{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,16]],"date-time":"2025-12-16T12:23:43Z","timestamp":1765887823106,"version":"3.37.3"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2016,10,6]],"date-time":"2016-10-06T00:00:00Z","timestamp":1475712000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"State of South Dakota Research Innovation Center, the Agriculture Experiment Station of South Dakota State University, National Science Foundation of United States","award":["0604755","1546869"],"award-info":[{"award-number":["0604755","1546869"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["61402194"],"award-info":[{"award-number":["61402194"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Biclustering is widely used to identify co-expressed genes under subsets of all the conditions in a large-scale transcriptomic dataset. The program, QUBIC, is recognized as one of the most efficient and effective biclustering methods for biological data interpretation. However, its availability is limited to a C implementation and to a low-throughput web interface.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>An R implementation of QUBIC is presented here with two unique features: (i) a 82% average improved efficiency by refactoring and optimizing the source C code of QUBIC; and (ii) a set of comprehensive functions to facilitate biclustering-based biological studies, including the qualitative representation (discretization) of expression data, query-based biclustering, bicluster expanding, biclusters comparison, heatmap visualization of any identified biclusters and co-expression networks elucidation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>The package is implemented in R (as of version 3.3) and is available from Bioconductor at the URL: http:\/\/bioconductor.org\/packages\/QUBIC, where installation and usage instructions can be found.<\/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\/btw635","type":"journal-article","created":{"date-parts":[[2016,9,30]],"date-time":"2016-09-30T19:05:53Z","timestamp":1475262353000},"page":"450-452","source":"Crossref","is-referenced-by-count":49,"title":["QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data"],"prefix":"10.1093","volume":"33","author":[{"given":"Yu","family":"Zhang","sequence":"first","affiliation":[{"name":"College of Computer Science and Technology, Jilin University, Changchun, China"},{"name":"Key Laboratory of Symbolic Computation and Knowledge Engineering (Jilin University), Ministry of Education, Changchun, China"}]},{"given":"Juan","family":"Xie","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, South Dakota State University, Brookings, SD, USA"},{"name":"Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA"}]},{"given":"Jinyu","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, South Dakota State University, Brookings, SD, USA"},{"name":"Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA"}]},{"given":"Anne","family":"Fennell","sequence":"additional","affiliation":[{"name":"Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA"},{"name":"BioSNTR, Brookings, SD, USA"}]},{"given":"Chi","family":"Zhang","sequence":"additional","affiliation":[{"name":"Center for Computational Biology and Bioinformatics and Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA"}]},{"given":"Qin","family":"Ma","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, South Dakota State University, Brookings, SD, USA"},{"name":"Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA"},{"name":"BioSNTR, Brookings, SD, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,10,6]]},"reference":[{"key":"2023020204402851100_btw635-B1","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1093\/bib\/bbs032","article-title":"A comparative analysis of biclustering algorithms for gene expression data","volume":"14","author":"Eren","year":"2013","journal-title":"Brief. 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