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Publications 2015

 

Erkenbrack, M. E. and Davidson, E. H. Evolutionary rewiring of gene regulatory network linkages at divergence of the echinoid subclasses. Proc Natl Acad Sci USA 2015. . ISSN 0027-8424. (In Press)

Yin, Z., Zhu, M., Davidson, E. H., Bottjer, D. J., Zhao, F.,Tafforeau, P. Sponge grade body fossil with cellular resolution dating 60 Myr before the Cambrian. Proc Natl Acad Sci U S A 2015 Mar 9;112(12):E1453-60.

Barsi, J. C., Li, E.,Davidson, E. H. Geometric control of ciliated band regulatory states in the sea urchin embryo.
Development 2015 Mar 5;142(5):953-61.

Gao, F., Thompson, J. R., Petsios, E., Erkenbrack, E., Moats, R. A., Bottjer, D. J., Davidson, E. H. Juvenile skeletogenesis in anciently diverged sea urchin clades. Dev Biol 2015 Apr 30;400(1):148-58.

Peter, I. S. and Davidson, E. H. Genomic Control Process. Development and Evolution. Academic Press/Elsevier, 2015


Publications 2014

 

Tu, Q., Cameron, R.A., Davidson, E. H. Quantitative developmental transcriptomes of the sea urchin Strongylocentrotus purpuratus. Dev. Biol. 385, 160-167, 2014

Barsi,J. C., Tu, Q. and Davidson, E. H. General approach for in vivo recovery of cell type specific effector gene sets. Genome Res. published online March 6, 2014. Access the most recent version at doi:10.1101/gr.167668.113

Li, E., Cui, M., Peter, I.S., Davidson, E. H. Encoding regulatory state boundaries in the pregastrular oral ectoderm of the sea urchin embryo. PNAS. published online February 1, 2014. Access the most recent version at doi: 10.1073/pnas.1323105111

Davidson E. H. The uncommon roles of common gene regulatory factors in the genomes of differentiating cells. EMBO J 2014 Jun 30;33(11):1193-4.

Cui, M., Siriwon, N.,Li, E. Davidson, E.H.,Peter, I. SSpecific functions of the Wnt signaling system in gene regulatory networks throughout the early sea urchin embryo. Proc Natl Acad Sci U S A 2014. Nov 10;111(47):E5029-38.

Davidson, E. H. A very brief scientific reminiscience of John Gurdon. Differentiation. Differentiation 2014 Jul;88(1)

 

 

Publications 2013

 

Ben-Tabou de-Leon,S., Su, Y.-H., Lin,. K.-T., Li; E., Davidson, E. H. Lockdown gene regulatory control in the sea urchin aboral ectoderm: Spatial initiation, signaling inputs, and cell fate. Dev. Biol. 374, 245-254, 2013. PMID: 23211652; PMCID:PMC3548969

Materna, S. C. and Davidson, E. H. A comprehensive analysis of Delta signaling in pre-gastrular sea urchin eembryos. Dev. Biol. 364, 77-87, 2013. PMCID: PMC3294105

Materna, S. C., Ransick, A., Li, E, Davidson, E. H. Diversification of oral and aboral mesodermal regulatory states in pregastrular sea urchin embryos. Dev. Biol. 375, 92-104, 2013. PMID: 23261933. PMCID: PMC3570723

Faure, E., Peter, I. S., Davidson, E. H. A new software package for predictive GRN modeling and redesign. J. Comp. Biol. 20, 419-423, 2013. PMID: 23614576

Peter I.S. and Davidson E.H. Transcriptional network logic:  the systems biology of development.In: Handbook of Systems Biology. Concepts and Insights. Eds A. J. Marian Walhout. M. Vidal and J. Dekker. Chapter 11, pages 211-228. Academic Press/Elsevier, 2013. PMC:N/A

Materna, S. C., Swartz, S. Z., Smith J. Notch and Nodal control expression of a forkhead factor in the specification network of a multipotent progenitor population in sea urchin. Development 140, 1796-1806, 2013. PMID 23533178

Li, E., Materna, S.C., Davidson, E. H. New regulatory circuit controlling spatial and temporal gene expression in the sea urchin embryo oral ectoderm GRN. Dev. Biol. 382, 268-279, 2013

 

Publications 2012

 


Damle, S. and Davidson, E. H.  An in vivo synthetic approach to network validation and discovery. Proc. Natl. Acad. Sci. USA. 109, 1548-1553. 2012.

Davidson, E. H. Retrospective. Roy J. Britten (1919-2012). Science 335, 1183, 2012.

Davidson, E. H. Reprospective. Roy J. Britten, 1919-2012: Our early years at Caltech. Proc. Natl. Acad. Sci. USA 109, 6358-6359, 2012.

Davidson, E. Q & A. Current Biology 22, R216-R217, 2012.

