Publications by authors named "Eric H Davidson"

100Publications

Conserved regulatory state expression controlled by divergent developmental gene regulatory networks in echinoids.

Development 2018 12 18;145(24). Epub 2018 Dec 18.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA

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http://dx.doi.org/10.1242/dev.167288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6307887PMC
December 2018

Developmental effector gene regulation: Multiplexed strategies for functional analysis.

Dev Biol 2019 01 28;445(1):68-79. Epub 2018 Oct 28.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States.

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https://linkinghub.elsevier.com/retrieve/pii/S00121606183020
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http://dx.doi.org/10.1016/j.ydbio.2018.10.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6321769PMC
January 2019

Assessing regulatory information in developmental gene regulatory networks.

Proc Natl Acad Sci U S A 2017 06;114(23):5862-5869

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125.

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http://dx.doi.org/10.1073/pnas.1610616114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5468647PMC
June 2017

Sequential Response to Multiple Developmental Network Circuits Encoded in an Intronic cis-Regulatory Module of Sea Urchin hox11/13b.

Cell Rep 2017 04;19(2):364-374

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.03.039DOI Listing
April 2017

Implications of Developmental Gene Regulatory Networks Inside and Outside Developmental Biology.

Curr Top Dev Biol 2016 1;117:237-51. Epub 2016 Feb 1.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA.

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http://dx.doi.org/10.1016/bs.ctdb.2015.12.014DOI Listing
December 2016

Genomics, "Discovery Science," Systems Biology, and Causal Explanation: What Really Works?

Authors:
Eric H Davidson

Perspect Biol Med 2015 ;58(2):165-81

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http://dx.doi.org/10.1353/pbm.2015.0025DOI Listing
October 2016

cis-Regulatory control of the initial neurogenic pattern of onecut gene expression in the sea urchin embryo.

Dev Biol 2016 Jan 30;409(1):310-318. Epub 2015 Oct 30.

Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Mail Code 156-29, Pasadena, CA 91125, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S00121606153010
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http://dx.doi.org/10.1016/j.ydbio.2015.10.021DOI Listing
January 2016

Genome-wide assessment of differential effector gene use in embryogenesis.

Development 2015 Nov 28;142(22):3892-901. Epub 2015 Sep 28.

Division of Biology and Bioengineering, Caltech, 1200 East California Boulevard, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1242/dev.127746DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4712884PMC
November 2015

Evolutionary rewiring of gene regulatory network linkages at divergence of the echinoid subclasses.

Proc Natl Acad Sci U S A 2015 Jul 13;112(30):E4075-84. Epub 2015 Jul 13.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125

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http://dx.doi.org/10.1073/pnas.1509845112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4522742PMC
July 2015

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. Epub 2015 Mar 9.

European Synchrotron Radiation Facility, Grenoble 38000, France.

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http://dx.doi.org/10.1073/pnas.1414577112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378401PMC
March 2015

Geometric control of ciliated band regulatory states in the sea urchin embryo.

Development 2015 Mar 5;142(5):953-61. Epub 2015 Feb 5.

Division of Biology and Biological Engineering, Caltech, Pasadena, CA 91125, USA

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http://dx.doi.org/10.1242/dev.117986DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4352983PMC
March 2015

Juvenile skeletogenesis in anciently diverged sea urchin clades.

Dev Biol 2015 Apr 30;400(1):148-58. Epub 2015 Jan 30.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, United States. Electronic address:

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http://dx.doi.org/10.1016/j.ydbio.2015.01.017DOI Listing
April 2015

A very brief scientific reminiscence of John Gurdon.

Authors:
Eric H Davidson

Differentiation 2014 Jul;88(1)

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http://dx.doi.org/10.1016/j.diff.2014.09.006DOI Listing
July 2014

Specific 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. Epub 2014 Nov 10.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125

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http://dx.doi.org/10.1073/pnas.1419141111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4250154PMC
November 2014

The uncommon roles of common gene regulatory factors in the genomes of differentiating cells.

Authors:
Eric H Davidson

EMBO J 2014 Jun 30;33(11):1193-4. Epub 2014 Apr 30.

Division of Biology, California Institute of Technology, Pasadena, CA, USA.

