{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:55Z","timestamp":1772138035664,"version":"3.50.1"},"reference-count":53,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2020,12,16]],"date-time":"2020-12-16T00:00:00Z","timestamp":1608076800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"International Deutsche Forschungsgemeinschaft Research Training Group","award":["1906"],"award-info":[{"award-number":["1906"]}]},{"name":"Arbeitsgruppe Bioinformatik"},{"name":"Medical Informatik of Bielefeld University"},{"name":"Natural Sciences and Engineering Research Council of Canada Discovery"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Identification of differentially expressed genes is necessary for unraveling disease pathogenesis. This task is complicated by the fact that many diseases are heterogeneous at the molecular level and samples representing distinct disease subtypes may demonstrate different patterns of dysregulation. Biclustering methods are capable of identifying genes that follow a similar expression pattern only in a subset of samples and hence can consider disease heterogeneity. However, identifying biologically significant and reproducible sets of genes and samples remain challenging for the existing tools. Many recent studies have shown that the integration of gene expression and protein interaction data improves the robustness of prediction and classification and advances biomarker discovery.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present DESMOND, a new method for identification of Differentially ExpreSsed gene MOdules iN Diseases. DESMOND performs network-constrained biclustering on gene expression data and identifies gene modules\u2014connected sets of genes up- or down-regulated in subsets of samples. We applied DESMOND on expression profiles of samples from two large breast cancer cohorts and have shown that the capability of DESMOND to incorporate protein interactions allows identifying the biologically meaningful gene and sample subsets and improves the reproducibility of the results.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/github.com\/ozolotareva\/DESMOND.<\/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\/btaa1038","type":"journal-article","created":{"date-parts":[[2020,12,2]],"date-time":"2020-12-02T17:38:58Z","timestamp":1606930738000},"page":"1691-1698","source":"Crossref","is-referenced-by-count":8,"title":["Identification of differentially expressed gene modules in heterogeneous diseases"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9424-8052","authenticated-orcid":false,"given":"Olga","family":"Zolotareva","sequence":"first","affiliation":[{"name":"International Research Training Group \u201cComputational Methods for the Analysis of the Diversity and Dynamics of Genomes\u201d and Genome Informatics, Faculty of Technology and Center for Biotechnology, Bielefeld University , Bielefeld, Germany"},{"name":"Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich , Munich, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5178-0188","authenticated-orcid":false,"given":"Sahand","family":"Khakabimamaghani","sequence":"additional","affiliation":[{"name":"School of Computing Science, Simon Fraser University , Burnaby, BC, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7377-0944","authenticated-orcid":false,"given":"Olga I","family":"Isaeva","sequence":"additional","affiliation":[{"name":"Center of Life Sciences, Skolkovo Institute of Science and Technology , Moscow, Russia"},{"name":"BostonGene Corporation , Waltham, MA 02453, USA"},{"name":"Divisions of Molecular Oncology & Immunology, Tumor Biology & Immunology, Molecular Carcinogenesis, The Netherlands Cancer Institute , Amsterdam, The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4726-3217","authenticated-orcid":false,"given":"Zoe","family":"Chervontseva","sequence":"additional","affiliation":[{"name":"Center of Life Sciences, Skolkovo Institute of Science and Technology , Moscow, Russia"},{"name":"A.A. 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