Li, E., Materna, S. C., Davidson, E. H. Direct and indirect control of oral ectoderm regulatory gene expression by Nodal signaling in the sea urchin embryo. Dev. Biol. 369, 377-385, 2012. PMID: 22771578; PMCID:PMC3423475

Nam, J., Davidson, E. H. Barcoded DNA-tag reporters for multiplex cis-regulatory analysis.. PLoS ONE 7(4): e35934. doi:10.1371/journal.pone.0035934, 2012.

Materna, S. C. and Davidson, E. H. A comprehensive analysis of Delta signaling in pre-gastrular sea urchin embryos.  Dev. Biol. 364, 77-87, 2012.

Ransick, A. and Davidson, E. H. Cis-regulatory logic driving glial cells missing: Self-sustaining circuitry in later embryogenesis. Dev. Biol. 364, 259-267, 2012

Peter I.S. and Davidson E.H. Pattern formation in sea urchin endomesoderm as instructed by gene regulatory network topologies. In: Pattern Formation in Morphogenesis. Vol. 15. Eds V. Capasso, M. Gromov, A. Harel-Bellan, N. Morozova, L. L. Pritchard. Pp.75-92. Springer-Verlag, Heidelberg. 2012. PMC:N/A

Peter, I. S., Faure, E., and Davidson, E. H. Predictive computation of genomic logic processing functions in embryonic development. Proc. Natl. Acad. Sci. USA, 109, 16434-16442, 2012. PMCID: PMC3478651.

Tu, Q., Cameron, R. A., Worley, K.C.,Gibbs, R. A. and Davidson, E. H. Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis. Genome Res. 22, 2079-2087, 2012. PMCID: PMC3460201.

 

Publications 2011

 

Peter, I. S. and Davidson, E. H.  Evolution of gene regulatory networks controlling embryonic development.  Cell 144, 970-985, 2011. (PMC3076009)

Davidson, E. H.  Evolutionary bioscience as regulatory systems biology.  Dev. Biol. 357, 35-40, 2011.

Peter, I. S. and Davidson, E. H. A gene regulatory network controlling the embryonic specification of endoderm. Nature 474, 635-639, 2011.

Damle, S. and Davidson, E. H.  Precise cis-regulatory control of spatial and temporal expression of the alx-1 gene in the skeletogenic lineage of S. purpuratus.  Dev. Biol. 357, 505-517, 2011.

Royo, J. O., Maeso, I., Irimia, M., Gao, F., Renfer, E., Peter, I. S., Lopes, C., D'Aniello, S., Technau, U., Casares, F., Daviidson, E. H., Garcia-Fernández, J. and Gómez-Skarmeta, J. L.  A neuronal regulatory state utilized from sea anemone to man, and its evolutionary co-option for brain development. Proc. Natl. Acad. Sci. USA 108, 14186-14191, 2011.

Deichmann, U., Morange, M. and Davidson, E. H. Introductory comment on six papers from a Symposium on experimental and historical aspects of evolutionary bioscience. Dev. Biol. 357, 2, 2011.

 

Publications 2010

 

Davidson, E. H. and Erwin, D. H.  Evolutionary innovation and stability in animal gene networks.  J. Exp. Zool. (Mol. Dev. Evol.) 314B, 182-186, 2010.

Nam, J., Dong, P., Tarpine, R., Istrail, S. and Davidson, E. H.  Functional cis-regulatory genomics for systems biology.  Proc. Natl. Acad. Sci. USA 107, 3930-3935, 2010. (PMC2840491)

Ptashne, M., Hobert, O. and Davidson, E.  Questions over the scientific basis of epigenome project.  Nature 464, 487, 2010.

Bolouri, H. and Davidson, E. H.  The gene regulatory network basis of the "community effect," and analysis of a sea urchin embryo example.  Dev. Biol. 340, 170-178, 2010. (PMC2854306)

Peter, I. S. and Davidson, E. H.  The endoderm gene regulatory network in sea urchin embryos up to mid-blastula stage.  Dev. Biol. 340, 188-199, 2010.

Davidson, E. H.  Leader for DB "Developmental Gene Regulatory Networks" Collection.  Dev. Biol. 340, 160, 2010.

Davidson, E. H. and Erwin, D. H.  An integrated view of Precambrian eumetazoan evolution.  Cold Spring Harbor Symp. Quant. Biol. 74, 65-80, 2010.

Materna, S. C., Nam, J. and Davidson, E. H.  High accuracy, high-resolution prevalence measurement for the majority of locally expressed regulatory genes in early sea urchin development.  Gene Expression Patterns 10, 177-184, 2010. (PMC2902461)

Ben-Tabou de-Leon, S. and Davidson, E. H.  Information processing at the foxa node of the sea urchin endomesoderm specification network.  Proc. Natl. Acad. Sci. USA 107, 10103-10108, 2010. (PMC2890479)

Davidson, E. H.  Emerging properties of animal gene regulatory networks. 
Nature 468, 911-920, 2010.