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http://dx.doi.org/10.1002/embj.201488693DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4198022PMC
June 2014

General approach for in vivo recovery of cell type-specific effector gene sets.

Genome Res 2014 May 6;24(5):860-8. Epub 2014 Mar 6.

Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.

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http://dx.doi.org/10.1101/gr.167668.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009615PMC
May 2014

Encoding regulatory state boundaries in the pregastrular oral ectoderm of the sea urchin embryo.

Proc Natl Acad Sci U S A 2014 Mar 20;111(10):E906-13. Epub 2014 Feb 20.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125.

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http://dx.doi.org/10.1073/pnas.1323105111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3956148PMC
March 2014

Quantitative developmental transcriptomes of the sea urchin Strongylocentrotus purpuratus.

Dev Biol 2014 Jan 26;385(2):160-7. Epub 2013 Nov 26.

Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ydbio.2013.11.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3898891PMC
January 2014

New regulatory circuit controlling spatial and temporal gene expression in the sea urchin embryo oral ectoderm GRN.

Dev Biol 2013 Oct 6;382(1):268-79. Epub 2013 Aug 6.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1016/j.ydbio.2013.07.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783610PMC
October 2013

A new software package for predictive gene regulatory network modeling and redesign.

J Comput Biol 2013 Jun 24;20(6):419-23. Epub 2013 Apr 24.

Division of Biology, MC 156-29, California Institute of Technology, Pasadena, California, USA.

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http://dx.doi.org/10.1089/cmb.2012.0297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3667423PMC
June 2013

Diversification of oral and aboral mesodermal regulatory states in pregastrular sea urchin embryos.

Dev Biol 2013 Mar 19;375(1):92-104. Epub 2012 Dec 19.

California Institute of Technology, Division of Biology, m/c 156-29, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1016/j.ydbio.2012.11.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3570723PMC
March 2013

Gene regulatory control in the sea urchin aboral ectoderm: spatial initiation, signaling inputs, and cell fate lockdown.

Dev Biol 2013 Feb 2;374(1):245-54. Epub 2012 Dec 2.

Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 31905, Israel.

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https://linkinghub.elsevier.com/retrieve/pii/S00121606120063
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http://dx.doi.org/10.1016/j.ydbio.2012.11.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3548969PMC
February 2013

Predictive computation of genomic logic processing functions in embryonic development.

Proc Natl Acad Sci U S A 2012 Oct 27;109(41):16434-42. Epub 2012 Aug 27.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1073/pnas.1207852109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3478651PMC
October 2012

Direct and indirect control of oral ectoderm regulatory gene expression by Nodal signaling in the sea urchin embryo.

Dev Biol 2012 Sep 6;369(2):377-85. Epub 2012 Jul 6.

Division of Biology, California Institute of Technology, Pasadena, 91125, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S00121606120035
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http://dx.doi.org/10.1016/j.ydbio.2012.06.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3423475PMC
September 2012

Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis.

Genome Res 2012 Oct 18;22(10):2079-87. Epub 2012 Jun 18.

Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.

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http://dx.doi.org/10.1101/gr.139170.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460201PMC
October 2012

Barcoded DNA-tag reporters for multiplex cis-regulatory analysis.

PLoS One 2012 26;7(4):e35934. Epub 2012 Apr 26.

Division of Biology, California Institute of Technology, Pasadena, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0035934PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3339872PMC
September 2012

Cis-regulatory logic driving glial cells missing: self-sustaining circuitry in later embryogenesis.

Dev Biol 2012 Apr;364(2):259-67

California Institute of Technology, Pasadena, CA 91125, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561781PMC
http://dx.doi.org/10.1016/j.ydbio.2012.02.003DOI Listing
April 2012

Roy J. Britten, 1919-2012: our early years at Caltech.

Authors:
Eric H Davidson

Proc Natl Acad Sci U S A 2012 Apr 12;109(17):6358-9. Epub 2012 Apr 12.

Division of Biology, Caltech, Pasadena, CA 91125, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1204420109
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http://dx.doi.org/10.1073/pnas.1204420109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3340058PMC
April 2012

Retrospective. Roy J. Britten (1919-2012).

