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University of Florida

Publications

Veronica Hinman, Ph.D.

orcid.org/0000-0003-3414-1357
h-index: 34
i10 index: 55
Underlined: student and postdoc authors from my lab

Research Publications:

  1. Cheryl A Telmer, Kamran Karimi, Macie M Chess, Sergei Agalakov, Bradley I Arshinoff, Vaneet Lotay, Dong Zhuo Wang, Stanley Chu, Troy J Pells, Peter D Vize, Veronica F Hinman, Charles A Ettensohn (2024). Echinobase: a resource to support the echinoderm research community. Genetics, Volume 227, Issue 1, May 2024, iyae002, https://doi.org/10.1093/genetics/iyae002
  2. A Meyer, C Ku, W Hatleberg, CA Telmer, V Hinman (2023) New hypotheses of cell type diversity and novelty from a comparative single cell and nuclei transcriptomics in echinoderms. eLife 12, e80090
  3. O Zueva, V Hinman (2023). Inducible in vivo genome editing in the sea star Patiria miniata. BioRxiv,01. 09.523328
  4. A Meyer, V Hinman (2022). The arm of the starfish: The far-reaching applications of Patiria miniata as a model system in evolutionary, developmental, and regenerative biology. Current Topics in Developmental Biology, 2022
  5. S Foley, A Vlasova, M Marcet-Houben, T Gabaldón, VF Hinman (2022) Evolutionary analyses of genes in Echinodermata offer insights towards the origin of metazoan phyla. Genomics 114 (4), 110431
  6. Ramesha Thimmappa, Shi Wang, Minyan Zheng, Rajesh Chandra Misra, Ancheng C Huang, Gerhard Saalbach, Yaqing Chang, Zunchun Zhou, Veronica Hinman, Zhenmin Bao, Anne Osbourn (2022). Biosynthesis of saponin defensive compounds in sea cucumbers. Nature Chemical Biology 18:774-781
  7. M Zheng, O Zueva, V Hinman (2022) Regeneration of the larval sea star nervous system by wounding induced respecification to the sox2 lineage Elife 11, e72983, 1,2022
  8. Bradley I Arshinoff, Gregory A Cary, Kamran Karimi, Saoirse Foley, Sergei Agalakov, Francisco Delgado, Vaneet S Lotay, Carolyn J Ku, Troy J Pells, Thomas R Beatman, Eugene Kim, R Andrew Cameron, Peter D Vize, Cheryl A Telmer, Jenifer C Croce, Charles A Ettensohn, Veronica F Hinman (2022) Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms Nucleic acids research 50 (D1), D970-D979, 2022
  9. S Foley, C Ku, B Arshinoff, V Lotay, K Karimi, PD Vize, V Hinman (2021) Integration of 1: 1 orthology maps and updated datasets into Echinobase. Database 2021
  10. Kamran Karimi, Sergei Agalakov, Cheryl A Telmer, Thomas R Beatman, Troy J Pells, Bradley IM Arshinoff, Carolyn J Ku, Saoirse Foley, Veronica F Hinman, Charles A Ettensohn, Peter D Vize (2021) Classifying domain-specific text documents containing ambiguous keywords, Database 2021
  11. TR Beatman, KM Buckley, GA Cary, VF Hinman, CA Ettensohn (2021) A Nomenclature for echinoderm genes. Database, 2021
  12. A Wolff, V Hinman (2021). The Use of Larval Sea Stars and Sea Urchins in the Discovery of Shared Mechanisms of Metazoan Whole-Body Regeneration. Genes 12 (7), 1063
  13. C Hoencamp, O Dudchenko, AMO Elbatsh, S Brahmachari, ..Hinman VF, et , (2021).3D genomics across the tree of life reveals condensin II as a determinant of architecture type. Science 372 (6545), 984-989          
  14. WL Hatleberg, VF Hinman (2021). Modularity and hierarchy in biological systems: Using gene regulatory networks to understand evolutionary change. Current Topics in Developmental Biology 141, 39-73
  15. GA Cary, BS McCauley, O Zueva, J Pattinato, W Longabaugh, VF Hinman (2020). Systematic comparison of sea urchin and sea star developmental gene regulatory networks explains how novelty is incorporated in early developmen Nature Communications 11 (1), 1-9
  16. Cary, GA, Cameron, RA, Hinman, VF (2019). Genomic resources for the study of echinoderm development and evolution. Methods in Molecular Biology.  Academic Press. 2019;151:65-88. doi: 10.1016/bs.mcb.2018.11.019
  17. G Cary, A Wolff, O Zueva, J Pattinato, V Hinman (2019). Analysis of sea star larval regeneration reveals conserved processes of whole-body regeneration across the metazoa.  BMC Biol. 2019 Feb 22;17(1):16. doi: 10.1186/s12915-019-0633-9..   BioRxiv 2017/118232.  
