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Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline
Cris L Luengo Hendriks, Soile VE Keränen, Charless C Fowlkes, Lisa Simirenko, Gunther H Weber, Angela H DePace, Clara Henriquez, David W Kaszuba, Bernd Hamann, Michael B Eisen, Jitendra Malik, Damir Sudar, Mark D Biggin, David W Knowles
Genome Biol. 2006; 7(12): R123. Published online 2006 December 21. doi: 10.1186/gb-2006-7-12-r123
PMCID:
PMC1794436
Abstract Full Text PDF–3.3M
 Is Cited by the Following 26 Articles in this Archive:
Analysis of Gap Gene Regulation in a 3D Organism-Scale Model of the Drosophila melanogaster Embryo
James B. Hengenius, Michael Gribskov, Ann E. Rundell, Charless C. Fowlkes, David M. Umulis
PLoS One. 2011; 6(11): e26797. Published online 2011 November 16. doi: 10.1371/journal.pone.0026797
PMCID:
PMC3217930
Abstract Full Text PDF–677K Supplementary Material
A Conserved Developmental Patterning Network Produces Quantitatively Different Output in Multiple Species of Drosophila
Charless C. Fowlkes, Kelly B. Eckenrode, Meghan D. Bragdon, Miriah Meyer, Zeba Wunderlich, Lisa Simirenko, Cris L. Luengo Hendriks, Soile V. E. Keränen, Clara Henriquez, David W. Knowles, Mark D. Biggin, Michael B. Eisen, Angela H. DePace
PLoS Genet. 2011 October; 7(10): e1002346. Published online 2011 October 27. doi: 10.1371/journal.pgen.1002346
PMCID:
PMC3203197
Abstract Full Text PDF–8.2M Supplementary Material
Simultaneous recognition and segmentation of cells: application in C.elegans
Lei Qu, Fuhui Long, Xiao Liu, Stuart Kim, Eugene Myers, Hanchuan Peng
Bioinformatics. 2011 October 15; 27(20): 2895–2902. Published online 2011 August 17. doi: 10.1093/bioinformatics/btr480
PMCID:
PMC3187651
Abstract Full Text PDF–1.3M
Multicolor fluorescent in situ hybridization to define abutting and overlapping gene expression in the embryonic zebrafish brain
Gilbert Lauter, Iris Söll, Giselbert Hauptmann
Neural Dev. 2011; 6: 10. Published online 2011 April 5. doi: 10.1186/1749-8104-6-10
PMCID:
PMC3088888
Abstract Full Text PDF–8.3M Supplementary Material
Artificial selection on egg size perturbs early pattern formation in Drosophila melanogaster
CM Miles, SE Lott, CL Luengo Hendriks, MZ Ludwig, Manu, CL Williams, M Kreitman
Evolution. Author manuscript; available in PMC 2012 January 1.
Published in final edited form as: Evolution. 2011 January; 65(1): 33–42. doi: 10.1111/j.1558-5646.2010.01088.x
PMCID:
PMC2988983
Abstract Full Text PDF–1.1M Supplementary Material
The gap gene network
Johannes Jaeger
Cell Mol Life Sci. 2011 January; 68(2): 243–274. Published online 2010 October 8. doi: 10.1007/s00018-010-0536-y
PMCID:
PMC3016493
Abstract Full Text PDF–1.1M
Nonparametric identification of regulatory interactions from spatial and temporal gene expression data
Anil Aswani, Soile VE Keränen, James Brown, Charless C Fowlkes, David W Knowles, Mark D Biggin, Peter Bickel, Claire J Tomlin
BMC Bioinformatics. 2010; 11: 413. Published online 2010 August 4. doi: 10.1186/1471-2105-11-413
PMCID:
PMC2933715
Abstract Full Text PDF–4.0M Supplementary Material
Distance measurements via the morphogen gradient of Bicoid in Drosophila embryos
Feng He, Ying Wen, David Cheung, Jingyuan Deng, Long J Lu, Renjie Jiao, Jun Ma
BMC Dev Biol. 2010; 10: 80. Published online 2010 August 2. doi: 10.1186/1471-213X-10-80
PMCID:
PMC2919471
Abstract Full Text PDF–1.0M Supplementary Material
Quantifying Phenotypic Variation in Isogenic Caenorhabditis elegans Expressing Phsp-16.2::gfp by Clustering 2D Expression Patterns
Alexander K. Seewald, James Cypser, Alexander Mendenhall, Thomas Johnson
PLoS One. 2010; 5(7): e11426. Published online 2010 July 19. doi: 10.1371/journal.pone.0011426
PMCID:
PMC2906502
Abstract Full Text PDF–441K
Quantitative imaging of the Dorsal nuclear gradient reveals limitations to threshold-dependent patterning in Drosophila
Louisa M. Liberman, Gregory T. Reeves, Angelike Stathopoulos
Proc Natl Acad Sci U S A. 2009 December 29; 106(52): 22317–22322. Published online 2009 December 16. doi: 10.1073/pnas.0906227106
PMCID:
PMC2799780
Abstract Full Text PDF–2.4M Supplementary Material
More than a decade of developmental gene expression atlases: where are we now?
