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Previously short time series gene expression data has been mainly analyzed using more general gene expression analysis tools not designed for the unique challenges and opportunities inherent in short time series gene expression data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We introduce the Short Time-series Expression Miner (STEM) the first software program specifically designed for the analysis of short time series microarray gene expression data. STEM implements unique methods to cluster, compare, and visualize such data. STEM also supports efficient and statistically rigorous biological interpretations of short time series data through its integration with the Gene Ontology.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      The unique algorithms STEM implements to cluster and compare short time series gene expression data combined with its visualization capabilities and integration with the Gene Ontology should make STEM useful in the analysis of data from a significant portion of all microarray studies. STEM is available for download for free to academic and non-profit users at\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.cs.cmu.edu\/~jernst\/stem\" ext-link-type=\"uri\">http:\/\/www.cs.cmu.edu\/~jernst\/stem<\/jats:ext-link>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/1471-2105-7-191","type":"journal-article","created":{"date-parts":[[2006,4,20]],"date-time":"2006-04-20T10:27:09Z","timestamp":1145528829000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1511,"title":["STEM: a tool for the analysis of short time series gene expression data"],"prefix":"10.1186","volume":"7","author":[{"given":"Jason","family":"Ernst","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ziv","family":"Bar-Joseph","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2006,4,5]]},"reference":[{"issue":"12","key":"930_CR1","doi-asserted-by":"publisher","first-page":"3273","DOI":"10.1091\/mbc.9.12.3273","volume":"9","author":"PT Spellman","year":"1998","unstructured":"Spellman PT, Sherlock G, Zhang M, Iyer V, Anders K, Eisen M, Brown P, Botstein D, Futcher B: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. 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