David McClay - Publications

Publications (131)

ECB-PERS-4068

Publications By David McClay

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Single-Cell Transcriptomics Reveals Evolutionary Reconfiguration of Embryonic Cell Fate Specification in the Sea Urchin Heliocidaris erythrogramma., Massri AJ, Berrio A, Afanassiev A, Greenstreet L, Pipho K, Byrne M, Schiebinger G, McClay DR, Wray GA., Genome Biol Evol. January 6, 2025; 17 (1):
Reprogramming of cells during embryonic transfating: overcoming a reprogramming block., Berrio A, Miranda E, Massri AJ, Afanassiev A, Schiebinger G, Wray GA, McClay DR., Development. December 4, 2024;
An RNA interference approach for functional studies in the sea urchin and its use in analysis of nodal signaling gradients., Wilson K, Manner C, Miranda E, Berrio A, Wray GA, McClay DR., Dev Biol. December 3, 2024; 516 59-70.
A molecular basis for spine color morphs in the sea urchin Lytechinus variegatus., Wise M, Silvia M, Reyes G, Dunn R, Onorato TM, Pieplow C, Furze A, Hebert E, Oulhen N, Ritschoff D, McClay DR, Wessel G., Sci Rep. November 18, 2024; 14 (1): 28518.
Feedback circuits are numerous in embryonic gene regulatory networks and offer a stabilizing influence on evolution of those networks., Massri AJ, McDonald B, Wray GA, McClay DR., Evodevo. June 16, 2023; 14 (1): 10.
Wound repair in sea urchin larvae involves pigment cells and blastocoelar cells., Allen RL, George AN, Miranda E, Phillips TM, Crawford JM, Kiehart DP, McClay DR., Dev Biol. November 1, 2022; 491 56-65.
Development of a larval nervous system in the sea urchin., McClay DR., Curr Top Dev Biol. January 1, 2022; 146 25-48.
Reprint of: Conditional specification of endomesoderm., McClay DR, Croce JC, Warner JF., Cells Dev. December 1, 2021; 168 203731.
Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin embryo., Massri AJ, Greenstreet L, Afanassiev A, Berrio A, Wray GA, Schiebinger G, McClay DR., Development. October 1, 2021; 148 (19):
Conditional specification of endomesoderm., McClay DR, Croce JC, Warner JF., Cells Dev. September 1, 2021; 167 203716.
Methodologies for Following EMT In Vivo at Single Cell Resolution., Massri AJ, Schiebinger GR, Berrio A, Wang L, Wray GA, McClay DR., Methods Mol Biol. January 1, 2021; 2179 303-314.
Perspective on Epithelial-Mesenchymal Transitions in Embryos., McClay DR., Methods Mol Biol. January 1, 2021; 2179 7-12.
Chromosomal-Level Genome Assembly of the Sea Urchin Lytechinus variegatus Substantially Improves Functional Genomic Analyses., Davidson PL, Guo H, Wang L, Berrio A, Zhang H, Chang Y, Soborowski AL, McClay DR, Fan G, Wray GA., Genome Biol Evol. July 1, 2020; 12 (7): 1080-1086.
Developmental origin of peripheral ciliary band neurons in the sea urchin embryo., Slota LA, Miranda E, Peskin B, McClay DR., Dev Biol. March 15, 2020; 459 (2): 72-78.
Gastrulation in the sea urchin., McClay DR, Warner J, Martik M, Miranda E, Slota L., Curr Top Dev Biol. January 1, 2020; 136 195-218.
Methods for transplantation of sea urchin blastomeres., George AN, McClay DR., Methods Cell Biol. January 1, 2019; 150 223-233.
Spatial and temporal patterns of gene expression during neurogenesis in the sea urchin Lytechinus variegatus., Slota LA, Miranda EM, McClay DR., Evodevo. January 1, 2019; 10 2.
Unlocking mechanisms of development through advances in tools., McClay D., Methods Cell Biol. January 1, 2019; 151 37-41.
Neurogenesis in the sea urchin embryo is initiated uniquely in three domains., McClay DR, Miranda E, Feinberg SL., Development. November 9, 2018; 145 (21):
Identification of neural transcription factors required for the differentiation of three neuronal subtypes in the sea urchin embryo., Slota LA, McClay DR., Dev Biol. January 15, 2018; 435 (2): 138-149.
New insights from a high-resolution look at gastrulation in the sea urchin, Lytechinus variegatus., Martik ML, McClay DR., Mech Dev. December 1, 2017; 148 3-10.
Contribution of hedgehog signaling to the establishment of left-right asymmetry in the sea urchin., Warner JF, Miranda EL, McClay DR., Dev Biol. March 15, 2016; 411 (2): 314-324.
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.
Developmental gene regulatory networks in sea urchins and what we can learn from them., Martik ML, Lyons DC, McClay DR., F1000Res. February 22, 2016; 5
Sea Urchin Morphogenesis., McClay DR., Curr Top Dev Biol. January 1, 2016; 117 15-29.