Authors:
Eric H Davidson

Science 2012 Mar;335(6073):1183

California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1126/science.1220828DOI Listing
March 2012

A comprehensive analysis of Delta signaling in pre-gastrular sea urchin embryos.

Dev Biol 2012 Apr 27;364(1):77-87. Epub 2012 Jan 27.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1016/j.ydbio.2012.01.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294105PMC
April 2012

Synthetic in vivo validation of gene network circuitry.

Proc Natl Acad Sci U S A 2012 Jan 11;109(5):1548-53. Epub 2012 Jan 11.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1073/pnas.1119905109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3277137PMC
January 2012

Transphyletic conservation of developmental regulatory state in animal evolution.

Proc Natl Acad Sci U S A 2011 Aug 15;108(34):14186-91. Epub 2011 Aug 15.

Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Cientificas - Universidad Pablo de Olavide, E-41013 Sevilla, Spain.

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http://dx.doi.org/10.1073/pnas.1109037108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3161536PMC
August 2011

Precise cis-regulatory control of spatial and temporal expression of the alx-1 gene in the skeletogenic lineage of s. purpuratus.

Dev Biol 2011 Sep 30;357(2):505-17. Epub 2011 Jun 30.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S001216061101074
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http://dx.doi.org/10.1016/j.ydbio.2011.06.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3164750PMC
September 2011

A gene regulatory network controlling the embryonic specification of endoderm.

Nature 2011 May 29;474(7353):635-9. Epub 2011 May 29.

Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.

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http://www.nature.com/doifinder/10.1038/nature10100
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http://dx.doi.org/10.1038/nature10100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3976212PMC
May 2011

Evolution of gene regulatory networks controlling body plan development.

Cell 2011 Mar;144(6):970-85

Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1016/j.cell.2011.02.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3076009PMC
March 2011

Evolutionary bioscience as regulatory systems biology.

Authors:
Eric H Davidson

Dev Biol 2011 Sep 12;357(1):35-40. Epub 2011 Feb 12.

Division of Biology, California Institute of Technology, Pasadena, 91125, USA.

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http://dx.doi.org/10.1016/j.ydbio.2011.02.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3135751PMC
September 2011

Emerging properties of animal gene regulatory networks.

Authors:
Eric H Davidson

Nature 2010 Dec;468(7326):911-20

Division of Biology 156-29, California Institute of Technology, Pasadena, California 91125, USA.

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http://dx.doi.org/10.1038/nature09645DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967874PMC
December 2010

Information processing at the foxa node of the sea urchin endomesoderm specification network.

Proc Natl Acad Sci U S A 2010 Jun 17;107(22):10103-8. Epub 2010 May 17.

Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1073/pnas.1004824107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2890477PMC
June 2010

High accuracy, high-resolution prevalence measurement for the majority of locally expressed regulatory genes in early sea urchin development.

Gene Expr Patterns 2010 Jun 14;10(4-5):177-84. Epub 2010 Apr 14.

Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1016/j.gep.2010.04.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902461PMC
June 2010

Experimentally based sea urchin gene regulatory network and the causal explanation of developmental phenomenology.

Wiley Interdiscip Rev Syst Biol Med 2009 Sep-Oct;1(2):237-246

Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1002/wsbm.24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836836PMC
January 2011

Functional cis-regulatory genomics for systems biology.

Proc Natl Acad Sci U S A 2010 Feb 8;107(8):3930-5. Epub 2010 Feb 8.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1073/pnas.1000147107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2840491PMC
February 2010

Evolutionary innovation and stability in animal gene networks.

J Exp Zool B Mol Dev Evol 2010 May;314(3):182-6

Division of Biology 156-29, California Institute of Technology, Pasadena, California, USA.

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http://dx.doi.org/10.1002/jez.b.21329DOI Listing
May 2010

Modularity and design principles in the sea urchin embryo gene regulatory network.

FEBS Lett 2009 Dec;583(24):3948-58

California Institute of Technology, Division of Biology, Pasadena, CA 91125, USA.

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http://doi.wiley.com/10.1016/j.febslet.2009.11.060
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http://dx.doi.org/10.1016/j.febslet.2009.11.060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2810318PMC
December 2009

Network design principles from the sea urchin embryo.