  18. Burke RD and Hinman VF (2018). The Development and Evolution of Larval Echinoderm Nervous Systems. Wiley Interdisciplinary Reviews: Developmental Biology, e316
  19. Cary GA, Cameron RA, Hinman VF (2018). EchinoBase: tools for echinoderm genome analyses.  Eukaryotic Genomic Databases, 349-369
  20. Cary GA, Jarvela CA, Francolini R., Hinman V.F (2017). Genome-wide use of evolvable high and low affinity Tbrain transcription factor binding sites.  Proc Natl Acad Sci U S A. 114(23):5854-5861. doi: 10.1073/pnas.1610611114.
  21. Thompson, Erkenbrack, Hinman, V.F., McCauley B.S. , Petsios, Bottjer. (2017). Paleogenomics of echinoids reveals an ancient origin for the double-negative specification of micromeres in sea urchins. Proc Natl Acad Sci U S A. 14(23):5870-5877. doi: 10.1073/pnas.1610603114.
  22. Cary GA, Hinman, V.F (2017). Echinoderm development and evolution in the post-genomic era. Developmental Biology. Feb 6. pii: S0012-1606(16)30574-7. doi: 10.1016/j.ydbio.2017.02.003. Featured cover
  23. Hinman V. and Cary G, (2017). The evolution of gene regulation. Elife. 2017 May 12;6. pii: e27291. doi: 10.7554/eLife.27291
  24. Tsvia Gildor, Hinman, V.F and Smadar Ben-Tabou de-Leon. (2017). Regulatory heterochronies and loose temporal scaling between the sea star and sea urchin regulatory circuits. Int J. Dev  Bio. 61: 347 – 356. doi: 10.1387/ijdb.160331sb
  25. Cheatle Jarvela, A., Yankura, K. and Hinman, V. F (2016). A gene regulatory network for apical organ neurogenesis and its spatial control in sea star embryos. Development.  DOI: 1242/dev.134999. BioRxiv https://doi.org/10.1101/036624.   Featured Cover
  26. Hinman V.F. Eric Davidson (1937-2015) and the past, present and future of EvoDevo (2016). Evol Dev. 2016 Mar-Apr;18(2):67-8. doi: 10.1111/ede.12180. PMID 26766743
  27. Hinman V.F. (2016) Ch 130: Conservation and evolution of gene networks driving development. The Encyclopedia of Evolutionary Biology. Elsevier.
  28. Rebiez, M., Patel, N., Hinman VF.(2015) Unraveling the tangled skein: the evolution of transcriptional regulatory networks in development. Annu Rev Genomics Hum Genet. 2015;16:103-31.
  29. Cheatle Jarvela AM, Hinman VF. (2015). Evolution of transcription factor function as a mechanism for changing metazoan developmental gene regulatory networks. Evodevo. 2015 Jan 29;6(1):3. doi: 10.1186/2041-9139-6-3
  30. McCauley B.S. Akyar E., Saad, R., Hinman V.F. (2015). Dose-dependent nuclear -catenin response segregates endomesoderm along the sea star primary axis. Development. 2015 Jan 1;142(1):207-17. doi: 10.1242/dev.113043.
  31. Cheatle Jarvela AM, Brubaker L, Vedenko A, Gupta A, , Armitage B, Bulyk M, Hinman V.F. (2014) Modular Evolution of DNA Binding Preference of a Tbrain Transcription Factor Provides a Mechanism for Modifying Gene Regulatory Networks. Molecular Biology and Evolution. Oct;31(10):2672-88. doi: 10.1093/molbev/msu213Jul 12. . Featured as Editor’s Choice in Science: http://www.sciencemag.org/content/345/6197/634.2.full.