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
Specification to biomineralization: following a single cell type as it constructs a skeleton., Lyons DC, Martik ML, Saunders LR, McClay DR., Integr Comp Biol. October 1, 2014; 54 (4): 723-33.
Delayed transition to new cell fates during cellular reprogramming., Cheng X, Lyons DC, Socolar JE, McClay DR., Dev Biol. July 15, 2014; 391 (2): 147-57.
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.
Branching out: origins of the sea urchin larval skeleton in development and evolution., McIntyre DC, Lyons DC, Martik M, McClay DR., Genesis. March 1, 2014; 52 (3): 173-85.
Hedgehog signaling requires motile cilia in the sea urchin., Warner JF, McCarthy AM, Morris RL, McClay DR., Mol Biol Evol. January 1, 2014; 31 (1): 18-22.
Perturbations to the hedgehog pathway in sea urchin embryos., Warner JF, McClay DR., Methods Mol Biol. January 1, 2014; 1128 211-21.
Short-range Wnt5 signaling initiates specification of sea urchin posterior ectoderm., McIntyre DC, Seay NW, Croce JC, McClay DR., Development. December 1, 2013; 140 (24): 4881-9.
Frizzled1/2/7 signaling directs β-catenin nuclearisation and initiates endoderm specification in macromeres during sea urchin embryogenesis., Lhomond G, McClay DR, Gache C, Croce JC., Development. February 1, 2012; 139 (4): 816-25.
Left-right asymmetry in the sea urchin embryo: BMP and the asymmetrical origins of the adult., Warner JF, Lyons DC, McClay DR., PLoS Biol. January 1, 2012; 10 (10): e1001404.
Morphogenesis in sea urchin embryos: linking cellular events to gene regulatory network states., Lyons DC, Kaltenbach SL, McClay DR., Wiley Interdiscip Rev Dev Biol. January 1, 2012; 1 (2): 231-52.
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.
Evolutionary crossroads in developmental biology: sea urchins., McClay DR., Development. July 1, 2011; 138 (13): 2639-48.
The control of foxN2/3 expression in sea urchin embryos and its function in the skeletogenic gene regulatory network., Rho HK, McClay DR., Development. March 1, 2011; 138 (5): 937-45.
Dynamics of Delta/Notch signaling on endomesoderm segregation in the sea urchin embryo., Croce JC, McClay DR., Development. January 1, 2010; 137 (1): 83-91.
Hedgehog signaling patterns mesoderm in the sea urchin., Walton KD, Warner J, Hertzler PH, McClay DR., Dev Biol. July 1, 2009; 331 (1): 26-37.
Blocking Dishevelled signaling in the noncanonical Wnt pathway in sea urchins disrupts endoderm formation and spiculogenesis, but not secondary mesoderm formation., Byrum CA, Xu R, Bince JM, McClay DR, Wikramanayake AH., Dev Dyn. July 1, 2009; 238 (7): 1649-65.
Chordin is required for neural but not axial development in sea urchin embryos., Bradham CA, Oikonomou C, Kühn A, Core AB, Modell JW, McClay DR, Poustka AJ., Dev Biol. April 15, 2009; 328 (2): 221-33.
LvNumb works synergistically with Notch signaling to specify non-skeletal mesoderm cells in the sea urchin embryo., Range RC, Glenn TD, Miranda E, McClay DR., Development. August 1, 2008; 135 (14): 2445-54.
Twist is an essential regulator of the skeletogenic gene regulatory network in the sea urchin embryo., Wu SY, Yang YP, McClay DR., Dev Biol. July 15, 2008; 319 (2): 406-15.
Vasa protein expression is restricted to the small micromeres of the sea urchin, but is inducible in other lineages early in development., Voronina E, Lopez M, Juliano CE, Gustafson E, Song JL, Extavour C, George S, Oliveri P, McClay D, Wessel G., Dev Biol. February 15, 2008; 314 (2): 276-86.
FGF signals guide migration of mesenchymal cells, control skeletal morphogenesis [corrected] and regulate gastrulation during sea urchin development., Röttinger E, Saudemont A, Duboc V, Besnardeau L, McClay D, Lepage T., Development. January 1, 2008; 135 (2): 353-65.
Ingression of primary mesenchyme cells of the sea urchin embryo: a precisely timed epithelial mesenchymal transition., Wu SY, Ferkowicz M, McClay DR., Birth Defects Res C Embryo Today. December 1, 2007; 81 (4): 241-52.
The Snail repressor is required for PMC ingression in the sea urchin embryo., Wu SY, McClay DR., Development. March 1, 2007; 134 (6): 1061-70.
The genomic underpinnings of apoptosis in Strongylocentrotus purpuratus., Robertson AJ, Croce J, Carbonneau S, Voronina E, Miranda E, McClay DR, Coffman JA., Dev Biol. December 1, 2006; 300 (1): 321-34.