Authors:
Eric H Davidson

Curr Opin Genet Dev 2009 Dec 11;19(6):535-40. Epub 2009 Nov 11.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S0959437X0900155
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http://dx.doi.org/10.1016/j.gde.2009.10.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3428372PMC
December 2009

The endoderm gene regulatory network in sea urchin embryos up to mid-blastula stage.

Dev Biol 2010 Apr 3;340(2):188-99. Epub 2009 Nov 3.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1016/j.ydbio.2009.10.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3981691PMC
April 2010

Regulative recovery in the sea urchin embryo and the stabilizing role of fail-safe gene network wiring.

Proc Natl Acad Sci U S A 2009 Oct 12;106(43):18291-6. Epub 2009 Oct 12.

Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1073/pnas.0910007106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775351PMC
October 2009

Flexibility of transcription factor target site position in conserved cis-regulatory modules.

Dev Biol 2009 Dec 18;336(1):122-35. Epub 2009 Sep 18.

Division of Biology and the Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S001216060901203
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http://dx.doi.org/10.1016/j.ydbio.2009.09.018DOI Listing
December 2009

Building developmental gene regulatory networks.

Birth Defects Res C Embryo Today 2009 Jun;87(2):123-30

Division of Biology, California Institute of Technology, Pasadena, California 911025, USA.

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http://dx.doi.org/10.1002/bdrc.20152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747644PMC
June 2009

The gene regulatory network basis of the "community effect," and analysis of a sea urchin embryo example.

Dev Biol 2010 Apr 10;340(2):170-8. Epub 2009 Jun 10.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1016/j.ydbio.2009.06.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2854306PMC
April 2010

Genomic control of patterning.

Int J Dev Biol 2009 ;53(5-6):707-16

California Institute of Technology, Pasadena, 91125, USA.

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http://www.intjdevbiol.com/paper.php?doi=072495ip
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http://dx.doi.org/10.1387/ijdb.072495ipDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967875PMC
September 2009

The evolution of hierarchical gene regulatory networks.

Nat Rev Genet 2009 Feb 13;10(2):141-8. Epub 2009 Jan 13.

Department of Paleobiology, MRC-121, National Museum of Natural History, PO BOX 37012, Washington, Washington DC 20013-7012, USA.

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http://www.nature.com/articles/nrg2499
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http://dx.doi.org/10.1038/nrg2499DOI Listing
February 2009

Gene regulatory network subcircuit controlling a dynamic spatial pattern of signaling in the sea urchin embryo.

Proc Natl Acad Sci U S A 2008 Dec 22;105(51):20089-94. Epub 2008 Dec 22.

Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0806442105
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http://dx.doi.org/10.1073/pnas.0806442105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2629318PMC
December 2008

Properties of developmental gene regulatory networks.

Proc Natl Acad Sci U S A 2008 Dec 22;105(51):20063-6. Epub 2008 Dec 22.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0806007105
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http://dx.doi.org/10.1073/pnas.0806007105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2629280PMC
December 2008

Developmental biology at the systems level.

Authors:
Eric H Davidson

Biochim Biophys Acta 2009 Apr 12;1789(4):248-9. Epub 2008 Nov 12.

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http://linkinghub.elsevier.com/retrieve/pii/S187493990800240
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http://dx.doi.org/10.1016/j.bbagrm.2008.11.001DOI Listing
April 2009

Modeling the dynamics of transcriptional gene regulatory networks for animal development.

Dev Biol 2009 Jan 12;325(2):317-28. Epub 2008 Nov 12.

Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S00121606080131
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http://dx.doi.org/10.1016/j.ydbio.2008.10.043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4100934PMC
January 2009

Visualization, documentation, analysis, and communication of large-scale gene regulatory networks.

Biochim Biophys Acta 2009 Apr 6;1789(4):363-74. Epub 2008 Aug 6.

Institute for Systems Biology, Seattle, WA 98103-8904, USA.

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http://dx.doi.org/10.1016/j.bbagrm.2008.07.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2762351PMC
April 2009

A new method, using cis-regulatory control, for blocking embryonic gene expression.

Dev Biol 2008 Jun 14;318(2):360-5. Epub 2008 Mar 14.

Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S00121606080018
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http://dx.doi.org/10.1016/j.ydbio.2008.02.056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929273PMC
June 2008

Global regulatory logic for specification of an embryonic cell lineage.

Proc Natl Acad Sci U S A 2008 Apr 14;105(16):5955-62. Epub 2008 Apr 14.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0711220105
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http://dx.doi.org/10.1073/pnas.0711220105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2329687PMC
April 2008

Transfer of a large gene regulatory apparatus to a new developmental address in echinoid evolution.

Proc Natl Acad Sci U S A 2008 Apr 14;105(16):6091-6. Epub 2008 Apr 14.

Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA.

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April 2008

Boveri's long experiment: sea urchin merogones and the establishment of the role of nuclear chromosomes in development.

Dev Biol 2008 Feb 3;314(1):1-11. Epub 2007 Dec 3.

School of Life Sciences, Center for Biology and Society, Arizona State University, Tempe, AZ 85287-4501, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2247478PMC
February 2008

Evolutionary plasticity of developmental gene regulatory network architecture.

Proc Natl Acad Sci U S A 2007 Dec 27;104(49):19404-9. Epub 2007 Nov 27.

Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2148302PMC
December 2007

A gene regulatory network subcircuit drives a dynamic pattern of gene expression.

Science 2007 Nov;318(5851):794-7

Division of Biology, 156-29, California Institute of Technology, Pasadena, CA 91125, USA.

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November 2007

Caught in the evolutionary act: precise cis-regulatory basis of difference in the organization of gene networks of sea stars and sea urchins.

Dev Biol 2007 Dec 16;312(2):584-95. Epub 2007 Sep 16.

Department of Biological Sciences, Carnegie Mellon University, PA 15213, USA.

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December 2007

The regulatory genome and the computer.

Dev Biol 2007 Oct 10;310(2):187-95. Epub 2007 Aug 10.

Center for Computational Molecular Biology and Department of Computer Science, Brown University, Providence, RI 02912, USA.

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October 2007

Logic of gene regulatory networks.

Curr Opin Biotechnol 2007 Aug 6;18(4):351-4. Epub 2007 Aug 6.

California Institute of Technology, Division of Biology, m/c 156-29, 1200 E. California Blvd., Pasadena, CA 91125, USA.

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August 2007

A missing link in the sea urchin embryo gene regulatory network: hesC and the double-negative specification of micromeres.

Proc Natl Acad Sci U S A 2007 Jul 16;104(30):12383-8. Epub 2007 Jul 16.

Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA.

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July 2007

Exclusive developmental functions of gatae cis-regulatory modules in the Strongylocentrorus purpuratus embryo.

Dev Biol 2007 Jul 10;307(2):434-45. Epub 2007 May 10.

Division of Biology, California Institute of Technology, 1200 E. California Blvd., Mail Code 156-29, Pasadena, CA 9112, USA.

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July 2007

A basal deuterostome genome viewed as a natural experiment.

Gene 2007 Dec 6;406(1-2):1-7. Epub 2007 May 6.

Beckman Institute 139-74, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, United States.

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http://dx.doi.org/10.1016/j.gene.2007.04.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2200295PMC
December 2007

Cis-regulatory control of the nodal gene, initiator of the sea urchin oral ectoderm gene network.

Dev Biol 2007 Jun 28;306(2):860-9. Epub 2007 Mar 28.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063469PMC
June 2007

Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning.

Development 2007 May 18;134(10):1977-89. Epub 2007 Apr 18.

Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.

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May 2007

Development. Built to run, not fail.

Science 2007 Mar;315(5818):1510-1

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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March 2007

Gene regulation: gene control network in development.

Annu Rev Biophys Biomol Struct 2007 ;36:191

Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.

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August 2007

Deciphering the underlying mechanism of specification and differentiation: the sea urchin gene regulatory network.

Sci STKE 2006 Nov 14;2006(361):pe47. Epub 2006 Nov 14.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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November 2006

Paleogenomics of echinoderms.

Science 2006 Nov;314(5801):956-60

Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089-0740, USA.

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November 2006

The genome of the sea urchin Strongylocentrotus purpuratus.