  32. Chealte Jarvela AM, Hinman VF (2014). Method for Microinjection of Patiria minata J. Vis. Exp. (91), e51913, doi:10.3791/51913
  33. Hinman V. F. Cheatle Jarvela AM. (2014) Developmental gene regulatory network evolution: Insights from comparative studies in echinoderms. Genesis. 2014 Feb 18. doi: 10.1002/dvg.22757
  34. Yankura, K.A., Koechelin, C., Cryan, A., Cheatle, A., Hinman V. F. (2013) A gene regulatory network for neurogenesis in a sea star embryo connects broad neural specification and localized pattering. Proc Natl Acad Sci U S A. 21;110(21):8591-6. doi: 10.1073/pnas.1220903110
  35. McCauley B.M. Akyar E., Filliger, L., Hinman V.F. (2013). Expression of Wnt and Frizzled genes during early sea star Gene Expr Patterns 13(8). 437-444.
  36. Le HS., Schulz, M. McCauley B.M., Hinman, V.F., Bar-Joseph Z. (2013). Probabilistic error correction for RNA sequencing. Nucleic Acids Research, 41(10):e109. doi: 10.1093/nar/gkt215
  37. McCauley BS, Wright EP, Exner C, Kitazawa C, Hinman V.F. (2012) Development of an embryonic skeletogenic mesenchyme lineage in a sea cucumber reveals the trajectory of change for the evolution of novel structures in echinoderms. Evodevo. 2012 Aug 9;3(1):17. doi: 10.1186/2041-9139-3-17.
  38. Kadri S, Hinman V.F., Benos PV. (2011). RNA deep sequencing reveals differential microRNA expression during development of sea urchin and sea star. PLoS One. 2011;6(12):e29217.
  39. Yankura KA, Martik ML, Jennings CK, Hinman VF. (2010). Uncoupling of complex regulatory patterning during evolution of larval development in echinoderms. BMC Biology. 2010 Nov 30;8:143.
    1. Featured commentary: BMC Biology 2011, 9:6. Highlighted F1000 review.
  40. McCauley B.S., Weideman, E. Hinman V.F. (2010). A conserved gene regulatory network subcircuit drives different developmental fates in the vegetal pole of highly divergent echinoderm embryos. Developmental Biology. Apr 15;340(2):200-8
  41. Kadri S, Hinman V, Benos PV. (2009). Efficient de novo prediction of microRNAs using hierarchical hidden Markov models. BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S35.
  42. Hinman, V. F., Yankura KA, McCauley B.S. (2009). Evolution of gene regulatory network architectures: Examples of subcircuit conservation and plasticity between classes of echinoderms. Biochim Biophys Acta.1789(4):326-32.
  43. Hinman, V.F., and Davidson E.H. (2007). Evolutionary plasticity of developmental gene regulatory network architecture. Proc Natl Acad Sci U S A 104(49):19404-9.
  44. Hinman, V. F., Nguyen A., Davidson E.H. (2007). Caught in the evolutionary act: precise cis-regulatory basis of difference in organization of gene networks of sea stars and sea urchins. Developmental Biology. 312(2):584-95
  45. Larroux, C., Fahey, B., Liubicich, D., Hinman, V. F., et al., (2006). Developmental expression of transcription factor genes in a demosponge: insights into the origin of metazoan multicellularity. Evolution & Development. 8, 150-173.
  46. Otim, O., Hinman, V. F., Davidson, E. H., (2005). Expression of AmHNF6, a sea star orthologue of a transcription factor with multiple distinct roles in sea urchin development. Gene Expression Patterns. 5, 381-386.
  47. Hinman, V. F., and Davidson, E. H. (2004). System-level Properties Revealed by a Gene Regulatory Network Analysis of Pregastrular Specification in Sea Urchins.  In ‘Gastrulation’. Ed. C. Stern.  Cold Spring Harbor Laboratory Press.  Cold Spring Habor.
  48. Hinman, V. F., and Davidson, E. H. (2003). Expression of a gene encoding a Gata transcription factor during embryogenesis of the starfish Asterina miniata. Gene Expression Patterns 3, 419-422.