Single-Cell Transcriptomics Reveals Evolutionary Reconfiguration of Embryonic Cell Fate Specification in the Sea Urchin Heliocidaris erythrogramma., Massri AJ, Berrio A, Afanassiev A, Greenstreet L, Pipho K, Byrne M, Schiebinger G, McClay DR, Wray GA., Genome Biol Evol. January 6, 2025; 17 (1):

Reprogramming of cells during embryonic transfating: overcoming a reprogramming block., Berrio A, Miranda E, Massri AJ, Afanassiev A, Schiebinger G, Wray GA, McClay DR., Development. December 4, 2024;

An RNA interference approach for functional studies in the sea urchin and its use in analysis of nodal signaling gradients., Wilson K, Manner C, Miranda E, Berrio A, Wray GA, McClay DR., Dev Biol. December 3, 2024; 516 59-70.

A molecular basis for spine color morphs in the sea urchin Lytechinus variegatus., Wise M, Silvia M, Reyes G, Dunn R, Onorato TM, Pieplow C, Furze A, Hebert E, Oulhen N, Ritschoff D, McClay DR, Wessel G., Sci Rep. November 18, 2024; 14 (1): 28518.

Feedback circuits are numerous in embryonic gene regulatory networks and offer a stabilizing influence on evolution of those networks., Massri AJ, McDonald B, Wray GA, McClay DR., Evodevo. June 16, 2023; 14 (1): 10.

Wound repair in sea urchin larvae involves pigment cells and blastocoelar cells., Allen RL, George AN, Miranda E, Phillips TM, Crawford JM, Kiehart DP, McClay DR., Dev Biol. November 1, 2022; 491 56-65.

Development of a larval nervous system in the sea urchin., McClay DR., Curr Top Dev Biol. January 1, 2022; 146 25-48.

Reprint of: Conditional specification of endomesoderm., McClay DR, Croce JC, Warner JF., Cells Dev. December 1, 2021; 168 203731.

Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin embryo., Massri AJ, Greenstreet L, Afanassiev A, Berrio A, Wray GA, Schiebinger G, McClay DR., Development. October 1, 2021; 148 (19):

Conditional specification of endomesoderm., McClay DR, Croce JC, Warner JF., Cells Dev. September 1, 2021; 167 203716.

Methodologies for Following EMT In Vivo at Single Cell Resolution., Massri AJ, Schiebinger GR, Berrio A, Wang L, Wray GA, McClay DR., Methods Mol Biol. January 1, 2021; 2179 303-314.

Perspective on Epithelial-Mesenchymal Transitions in Embryos., McClay DR., Methods Mol Biol. January 1, 2021; 2179 7-12.

Chromosomal-Level Genome Assembly of the Sea Urchin Lytechinus variegatus Substantially Improves Functional Genomic Analyses., Davidson PL, Guo H, Wang L, Berrio A, Zhang H, Chang Y, Soborowski AL, McClay DR, Fan G, Wray GA., Genome Biol Evol. July 1, 2020; 12 (7): 1080-1086.

Developmental origin of peripheral ciliary band neurons in the sea urchin embryo., Slota LA, Miranda E, Peskin B, McClay DR., Dev Biol. March 15, 2020; 459 (2): 72-78.

Gastrulation in the sea urchin., McClay DR, Warner J, Martik M, Miranda E, Slota L., Curr Top Dev Biol. January 1, 2020; 136 195-218.

Methods for transplantation of sea urchin blastomeres., George AN, McClay DR., Methods Cell Biol. January 1, 2019; 150 223-233.

Spatial and temporal patterns of gene expression during neurogenesis in the sea urchin Lytechinus variegatus., Slota LA, Miranda EM, McClay DR., Evodevo. January 1, 2019; 10 2.

Unlocking mechanisms of development through advances in tools., McClay D., Methods Cell Biol. January 1, 2019; 151 37-41.

Neurogenesis in the sea urchin embryo is initiated uniquely in three domains., McClay DR, Miranda E, Feinberg SL., Development. November 9, 2018; 145 (21):

Identification of neural transcription factors required for the differentiation of three neuronal subtypes in the sea urchin embryo., Slota LA, McClay DR., Dev Biol. January 15, 2018; 435 (2): 138-149.

New insights from a high-resolution look at gastrulation in the sea urchin, Lytechinus variegatus., Martik ML, McClay DR., Mech Dev. December 1, 2017; 148 3-10.

Contribution of hedgehog signaling to the establishment of left-right asymmetry in the sea urchin., Warner JF, Miranda EL, McClay DR., Dev Biol. March 15, 2016; 411 (2): 314-324.

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.

Developmental gene regulatory networks in sea urchins and what we can learn from them., Martik ML, Lyons DC, McClay DR., F1000Res. February 22, 2016; 5

Sea Urchin Morphogenesis., McClay DR., Curr Top Dev Biol. January 1, 2016; 117 15-29.

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

Specification to biomineralization: following a single cell type as it constructs a skeleton., Lyons DC, Martik ML, Saunders LR, McClay DR., Integr Comp Biol. October 1, 2014; 54 (4): 723-33.

Delayed transition to new cell fates during cellular reprogramming., Cheng X, Lyons DC, Socolar JE, McClay DR., Dev Biol. July 15, 2014; 391 (2): 147-57.

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.

Branching out: origins of the sea urchin larval skeleton in development and evolution., McIntyre DC, Lyons DC, Martik M, McClay DR., Genesis. March 1, 2014; 52 (3): 173-85.

Hedgehog signaling requires motile cilia in the sea urchin., Warner JF, McCarthy AM, Morris RL, McClay DR., Mol Biol Evol. January 1, 2014; 31 (1): 18-22.

Perturbations to the hedgehog pathway in sea urchin embryos., Warner JF, McClay DR., Methods Mol Biol. January 1, 2014; 1128 211-21.

