Veronica F Hinman - Publications

Publications (44)

ECB-PERS-4136

Publications By Veronica F Hinman

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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. May 7, 2024; 227 (1):
New hypotheses of cell type diversity and novelty from orthology-driven comparative single cell and nuclei transcriptomics in echinoderms., Meyer A, Ku C, Hatleberg WL, Telmer CA, Hinman V., Elife. July 20, 2023; 12
Evolutionary analyses of genes in Echinodermata offer insights towards the origin of metazoan phyla., Foley S, Vlasova A, Marcet-Houben M, Gabaldón T, Hinman VF., Genomics. July 1, 2022; 114 (4): 110431.
Biosynthesis of saponin defensive compounds in sea cucumbers., Thimmappa R, Wang S, Zheng M, Misra RC, Huang AC, Saalbach G, Chang Y, Zhou Z, Hinman V, Bao Z, Osbourn A., Nat Chem Biol. July 1, 2022; 18 (7): 774-781.
Regeneration of the larval sea star nervous system by wounding induced respecification to the Sox2 lineage., Zheng M, Zueva O, Hinman VF., Elife. January 14, 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.
The arm of the starfish: The far-reaching applications of Patiria miniata as a model system in evolutionary, developmental, and regenerative biology., Meyer A, Hinman V., Curr Top Dev Biol. January 1, 2022; 147 523-543.
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
A nomenclature for echinoderm genes., Beatman TR, Buckley KM, Cary GA, Hinman VF, Ettensohn CA., Database (Oxford). August 7, 2021; 2021
The Use of Larval Sea Stars and Sea Urchins in the Discovery of Shared Mechanisms of Metazoan Whole-Body Regeneration., Wolff A, Hinman V., Genes (Basel). July 13, 2021; 12 (7):
Integration of 1:1 orthology maps and updated datasets into Echinobase., Foley S, Ku C, Arshinoff B, Lotay V, Karimi K, Vize PD, Hinman V., Database (Oxford). May 19, 2021; 2021
Modularity and hierarchy in biological systems: Using gene regulatory networks to understand evolutionary change., Hatleberg WL, Hinman VF., Curr Top Dev Biol. January 1, 2021; 141 39-73.
Systematic comparison of sea urchin and sea star developmental gene regulatory networks explains how novelty is incorporated in early development., Cary GA, McCauley BS, Zueva O, Pattinato J, Longabaugh W, Hinman VF., Nat Commun. December 4, 2020; 11 (1): 6235.
Developmental transcriptomes of the sea star, Patiria miniata, illuminate how gene expression changes with evolutionary distance., Gildor T, Cary GA, Lalzar M, Hinman VF, Ben-Tabou de-Leon S., Sci Rep. November 7, 2019; 9 (1): 16201.
Analysis of sea star larval regeneration reveals conserved processes of whole-body regeneration across the metazoa., Cary GA, Wolff A, Zueva O, Pattinato J, Hinman VF., BMC Biol. February 22, 2019; 17 (1): 16.
Genomic resources for the study of echinoderm development and evolution., Cary GA, Cameron RA, Hinman VF., Methods Cell Biol. January 1, 2019; 151 65-88.
Embryonic neurogenesis in echinoderms., Hinman VF, Burke RD., Wiley Interdiscip Rev Dev Biol. July 1, 2018; 7 (4): e316.
EchinoBase: Tools for Echinoderm Genome Analyses., Cary GA, Cameron RA, Hinman VF., Methods Mol Biol. January 1, 2018; 1757 349-369.
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.
Regulatory heterochronies and loose temporal scaling between sea star and sea urchin regulatory circuits., Gildor T, Hinman V, Ben-Tabou-De-Leon S., Int J Dev Biol. January 1, 2017; 61 (3-4-5): 347-356.
A gene regulatory network for apical organ neurogenesis and its spatial control in sea star embryos., Cheatle Jarvela AM, Yankura KA, Hinman VF., Development. November 15, 2016; 143 (22): 4214-4223.
Dose-dependent nuclear β-catenin response segregates endomesoderm along the sea star primary axis., McCauley BS, Akyar E, Saad HR, Hinman VF., Development. January 1, 2015; 142 (1): 207-17.
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.
A method for microinjection of Patiria miniata zygotes., Cheatle Jarvela AM, Hinman V., J Vis Exp. September 1, 2014; (91): e51913.
