Publications By Charles A. Ettensohn

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Echinobase: a resource to support the echinoderm research community., Telmer CA, Karimi K, Chess MM, Agalakov S, Arshinoff BI, Lotay V, Wang DZ, Chu S, Pells TJ, Vize PD, Hinman VF, Ettensohn CA., Genetics. January 23, 2024;

Genome-wide identification and spatiotemporal expression analysis of cadherin superfamily members in echinoderms., Chess MM, Douglas W, Saunders J, Ettensohn CA., Evodevo. December 20, 2023; 14 (1): 15.

Molecular compartmentalization in a syncytium: restricted mobility of proteins within the sea urchin skeletogenic mesenchyme., Khor JM, Guerrero-Santoro J, Ettensohn CA., Development. October 30, 2023;

An optimized Tet-On system for conditional control of gene expression in sea urchins., Khor JM, Ettensohn CA., Development. January 1, 2023; 150 (1):

Architecture and evolution of the cis-regulatory system of the echinoderm kirrelL gene., Khor JM, Ettensohn CA., Elife. February 25, 2022; 11

Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms., Arshinoff BI, Cary GA, Karimi K, Foley S, Agalakov S, Delgado F, Lotay VS, Ku CJ, Pells TJ, Beatman TR, Kim E, Cameron RA, Vize PD, Telmer CA, Croce JC, Ettensohn CA, Hinman VF., Nucleic Acids Res. January 7, 2022; 50 (D1): D970-D979.

Lessons from a transcription factor: Alx1 provides insights into gene regulatory networks, cellular reprogramming, and cell type evolution., Ettensohn CA, Guerrero-Santoro J, Khor JM., Curr Top Dev Biol. January 1, 2022; 146 113-148.

Classifying domain-specific text documents containing ambiguous keywords., Karimi K, Agalakov S, Telmer CA, Beatman TR, Pells TJ, Arshinoff BI, Ku CJ, Foley S, Hinman VF, Ettensohn CA, Vize PD., Database (Oxford). September 29, 2021; 2021

Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling., Khor JM, Guerrero-Santoro J, Douglas W, Ettensohn CA., Genome Res. September 1, 2021; 31 (9): 1680-1692.

A nomenclature for echinoderm genes., Beatman TR, Buckley KM, Cary GA, Hinman VF, Ettensohn CA., Database (Oxford). August 7, 2021; 2021

Conditional gene knockdowns in sea urchins using caged morpholinos., Bardhan A, Deiters A, Ettensohn CA., Dev Biol. July 1, 2021; 475 21-29.

Analysis of the DNA-binding properties of Alx1, an evolutionarily conserved regulator of skeletogenesis in echinoderms., Guerrero-Santoro J, Khor JM, Açıkbaş AH, Jaynes JB, Ettensohn CA., J Biol Chem. July 1, 2021; 297 (1): 100901.

The gene regulatory control of sea urchin gastrulation., Ettensohn CA., Mech Dev. June 1, 2020; 162 103599.

Transcription Factors of the Alx Family: Evolutionarily Conserved Regulators of Deuterostome Skeletogenesis., Khor JM, Ettensohn CA., Front Genet. April 30, 2020; 11 569314.

The evolution of a new cell type was associated with competition for a signaling ligand., Ettensohn CA, Adomako-Ankomah A., PLoS Biol. September 18, 2019; 17 (9): e3000460.

Genome-wide identification of binding sites and gene targets of Alx1, a pivotal regulator of echinoderm skeletogenesis., Khor JM, Guerrero-Santoro J, Ettensohn CA., Development. August 19, 2019; 146 (16):

Genome-wide analysis of chromatin accessibility using ATAC-seq., Shashikant T, Ettensohn CA., Methods Cell Biol. January 1, 2019; 151 219-235.

Techniques for analyzing gene expression using BAC-based reporter constructs., Buckley KM, Ettensohn CA., Methods Cell Biol. January 1, 2019; 151 197-218.

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.

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.

Functional divergence of paralogous transcription factors supported the evolution of biomineralization in echinoderms., Khor JM, Ettensohn CA., Elife. November 20, 2017; 6

KirrelL, a member of the Ig-domain superfamily of adhesion proteins, is essential for fusion of primary mesenchyme cells in the sea urchin embryo., Ettensohn CA, Dey D., Dev Biol. January 15, 2017; 421 (2): 258-270.

TGF-β sensu stricto signaling regulates skeletal morphogenesis in the sea urchin embryo., Sun Z, Ettensohn CA., Dev Biol. January 15, 2017; 421 (2): 149-160.