Short-range Wnt5 signaling initiates specification of sea urchin posterior ectoderm., McIntyre DC, Seay NW, Croce JC, McClay DR., Development. December 1, 2013; 140 (24): 4881-9.

Frizzled1/2/7 signaling directs β-catenin nuclearisation and initiates endoderm specification in macromeres during sea urchin embryogenesis., Lhomond G, McClay DR, Gache C, Croce JC., Development. February 1, 2012; 139 (4): 816-25.

Left-right asymmetry in the sea urchin embryo: BMP and the asymmetrical origins of the adult., Warner JF, Lyons DC, McClay DR., PLoS Biol. January 1, 2012; 10 (10): e1001404.

Morphogenesis in sea urchin embryos: linking cellular events to gene regulatory network states., Lyons DC, Kaltenbach SL, McClay DR., Wiley Interdiscip Rev Dev Biol. January 1, 2012; 1 (2): 231-52.

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.

Evolutionary crossroads in developmental biology: sea urchins., McClay DR., Development. July 1, 2011; 138 (13): 2639-48.

The control of foxN2/3 expression in sea urchin embryos and its function in the skeletogenic gene regulatory network., Rho HK, McClay DR., Development. March 1, 2011; 138 (5): 937-45.

Dynamics of Delta/Notch signaling on endomesoderm segregation in the sea urchin embryo., Croce JC, McClay DR., Development. January 1, 2010; 137 (1): 83-91.

Hedgehog signaling patterns mesoderm in the sea urchin., Walton KD, Warner J, Hertzler PH, McClay DR., Dev Biol. July 1, 2009; 331 (1): 26-37.

Blocking Dishevelled signaling in the noncanonical Wnt pathway in sea urchins disrupts endoderm formation and spiculogenesis, but not secondary mesoderm formation., Byrum CA, Xu R, Bince JM, McClay DR, Wikramanayake AH., Dev Dyn. July 1, 2009; 238 (7): 1649-65.

Chordin is required for neural but not axial development in sea urchin embryos., Bradham CA, Oikonomou C, Kühn A, Core AB, Modell JW, McClay DR, Poustka AJ., Dev Biol. April 15, 2009; 328 (2): 221-33.

LvNumb works synergistically with Notch signaling to specify non-skeletal mesoderm cells in the sea urchin embryo., Range RC, Glenn TD, Miranda E, McClay DR., Development. August 1, 2008; 135 (14): 2445-54.

Twist is an essential regulator of the skeletogenic gene regulatory network in the sea urchin embryo., Wu SY, Yang YP, McClay DR., Dev Biol. July 15, 2008; 319 (2): 406-15.

Vasa protein expression is restricted to the small micromeres of the sea urchin, but is inducible in other lineages early in development., Voronina E, Lopez M, Juliano CE, Gustafson E, Song JL, Extavour C, George S, Oliveri P, McClay D, Wessel G., Dev Biol. February 15, 2008; 314 (2): 276-86.

FGF signals guide migration of mesenchymal cells, control skeletal morphogenesis [corrected] and regulate gastrulation during sea urchin development., Röttinger E, Saudemont A, Duboc V, Besnardeau L, McClay D, Lepage T., Development. January 1, 2008; 135 (2): 353-65.

Ingression of primary mesenchyme cells of the sea urchin embryo: a precisely timed epithelial mesenchymal transition., Wu SY, Ferkowicz M, McClay DR., Birth Defects Res C Embryo Today. December 1, 2007; 81 (4): 241-52.

The Snail repressor is required for PMC ingression in the sea urchin embryo., Wu SY, McClay DR., Development. March 1, 2007; 134 (6): 1061-70.

The genomic underpinnings of apoptosis in Strongylocentrotus purpuratus., Robertson AJ, Croce J, Carbonneau S, Voronina E, Miranda E, McClay DR, Coffman JA., Dev Biol. December 1, 2006; 300 (1): 321-34.

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