{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T09:33:06Z","timestamp":1763458386140,"version":"3.41.2"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2024,8,11]],"date-time":"2024-08-11T00:00:00Z","timestamp":1723334400000},"content-version":"vor","delay-in-days":10,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union Horizon 2020 research and innovation program","award":["847941"],"award-info":[{"award-number":["847941"]}]},{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","award":["310030_185292"],"award-info":[{"award-number":["310030_185292"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,8,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Mendelian randomization (MR) is a widely used approach to estimate causal effect of variation in gene expression on complex traits. Among several MR-based algorithms, transcriptome-wide summary statistics-based Mendelian Randomization approach (TWMR) enables the uses of multiple SNPs as instruments and multiple gene expression traits as exposures to facilitate causal inference in observational studies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here we present a Python-based implementation of TWMR and revTWMR. Our implementation offers GPU computational support for faster computations and robust computation mode resilient to highly correlated gene expressions and genetic variants<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>pyTWMR is available at github.com\/soreshkov\/pyTWMR.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae505","type":"journal-article","created":{"date-parts":[[2024,8,10]],"date-time":"2024-08-10T00:26:28Z","timestamp":1723249588000},"source":"Crossref","is-referenced-by-count":1,"title":["pyTWMR: transcriptome-wide Mendelian randomization in python"],"prefix":"10.1093","volume":"40","author":[{"given":"Sergey","family":"Oreshkov","sequence":"first","affiliation":[{"name":"Endocrine, Diabetes and Metabolism Service, Centre Hospitalier Universitaire Vaudois (CHUV) , Lausanne 1005, Switzerland"},{"name":"Faculty of Biology and Medicine, University of Lausanne , Lausanne 1005, Switzerland"}]},{"given":"Kaido","family":"Lepik","sequence":"additional","affiliation":[{"name":"Department of Computational Biology, University of Lausanne , Lausanne 1015, Switzerland"},{"name":"University Center for Primary Care and Public Health, University of Lausanne , Lausanne 1005, Switzerland"},{"name":"Swiss Institute of Bioinformatics , Lausanne 1015, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3258-4747","authenticated-orcid":false,"given":"Federico","family":"Santoni","sequence":"additional","affiliation":[{"name":"Endocrine, Diabetes and Metabolism Service, Centre Hospitalier Universitaire Vaudois (CHUV) , Lausanne 1005, Switzerland"},{"name":"Faculty of Biology and Medicine, University of Lausanne , Lausanne 1005, Switzerland"},{"name":"Institute for Genetic and Biomedical Research (IRGB) - CNR , Monserrato 09042, Italy"}]}],"member":"286","published-online":{"date-parts":[[2024,8,10]]},"reference":[{"key":"2024082223014514500_btae505-B1","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1002\/gepi.21758","article-title":"Mendelian randomization analysis with multiple genetic variants using summarized data","volume":"37","author":"Burgess","year":"2013","journal-title":"Genet Epidemiol"},{"key":"2024082223014514500_btae505-B3","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1080\/00031305.2012.687494","article-title":"Who invented the Delta method?","volume":"66","author":"Ver Hoef","year":"2012","journal-title":"Am Stat"},{"key":"2024082223014514500_btae505-B4","doi-asserted-by":"crossref","first-page":"D896","DOI":"10.1093\/nar\/gkw1133","article-title":"The new NHGRI-EBI catalog of published genome-wide association studies (GWAS catalog)","volume":"45","author":"MacArthur","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2024082223014514500_btae505-B5","doi-asserted-by":"crossref","first-page":"5647","DOI":"10.1038\/s41467-021-25805-y","article-title":"Differentially expressed genes reflect disease-induced rather than disease-causing changes in the transcriptome","volume":"12","author":"Porcu","year":"2021","journal-title":"Nat Commun"},{"key":"2024082223014514500_btae505-B6","doi-asserted-by":"crossref","first-page":"3300","DOI":"10.1038\/s41467-019-10936-0","article-title":"Mendelian randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits","volume":"10","author":"Porcu","year":"2019","journal-title":"Nat Commun"},{"key":"2024082223014514500_btae505-B7","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1038\/s41576-019-0127-1","article-title":"Benefits and limitations of genome-wide association studies","volume":"20","author":"Tam","year":"2019","journal-title":"Nat Rev Genet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae505\/58796765\/btae505.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/8\/btae505\/58894645\/btae505.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/8\/btae505\/58894645\/btae505.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,22]],"date-time":"2024-08-22T23:55:52Z","timestamp":1724370952000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btae505\/7731496"}},"subtitle":[],"editor":[{"given":"Russell","family":"Schwartz","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2024,8]]},"references-count":6,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2024,8,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btae505","relation":{},"ISSN":["1367-4811"],"issn-type":[{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2024,8]]},"published":{"date-parts":[[2024,8]]},"article-number":"btae505"}}