Eric H Davidson - Publications

Publications (295)

ECB-PERS-4294

Publications By Eric H Davidson

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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.
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.
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. June 15, 2011; 357 (2): 505-17.
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.
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.
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. August 15, 2009; 335 (2): 428-41.
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.
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.
A new method, using cis-regulatory control, for blocking embryonic gene expression., Smith J, Davidson EH., Dev Biol. March 15, 2008; 318 (2): 360-5.
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.

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.

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.

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. June 15, 2011; 357 (2): 505-17.

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.

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.

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. August 15, 2009; 335 (2): 428-41.

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.

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.

A new method, using cis-regulatory control, for blocking embryonic gene expression., Smith J, Davidson EH., Dev Biol. March 15, 2008; 318 (2): 360-5.

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.

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