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.

Horizontal transfer of the msp130 gene supported the evolution of metazoan biomineralization., Ettensohn CA., Evol Dev. May 1, 2014; 16 (3): 139-48.

Growth factors and early mesoderm morphogenesis: insights from the sea urchin embryo., Adomako-Ankomah A, Ettensohn CA., Genesis. March 1, 2014; 52 (3): 158-72.

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.

Growth factor-mediated mesodermal cell guidance and skeletogenesis during sea urchin gastrulation., Adomako-Ankomah A, Ettensohn CA., Development. October 1, 2013; 140 (20): 4214-25.

Encoding anatomy: developmental gene regulatory networks and morphogenesis., Ettensohn CA., Genesis. June 1, 2013; 51 (6): 383-409.

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.

High-resolution, three-dimensional mapping of gene expression using GeneExpressMap (GEM)., Flynn CJ, Sharma T, Ruffins SW, Guerra SL, Crowley JC, Ettensohn CA., Dev Biol. September 15, 2011; 357 (2): 532-40.

Regulative deployment of the skeletogenic gene regulatory network during sea urchin development., Sharma T, Ettensohn CA., Development. June 1, 2011; 138 (12): 2581-90.

P58-A and P58-B: novel proteins that mediate skeletogenesis in the sea urchin embryo., Adomako-Ankomah A, Ettensohn CA., Dev Biol. May 1, 2011; 353 (1): 81-93.

Activation of the skeletogenic gene regulatory network in the early sea urchin embryo., Sharma T, Ettensohn CA., Development. April 1, 2010; 137 (7): 1149-57.

The expression and distribution of Wnt and Wnt receptor mRNAs during early sea urchin development., Stamateris RE, Rafiq K, Ettensohn CA., Gene Expr Patterns. January 1, 2010; 10 (1): 60-4.

Cell micromanipulation with an active handheld micromanipulator., Cuevas Tabares J, Maclachlan RA, Ettensohn CA, Riviere CN., Annu Int Conf IEEE Eng Med Biol Soc. January 1, 2010; 2010 4363-6.

Lessons from a gene regulatory network: echinoderm skeletogenesis provides insights into evolution, plasticity and morphogenesis., Ettensohn CA., Development. January 1, 2009; 136 (1): 11-21.

Mesenchymal cell fusion in the sea urchin embryo., Hodor PG, Ettensohn CA., Methods Mol Biol. January 1, 2008; 475 315-34.

Gene regulatory networks and developmental plasticity in the early sea urchin embryo: alternative deployment of the skeletogenic gene regulatory network., Ettensohn CA, Kitazawa C, Cheers MS, Leonard JD, Sharma T., Development. September 1, 2007; 134 (17): 3077-87.

Analysis of dishevelled localization and function in the early sea urchin embryo., Leonard JD, Ettensohn CA., Dev Biol. June 1, 2007; 306 (1): 50-65.

A genome-wide analysis of biomineralization-related proteins in the sea urchin Strongylocentrotus purpuratus., Livingston BT, Killian CE, Wilt F, Cameron A, Landrum MJ, Ermolaeva O, Sapojnikov V, Maglott DR, Buchanan AM, Ettensohn CA., Dev Biol. December 1, 2006; 300 (1): 335-48.

A functional genomic and proteomic perspective of sea urchin calcium signaling and egg activation., Roux MM, Townley IK, Raisch M, Reade A, Bradham C, Humphreys G, Gunaratne HJ, Killian CE, Moy G, Su YH, Ettensohn CA, Wilt F, Vacquier VD, Burke RD, Wessel G, Foltz KR., Dev Biol. December 1, 2006; 300 (1): 416-33.

The emergence of pattern in embryogenesis: regulation of beta-catenin localization during early sea urchin development., Ettensohn CA., Sci STKE. November 14, 2006; 2006 (361): pe48.