Developmental gene regulatory network evolution: insights from comparative studies in echinoderms., Hinman VF, Cheatle Jarvela AM., Genesis. March 1, 2014; 52 (3): 193-207.
Expression of wnt and frizzled genes during early sea star development., McCauley BS, Akyar E, Filliger L, Hinman VF., Gene Expr Patterns. December 1, 2013; 13 (8): 437-44.
Gene regulatory network for neurogenesis in a sea star embryo connects broad neural specification and localized patterning., Yankura KA, Koechlein CS, Cryan AF, Cheatle A, Hinman VF., Proc Natl Acad Sci U S A. May 21, 2013; 110 (21): 8591-6.
Probabilistic error correction for RNA sequencing., Le HS, Schulz MH, McCauley BM, Hinman VF, Bar-Joseph Z., Nucleic Acids Res. May 1, 2013; 41 (10): e109.
Development of an embryonic skeletogenic mesenchyme lineage in a sea cucumber reveals the trajectory of change for the evolution of novel structures in echinoderms., McCauley BS, Wright EP, Exner C, Kitazawa C, Hinman VF., Evodevo. August 9, 2012; 3 (1): 17.
RNA deep sequencing reveals differential microRNA expression during development of sea urchin and sea star., Kadri S, Hinman VF, Benos PV., PLoS One. January 1, 2011; 6 (12): e29217.
Uncoupling of complex regulatory patterning during evolution of larval development in echinoderms., Yankura KA, Martik ML, Jennings CK, Hinman VF., BMC Biol. November 30, 2010; 8 143.
A conserved gene regulatory network subcircuit drives different developmental fates in the vegetal pole of highly divergent echinoderm embryos., McCauley BS, Weideman EP, Hinman VF., Dev Biol. April 15, 2010; 340 (2): 200-8.
Evolution of gene regulatory network architectures: examples of subcircuit conservation and plasticity between classes of echinoderms., Hinman VF, Yankura KA, McCauley BS., Biochim Biophys Acta. April 1, 2009; 1789 (4): 326-32.
Caught in the evolutionary act: precise cis-regulatory basis of difference in the organization of gene networks of sea stars and sea urchins., Hinman VF, Nguyen A, Davidson EH., Dev Biol. December 15, 2007; 312 (2): 584-95.
Evolutionary plasticity of developmental gene regulatory network architecture., Hinman VF, Davidson EH., Proc Natl Acad Sci U S A. December 4, 2007; 104 (49): 19404-9.
Expression of AmHNF6, a sea star orthologue of a transcription factor with multiple distinct roles in sea urchin development., Otim O, Hinman VF, Davidson EH., Gene Expr Patterns. February 1, 2005; 5 (3): 381-6.
Developmental gene regulatory network architecture across 500 million years of echinoderm evolution., Hinman VF, Nguyen AT, Cameron RA, Davidson EH., Proc Natl Acad Sci U S A. November 11, 2003; 100 (23): 13356-61.
Expression and function of a starfish Otx ortholog, AmOtx: a conserved role for Otx proteins in endoderm development that predates divergence of the eleutherozoa., Hinman VF, Nguyen AT, Davidson EH., Mech Dev. October 1, 2003; 120 (10): 1165-76.
Expression of a gene encoding a Gata transcription factor during embryogenesis of the starfish Asterina miniata., Hinman VF, Davidson EH., Gene Expr Patterns. August 1, 2003; 3 (4): 419-22.
Expression of AmKrox, a starfish ortholog of a sea urchin transcription factor essential for endomesodermal specification., Hinman VF, Davidson EH., Gene Expr Patterns. August 1, 2003; 3 (4): 423-6.
A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo., Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, Yuh CH, Minokawa T, Amore G, Hinman V, Arenas-Mena C, Otim O, Brown CT, Livi CB, Lee PY, Revilla R, Schilstra MJ, Clarke PJ, Rust AG, Pan Z, Arnone MI, Rowen L, Cameron RA, McClay DR, Hood L, Bolouri H., Dev Biol. June 1, 2002; 246 (1): 162-90.
A genomic regulatory network for development., Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, Yuh CH, Minokawa T, Amore G, Hinman V, Arenas-Mena C, Otim O, Brown CT, Livi CB, Lee PY, Revilla R, Rust AG, Pan Zj, Schilstra MJ, Clarke PJ, Arnone MI, Rowen L, Cameron RA, McClay DR, Hood L, Bolouri H., Science. March 1, 2002; 295 (5560): 1669-78.