Bouke A. de Boer, Jan M. Ruijter, Frans P. J. M. Voorbraak, Antoon F. M. Moorman
Nucleic Acids Res. 2009 December; 37(22): 7349–7359. Published online 2009 December. doi: 10.1093/nar/gkp819
Correction in:
Nucleic Acids Res. 2010 May; 38(9): 3147.
PMCID:
PMC2794177
Abstract Full Text PDF–1.4M Correction
Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions
Stewart MacArthur, Xiao-Yong Li, Jingyi Li, James B Brown, Hou Cheng Chu, Lucy Zeng, Brandi P Grondona, Aaron Hechmer, Lisa Simirenko, Soile VE Keränen, David W Knowles, Mark Stapleton, Peter Bickel, Mark D Biggin, Michael B Eisen
Genome Biol. 2009; 10(7): R80. Published online 2009 July 23. doi: 10.1186/gb-2009-10-7-r80
PMCID:
PMC2728534
Abstract Full Text PDF–1.7M Supplementary Material
Mapping mammary gland architecture using multi-scale in situ analysis
Rodrigo Fernandez-Gonzalez, Irineu Illa-Bochaca, Bryan E. Welm, Markus C. Fleisch, Zena Werb, Carlos Ortiz-de-Solorzano, Mary Helen Barcellos-Hoff
Integr Biol (Camb) Author manuscript; available in PMC 2010 March 30.
Published in final edited form as: Integr Biol (Camb). 2009 January; 1(1): 80–89. Published online 2008 December 5. doi: 10.1039/b816933k
PMCID:
PMC2847439
Abstract Full Text PDF–3.9M
A combinatorial code for pattern formation in Drosophila oogenesis
N. Yakoby, C.A. Bristow, D. Gong, X. Schafer, J. Lembong, J.J. Zartman, M.S. Halfon, T. Schüpbach, S.Y. Shvartsman
Dev Cell. Author manuscript; available in PMC 2010 February 16.
Published in final edited form as: Dev Cell. 2008 November; 15(5): 725. doi: 10.1016/j.devcel.2008.09.008
PMCID:
PMC2822874
Abstract Full Text PDF–1.9M Supplementary Material
Image Processing and Analysis for Quantifying Gene Expression from Early Drosophila Embryos
Ahmet Ay, Walid D. Fakhouri, Chichia Chiu, David N. Arnosti
Tissue Eng Part A. 2008 September; 14(9): 1517–1526. doi: 10.1089/ten.tea.2008.0202
PMCID:
PMC2630463
Abstract Full Text PDF–319K
Bioimage informatics: a new area of engineering biology
Hanchuan Peng
Bioinformatics. 2008 September 1; 24(17): 1827–1836. Published online 2008 July 4. doi: 10.1093/bioinformatics/btn346
PMCID:
PMC2519164
Abstract Full Text PDF–744K Supplementary Material
Precise registration of gene expression boundaries by a repressive morphogen in Drosophila
Danyang Yu, Stephen Small
Curr Biol. Author manuscript; available in PMC 2009 June 24.
Published in final edited form as: Curr Biol. 2008 June 24; 18(12): 868–876. doi: 10.1016/j.cub.2008.05.050
PMCID:
PMC2481289
Abstract Full Text PDF–2.7M Supplementary Material
Methods for Acquisition of Quantitative Data from Confocal Images of Gene Expression in situ
S. Yu. Surkova, E. M. Myasnikova, K. N. Kozlov, A. A. Samsonova, J. Reinitz, M. G. Samsonova
Cell and tissue biol. Author manuscript; available in PMC 2009 April 1.
