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Coup-TF: A maternal factor essential for differentiation along the embryonic axes in the sea urchin Paracentrotus lividus. , Tsironis I, Paganos P , Gouvi G, Tsimpos P, Stamopoulou A, Arnone MI , Flytzanis CN., Dev Biol. July 1, 2021; 475 131-144.
The gene regulatory control of sea urchin gastrulation. , Ettensohn CA ., Mech Dev. June 1, 2020; 162 103599.
A biphasic role of non-canonical Wnt16 signaling during early anterior-posterior patterning and morphogenesis of the sea urchin embryo. , Martínez-Bartolomé M , Range RC ., Development. December 16, 2019; 146 (24):
How Does the Regulatory Genome Work? , Istrail S, Peter IS ., J Comput Biol. July 1, 2019; 26 (7): 685-695.
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.
Methods for the experimental and computational analysis of gene regulatory networks in sea urchins. , Peter IS ., Methods Cell Biol. January 1, 2019; 151 89-113.
The Axial Organ and the Pharynx Are Sites of Hematopoiesis in the Sea Urchin. , Golconda P, Buckley KM , Reynolds CR, Romanello JP, Smith LC ., Front Immunol. January 1, 2019; 10 870.
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):
Canonical and non-canonical Wnt signaling pathways define the expression domains of Frizzled 5/8 and Frizzled 1/2/7 along the early anterior-posterior axis in sea urchin embryos. , Range RC ., Dev Biol. December 15, 2018; 444 (2): 83-92.
From genome to anatomy: The architecture and evolution of the skeletogenic gene regulatory network of sea urchins and other echinoderms. , Shashikant T, Khor JM, Ettensohn CA ., Genesis. October 1, 2018; 56 (10): e23253.
Bacterial artificial chromosomes as recombinant reporter constructs to investigate gene expression and regulation in echinoderms. , Buckley KM , Dong P, Cameron RA , Rast JP., Brief Funct Genomics. September 27, 2018; 17 (5): 362-371.
Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling. , Shashikant T, Khor JM, Ettensohn CA ., BMC Genomics. March 20, 2018; 19 (1): 206.
A novel gene''s role in an ancient mechanism: secreted Frizzled-related protein 1 is a critical component in the anterior-posterior Wnt signaling network that governs the establishment of the anterior neuroectoderm in sea urchin embryos. , Khadka A, Martínez-Bartolomé M , Burr SD, Range RC ., Evodevo. January 22, 2018; 9 1.
Omics approaches to study gene regulatory networks for development in echinoderms. , Lowe EK, Cuomo C, Arnone MI ., Brief Funct Genomics. September 1, 2017; 16 (5): 299-308.
Echinoderm development and evolution in the post-genomic era. , Cary GA , Hinman VF ., Dev Biol. July 15, 2017; 427 (2): 203-211.
Paleogenomics of echinoids reveals an ancient origin for the double-negative specification of micromeres in sea urchins. , Thompson JR, Erkenbrack EM , Hinman VF , McCauley BS, Petsios E, Bottjer DJ., Proc Natl Acad Sci U S A. June 6, 2017; 114 (23): 5870-5877.
Genome-wide use of high- and low-affinity Tbrain transcription factor binding sites during echinoderm development. , Cary GA , Cheatle Jarvela AM, Francolini RD, Hinman VF ., Proc Natl Acad Sci U S A. June 6, 2017; 114 (23): 5854-5861.
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.
An Organismal Model for Gene Regulatory Networks in the Gut-Associated Immune Response. , Buckley KM , Rast JP., Front Immunol. March 13, 2017; 8 1297.
Divergence of ectodermal and mesodermal gene regulatory network linkages in early development of sea urchins. , Erkenbrack EM ., Proc Natl Acad Sci U S A. November 15, 2016; 113 (46): E7202-E7211.
Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris. , Israel JW, Martik ML, Byrne M , Raff EC, Raff RA, McClay DR , Wray GA ., PLoS Biol. March 1, 2016; 14 (3): e1002391.
Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks. , Dylus DV , Czarkwiani A, Stångberg J, Ortega-Martinez O, Dupont S, Oliveri P ., Evodevo. January 1, 2016; 7 2.