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. May 7, 2024; 227 (1):

New hypotheses of cell type diversity and novelty from orthology-driven comparative single cell and nuclei transcriptomics in echinoderms., Meyer A, Ku C, Hatleberg WL, Telmer CA, Hinman V., Elife. July 20, 2023; 12

Evolutionary analyses of genes in Echinodermata offer insights towards the origin of metazoan phyla., Foley S, Vlasova A, Marcet-Houben M, Gabaldón T, Hinman VF., Genomics. July 1, 2022; 114 (4): 110431.

Biosynthesis of saponin defensive compounds in sea cucumbers., Thimmappa R, Wang S, Zheng M, Misra RC, Huang AC, Saalbach G, Chang Y, Zhou Z, Hinman V, Bao Z, Osbourn A., Nat Chem Biol. July 1, 2022; 18 (7): 774-781.

Regeneration of the larval sea star nervous system by wounding induced respecification to the Sox2 lineage., Zheng M, Zueva O, Hinman VF., Elife. January 14, 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.

The arm of the starfish: The far-reaching applications of Patiria miniata as a model system in evolutionary, developmental, and regenerative biology., Meyer A, Hinman V., Curr Top Dev Biol. January 1, 2022; 147 523-543.

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

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

The Use of Larval Sea Stars and Sea Urchins in the Discovery of Shared Mechanisms of Metazoan Whole-Body Regeneration., Wolff A, Hinman V., Genes (Basel). July 13, 2021; 12 (7):

Integration of 1:1 orthology maps and updated datasets into Echinobase., Foley S, Ku C, Arshinoff B, Lotay V, Karimi K, Vize PD, Hinman V., Database (Oxford). May 19, 2021; 2021

Modularity and hierarchy in biological systems: Using gene regulatory networks to understand evolutionary change., Hatleberg WL, Hinman VF., Curr Top Dev Biol. January 1, 2021; 141 39-73.

Systematic comparison of sea urchin and sea star developmental gene regulatory networks explains how novelty is incorporated in early development., Cary GA, McCauley BS, Zueva O, Pattinato J, Longabaugh W, Hinman VF., Nat Commun. December 4, 2020; 11 (1): 6235.

Developmental transcriptomes of the sea star, Patiria miniata, illuminate how gene expression changes with evolutionary distance., Gildor T, Cary GA, Lalzar M, Hinman VF, Ben-Tabou de-Leon S., Sci Rep. November 7, 2019; 9 (1): 16201.

Analysis of sea star larval regeneration reveals conserved processes of whole-body regeneration across the metazoa., Cary GA, Wolff A, Zueva O, Pattinato J, Hinman VF., BMC Biol. February 22, 2019; 17 (1): 16.

Genomic resources for the study of echinoderm development and evolution., Cary GA, Cameron RA, Hinman VF., Methods Cell Biol. January 1, 2019; 151 65-88.

Embryonic neurogenesis in echinoderms., Hinman VF, Burke RD., Wiley Interdiscip Rev Dev Biol. July 1, 2018; 7 (4): e316.

EchinoBase: Tools for Echinoderm Genome Analyses., Cary GA, Cameron RA, Hinman VF., Methods Mol Biol. January 1, 2018; 1757 349-369.

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.

Regulatory heterochronies and loose temporal scaling between sea star and sea urchin regulatory circuits., Gildor T, Hinman V, Ben-Tabou-De-Leon S., Int J Dev Biol. January 1, 2017; 61 (3-4-5): 347-356.

A gene regulatory network for apical organ neurogenesis and its spatial control in sea star embryos., Cheatle Jarvela AM, Yankura KA, Hinman VF., Development. November 15, 2016; 143 (22): 4214-4223.

Dose-dependent nuclear β-catenin response segregates endomesoderm along the sea star primary axis., McCauley BS, Akyar E, Saad HR, Hinman VF., Development. January 1, 2015; 142 (1): 207-17.

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.

A method for microinjection of Patiria miniata zygotes., Cheatle Jarvela AM, Hinman V., J Vis Exp. September 1, 2014; (91): e51913.

Developmental gene regulatory network evolution: insights from comparative studies in echinoderms., Hinman VF, Cheatle Jarvela AM., Genesis. March 1, 2014; 52 (3): 193-207.

