{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T03:21:00Z","timestamp":1769916060717,"version":"3.49.0"},"reference-count":16,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,2,15]],"date-time":"2019-02-15T00:00:00Z","timestamp":1550188800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,2,15]],"date-time":"2019-02-15T00:00:00Z","timestamp":1550188800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000182","name":"Medical Research and Materiel Command","doi-asserted-by":"publisher","award":["09284002"],"award-info":[{"award-number":["09284002"]}],"id":[{"id":"10.13039\/100000182","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2019,12]]},"DOI":"10.1186\/s12859-019-2657-0","type":"journal-article","created":{"date-parts":[[2019,2,15]],"date-time":"2019-02-15T13:06:00Z","timestamp":1550235960000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Functional Heatmap: an automated and interactive pattern recognition tool to integrate time with multi-omics assays"],"prefix":"10.1186","volume":"20","author":[{"given":"Joshua R.","family":"Williams","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8289-1999","authenticated-orcid":false,"given":"Ruoting","family":"Yang","sequence":"additional","affiliation":[]},{"given":"John L.","family":"Clifford","sequence":"additional","affiliation":[]},{"given":"Daniel","family":"Watson","sequence":"additional","affiliation":[]},{"given":"Ross","family":"Campbell","sequence":"additional","affiliation":[]},{"given":"Derese","family":"Getnet","sequence":"additional","affiliation":[]},{"given":"Raina","family":"Kumar","sequence":"additional","affiliation":[]},{"given":"Rasha","family":"Hammamieh","sequence":"additional","affiliation":[]},{"given":"Marti","family":"Jett","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2019,2,15]]},"reference":[{"issue":"8","key":"2657_CR1","doi-asserted-by":"publisher","first-page":"552","DOI":"10.1038\/nrg3244","volume":"13","author":"Z Bar-Joseph","year":"2012","unstructured":"Bar-Joseph Z, Gitter A, Simon I. Studying and modelling dynamic biological processes using time-series gene expression data. Nat Rev Genet. 2012;13(8):552.","journal-title":"Nat Rev Genet"},{"issue":"25","key":"2657_CR2","doi-asserted-by":"publisher","first-page":"14863","DOI":"10.1073\/pnas.95.25.14863","volume":"95","author":"MB Eisen","year":"1998","unstructured":"Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci. 1998;95(25):14863\u20138.","journal-title":"Proc Natl Acad Sci"},{"issue":"1","key":"2657_CR3","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/1471-2105-12-13","volume":"12","author":"A Sinha","year":"2011","unstructured":"Sinha A, Markatou M. A platform for processing expression of short time series (PESTS). BMC Bioinformatics. 2011;12(1):13.","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"2657_CR4","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1186\/1756-0500-2-124","volume":"2","author":"JP Gon\u00e7alves","year":"2009","unstructured":"Gon\u00e7alves JP, Madeira SC, Oliveira AL. BiGGEsTS: integrated environment for biclustering analysis of time series gene expression data. BMC Res Notes. 2009;2(1):124.","journal-title":"BMC Res Notes"},{"issue":"14","key":"2657_CR5","doi-asserted-by":"publisher","first-page":"9121","DOI":"10.1073\/pnas.132656399","volume":"99","author":"MF Ramoni","year":"2002","unstructured":"Ramoni MF, Sebastiani P, Kohane IS. Cluster analysis of gene expression dynamics. Proc Natl Acad Sci. 2002;99(14):9121\u20136.","journal-title":"Proc Natl Acad Sci"},{"issue":"suppl_2","key":"2657_CR6","doi-asserted-by":"publisher","first-page":"W239","DOI":"10.1093\/nar\/gkq488","volume":"38","author":"MJ Nueda","year":"2010","unstructured":"Nueda MJ, Carbonell J, Medina I, Dopazo JN, Conesa A. Serial expression analysis: a web tool for the analysis of serial gene expression data. Nucleic Acids Res. 2010;38(suppl_2):W239\u201345.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"2657_CR7","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1186\/1471-2105-9-415","volume":"9","author":"C Angelini","year":"2008","unstructured":"Angelini C, Cutillo L, De Canditiis D, Mutarelli M, Pensky M. BATS: a Bayesian user-friendly software for analyzing time series microarray experiments. BMC Bioinformatics. 2008;9(1):415.","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"2657_CR8","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1186\/1471-2105-7-191","volume":"7","author":"J Ernst","year":"2006","unstructured":"Ernst J, Bar-Joseph Z. STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics. 2006;7(1):191.","journal-title":"BMC Bioinformatics"},{"issue":"23","key":"2657_CR9","doi-asserted-by":"crossref","first-page":"3827","DOI":"10.1093\/bioinformatics\/btw780","volume":"33","author":"I Jung","year":"2017","unstructured":"Jung I, Jo K, Kang H, Ahn H, Yu Y, Kim S. TimesVector: a vectorized clustering approach to the analysis of time series transcriptome data from multiple phenotypes. Bioinformatics. 2017;33(23):3827\u201335.","journal-title":"Bioinformatics"},{"key":"2657_CR10","unstructured":"Phang TL, Neville MC, Rudolph M, Hunter L. Trajectory clustering: a non-parametric method for grouping gene expression time courses, with applications to mammary development. Pac Symp Biocomput. 2003;(5):351\u201362."},{"issue":"1","key":"2657_CR11","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","volume":"28","author":"M Kanehisa","year":"2000","unstructured":"Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27\u201330.","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2657_CR12","doi-asserted-by":"publisher","first-page":"D661","DOI":"10.1093\/nar\/gkx1064","volume":"46","author":"DN Slenter","year":"2017","unstructured":"Slenter DN, Kutmon M, Hanspers K, Riutta A, Windsor J, Nunes N, M\u00e9lius J, Cirillo E, Coort SL, Digles D. WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. Nucleic Acids Res. 2017;46(D1):D661\u20137.","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"2657_CR13","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1089\/152791601750294344","volume":"2","author":"D Nishimura","year":"2001","unstructured":"Nishimura D. BioCarta. Biotech Softw Internet Rep. 2001;2(3):117\u201320.","journal-title":"Biotech Softw Internet Rep"},{"issue":"suppl_1","key":"2657_CR14","first-page":"D428","volume":"33","author":"G Joshi-Tope","year":"2005","unstructured":"Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath G, Wu G, Matthews L. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res. 2005;33(suppl_1):D428\u201332.","journal-title":"Nucleic Acids Res"},{"issue":"43","key":"2657_CR15","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","volume":"102","author":"A Subramanian","year":"2005","unstructured":"Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci. 2005;102(43):15545\u201350.","journal-title":"Proc Natl Acad Sci"},{"issue":"4","key":"2657_CR16","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1093\/bioinformatics\/btk005","volume":"22","author":"JT Leek","year":"2006","unstructured":"Leek JT, Monsen E, Dabney AR, Storey JD. EDGE: extraction and analysis of differential gene expression. Bioinformatics. 2006;22(4):507\u20138.","journal-title":"Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2657-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-019-2657-0\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2657-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,13]],"date-time":"2023-09-13T17:39:34Z","timestamp":1694626774000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-019-2657-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,2,15]]},"references-count":16,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2019,12]]}},"alternative-id":["2657"],"URL":"https:\/\/doi.org\/10.1186\/s12859-019-2657-0","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,2,15]]},"assertion":[{"value":"1 October 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 January 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 February 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"81"}}