{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,24]],"date-time":"2026-01-24T18:00:31Z","timestamp":1769277631415,"version":"3.49.0"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,3,25]],"date-time":"2025-03-25T00:00:00Z","timestamp":1742860800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1R01GM148974-01"],"award-info":[{"award-number":["1R01GM148974-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DMS-2112943"],"award-info":[{"award-number":["DMS-2112943"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Mendelian randomization (MR) infers causal relationships between exposures and outcomes using genetic variants as instrumental variables. Typically, MR considers only a pair of exposure and outcome at a time, limiting its capability of capturing the entire causal network. We overcome this limitation by developing MR.RGM (Mendelian randomization via reciprocal graphical model), a fast R-package that implements the Bayesian reciprocal graphical model and enables practitioners to construct holistic causal networks with possibly cyclic\/reciprocal causation and proper uncertainty quantifications, offering a comprehensive understanding of complex biological systems and their interconnections.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed MR.RGM, an open-source R package that applies bidirectional MR using a network-based strategy, enabling the exploration of causal relationships among multiple variables in complex biological systems. MR.RGM holds the promise of unveiling intricate interactions and advancing our understanding of genetic networks, disease risks, and phenotypic complexities.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>MR.RGM is available at CRAN (https:\/\/CRAN.R-project.org\/package=MR.RGM, DOI: 10.32614\/CRAN.package.MR.RGM) and https:\/\/github.com\/bitansa\/MR.RGM.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf130","type":"journal-article","created":{"date-parts":[[2025,3,28]],"date-time":"2025-03-28T21:01:31Z","timestamp":1743195691000},"source":"Crossref","is-referenced-by-count":2,"title":["MR.RGM: an R package for fitting Bayesian multivariate bidirectional Mendelian randomization networks"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-5178-5934","authenticated-orcid":false,"given":"Bitan","family":"Sarkar","sequence":"first","affiliation":[{"name":"De , College Station, TX 77843,","place":["United States"]},{"name":"partment of Statistics, Texas A&M University , College Station, TX 77843,","place":["United States"]}]},{"given":"Yang","family":"Ni","sequence":"additional","affiliation":[{"name":"De , College Station, TX 77843,","place":["United States"]},{"name":"partment of Statistics, Texas A&M University , College Station, TX 77843,","place":["United States"]},{"name":"The University of Texas Department of Statistics and Data Sciences, , Austin, TX 78705,","place":["United States"]}]}],"member":"286","published-online":{"date-parts":[[2025,3,24]]},"reference":[{"key":"2025041602171794000_btaf130-B1","doi-asserted-by":"publisher","author":"Badsha","DOI":"10.32614\/CRAN.package.MRPC"},{"key":"2025041602171794000_btaf130-B2","author":"Bottolo"},{"key":"2025041602171794000_btaf130-B3","doi-asserted-by":"publisher","first-page":"512","DOI":"10.1093\/ije\/dyv080","article-title":"Mendelian randomization with invalid instruments: effect estimation and bias detection through Egger regression","volume":"44","author":"Bowden","year":"2015","journal-title":"Int J Epidemiol"},{"key":"2025041602171794000_btaf130-B4","doi-asserted-by":"publisher","author":"Burgess","DOI":"10.32614\/CRAN.package.MendelianRandomization"},{"key":"2025041602171794000_btaf130-B5","doi-asserted-by":"publisher","first-page":"1318","DOI":"10.1126\/science.aaz1776","article-title":"The GTEx Consortium atlas of genetic regulatory effects across human tissues","volume":"369","author":"GTEx Consortium","year":"2020","journal-title":"Science"},{"key":"2025041602171794000_btaf130-B6","doi-asserted-by":"publisher","first-page":"e34408","DOI":"10.7554\/eLife.34408","article-title":"The MR-Base platform supports systematic causal inference across the human phenome","volume":"7","author":"Hemani","year":"2018","journal-title":"eLife"},{"key":"2025041602171794000_btaf130-B7","doi-asserted-by":"publisher","first-page":"1095","DOI":"10.1214\/17-BA1087","volume-title":"Bayesian Anal","author":"Ni"},{"key":"2025041602171794000_btaf130-B8","doi-asserted-by":"publisher","author":"Palmer","year":", :     (), 2023.","DOI":"10.32614\/CRAN.package.OneSampleMR"},{"key":"2025041602171794000_btaf130-B9","doi-asserted-by":"publisher","first-page":"5434","DOI":"10.1002\/sim.9133","article-title":"Testing and correcting for weak and pleiotropic instruments in two-sample multivariable Mendelian randomization","volume":"40","author":"Sanderson","year":"2021","journal-title":"Stat Med"},{"key":"2025041602171794000_btaf130-B10","doi-asserted-by":"publisher","author":"Sarkar","year":", :     (), 2024.","DOI":"10.32614\/CRAN.package.MR.RGM"},{"key":"2025041602171794000_btaf130-B11","doi-asserted-by":"publisher","first-page":"658","DOI":"10.1002\/gepi.21758","article-title":"Mendelian randomization analysis with multiple genetic variants using summarized data","volume":"37","author":"Thompson","year":"2013","journal-title":"Genet Epidemiol"},{"key":"2025041602171794000_btaf130-B12","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1093\/ije\/dyaa191","article-title":"Software application profile: Bayesian estimation of inverse variance weighted and MR-Egger models for two-sample Mendelian randomization studies\u2014mrbayes","volume":"50","author":"Uche-Ikonne","year":"2021","journal-title":"Int J Epidemiol"},{"key":"2025041602171794000_btaf130-B13","doi-asserted-by":"publisher","author":"Xu","year":", :     (), 2022.","DOI":"10.32614\/CRAN.package.mr.pivw"},{"key":"2025041602171794000_btaf130-B14","doi-asserted-by":"publisher","author":"Yuan","year":", :     (), 2019.","DOI":"10.32614\/CRAN.package.PPMR"},{"key":"2025041602171794000_btaf130-B15","author":"Zhao","year":", :     (), 2018."},{"key":"2025041602171794000_btaf130-B16","doi-asserted-by":"publisher","author":"Zuber","year":"2024","DOI":"10.1101\/2024.06.18.599498"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf130\/62593531\/btaf130.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/4\/btaf130\/62593531\/btaf130.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/4\/btaf130\/62593531\/btaf130.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,16]],"date-time":"2025-04-16T06:17:27Z","timestamp":1744784247000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btaf130\/8092866"}},"subtitle":[],"editor":[{"given":"Lenore","family":"Cowen","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2025,3,24]]},"references-count":16,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2025,3,29]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf130","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,4]]},"published":{"date-parts":[[2025,3,24]]},"article-number":"btaf130"}}