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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
 Is Cited by the Following 19 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
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
Shaping a Morphogen Gradient for Positional Precision
Feng He, Timothy E. Saunders, Ying Wen, David Cheung, Renjie Jiao, Pieter Rein ten Wolde, Martin Howard, Jun Ma
Biophys J. 2010 August 4; 99(3): 697–707. doi: 10.1016/j.bpj.2010.04.073
PMCID:
PMC2913175
Abstract Full Text PDF–543K 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
Deciphering the genome’s regulatory code: The many languages of DNA
Jens Rister, Claude Desplan
Bioessays. Author manuscript; available in PMC 2011 May 1.
Published in final edited form as: Bioessays. 2010 May; 32(5): 381–384. doi: 10.1002/bies.200900197
PMCID:
PMC3024831
Abstract Full Text PDF–162K
Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images
Daniel L. Mace, Nicole Varnado, Weiping Zhang, Erwin Frise, Uwe Ohler
Bioinformatics. 2010 March 15; 26(6): 761–769. Published online 2009 November 26. doi: 10.1093/bioinformatics/btp658
PMCID:
PMC3140183
Abstract Full Text PDF–580K Supplementary Material
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
Canalization of Gene Expression and Domain Shifts in the Drosophila Blastoderm by Dynamical Attractors
Manu, Svetlana Surkova, Alexander V. Spirov, Vitaly V. Gursky, Hilde Janssens, Ah-Ram Kim, Ovidiu Radulescu, Carlos E. Vanario-Alonso, David H. Sharp, Maria Samsonova, John Reinitz
PLoS Comput Biol. 2009 March; 5(3): e1000303. Published online 2009 March 13. doi: 10.1371/journal.pcbi.1000303
PMCID:
PMC2646127
Abstract Full Text PDF–1.2M Supplementary Material
The Intersection of Theory and Application in Elucidating Pattern Formation in Developmental Biology
Hans G. Othmer, Kevin Painter, David Umulis, Chuan Xue
Math Model Nat Phenom. Author manuscript; available in PMC 2009 October 19.
Published in final edited form as: Math Model Nat Phenom. 2009 January 1; 4(4): 3–82. doi: 10.1051/mmnp/20094401
PMCID:
PMC2763616
Abstract Full Text PDF–7.3M
Design Flexibility in cis-Regulatory Control of Gene Expression: Synthetic and Comparative Evidence
Louisa M. Liberman, Angelike M. Stathopoulos
Dev Biol. Author manuscript; available in PMC 2010 March 15.
Published in final edited form as: Dev Biol. 2009 March 15; 327(2): 578–589. Published online 2008 December 25. doi: 10.1016/j.ydbio.2008.12.020
PMCID:
PMC2746413
Abstract Full Text PDF–2.3M Supplementary Material
A Precise Bicoid Gradient Is Nonessential during Cycles 11–13 for Precise Patterning in the Drosophila Blastoderm
Elena M. Lucchetta, Meghan E. Vincent, Rustem F. Ismagilov
PLoS ONE. 2008; 3(11): e3651. Published online 2008 November 7. doi: 10.1371/journal.pone.0003651
PMCID:
PMC2578877
Abstract Full Text PDF–1.0M Supplementary Material
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
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 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
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