Authors:
Erica Sodergren George M Weinstock Eric H Davidson R Andrew Cameron Richard A Gibbs Robert C Angerer Lynne M Angerer Maria Ina Arnone David R Burgess Robert D Burke James A Coffman Michael Dean Maurice R Elphick Charles A Ettensohn Kathy R Foltz Amro Hamdoun Richard O Hynes William H Klein William Marzluff David R McClay Robert L Morris Arcady Mushegian Jonathan P Rast L Courtney Smith Michael C Thorndyke Victor D Vacquier Gary M Wessel Greg Wray Lan Zhang Christine G Elsik Olga Ermolaeva Wratko Hlavina Gretchen Hofmann Paul Kitts Melissa J Landrum Aaron J Mackey Donna Maglott Georgia Panopoulou Albert J Poustka Kim Pruitt Victor Sapojnikov Xingzhi Song Alexandre Souvorov Victor Solovyev Zheng Wei Charles A Whittaker Kim Worley K James Durbin Yufeng Shen Olivier Fedrigo David Garfield Ralph Haygood Alexander Primus Rahul Satija Tonya Severson Manuel L Gonzalez-Garay Andrew R Jackson Aleksandar Milosavljevic Mark Tong Christopher E Killian Brian T Livingston Fred H Wilt Nikki Adams Robert Bellé Seth Carbonneau Rocky Cheung Patrick Cormier Bertrand Cosson Jenifer Croce Antonio Fernandez-Guerra Anne-Marie Genevière Manisha Goel Hemant Kelkar Julia Morales Odile Mulner-Lorillon Anthony J Robertson Jared V Goldstone Bryan Cole David Epel Bert Gold Mark E Hahn Meredith Howard-Ashby Mark Scally John J Stegeman Erin L Allgood Jonah Cool Kyle M Judkins Shawn S McCafferty Ashlan M Musante Robert A Obar Amanda P Rawson Blair J Rossetti Ian R Gibbons Matthew P Hoffman Andrew Leone Sorin Istrail Stefan C Materna Manoj P Samanta Viktor Stolc Waraporn Tongprasit Qiang Tu Karl-Frederik Bergeron Bruce P Brandhorst James Whittle Kevin Berney David J Bottjer Cristina Calestani Kevin Peterson Elly Chow Qiu Autumn Yuan Eran Elhaik Dan Graur Justin T Reese Ian Bosdet Shin Heesun Marco A Marra Jacqueline Schein Michele K Anderson Virginia Brockton Katherine M Buckley Avis H Cohen Sebastian D Fugmann Taku Hibino Mariano Loza-Coll Audrey J Majeske Cynthia Messier Sham V Nair Zeev Pancer David P Terwilliger Cavit Agca Enrique Arboleda Nansheng Chen Allison M Churcher F Hallböök Glen W Humphrey Mohammed M Idris Takae Kiyama Shuguang Liang Dan Mellott Xiuqian Mu Greg Murray Robert P Olinski Florian Raible Matthew Rowe John S Taylor Kristin Tessmar-Raible D Wang Karen H Wilson Shunsuke Yaguchi Terry Gaasterland Blanca E Galindo Herath J Gunaratne Celina Juliano Masashi Kinukawa Gary W Moy Anna T Neill Mamoru Nomura Michael Raisch Anna Reade Michelle M Roux Jia L Song Yi-Hsien Su Ian K Townley Ekaterina Voronina Julian L Wong Gabriele Amore Margherita Branno Euan R Brown Vincenzo Cavalieri Véronique Duboc Louise Duloquin Constantin Flytzanis Christian Gache François Lapraz Thierry Lepage Annamaria Locascio Pedro Martinez Giorgio Matassi Valeria Matranga Ryan Range Francesca Rizzo Eric Röttinger Wendy Beane Cynthia Bradham Christine Byrum Tom Glenn Sofia Hussain Gerard Manning Esther Miranda Rebecca Thomason Katherine Walton Athula Wikramanayke Shu-Yu Wu Ronghui Xu C Titus Brown Lili Chen Rachel F Gray Pei Yun Lee Jongmin Nam Paola Oliveri Joel Smith Donna Muzny Stephanie Bell Joseph Chacko Andrew Cree Stacey Curry Clay Davis Huyen Dinh Shannon Dugan-Rocha Jerry Fowler Rachel Gill Cerrissa Hamilton Judith Hernandez Sandra Hines Jennifer Hume Laronda Jackson Angela Jolivet Christie Kovar Sandra Lee Lora Lewis George Miner Margaret Morgan Lynne V Nazareth Geoffrey Okwuonu David Parker Ling-Ling Pu Rachel Thorn Rita Wright

Science 2006 Nov;314(5801):941-52

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November 2006

The sea urchin genome: where will it lead us?

