Cis-regulatory logic in the endo16 gene: switching from a specification to a differentiation mode of control

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Ransick, A., Ernst, S., Britten, R. J. and Davidson, E. H (1993). Wholemount insitu hybridization shows Endo-16 to be a marker forthevegetal plate territory in sea urchin embryos. Mech. Dev 42, 117-124.[Medline]

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Yuh, C.-H. and Davidson, E. H (1996). Modular cis -regulatory organization of Endo16 , a gut-specific gene of the sea urchin embryo. Development 122, 1069-1082.[Abstract]

Yuh, C.-H., Ransick, A., Martinez, P., Britten, R. J. and Davidson, E. H (1994). Complexity and organization of DNA-protein interactions in the 5regulatory region of an endoderm-specific marker gene in the sea urchin embryo. Mech. Dev 47, 165-186.[Medline]

Yuh, C.-H., Moore, J. G. and Davidson, E. H (1996). Quantitative functional interrelations within the cis -regulatory system of the S. purpuratus Endo16 gene. Development 122, 4045-4056.[Abstract]

Yuh, C. H., Bolouri, H. and Davidson, E. H (1998). Genomic cis -regulatory logic: Functional analysis and computational model of a sea urchin gene control system. Science 279, 1896-1902.[Abstract/Free Full Text]

Zeller, R. W., Coffman, J. A., Harrington, M. G., Britten, R. J. and Davidson, E. H (1995). SpGCF1, a sea urchin embryo transcription factor, exists as five nested variants encoded by a single mRNA. Dev. Biol 169, 713-727.[Medline]

Zeller, R. W., Griffith, J. D., Moore, J. G., Kirchhamer, C. V., Britten, R. J. and Davidson, E. H (1995). A multimerizing transcription factor of sea urchin embryos capable of looping DNA. Proc. Natl. Acad. Sci. USA 92, 2989-2993.[Abstract/Free Full Text]

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Articles by Yuh, C. H.

Articles by Davidson, E. H.

				P. Oliveri, Q. Tu, and E. H. Davidson From the Cover: Feature Article: Global regulatory logic for specification of an embryonic cell lineage PNAS, April 22, 2008; 105(16): 5955 - 5962. [Abstract] [Full Text] [PDF]

				L. Hood Gene regulatory networks and embryonic specification PNAS, April 22, 2008; 105(16): 5951 - 5952. [Full Text] [PDF]

				R. Albert Network Inference, Analysis, and Modeling in Systems Biology PLANT CELL, November 1, 2007; 19(11): 3327 - 3338. [Full Text] [PDF]

				A. V. Werhli, M. Grzegorczyk, and D. Husmeier Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks Bioinformatics, October 15, 2006; 22(20): 2523 - 2531. [Abstract] [Full Text] [PDF]

				M. Freeling and B. C. Thomas Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity Genome Res., July 1, 2006; 16(7): 805 - 814. [Abstract] [Full Text] [PDF]

				G. A. Wray The evolution of embryonic gene expression in sea urchins Integr. Comp. Biol., June 1, 2006; 46(3): 233 - 242. [Abstract] [Full Text] [PDF]

				S. Gorski and T. Misteli Systems biology in the cell nucleus J. Cell Sci., September 15, 2005; 118(18): 4083 - 4092. [Abstract] [Full Text] [PDF]

				R. A. Cameron, S. H. Chow, K. Berney, T.-Y. Chiu, Q.-A. Yuan, A. Kramer, A. Helguero, A. Ransick, M. Yun, and E. H. Davidson An evolutionary constraint: Strongly disfavored class of change in DNA sequence during divergence of cis-regulatory modules PNAS, August 16, 2005; 102(33): 11769 - 11774. [Abstract] [Full Text] [PDF]

				J. P. Balhoff and G. A. Wray Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites PNAS, June 14, 2005; 102(24): 8591 - 8596. [Abstract] [Full Text] [PDF]

