{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T00:56:00Z","timestamp":1767920160417,"version":"3.49.0"},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2022,8,30]],"date-time":"2022-08-30T00:00:00Z","timestamp":1661817600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Laboratory of Multivariate Statistics, Department of Brain and Behavioural Sciences, Medical and Genomic Statistics Unit"},{"DOI":"10.13039\/501100004769","name":"University of Pavia","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004769","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,10,14]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>With the advent of high-throughput sequencing in molecular biology and medicine, the need for scalable statistical solutions for modeling complex biological systems has become of critical importance. The increasing number of platforms and possible experimental scenarios raised the problem of integrating large amounts of new heterogeneous data and current knowledge, to test novel hypotheses and improve our comprehension of physiological processes and diseases.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Combining network analysis and causal inference within the framework of structural equation modeling (SEM), we developed the R package SEMgraph. It provides a fully automated toolkit, managing complex biological systems as multivariate networks, ensuring robustness and reproducibility through data-driven evaluation of model architecture and perturbation, which is readily interpretable in terms of causal effects among system components.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>SEMgraph package is available at https:\/\/cran.r-project.org\/web\/packages\/SEMgraph.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac567","type":"journal-article","created":{"date-parts":[[2022,8,29]],"date-time":"2022-08-29T20:17:22Z","timestamp":1661804242000},"page":"4829-4830","source":"Crossref","is-referenced-by-count":16,"title":["SEMgraph: an R package for causal network inference of high-throughput data with structural equation models"],"prefix":"10.1093","volume":"38","author":[{"given":"Mario","family":"Grassi","sequence":"first","affiliation":[{"name":"Department of Brain and Behavioral Sciences, University of Pavia , Pavia 27100, Italy"}]},{"given":"Fernando","family":"Palluzzi","sequence":"additional","affiliation":[{"name":"Department of Brain and Behavioral Sciences, University of Pavia , Pavia 27100, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6384-2561","authenticated-orcid":false,"given":"Barbara","family":"Tarantino","sequence":"additional","affiliation":[{"name":"Department of Brain and Behavioral Sciences, University of Pavia , Pavia 27100, Italy"}]}],"member":"286","published-online":{"date-parts":[[2022,8,30]]},"reference":[{"key":"2022101415191277700_btac567-B1","doi-asserted-by":"crossref","DOI":"10.1002\/9781118619179","volume-title":"Structural Equations With Latent Variables","author":"Bollen","year":"1989","edition":"1st edn"},{"key":"2022101415191277700_btac567-B2","doi-asserted-by":"crossref","first-page":"e0127376","DOI":"10.1371\/journal.pone.0127376","article-title":"C9ORF72 GGGGCC expanded repeats produce splicing dysregulation which correlates with disease severity in amyotrophic lateral sclerosis","volume":"10","author":"Cooper-Knock","year":"2015","journal-title":"PLoS One"},{"key":"2022101415191277700_btac567-B3","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511803161","volume-title":"Causality: Models, Reasoning, and Inference","author":"Pearl","year":"2009","edition":"2nd edn"},{"key":"2022101415191277700_btac567-B4","first-page":"1","article-title":"On efficient adjustment in causal graphs","volume":"21","author":"Witte","year":"2020","journal-title":"J. Mach. Learn. 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