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Developmental effector gene regulation: Multiplexed strategies for functional analysis. , Wang L, Koppitch K, Cutting A, Dong P, Kudtarkar P, Zeng J, Cameron RA , Davidson EH ., Dev Biol. January 1, 2019; 445 (1): 68-79.
Conserved regulatory state expression controlled by divergent developmental gene regulatory networks in echinoids. , Erkenbrack EM , Davidson EH , Peter IS ., Development. December 18, 2018; 145 (24):
Assessing regulatory information in developmental gene regulatory networks. , Peter IS , Davidson EH ., Proc Natl Acad Sci U S A. June 6, 2017; 114 (23): 5862-5869.
Sequential Response to Multiple Developmental Network Circuits Encoded in an Intronic cis-Regulatory Module of Sea Urchin hox11/13b. , Cui M, Vielmas E, Davidson EH , Peter IS ., Cell Rep. April 11, 2017; 19 (2): 364-374.
Mapping a multiplexed zoo of mRNA expression. , Choi HM, Calvert CR, Husain N, Huss D, Barsi JC , Deverman BE, Hunter RC, Kato M, Lee SM, Abelin AC, Rosenthal AZ, Akbari OS, Li Y, Hay BA, Sternberg PW, Patterson PH, Davidson EH , Mazmanian SK, Prober DA, van de Rijn M, Leadbetter JR, Newman DK, Readhead C, Bronner ME, Wold B, Lansford R, Sauka-Spengler T, Fraser SE, Pierce NA., Development. October 1, 2016; 143 (19): 3632-3637.
cis-Regulatory control of the initial neurogenic pattern of onecut gene expression in the sea urchin embryo. , Barsi JC , Davidson EH ., Dev Biol. January 1, 2016; 409 (1): 310-318.
Genome-wide assessment of differential effector gene use in embryogenesis. , Barsi JC , Tu Q, Calestani C , Davidson EH ., Development. November 15, 2015; 142 (22): 3892-901.
Reorganization of sea urchin gene regulatory networks at least 268 million years ago as revealed by oldest fossil cidaroid echinoid. , Thompson JR, Petsios E, Davidson EH , Erkenbrack EM , Gao F, Bottjer DJ., Sci Rep. October 21, 2015; 5 15541.
Evolutionary rewiring of gene regulatory network linkages at divergence of the echinoid subclasses. , Erkenbrack EM , Davidson EH ., Proc Natl Acad Sci U S A. July 28, 2015; 112 (30): E4075-84.
Juvenile skeletogenesis in anciently diverged sea urchin clades. , Gao F, Thompson JR, Petsios E, Erkenbrack E , Moats RA, Bottjer DJ, Davidson EH ., Dev Biol. April 1, 2015; 400 (1): 148-58.
Geometric control of ciliated band regulatory states in the sea urchin embryo. , Barsi JC , Li E, Davidson EH ., Development. March 1, 2015; 142 (5): 953-61.
Specific functions of the Wnt signaling system in gene regulatory networks throughout the early sea urchin embryo. , Cui M, Siriwon N, Li E, Davidson EH , Peter IS ., Proc Natl Acad Sci U S A. November 25, 2014; 111 (47): E5029-38.
General approach for in vivo recovery of cell type-specific effector gene sets. , Barsi JC , Tu Q, Davidson EH ., Genome Res. May 1, 2014; 24 (5): 860-8.
Encoding regulatory state boundaries in the pregastrular oral ectoderm of the sea urchin embryo. , Li E, Cui M, Peter IS , Davidson EH ., Proc Natl Acad Sci U S A. March 11, 2014; 111 (10): E906-13.
Quantitative developmental transcriptomes of the sea urchin Strongylocentrotus purpuratus. , Tu Q, Cameron RA , Davidson EH ., Dev Biol. January 15, 2014; 385 (2): 160-7.
Brief notes on the meaning of a genomic control system for animal embryogenesis. , Davidson E ., Perspect Biol Med. January 1, 2014; 57 (1): 78-86.
New regulatory circuit controlling spatial and temporal gene expression in the sea urchin embryo oral ectoderm GRN. , Li E, Materna SC, Davidson EH ., Dev Biol. October 1, 2013; 382 (1): 268-79.
Diversification of oral and aboral mesodermal regulatory states in pregastrular sea urchin embryos. , Materna SC, Ransick A, Li E, Davidson EH ., Dev Biol. March 1, 2013; 375 (1): 92-104.
Gene regulatory control in the sea urchin aboral ectoderm: spatial initiation, signaling inputs, and cell fate lockdown. , Ben-Tabou de-Leon S, Su YH , Lin KT, Li E, Davidson EH ., Dev Biol. February 1, 2013; 374 (1): 245-54.
Predictive computation of genomic logic processing functions in embryonic development. , Peter IS , Faure E, Davidson EH ., Proc Natl Acad Sci U S A. October 9, 2012; 109 (41): 16434-42.
Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis. , Tu Q, Cameron RA , Worley KC, Gibbs RA, Davidson EH ., Genome Res. October 1, 2012; 22 (10): 2079-87.
Direct and indirect control of oral ectoderm regulatory gene expression by Nodal signaling in the sea urchin embryo. , Li E, Materna SC, Davidson EH ., Dev Biol. September 15, 2012; 369 (2): 377-85.
Cis-regulatory logic driving glial cells missing: self-sustaining circuitry in later embryogenesis. , Ransick A, Davidson EH ., Dev Biol. April 15, 2012; 364 (2): 259-67.
