{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T00:53:19Z","timestamp":1773103999639,"version":"3.50.1"},"reference-count":73,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2021,2,3]],"date-time":"2021-02-03T00:00:00Z","timestamp":1612310400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institute of Health","doi-asserted-by":"publisher","award":["P01HL032262"],"award-info":[{"award-number":["P01HL032262"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institute of Health","doi-asserted-by":"publisher","award":["DP2HL137300"],"award-info":[{"award-number":["DP2HL137300"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institute of Health","doi-asserted-by":"publisher","award":["R00HG008399"],"award-info":[{"award-number":["R00HG008399"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institute of Health","doi-asserted-by":"publisher","award":["R35HG010717"],"award-info":[{"award-number":["R35HG010717"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Integrated Infrastructure for Social Mining and Big Data Analytics","award":["871042"],"award-info":[{"award-number":["871042"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Genome-wide association studies (GWASs) have identified thousands of common trait-associated genetic variants but interpretation of their function remains challenging. These genetic variants can overlap the binding sites of transcription factors (TFs) and therefore could alter gene expression. However, we currently lack a systematic understanding on how this mechanism contributes to phenotype.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present Motif-Raptor, a TF-centric computational tool that integrates sequence-based predictive models, chromatin accessibility, gene expression datasets and GWAS summary statistics to systematically investigate how TF function is affected by genetic variants. Given trait-associated non-coding variants, Motif-Raptor can recover relevant cell types and critical TFs to drive hypotheses regarding their mechanism of action. We tested Motif-Raptor on complex traits such as rheumatoid arthritis and red blood cell count and demonstrated its ability to prioritize relevant cell types, potential regulatory TFs and non-coding SNPs which have been previously characterized and validated.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Motif-Raptor is freely available as a Python package at: https:\/\/github.com\/pinellolab\/MotifRaptor.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab072","type":"journal-article","created":{"date-parts":[[2021,1,28]],"date-time":"2021-01-28T18:40:40Z","timestamp":1611859240000},"page":"2103-2111","source":"Crossref","is-referenced-by-count":10,"title":["Motif-Raptor: a cell type-specific and transcription factor centric approach for post-GWAS prioritization of causal regulators"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9974-8788","authenticated-orcid":false,"given":"Qiuming","family":"Yao","sequence":"first","affiliation":[{"name":"Department of Pathology, Massachusetts General Hospital , Charlestown, MA 02129, USA"},{"name":"Division of Hematology\/Oncology, Boston Children\u2019s Hospital , Boston, MA 02115, USA"},{"name":"Harvard Medical School , Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paolo","family":"Ferragina","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Pisa , Pisa 56128, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yakir","family":"Reshef","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Harvard University , Cambridge, MA 02138, USA"},{"name":"Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7740-3399","authenticated-orcid":false,"given":"Guillaume","family":"Lettre","sequence":"additional","affiliation":[{"name":"Faculty of Medicine, Universit\u00e9 de Montr\u00e9al , Montreal, Quebec H3C3J7, Canada"},{"name":"Montreal Heart Institute , Montreal, Quebec H1T1C8, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel E","family":"Bauer","sequence":"additional","affiliation":[{"name":"Division of Hematology\/Oncology, Boston Children\u2019s Hospital , Boston, MA 02115, USA"},{"name":"Harvard Medical School , Boston, MA 02115, USA"},{"name":"Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"},{"name":"Department of Pediatric Oncology, Dana-Farber Cancer Institute , Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1109-3823","authenticated-orcid":false,"given":"Luca","family":"Pinello","sequence":"additional","affiliation":[{"name":"Department of Pathology, Massachusetts General Hospital , Charlestown, MA 02129, USA"},{"name":"Harvard Medical School , Boston, MA 02115, USA"},{"name":"Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,2,3]]},"reference":[{"key":"2024041009305100900_btab072-B1","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1038\/nbt.3300","article-title":"Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning","volume":"33","author":"Alipanahi","year":"2015","journal-title":"Nat. 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