{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:09Z","timestamp":1772138049464,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,9,16]],"date-time":"2021-09-16T00:00:00Z","timestamp":1631750400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Biomedical Research Program"},{"DOI":"10.13039\/100019460","name":"Weill Cornell Medical College in Qatar","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100019460","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Qatar Foundation and multiple grants from the Qatar National Research Fund"},{"name":"National Institute of Aging of the National Institutes of Health under","award":["1U19AG063744"],"award-info":[{"award-number":["1U19AG063744"]}]},{"name":"National Institute of Aging of the National Institutes of Health under","award":["1R01AG069901-01A1"],"award-info":[{"award-number":["1R01AG069901-01A1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>The \u2018Subgroup Identification\u2019 (SGI) toolbox provides an algorithm to automatically detect clinical subgroups of samples in large-scale omics datasets. It is based on hierarchical clustering trees in combination with a specifically designed association testing and visualization framework that can process an arbitrary number of clinical parameters and outcomes in a systematic fashion. A multi-block extension allows for the simultaneous use of multiple omics datasets on the same samples. In this article, we first describe the functionality of the toolbox and then demonstrate its capabilities through application examples on a type 2 diabetes metabolomics study as well as two copy number variation datasets from The Cancer Genome Atlas.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>SGI is an open-source package implemented in R. Package source codes and hands-on tutorials are available at https:\/\/github.com\/krumsieklab\/sgi. The QMdiab metabolomics data is included in the package and can be downloaded from https:\/\/doi.org\/10.6084\/m9.figshare.5904022.<\/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\/btab656","type":"journal-article","created":{"date-parts":[[2021,9,13]],"date-time":"2021-09-13T15:14:43Z","timestamp":1631546083000},"page":"573-576","source":"Crossref","is-referenced-by-count":3,"title":["SGI: automatic clinical subgroup identification in omics datasets"],"prefix":"10.1093","volume":"38","author":[{"given":"Mustafa","family":"Buyukozkan","sequence":"first","affiliation":[{"name":"Department of Physiology and Biophysics, Institute for Computational Biomedicine , New York, NY 10021, USA"},{"name":"Englander Institute for Precision Medicine, Weill Cornell Medicine , New York, NY 10021, USA"}]},{"given":"Karsten","family":"Suhre","sequence":"additional","affiliation":[{"name":"Englander Institute for Precision Medicine, Weill Cornell Medicine , New York, NY 10021, USA"},{"name":"Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City , 24144 Doha, Qatar"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4734-3791","authenticated-orcid":false,"given":"Jan","family":"Krumsiek","sequence":"additional","affiliation":[{"name":"Department of Physiology and Biophysics, Institute for Computational Biomedicine , New York, NY 10021, USA"},{"name":"Englander Institute for Precision Medicine, Weill Cornell Medicine , New York, NY 10021, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,9,16]]},"reference":[{"key":"2023020108442311400_btab656-B1","doi-asserted-by":"crossref","first-page":"1493","DOI":"10.1172\/JCI124611","article-title":"Precision medicine and phenotypes, endotypes, genotypes, regiotypes, and theratypes of allergic diseases","volume":"129","author":"Agache","year":"2019","journal-title":"J. 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