Published in final edited form as: Cell and tissue biol. 2008 April; 2(2): 200–215. doi: 10.1134/S1990519X08020156
PMCID:
PMC2630218
Abstract Full Text PDF–7.7M
Intron Delays and Transcriptional Timing during Development
Ian A. Swinburne, Pamela A. Silver
Dev Cell. Author manuscript; available in PMC 2010 February 19.
Published in final edited form as: Dev Cell. 2008 March; 14(3): 324–330. doi: 10.1016/j.devcel.2008.02.002
PMCID:
PMC2825037
Abstract Full Text PDF–243K
Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm
Xiao-yong Li, Stewart MacArthur, Richard Bourgon, David Nix, Daniel A Pollard, Venky N Iyer, Aaron Hechmer, Lisa Simirenko, Mark Stapleton, Cris L. Luengo Hendriks, Hou Cheng Chu, Nobuo Ogawa, William Inwood, Victor Sementchenko, Amy Beaton, Richard Weiszmann, Susan E Celniker, David W Knowles, Tom Gingeras, Terence P Speed, Michael B Eisen, Mark D Biggin
PLoS Biol. 2008 February; 6(2): e27. Published online 2008 February 12. doi: 10.1371/journal.pbio.0060027
Correction in:
PLoS Biol. 2008 July; 6(7): e190.
PMCID:
PMC2235902
Abstract Full Text PDF–1.9M Supplementary Material Correction
Semi-supervised learning for the identification of syn-expressed genes from fused microarray and in situ image data
Ivan G Costa, Roland Krause, Lennart Opitz, Alexander Schliep
BMC Bioinformatics. 2007; 8(Suppl 10): S3. Published online 2007 December 21. doi: 10.1186/1471-2105-8-S10-S3
PMCID:
PMC2230504
Abstract Full Text PDF–2.3M
Straightening Caenorhabditis elegans images
Hanchuan Peng, Fuhui Long, Xiao Liu, Stuart K. Kim, Eugene W. Myers
Bioinformatics. 2008 January 15; 24(2): 234–242. Published online 2007 November 19. doi: 10.1093/bioinformatics/btm569
PMCID:
PMC2940239
Abstract Full Text PDF–354K
Characterization of the Drosophila segment determination morphome
Svetlana Surkova, David Kosman, Konstantin Kozlov, Manu, Ekaterina Myasnikova, Anastasia A. Samsonova, Alexander Spirov, Carlos E. Vanario-Alonso, Maria Samsonova, John Reinitz
Dev Biol. Author manuscript; available in PMC 2009 January 15.
Published in final edited form as: Dev Biol. 2008 January 15; 313(2): 844–862. Published online 2007 November 4. doi: 10.1016/j.ydbio.2007.10.037
PMCID:
PMC2254320
Abstract Full Text PDF–7.2M Supplementary Material
Global analysis of patterns of gene expression during Drosophila embryogenesis
Pavel Tomancak, Benjamin P Berman, Amy Beaton, Richard Weiszmann, Elaine Kwan, Volker Hartenstein, Susan E Celniker, Gerald M Rubin
Genome Biol. 2007; 8(7): R145. Published online 2007 July 23. doi: 10.1186/gb-2007-8-7-r145
PMCID:
PMC2323238
Abstract Full Text PDF–5.6M Supplementary Material
Interactive processing and visualization of image data for biomedical and life science applications
Oliver G Staadt, Vijay Natarajan, Gunther H Weber, David F Wiley, Bernd Hamann
BMC Cell Biol. 2007; 8(Suppl 1): S10. Published online 2007 July 10. doi: 10.1186/1471-2121-8-S1-S10
PMCID:
PMC1924506
Abstract Full Text PDF–5.0M
Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution II: dynamics
Soile VE Keränen, Charless C Fowlkes, Cris L Luengo Hendriks, Damir Sudar, David W Knowles, Jitendra Malik, Mark D Biggin
Genome Biol. 2006; 7(12): R124. Published online 2006 December 21. doi: 10.1186/gb-2006-7-12-r124
PMCID:
PMC1794437
Abstract Full Text PDF–3.2M Supplementary Material
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