The genome of the sea urchin Strongylocentrotus purpuratus., Sea Urchin Genome Sequencing Consortium, Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, Coffman JA, Dean M, Elphick MR, Ettensohn CA, Foltz KR, Hamdoun A, Hynes RO, Klein WH, Marzluff W, McClay DR, Morris RL, Mushegian A, Rast JP, Smith LC, Thorndyke MC, Vacquier VD, Wessel GM, Wray G, Zhang L, Elsik CG, Ermolaeva O, Hlavina W, Hofmann G, Kitts P, Landrum MJ, Mackey AJ, Maglott D, Panopoulou G, Poustka AJ, Pruitt K, Sapojnikov V, Song X, Souvorov A, Solovyev V, Wei Z, Whittaker CA, Worley K, Durbin KJ, Shen Y, Fedrigo O, Garfield D, Haygood R, Primus A, Satija R, Severson T, Gonzalez-Garay ML, Jackson AR, Milosavljevic A, Tong M, Killian CE, Livingston BT, Wilt FH, Adams N, Bellé R, Carbonneau S, Cheung R, Cormier P, Cosson B, Croce J, Fernandez-Guerra A, Genevière AM, Goel M, Kelkar H, Morales J, Mulner-Lorillon O, Robertson AJ, Goldstone JV, Cole B, Epel D, Gold B, Hahn ME, Howard-Ashby M, Scally M, Stegeman JJ, Allgood EL, Cool J, Judkins KM, McCafferty SS, Musante AM, Obar RA, Rawson AP, Rossetti BJ, Gibbons IR, Hoffman MP, Leone A, Istrail S, Materna SC, Samanta MP, Stolc V, Tongprasit W, Tu Q, Bergeron KF, Brandhorst BP, Whittle J, Berney K, Bottjer DJ, Calestani C, Peterson K, Chow E, Yuan QA, Elhaik E, Graur D, Reese JT, Bosdet I, Heesun S, Marra MA, Schein J, Anderson MK, Brockton V, Buckley KM, Cohen AH, Fugmann SD, Hibino T, Loza-Coll M, Majeske AJ, Messier C, Nair SV, Pancer Z, Terwilliger DP, Agca C, Arboleda E, Chen N, Churcher AM, Hallböök F, Humphrey GW, Idris MM, Kiyama T, Liang S, Mellott D, Mu X, Murray G, Olinski RP, Raible F, Rowe M, Taylor JS, Tessmar-Raible K, Wang D, Wilson KH, Yaguchi S, Gaasterland T, Galindo BE, Gunaratne HJ, Juliano C, Kinukawa M, Moy GW, Neill AT, Nomura M, Raisch M, Reade A, Roux MM, Song JL, Su YH, Townley IK, Voronina E, Wong JL, Amore G, Branno M, Brown ER, Cavalieri V, Duboc V, Duloquin L, Flytzanis C, Gache C, Lapraz F, Lepage T, Locascio A, Martinez P, Matassi G, Matranga V, Range R, Rizzo F, Röttinger E, Beane W, Bradham C, Byrum C, Glenn T, Hussain S, Manning G, Miranda E, Thomason R, Walton K, Wikramanayke A, Wu SY, Xu R, Brown CT, Chen L, Gray RF, Lee PY, Nam J, Oliveri P, Smith J, Muzny D, Bell S, Chacko J, Cree A, Curry S, Davis C, Dinh H, Dugan-Rocha S, Fowler J, Gill R, Hamilton C, Hernandez J, Hines S, Hume J, Jackson L, Jolivet A, Kovar C, Lee S, Lewis L, Miner G, Morgan M, Nazareth LV, Okwuonu G, Parker D, Pu LL, Thorn R, Wright R., Science. November 10, 2006; 314 (5801): 941-52.

P16 is an essential regulator of skeletogenesis in the sea urchin embryo., Cheers MS, Ettensohn CA., Dev Biol. July 15, 2005; 283 (2): 384-96.

Differential stability of beta-catenin along the animal-vegetal axis of the sea urchin embryo mediated by dishevelled., Weitzel HE, Illies MR, Byrum CA, Xu R, Wikramanayake AH, Ettensohn CA., Development. June 1, 2004; 131 (12): 2947-56.

Rapid microinjection of fertilized eggs., Cheers MS, Ettensohn CA., Methods Cell Biol. January 1, 2004; 74 287-310.

Alx1, a member of the Cart1/Alx3/Alx4 subfamily of Paired-class homeodomain proteins, is an essential component of the gene network controlling skeletogenic fate specification in the sea urchin embryo., Ettensohn CA, Illies MR, Oliveri P, De Jong DL., Development. July 1, 2003; 130 (13): 2917-28.

Identification and developmental expression of new biomineralization proteins in the sea urchin Strongylocentrotus purpuratus., Illies MR, Peeler MT, Dechtiaruk AM, Ettensohn CA., Dev Genes Evol. October 1, 2002; 212 (9): 419-31.

Cloning and developmental expression of a novel, secreted frizzled-related protein from the sea urchin, Strongylocentrotus purpuratus., Illies MR, Peeler MT, Dechtiaruk A, Ettensohn CA., Mech Dev. April 1, 2002; 113 (1): 61-4.

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