{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T12:18:07Z","timestamp":1763727487760,"version":"3.37.3"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2019,5,22]],"date-time":"2019-05-22T00:00:00Z","timestamp":1558483200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"German Federal Ministry of Education and Research","award":["01ZZ1804D"],"award-info":[{"award-number":["01ZZ1804D"]}]},{"DOI":"10.13039\/501100011736","name":"Ministry of Economic Affairs, Labour and Housing of Baden-W\u00fcrttemberg","doi-asserted-by":"publisher","award":["3-4332.62-HSG\/84"],"award-info":[{"award-number":["3-4332.62-HSG\/84"]}],"id":[{"id":"10.13039\/501100011736","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>More and more affordable high-throughput techniques for measuring molecular features of biomedical samples have led to a huge increase in availability and size of different types of multi-omic datasets, containing, for example, genetic or histone modification data. Due to the multi-view characteristic of the data, established approaches for exploratory analysis are not directly applicable. Here we present web-rMKL, a web server that provides an integrative dimensionality reduction with subsequent clustering of samples based on data from multiple inputs. The underlying machine learning method rMKL-LPP performed best for clinical enrichment in a recent benchmark of state-of-the-art multi-view clustering algorithms. The method was introduced for a multi-omic cancer subtype discovery setting, however, it is not limited to this application scenario as exemplified by a presented use case for stem cell differentiation. web-rMKL offers an intuitive interface for uploading data and setting the parameters. rMKL-LPP runs on the back end and the user may receive notifications once the results are available. We also introduce a preprocessing tool for generating kernel matrices from tables containing numerical feature values. This program can be used to generate admissible input if no precomputed kernel matrices are available. The web server is freely available at web-rMKL.org.<\/jats:p>","DOI":"10.1093\/nar\/gkz422","type":"journal-article","created":{"date-parts":[[2019,5,9]],"date-time":"2019-05-09T15:21:10Z","timestamp":1557415270000},"page":"W605-W609","source":"Crossref","is-referenced-by-count":7,"title":["web-rMKL: a web server for dimensionality reduction and sample clustering of multi-view data based on unsupervised multiple kernel learning"],"prefix":"10.1093","volume":"47","author":[{"given":"Benedict","family":"R\u00f6der","sequence":"first","affiliation":[{"name":"Methods in Medical Informatics, Department of Computer Science, University of T\u00fcbingen, 72076 T\u00fcbingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicolas","family":"Kersten","sequence":"additional","affiliation":[{"name":"Methods in Medical Informatics, Department of Computer Science, University of T\u00fcbingen, 72076 T\u00fcbingen, Germany"},{"name":"FZI Forschungszentrum Informatik, Microelectronic System Design (SiM), 76131 Karlsruhe, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marius","family":"Herr","sequence":"additional","affiliation":[{"name":"Methods in Medical Informatics, Department of Computer Science, University of T\u00fcbingen, 72076 T\u00fcbingen, Germany"},{"name":"Institute for Translational Bioinformatics, University Hospital T\u00fcbingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nora K","family":"Speicher","sequence":"additional","affiliation":[{"name":"Institute for Translational Bioinformatics, University Hospital T\u00fcbingen, Germany"},{"name":"Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbr\u00fccken, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nico","family":"Pfeifer","sequence":"additional","affiliation":[{"name":"Methods in Medical Informatics, Department of Computer Science, University of T\u00fcbingen, 72076 T\u00fcbingen, Germany"},{"name":"Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbr\u00fccken, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,5,22]]},"reference":[{"key":"2019062808325184500_B1","doi-asserted-by":"crossref","first-page":"i268","DOI":"10.1093\/bioinformatics\/btv244","article-title":"Integrating different data types by regularized unsupervised multiple kernel learning with application to cancer subtype discovery","volume":"31","author":"Speicher","year":"2015","journal-title":"Bioinformatics"},{"key":"2019062808325184500_B2","doi-asserted-by":"crossref","first-page":"10546","DOI":"10.1093\/nar\/gky889","article-title":"Multi-omic and multi-view clustering algorithms: review and cancer benchmark","volume":"46","author":"Rappoport","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019062808325184500_B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2202\/1544-6115.1470","article-title":"Extensions of sparse canonical correlation analysis with applications to genomic data","volume":"8","author":"Witten","year":"2009","journal-title":"Stat. 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