We are interested in developping computational vision approaches to
understand better biological problems. For this purpose, we collaborate with the
Laurence Berkeley National Laboratory.
We are currently participating in the Berkeley Drosophila Transcription Network Project,
building a morphological and gene expression atlas in Drosophila,
and in the Protein Complex Analysis Project, detecting and reconstructing molecular structures in Electron Microscopy images.
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"Constructing a quantitative spatio-temporal atlas of gene
expression in the Drosophila blastoderm". C. Fowlkes, C. Luengo Hendriks, S. Keränen, G. Weber, O. Rübel, M-Y Huang, S. Chatoor, L. Simirenko, A. DePace C. Henriquez, A. Beaton, R. Weiszmann, S. Celniker, B. Hamann, D. Knowles, M. Biggin, M. Eisen, and J. Malik. Cell, 2008. [pdf] |
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"Expressing Genes" Felice Frankel interviews A. DePace, G. Weber and C. Fowlkes. American Scientist, 2007. [pdf] [html] |
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"3D Morphology and Gene Expression in the Drosophila Blastoderm
at Cellular Resolution II: Dynamics". S. Keränen, C. Fowlkes, C. Luengo Hendriks, D. Sudar, D. Knowles, J. Malik and M. Biggin. Genome Biology, 2006. [pdf] |
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"3D Morphology and Gene Expression in the Drosophila Blastoderm
at Cellular Resolution I: Data Acquisition Pipeline". C. Luengo-Hendriks, S. Keränen, C. Fowlkes, L. Simirenko, G. Weber, C. Henriquez, D. Kaszuba, B. Hamann, M. Eisen, J. Malik, D. Sudar, M. Biggin and D. Knowles. Genome Biology, 2006. [pdf] |
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"Inferring nuclear movements from fixed material" C. Fowlkes and J. Malik. Technical Report, U.C. Berkeley, 2006 [pdf] |
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"Registering Drosophila Embryos at Cellular Resolution to Build
a Quantitative 3D Map of Gene Expression Patterns and Morphology". C. Fowlkes, C. Luengo Hendriks, S. Keränen, M. Biggin, D. Knowles, D. Sudar and J. Malik. CSB 2005 Workshop on BioImage Data Minning and Informatics, 2005. [pdf] |