				S. Istrail and E. H. Davidson Gene Regulatory Networks Special Feature: Logic functions of the genomic cis-regulatory code PNAS, April 5, 2005; 102(14): 4954 - 4959. [Abstract] [Full Text] [PDF]

				M.-C. Marin, J.-R. Rodriguez, and A. Ferrus Transcription of Drosophila Troponin I Gene Is Regulated by Two Conserved, Functionally Identical, Synergistic Elements Mol. Biol. Cell, March 1, 2004; 15(3): 1185 - 1196. [Abstract] [Full Text] [PDF]

				H. F. Farhadi, P. Lepage, R. Forghani, H. C. H. Friedman, W. Orfali, L. Jasmin, W. Miller, T. J. Hudson, and A. C. Peterson A Combinatorial Network of Evolutionarily Conserved Myelin Basic Protein Regulatory Sequences Confers Distinct Glial-Specific Phenotypes J. Neurosci., November 12, 2003; 23(32): 10214 - 10223. [Abstract] [Full Text] [PDF]

				L. A. Romano and G. A. Wray Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation Development, September 1, 2003; 130(17): 4187 - 4199. [Abstract] [Full Text] [PDF]

				G. A. Wray, M. W. Hahn, E. Abouheif, J. P. Balhoff, M. Pizer, M. V. Rockman, and L. A. Romano The Evolution of Transcriptional Regulation in Eukaryotes Mol. Biol. Evol., September 1, 2003; 20(9): 1377 - 1419. [Abstract] [Full Text] [PDF]

				H. Bolouri and E. H. Davidson Transcriptional regulatory cascades in development: Initial rates, not steady state, determine network kinetics PNAS, August 5, 2003; 100(16): 9371 - 9376. [Abstract] [Full Text] [PDF]

				N. E. Buchler, U. Gerland, and T. Hwa On schemes of combinatorial transcription logic PNAS, April 29, 2003; 100(9): 5136 - 5141. [Abstract] [Full Text] [PDF]

				E. H. Davidson, D. R. McClay, and L. Hood Regulatory gene networks and the properties of the developmental process PNAS, February 18, 2003; 100(4): 1475 - 1480. [Abstract] [Full Text] [PDF]

				D. K. Jacobs and R. D. Gates Developmental Genes and the Reconstruction of Metazoan Evolution--Implications of Evolutionary Loss, Limits on Inference of Ancestry and Type 2 Errors Integr. Comp. Biol., February 1, 2003; 43(1): 11 - 18. [Abstract] [Full Text] [PDF]

				I. Manabe, T. Shindo, and R. Nagai Gene Expression in Fibroblasts and Fibrosis: Involvement in Cardiac Hypertrophy Circ. Res., December 13, 2002; 91(12): 1103 - 1113. [Abstract] [Full Text] [PDF]

				U. Gerland, J. D. Moroz, and T. Hwa Physical constraints and functional characteristics of transcription factor-DNA interaction PNAS, September 17, 2002; 99(19): 12015 - 12020. [Abstract] [Full Text] [PDF]

				D. Y.R. Stainier A glimpse into the molecular entrails of endoderm formation Genes & Dev., April 15, 2002; 16(8): 893 - 907. [Full Text] [PDF]

				E. H. Davidson, J. P. Rast, P. Oliveri, A. Ransick, C. Calestani, C.-H. Yuh, T. Minokawa, G. Amore, V. Hinman, C. Arenas-Mena, et al. A Genomic Regulatory Network for Development Science, March 1, 2002; 295(5560): 1669 - 1678. [Abstract] [Full Text] [PDF]

				F. J. Lovicu and J. W. McAvoy FGF-induced lens cell proliferation and differentiation is dependent on MAPK (ERK1/2) signalling Development, December 15, 2001; 128(24): 5075 - 5084. [Abstract] [Full Text] [PDF]

				I. Manabe and G. K. Owens The Smooth Muscle Myosin Heavy Chain Gene Exhibits Smooth Muscle Subtype-selective Modular Regulation in Vivo J. Biol. Chem., October 12, 2001; 276(42): 39076 - 39087. [Abstract] [Full Text] [PDF]