Authors:
Eric H Davidson

Science 2006 Nov;314(5801):939-40

Division of Biology, 156-29, California Institute of Technology, Pasadena, CA 91125, USA.

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November 2006

Sea urchin Forkhead gene family: phylogeny and embryonic expression.

Dev Biol 2006 Dec 22;300(1):49-62. Epub 2006 Sep 22.

Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA.

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December 2006

Gene families encoding transcription factors expressed in early development of Strongylocentrotus purpuratus.

Dev Biol 2006 Dec 22;300(1):90-107. Epub 2006 Aug 22.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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December 2006

Repression of mesodermal fate by foxa, a key endoderm regulator of the sea urchin embryo.

Development 2006 Nov;133(21):4173-81

Division of Biology, 156-29, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dev.biologists.org/cgi/doi/10.1242/dev.02577
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November 2006

The C2H2 zinc finger genes of Strongylocentrotus purpuratus and their expression in embryonic development.

Dev Biol 2006 Dec 22;300(1):108-20. Epub 2006 Aug 22.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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December 2006

Hindgut specification and cell-adhesion functions of Sphox11/13b in the endoderm of the sea urchin embryo.

Dev Growth Differ 2006 Sep;48(7):463-72

Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-4614, USA.

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September 2006

cis-regulatory processing of Notch signaling input to the sea urchin glial cells missing gene during mesoderm specification.

Dev Biol 2006 Sep 2;297(2):587-602. Epub 2006 Jun 2.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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September 2006

Confocal quantification of cis-regulatory reporter gene expression in living sea urchin.

Dev Biol 2006 Nov 14;299(2):543-50. Epub 2006 Jun 14.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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November 2006

Regulation of spblimp1/krox1a, an alternatively transcribed isoform expressed in midgut and hindgut of the sea urchin gastrula.

Gene Expr Patterns 2007 Jan 10;7(1-2):1-7. Epub 2006 May 10.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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January 2007

Phosphatized polar lobe-forming embryos from the Precambrian of southwest China.

Science 2006 Jun;312(5780):1644-6

Nanjing Institute of Geology and Paleontology, Institute of Evo/Developmental Biology, and State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, China.

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June 2006

Expression and function of blimp1/krox, an alternatively transcribed regulatory gene of the sea urchin endomesoderm network.

Dev Biol 2006 May;293(2):513-25

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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May 2006

cis-Regulatory control of cyclophilin, a member of the ETS-DRI skeletogenic gene battery in the sea urchin embryo.

Dev Biol 2006 May 30;293(2):555-64. Epub 2006 Mar 30.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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May 2006

Gene regulatory networks and the evolution of animal body plans.

Science 2006 Feb;311(5762):796-800

Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1113832
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February 2006

cis-Regulatory inputs of the wnt8 gene in the sea urchin endomesoderm network.

Dev Biol 2005 Dec 10;288(2):545-58. Epub 2005 Nov 10.

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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December 2005

Unusual gene order and organization of the sea urchin hox cluster.

J Exp Zool B Mol Dev Evol 2006 Jan;306(1):45-58

Division of Biology and the Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1002/jez.b.21070DOI Listing
January 2006

An evolutionary constraint: strongly disfavored class of change in DNA sequence during divergence of cis-regulatory modules.

Proc Natl Acad Sci U S A 2005 Aug 8;102(33):11769-74. Epub 2005 Aug 8.

Division of Biology and Center for Computational Regulatory Genomics of the Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0505291102
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1188003PMC
August 2005

Computational representation of developmental genetic regulatory networks.

Dev Biol 2005 Jul;283(1):1-16

Institute for Systems Biology, Seattle, WA 98103-8904, USA.

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July 2005