Expression of wnt and frizzled genes during early sea star development., McCauley BS, Akyar E, Filliger L, Hinman VF., Gene Expr Patterns. December 1, 2013; 13 (8): 437-44.

Gene regulatory network for neurogenesis in a sea star embryo connects broad neural specification and localized patterning., Yankura KA, Koechlein CS, Cryan AF, Cheatle A, Hinman VF., Proc Natl Acad Sci U S A. May 21, 2013; 110 (21): 8591-6.

Probabilistic error correction for RNA sequencing., Le HS, Schulz MH, McCauley BM, Hinman VF, Bar-Joseph Z., Nucleic Acids Res. May 1, 2013; 41 (10): e109.

Development of an embryonic skeletogenic mesenchyme lineage in a sea cucumber reveals the trajectory of change for the evolution of novel structures in echinoderms., McCauley BS, Wright EP, Exner C, Kitazawa C, Hinman VF., Evodevo. August 9, 2012; 3 (1): 17.

RNA deep sequencing reveals differential microRNA expression during development of sea urchin and sea star., Kadri S, Hinman VF, Benos PV., PLoS One. January 1, 2011; 6 (12): e29217.

Uncoupling of complex regulatory patterning during evolution of larval development in echinoderms., Yankura KA, Martik ML, Jennings CK, Hinman VF., BMC Biol. November 30, 2010; 8 143.

A conserved gene regulatory network subcircuit drives different developmental fates in the vegetal pole of highly divergent echinoderm embryos., McCauley BS, Weideman EP, Hinman VF., Dev Biol. April 15, 2010; 340 (2): 200-8.

Evolution of gene regulatory network architectures: examples of subcircuit conservation and plasticity between classes of echinoderms., Hinman VF, Yankura KA, McCauley BS., Biochim Biophys Acta. April 1, 2009; 1789 (4): 326-32.

Caught in the evolutionary act: precise cis-regulatory basis of difference in the organization of gene networks of sea stars and sea urchins., Hinman VF, Nguyen A, Davidson EH., Dev Biol. December 15, 2007; 312 (2): 584-95.

Evolutionary plasticity of developmental gene regulatory network architecture., Hinman VF, Davidson EH., Proc Natl Acad Sci U S A. December 4, 2007; 104 (49): 19404-9.

Expression of AmHNF6, a sea star orthologue of a transcription factor with multiple distinct roles in sea urchin development., Otim O, Hinman VF, Davidson EH., Gene Expr Patterns. February 1, 2005; 5 (3): 381-6.

Developmental gene regulatory network architecture across 500 million years of echinoderm evolution., Hinman VF, Nguyen AT, Cameron RA, Davidson EH., Proc Natl Acad Sci U S A. November 11, 2003; 100 (23): 13356-61.

Expression and function of a starfish Otx ortholog, AmOtx: a conserved role for Otx proteins in endoderm development that predates divergence of the eleutherozoa., Hinman VF, Nguyen AT, Davidson EH., Mech Dev. October 1, 2003; 120 (10): 1165-76.

Expression of a gene encoding a Gata transcription factor during embryogenesis of the starfish Asterina miniata., Hinman VF, Davidson EH., Gene Expr Patterns. August 1, 2003; 3 (4): 419-22.

Expression of AmKrox, a starfish ortholog of a sea urchin transcription factor essential for endomesodermal specification., Hinman VF, Davidson EH., Gene Expr Patterns. August 1, 2003; 3 (4): 423-6.

A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo., Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, Yuh CH, Minokawa T, Amore G, Hinman V, Arenas-Mena C, Otim O, Brown CT, Livi CB, Lee PY, Revilla R, Schilstra MJ, Clarke PJ, Rust AG, Pan Z, Arnone MI, Rowen L, Cameron RA, McClay DR, Hood L, Bolouri H., Dev Biol. June 1, 2002; 246 (1): 162-90.

A genomic regulatory network for development., Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, Yuh CH, Minokawa T, Amore G, Hinman V, Arenas-Mena C, Otim O, Brown CT, Livi CB, Lee PY, Revilla R, Rust AG, Pan Zj, Schilstra MJ, Clarke PJ, Arnone MI, Rowen L, Cameron RA, McClay DR, Hood L, Bolouri H., Science. March 1, 2002; 295 (5560): 1669-78.

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