{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T16:16:18Z","timestamp":1772554578595,"version":"3.50.1"},"reference-count":20,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,6,27]],"date-time":"2024-06-27T00:00:00Z","timestamp":1719446400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,6,27]],"date-time":"2024-06-27T00:00:00Z","timestamp":1719446400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100005416","name":"Norges Forskningsr\u00e5d","doi-asserted-by":"publisher","award":["248804"],"award-info":[{"award-number":["248804"]}],"id":[{"id":"10.13039\/501100005416","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005416","name":"Norges Forskningsr\u00e5d","doi-asserted-by":"publisher","award":["248804"],"award-info":[{"award-number":["248804"]}],"id":[{"id":"10.13039\/501100005416","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005416","name":"Norges Forskningsr\u00e5d","doi-asserted-by":"publisher","award":["262111"],"award-info":[{"award-number":["262111"]}],"id":[{"id":"10.13039\/501100005416","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005416","name":"Norges Forskningsr\u00e5d","doi-asserted-by":"publisher","award":["248804"],"award-info":[{"award-number":["248804"]}],"id":[{"id":"10.13039\/501100005416","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>The matched case\u2013control design, up until recently mostly pertinent to epidemiological studies, is becoming customary in biomedical applications as well. For instance, in omics studies, it is quite common to compare cancer and healthy tissue from the same patient. Furthermore, researchers today routinely collect data from various and variable sources that they wish to relate to the case\u2013control status. This highlights the need to develop and implement statistical methods that can take these tendencies into account.\n<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>We present an R package , that provides an implementation of the penalized conditional logistic regression model for analyzing matched case\u2013control studies. It allows for different penalties for different blocks of covariates, and it is therefore particularly useful in the presence of multi-source omics data. Both L1 and L2 penalties are implemented. Additionally, the package implements stability selection for variable selection in the considered regression model.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>The proposed method fills a gap in the available software for fitting high-dimensional conditional logistic regression models accounting for the matched design and block structure of predictors\/features. The output consists of a set of selected variables that are significantly associated with case\u2013control status. These variables can then be investigated in terms of functional interpretation or validation in further, more targeted studies.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-024-05850-2","type":"journal-article","created":{"date-parts":[[2024,6,27]],"date-time":"2024-06-27T13:05:23Z","timestamp":1719493523000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["penalizedclr: an R package for penalized conditional logistic regression for integration of multiple omics layers"],"prefix":"10.1186","volume":"25","author":[{"given":"Vera","family":"Djordjilovi\u0107","sequence":"first","affiliation":[]},{"given":"Erica","family":"Ponzi","sequence":"additional","affiliation":[]},{"given":"Therese Haugdahl","family":"N\u00f8st","sequence":"additional","affiliation":[]},{"given":"Magne","family":"Thoresen","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2024,6,27]]},"reference":[{"issue":"6","key":"5850_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-16-S6-S1","volume":"16","author":"M Avalos","year":"2015","unstructured":"Avalos M, Pouyes H, Grandvalet Y, et al. Sparse conditional logistic regression for analyzing large-scale matched data from epidemiological studies: a simple algorithm. BMC Bioinf. 2015;16(6):1\u201311.","journal-title":"BMC Bioinf."},{"issue":"4","key":"5850_CR2","doi-asserted-by":"publisher","first-page":"639","DOI":"10.1111\/rssc.12056","volume":"63","author":"R Balasubramanian","year":"2014","unstructured":"Balasubramanian R, Houseman EA, Coull BA, et al. Variable importance in matched case-control studies in settings of high dimensional data. J R Stat Soc Ser C Appl Stat. 2014;63(4):639\u201355.","journal-title":"J R Stat Soc Ser C Appl Stat."},{"key":"5850_CR3","doi-asserted-by":"publisher","DOI":"10.1155\/2017\/7691937","author":"AL Boulesteix","year":"2017","unstructured":"Boulesteix AL, De Bin R, Jiang X, et al. IPF-LASSO: integrative-penalized regression with penalty factors for prediction based on multi-omics data. 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More information is available in [].","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no Conflict of interest.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"226"}}