Evolutionary Modification of Development in Mammalian Teeth: Quantifying Gene Expression Patterns and Topography von Jernvall, J, Keränen, S V, Thesleff, I

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Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution II: dynamics von Keränen, Soile V E, Fowlkes, Charless C, Luengo Hendriks, Cris L, Sudar, Damir, Knowles, David W, Malik, Jitendra, Biggin, Mark D

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REDfly: An Integrated Knowledgebase for Insect Regulatory Genomics von Keränen, Soile V E, Villahoz-Baleta, Angel, Bruno, Andrew E, Halfon, Marc S

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REDfly: the transcriptional regulatory element database for Drosophila von Rivera, John, Keränen, Soile V E, Gallo, Steven M, Halfon, Marc S

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Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline von Luengo Hendriks, Cris L, Keränen, Soile V E, Fowlkes, Charless C, Simirenko, Lisa, Weber, Gunther H, DePace, Angela H, Henriquez, Clara, Kaszuba, David W, Hamann, Bernd, Eisen, Michael B, Malik, Jitendra, Sudar, Damir, Biggin, Mark D, Knowles, David W

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Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions von MacArthur, Stewart, Li, Xiao-Yong, Li, Jingyi, Brown, James B, Chu, Hou Cheng, Zeng, Lucy, Grondona, Brandi P, Hechmer, Aaron, Simirenko, Lisa, Keränen, Soile V E, Knowles, David W, Stapleton, Mark, Bickel, Peter, Biggin, Mark D, Eisen, Michael B

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A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila von Fowlkes, Charless C, Eckenrode, Kelly B, Bragdon, Meghan D, Meyer, Miriah, Wunderlich, Zeba, Simirenko, Lisa, Luengo Hendriks, Cris L, Keränen, Soile V E, Henriquez, Clara, Knowles, David W, Biggin, Mark D, Eisen, Michael B, DePace, Angela H

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Visual Exploration of Three-Dimensional Gene Expression Using Physical Views and Linked Abstract Views von Weber, Gunther H., Malik, Jitendra, Biggin, Mark D., Hamann, Bernd, Rubel, Oliver, Huang, Min-Yu, DePace, Angela H., Fowlkes, Charless C., Keranen, Soile V.E., Luengo Hendriks, Cris L., Hagen, Hans, Knowles, David W.

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Nonparametric identification of regulatory interactions from spatial and temporal gene expression data von Aswani, Anil, Keränen, Soile V E, Brown, James, Fowlkes, Charless C, Knowles, David W, Biggin, Mark D, Bickel, Peter, Tomlin, Claire J

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Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data von Rubel, O., Weber, G.H., Min-Yu Huang, Bethel, E.W., Biggin, M.D., Fowlkes, C.C., Luengo Hendriks, C.L., Keranen, S.V.E., Eisen, M.B., Knowles, D.W., Malik, J., Hagen, H., Hamann, B.

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A Quantitative Spatiotemporal Atlas of Gene Expression in the Drosophila Blastoderm von Fowlkes, Charless C., Hendriks, Cris L. Luengo, Keränen, Soile V.E., Weber, Gunther H., Rübel, Oliver, Huang, Min-Yu, Chatoor, Sohail, DePace, Angela H., Simirenko, Lisa, Henriquez, Clara, Beaton, Amy, Weiszmann, Richard, Celniker, Susan, Hamann, Bernd, Knowles, David W., Biggin, Mark D., Eisen, Michael B., Malik, Jitendra

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Coupling visualization and data analysis for knowledge discovery from multi-dimensional scientific data von Rübel, Oliver, Ahern, Sean, Bethel, E. Wes, Biggin, Mark D., Childs, Hank, Cormier-Michel, Estelle, DePace, Angela, Eisen, Michael B., Fowlkes, Charless C., Geddes, Cameron G.R., Hagen, Hans, Hamann, Bernd, Huang, Min-Yu, Keränen, Soile V.E., Knowles, David W., Hendriks, Cris L. Luengo, Malik, Jitendra, Meredith, Jeremy, Messmer, Peter, Prabhat, Ushizima, Daniela, Weber, Gunther H., Wu, Kesheng

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Visual Exploration of Three-Dimensional Gene Expression Using Physical Views and Linked Abstract Views von Weber, Gunther H, Rubel, Oliver, Huang, Min-Yu, Depace, Angela H, Fowlkes, Charless C, Keranen, Soile V E, Luengo Hendriks, Cris L, Hagen, Hans, Knowles, David W, Malik, Jitendra, Biggin, Mark D, Hamann, Bernd

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Simulation study on effects of signaling network structure on the developmental increase in complexity von Keranen, SVE

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A Conserved Developmental Patterning Network Produces Quantitatively Different Output in Multiple Species of Drosophila: e1002346 von Fowlkes, Charless C, Eckenrode, Kelly B, Bragdon, Meghan D, Meyer, Miriah, Wunderlich, Zeba, Simirenko, Lisa, Hendriks, Cris LLuengo, Keränen, Soile VE, Henriquez, Clara, Knowles, David W, Biggin, Mark D, Eisen, Michael B, DePace, Angela H

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Linking Advanced Visualization and MATLAB for the Analysis of 3D Gene Expression Data von Rübel, Oliver, Keränen, Soile V. E., Biggin, Mark, Knowles, David W., Weber, Gunther H., Hagen, Hans, Hamann, Bernd, Bethel, E. Wes

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Visually Relating Gene Expression and in vivo DNA Binding Data von Min-Yu Huang, Mackey, Lester, Keranen, Soile V. E., Weber, Gunther H., Jordan, Michael I., Knowles, David W., Biggin, Mark D., Hamann, Bernd

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REDfly: The Regulatory Element Database for Drosophila von Halfon, Marc S., Keränen, Soile V. E., Baleta, Angel Villahoz, Bruno, Andrew E., Gallo, Steven M.

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Three-dimensional morphology and gene expression in the Drosophilablastoderm at cellular resolution II: dynamics von Keränen, Soile VE, Fowlkes, Charless C, Luengo Hendriks, Cris L, Sudar, Damir, Knowles, David W, Malik, Jitendra, Biggin, Mark D

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Three-dimensional morphology and gene expression in the Drosophilablastoderm at cellular resolution I: data acquisition pipeline von Luengo Hendriks, Cris L, Keränen, Soile VE, Fowlkes, Charless C, Simirenko, Lisa, Weber, Gunther H, DePace, Angela H, Henriquez, Clara, Kaszuba, David W, Hamann, Bernd, Eisen, Michael B, Malik, Jitendra, Sudar, Damir, Biggin, Mark D, Knowles, David W

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