Ancestral state reconstruction by comparative analysis of a GRN kernel operating in echinoderms. , Erkenbrack EM , Ako-Asare K, Miller E, Tekelenburg S, Thompson JR, Romano L ., Dev Genes Evol. January 1, 2016; 226 (1): 37-45.
Robustness and Accuracy in Sea Urchin Developmental Gene Regulatory Networks. , Ben-Tabou de-Leon S., Front Genet. January 1, 2016; 7 16.
A deuterostome origin of the Spemann organiser suggested by Nodal and ADMPs functions in Echinoderms. , Lapraz F, Haillot E, Lepage T ., Nat Commun. October 1, 2015; 6 8434.
Deployment of a retinal determination gene network drives directed cell migration in the sea urchin embryo. , Martik ML, McClay DR ., Elife. September 24, 2015; 4
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.
Logics and properties of a genetic regulatory program that drives embryonic muscle development in an echinoderm. , Andrikou C, Pai CY, Su YH , Arnone MI ., Elife. July 28, 2015; 4
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.
Signal-dependent regulation of the sea urchin skeletogenic gene regulatory network. , Sun Z, Ettensohn CA ., Gene Expr Patterns. November 1, 2014; 16 (2): 93-103.
Modular evolution of DNA-binding preference of a Tbrain transcription factor provides a mechanism for modifying gene regulatory networks. , Cheatle Jarvela AM, Brubaker L, Vedenko A, Gupta A, Armitage BA, Bulyk ML, Hinman VF ., Mol Biol Evol. October 1, 2014; 31 (10): 2672-88.
Molecular conservation of metazoan gut formation: evidence from expression of endomesoderm genes in Capitella teleta (Annelida). , Boyle MJ, Yamaguchi E, Seaver EC., Evodevo. June 17, 2014; 5 39.
Sub-circuits of a gene regulatory network control a developmental epithelial-mesenchymal transition. , Saunders LR, McClay DR ., Development. April 1, 2014; 141 (7): 1503-13.
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.
Developmental gene regulatory network evolution: insights from comparative studies in echinoderms. , Hinman VF , Cheatle Jarvela AM., Genesis. March 1, 2014; 52 (3): 193-207.
Genome-wide analysis of the skeletogenic gene regulatory network of sea urchins. , Rafiq K, Shashikant T, McManus CJ, Ettensohn CA ., Development. February 1, 2014; 141 (4): 950-61.
Multicolor labeling in developmental gene regulatory network analysis. , Sethi AJ, Angerer RC , Angerer LM ., Methods Mol Biol. January 1, 2014; 1128 249-62.
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.
Cis-regulatory control of the nuclear receptor Coup-TF gene in the sea urchin Paracentrotus lividus embryo. , Kalampoki LG, Flytzanis CN., PLoS One. January 1, 2014; 9 (11): e109274.
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.
Encoding anatomy: developmental gene regulatory networks and morphogenesis. , Ettensohn CA ., Genesis. June 1, 2013; 51 (6): 383-409.
Networking development by Boolean logic. , Tu S, Pederson T, Weng Z., Nucleus. January 1, 2013; 4 (2): 89-91.
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.
Early developmental gene regulation in Strongylocentrotus purpuratus embryos in response to elevated CO₂ seawater conditions. , Hammond LM, Hofmann GE., J Exp Biol. July 15, 2012; 215 (Pt 14): 2445-54.
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.
The genomic regulatory control of skeletal morphogenesis in the sea urchin. , Rafiq K, Cheers MS, Ettensohn CA ., Development. February 1, 2012; 139 (3): 579-90.
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.
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.
Wnt6 activates endoderm in the sea urchin gene regulatory network. , Croce J , Range R , Wu SY, Miranda E, Lhomond G, Peng JC, Lepage T , McClay DR ., Development. August 1, 2011; 138 (15): 3297-306.
Regulative deployment of the skeletogenic gene regulatory network during sea urchin development. , Sharma T, Ettensohn CA ., Development. June 1, 2011; 138 (12): 2581-90.