A comprehensive analysis of Delta signaling in pre-gastrular sea urchin embryos. , Materna SC, Davidson EH ., Dev Biol. April 1, 2012; 364 (1): 77-87.
Synthetic in vivo validation of gene network circuitry. , Damle SS, Davidson EH ., Proc Natl Acad Sci U S A. January 31, 2012; 109 (5): 1548-53.
Barcoded DNA-tag reporters for multiplex cis-regulatory analysis. , Nam J , Davidson EH ., PLoS One. January 1, 2012; 7 (4): e35934.
Precise cis-regulatory control of spatial and temporal expression of the alx-1 gene in the skeletogenic lineage of s. purpuratus. , Damle S, Davidson EH ., Dev Biol. September 15, 2011; 357 (2): 505-17.
Transphyletic conservation of developmental regulatory state in animal evolution. , Royo JL, Maeso I, Irimia M, Gao F, Peter IS , Lopes CS, D'Aniello S, Casares F, Davidson EH , Garcia-Fernández J, Gómez-Skarmeta JL., Proc Natl Acad Sci U S A. August 23, 2011; 108 (34): 14186-91.
A gene regulatory network controlling the embryonic specification of endoderm. , Peter IS , Davidson EH ., Nature. May 29, 2011; 474 (7353): 635-9.
High accuracy, high-resolution prevalence measurement for the majority of locally expressed regulatory genes in early sea urchin development. , Materna SC, Nam J , Davidson EH ., Gene Expr Patterns. June 1, 2010; 10 (4-5): 177-84.
Information processing at the foxa node of the sea urchin endomesoderm specification network. , de-Leon SB , Davidson EH ., Proc Natl Acad Sci U S A. June 1, 2010; 107 (22): 10103-8.
The gene regulatory network basis of the "community effect," and analysis of a sea urchin embryo example. , Bolouri H, Davidson EH ., Dev Biol. April 15, 2010; 340 (2): 170-8.
The endoderm gene regulatory network in sea urchin embryos up to mid-blastula stage. , Peter IS , Davidson EH ., Dev Biol. April 15, 2010; 340 (2): 188-99.
Functional cis-regulatory genomics for systems biology. , Nam J , Dong P, Tarpine R, Istrail S, Davidson EH ., Proc Natl Acad Sci U S A. February 23, 2010; 107 (8): 3930-5.
Modularity and design principles in the sea urchin embryo gene regulatory network. , Peter IS , Davidson EH ., FEBS Lett. December 17, 2009; 583 (24): 3948-58.
Flexibility of transcription factor target site position in conserved cis-regulatory modules. , Cameron RA , Davidson EH ., Dev Biol. December 1, 2009; 336 (1): 122-35.
Network design principles from the sea urchin embryo. , Davidson EH ., Curr Opin Genet Dev. December 1, 2009; 19 (6): 535-40.
The cis-regulatory system of the tbrain gene: Alternative use of multiple modules to promote skeletogenic expression in the sea urchin embryo. , Wahl ME, Hahn J, Gora K, Davidson EH , Oliveri P ., Dev Biol. November 15, 2009; 335 (2): 428-41.
Regulative recovery in the sea urchin embryo and the stabilizing role of fail-safe gene network wiring. , Smith J, Davidson EH ., Proc Natl Acad Sci U S A. October 27, 2009; 106 (43): 18291-6.
Building developmental gene regulatory networks. , Li E, Davidson EH ., Birth Defects Res C Embryo Today. June 1, 2009; 87 (2): 123-30.
A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo. , Su YH , Li E, Geiss GK, Longabaugh WJ, Krämer A, Davidson EH ., Dev Biol. May 15, 2009; 329 (2): 410-21.
SpBase: the sea urchin genome database and web site. , Cameron RA , Samanta M, Yuan A, He D, Davidson E ., Nucleic Acids Res. January 1, 2009; 37 (Database issue): D750-4.
Genomic control of patterning. , Peter IS , Davidson EH ., Int J Dev Biol. January 1, 2009; 53 (5-6): 707-16.
Experimentally based sea urchin gene regulatory network and the causal explanation of developmental phenomenology. , Ben-Tabou de-Leon S, Davidson EH ., Wiley Interdiscip Rev Syst Biol Med. January 1, 2009; 1 (2): 237-246.
Properties of developmental gene regulatory networks. , Davidson EH , Levine MS., Proc Natl Acad Sci U S A. December 23, 2008; 105 (51): 20063-6.
Gene regulatory network subcircuit controlling a dynamic spatial pattern of signaling in the sea urchin embryo. , Smith J, Davidson EH ., Proc Natl Acad Sci U S A. December 23, 2008; 105 (51): 20089-94.
A new method, using cis-regulatory control, for blocking embryonic gene expression. , Smith J, Davidson EH ., Dev Biol. June 15, 2008; 318 (2): 360-5.
Transfer of a large gene regulatory apparatus to a new developmental address in echinoid evolution. , Gao F, Davidson EH ., Proc Natl Acad Sci U S A. April 22, 2008; 105 (16): 6091-6.
Global regulatory logic for specification of an embryonic cell lineage. , Oliveri P , Tu Q, Davidson EH ., Proc Natl Acad Sci U S A. April 22, 2008; 105 (16): 5955-62.
Boveri''s long experiment: sea urchin merogones and the establishment of the role of nuclear chromosomes in development. , Laubichler MD, Davidson EH ., Dev Biol. February 1, 2008; 314 (1): 1-11.