "orcid": "0000-0003-3419-5670", "researcher": {"href": "https://publications.scilifelab.se/researcher/68bbc313fcd344e2adb1ab5d8d7f8581.json"}}, {"family": "Brown", "given": "Ashley R", "initials": "AR", "orcid": "0000-0002-3091-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/31ed0f654aa3485e8b2a02f902981f32.json"}}, {"family": "Zhang", "given": "Xiaomeng", "initials": "X", "orcid": "0000-0002-8536-6460", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f4e1e573fa54ccc88171795e61d2a7a.json"}}, {"family": "Foley", "given": "Kathleen", "initials": "K", "orcid": "0000-0003-0923-1326", "researcher": {"href": "https://publications.scilifelab.se/researcher/03f76d7e48d843d39046582156da3615.json"}}, {"family": "Genereux", "given": "Diane P", "initials": "DP", "orcid": "0000-0001-5770-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dedda53aab044eabd09ae377084ff9d.json"}}, {"family": "Zoonomia Consortium**", "given": "", "initials": ""}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Meyer", "given": "Wynn K", "initials": "WK", "orcid": "0000-0001-7978-3877", "researcher": {"href": "https://publications.scilifelab.se/researcher/d168f23b63994217b3b082c3cd70561b.json"}}, {"family": "Pfenning", "given": "Andreas R", "initials": "AR", "orcid": "0000-0002-3447-9801", "researcher": {"href": "https://publications.scilifelab.se/researcher/579e32fe57da4d738b7fbf0a57fb6faf.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabm7993"}, "abstract": "Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.", "doi": "10.1126/science.abm7993", "pmid": "37104615", "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": "NIHMS1897368"}, {"db": "pmc", "key": "PMC10322212"}], "notes": [], "created": "2023-12-01T09:07:36.543Z", "modified": "2024-01-16T13:48:33.603Z"}, {"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.", 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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"}]}