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Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly <jats:italic>Drosophila melanogaster<\/jats:italic>. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide promising ways for addressing key scientific questions.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We develop a set of computational methods and open source tools for identifying co-expressed embryonic domains and the associated genes simultaneously. To map the expression patterns of many genes into the same coordinate space and account for the embryonic shape variations, we develop a mesh generation method to deform a meshed generic ellipse to each individual embryo. We then develop a co-clustering formulation to cluster the genes and the mesh elements, thereby identifying co-expressed embryonic domains and the associated genes simultaneously. Experimental results indicate that the gene and mesh co-clusters can be correlated to key developmental events during the stages of embryogenesis we study. The open source software tool has been made available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/compbio.cs.odu.edu\/fly\/\" ext-link-type=\"uri\">http:\/\/compbio.cs.odu.edu\/fly\/<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Our mesh generation and machine learning methods and tools improve upon the flexibility, ease-of-use and accuracy of existing methods.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-14-372","type":"journal-article","created":{"date-parts":[[2013,12,28]],"date-time":"2013-12-28T10:01:13Z","timestamp":1388224873000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["A mesh generation and machine learning framework for Drosophilagene expression pattern image analysis"],"prefix":"10.1186","volume":"14","author":[{"given":"Wenlu","family":"Zhang","sequence":"first","affiliation":[]},{"given":"Daming","family":"Feng","sequence":"additional","affiliation":[]},{"given":"Rongjian","family":"Li","sequence":"additional","affiliation":[]},{"given":"Andrey","family":"Chernikov","sequence":"additional","affiliation":[]},{"given":"Nikos","family":"Chrisochoides","sequence":"additional","affiliation":[]},{"given":"Christopher","family":"Osgood","sequence":"additional","affiliation":[]},{"given":"Charlotte","family":"Konikoff","sequence":"additional","affiliation":[]},{"given":"Stuart","family":"Newfeld","sequence":"additional","affiliation":[]},{"given":"Sudhir","family":"Kumar","sequence":"additional","affiliation":[]},{"given":"Shuiwang","family":"Ji","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,12,28]]},"reference":[{"key":"6237_CR1","volume-title":"Molecular Cell Biology","author":"H Lodish","year":"2007","unstructured":"Lodish H, Berk A, Kaiser CA, Krieger M, Scott MP, Bretscher A, Ploegh H, Matsudaira P: Molecular Cell Biology. 2007, New York: W. 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