  49. Hinman, V. F., and Davidson, E. H. (2003). Expression of AmKrox, a starfish ortholog of a sea urchin transcription factor essential for endomesodermal specification. Gene Expression Patterns 3, 423-426.
  50. Hinman, V. F., Nguyen, A. T., and Davidson, E. H. (2003). Expression and function of a starfish Otx ortholog, AmOtx: a conserved role for Otx proteins in endoderm development that predates divergence of the eleutherozoa. Mechanisms of Development 120, 1165-1176.
  51. Hinman, V. F., Nguyen, A. T., Cameron, R. A., and Davidson, E. H. (2003). Developmental gene regulatory network architecture across 500 MY of echinoderm evolution. Proceedings of the National Academy of Sciences of the United States of America, 100, 13356-13361.
  52. Hinman, V. F., O'Brien, E. K., Richards, G. S., and Degnan, B. M. (2003). Expression of anterior hox genes during larval development of the gastropod Haliotis asinina. Evolution and Development 5, 508-521.
  53. Davidson, E. H., Rast, J. P., Oliveri, P., Ransick, A., Calestani, C., Yuh, C. H., Minokawa, T., Amore, G., Hinman, V., Arenas-Mena, C., Otim, O., Brown, C. T., Livi, C. B., Lee, P. Y., Revilla, R., Rust, A. G., Pan, Z. J., Schilstra, M. J., Clarke, P. J. C., Arnone, M. I., Rowen, L., Cameron, R. A., McClay, D. R., Hood, L., and Bolouri, H. (2002). A genomic regulatory network for development. Science 295, 1669-1678.
  54. Davidson, E. H., Rast, J. P., Oliveri, P., Ransick, A., Calestani, C., Yuh, C. H., Minokawa, T., Amore, G., Hinman, V., Arenas-Mena, C., Otim, O., Brown, C. T., Livi, C. B., Lee, P. Y., Revilla, R., Schilstra, M. J., Clarke, P. J. C., Rust, A. G., Pan, Z. J., Arnone, M. I., Rowen, L., Cameron, R. A., McClay, D. R., Hood, L., and Bolouri, H. (2002). A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo. Developmental Biology 246, 162-190.
  55. Devine, C., Hinman, V. F., and Degnan, B. M. (2002). Evolution and developmental expression of nuclear receptor genes in the ascidian Herdmania. International Journal of Developmental Biology 46, 687-692.
  56. Hinman, V. F., and Degnan, B. M. (2002). Mox homeobox expression in muscle lineage of the gastropod Haliotis asinina: evidence for a conserved role in bilaterian myogenesis. Development Genes and Evolution 212, 141-144.
  57. Jackson, D., Leys, S. P., Hinman, V. F., Woods, R., Lavin, M. F., and Degnan, B. M. (2002). Ecological regulation of development: induction of marine invertebrate metamorphosis. International Journal of Developmental Biology 46, 679-686.
  58. Hinman, V. F., and Degnan, B. M. (2001). Homeobox genes, retinoic acid and the development and evolution of dual body plans in the ascidian Herdmania curvata. American Zoologist 41, 664-675.
  59. Giusti, A. F., Hinman, V. F., Degnan, S. M., Degnan, B. M., and Morse, D. E. (2000). Expression of a Scr/Hox5 gene in the larval central nervous system of the gastropod Haliotis, a non-segmented spiralian lophotrochozoan. Evolution & Development 2, 294-302.
  60. Hinman, V. F., Becker, E., and Degnan, B. M. (2000). Neuroectodermal and endodermal expression of the ascidian Cdx gene is separated by metamorphosis. Development Genes and Evolution 210, 212-216.
  61. Hinman, V. F., and Degnan, B. M. (2000). Retinoic acid perturbs Otx gene expression in the ascidian pharynx. Development Genes and Evolution 210, 129-139.
  62. Eri, R., Arnold, J. M., Hinman, V. F., Green, K. M., Jones, M. K., Degnan, B. M., and Lavin, M. F. (1999). Hemps, a novel EGF-like protein, plays a central role in ascidian metamorphosis. Development 126, 5809-5818.
  63. Hinman, V. F., and Degnan, B. M. (1998). Retinoic acid disrupts anterior ectodermal and endodermal development in ascidian larvae and postlarvae. Development Genes and Evolution 208, 336-345.