Carnegie Mellon University

Veronica F. Hinman

Department Head
Dr. Frederick A. Schwertz Distinguished Professor of Life Sciences

634A Mellon Institute
Department of Biological Sciences
Carnegie Mellon University
4400 Fifth Avenue
Pittsburgh, PA 15213

Phone: 412-268-9348
Fax: 412-268-7129


Lab website

Veronica Hinman


Ph.D., University of Queensland, Australia
Postdoctoral Appointment, California Institute of Technology


The research interests and experience within this laboratory falls into the area broadly defined as evolution of developmental mechanisms. Our particular approach for understanding conserved and divergent properties of animal development is to compare architectural organization of gene regulatory networks (GRNs). GRN models consider not only the expression domains and function of many regulatory genes (mostly transcription factors), but importantly their inter-relationships. The construction of GRNs involves the use of cutting edge embryological and molecular biological technologies to study gene expression and to undertake gene perturbation, gene transfer and cis -regulatory analyses. Since our work is comparative these techniques must often be adapted for use in non-model organisms. The relationships between regulatory genes are portrayed as a network diagrams.

We use a variety of marine invertebrates, particularly echinoderms, for our research. This is due largely to the fact that the most extensive GRN currently exists for the sea urchin embryo (see and the starfish has been shown to be an excellent comparative model. Also marine invertebrates represent the largest morphological diversity on the planet and present a wealth of opportunity to explore the association between development, phenotype and evolution.

We use a comparative GRN method to answer questions such as:

  1. What are conserved features of GRNs? These may be particular relationships of orthologous genes that can explain the preservation of phylotypic characters or may even represent developmental phenomena more widespread among the metazoa that are thus crucial for understanding animal development.
  2. How does the architecture of GRNs diverge with morphological differences in development and how did these architectural changes arise in evolution?
  3. What are the similarities and differences that underlie the GRN of two independently evolving taxa that converge upon the same morphological outcome?
  4. What is the cis -regulatory organization that underlies GRN structure and how has the cis regulatory logic evolved in conjunction with network architecture evolution? 
Hinman Lab


Karimi K, Agalakov S, Telmer CA, Beatman TR, Pells TJ, Arshinoff BI, Ku CJ, Foley S, Hinman VF, Ettensohn CA, Vize PD. Classifying domain-specific text documents containing ambiguous keywords. Database (Oxford). 2021 Sep 29;2021:baab062. doi: 10.1093/database/baab062. PMID: 34585729

Beatman TR, Buckley KM, Cary GA, Hinman VF, Ettensohn CA. A nomenclature for echinoderm genes. Database (Oxford). 2021 Aug 7;2021:baab052. doi: 10.1093/database/baab052. PMID: 34386815

Hatleberg WL, Hinman VF. Modularity and hierarchy in biological systems: Using gene regulatory networks to understand evolutionary change. Curr Top Dev Biol. 2021;141:39-73. doi: 10.1016/bs.ctdb.2020.11.004. Epub 2021 Feb 5. PMID: 33602494

Cary GA, McCauley BS, Zueva O, Pattinato J, Longabaugh W, Hinman VF. Systematic comparison of sea urchin and sea star developmental gene regulatory networks explains how novelty is incorporated in early development. Nat Commun. 2020 Dec 4;11(1):6235. doi: 10.1038/s41467-020-20023-4. PMID: 33277483

Gildor T, Cary GA, Lalzar M, Hinman VF, Ben-Tabou de-Leon S. Developmental transcriptomes of the sea star, Patiria miniata, illuminate how gene expression changes with evolutionary distance. Sci Rep. 2019 Nov 7;9(1):16201. doi: 10.1038/s41598-019-52577-9. PMID: 31700051

Cary GA, Cameron RA, Hinman VF. Genomic resources for the study of echinoderm development and evolution. Methods Cell Biol. 2019;151:65-88. doi: 10.1016/bs.mcb.2018.11.019. Epub 2019 Jan 9. PMID: 30948032

Cary GA, Wolff A, Zueva O, Pattinato J, Hinman VF. 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. PMID: 30795750

Cary GA, Cameron RA, Hinman VF. EchinoBase: Tools for Echinoderm Genome Analyses. Methods Mol Biol. 2018;1757:349-369. doi: 10.1007/978-1-4939-7737-6_12. PMID: 29761464

Hinman VF, Burke RD. Embryonic neurogenesis in echinoderms. Wiley Interdiscip Rev Dev Biol. 2018 Jul;7(4):e316. doi: 10.1002/wdev.316. Epub 2018 Feb 22. PMID: 29470839

Cary GA, Cheatle Jarvela AM, Francolini RD, Hinman VF. Genome-wide use of high- and low-affinity Tbrain transcription factor binding sites during echinoderm development. Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):5854-5861. doi: 10.1073/pnas.1610611114. PMID: 28584099

Thompson JR, Erkenbrack EM, Hinman VF, McCauley BS, Petsios E, Bottjer DJ. Paleogenomics of echinoids reveals an ancient origin for the double-negative specification of micromeres in sea urchins. Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):5870-5877. doi: 10.1073/pnas.1610603114. PMID: 28584090

Cary GA, Hinman VF. Echinoderm development and evolution in the post-genomic era. Dev Biol. 2017 Jul 15;427(2):203-211. doi: 10.1016/j.ydbio.2017.02.003. Epub 2017 Feb 7. PMID: 28185788

Cheatle Jarvela AM, Yankura KA, Hinman VF. A gene regulatory network for apical organ neurogenesis and its spatial control in sea star embryos. Development. 2016 Nov 15;143(22):4214-4223. doi: 10.1242/dev.134999. Epub 2016 Oct 5. PMID: 27707794

Rebeiz M, Patel NH, Hinman VF. Unraveling the Tangled Skein: The Evolution of Transcriptional Regulatory Networks in Development. Annu Rev Genomics Hum Genet. 2015;16:103-31. doi: 10.1146/annurev-genom-091212-153423. Epub 2015 May 20. PMID: 26079281

Cheatle Jarvela AM, Hinman VF. Evolution of transcription factor function as a mechanism for changing metazoan developmental gene regulatory networks. Evodevo. 2015 Jan 29;6(1):3.

Cheatle Jarvela AM, Hinman V. A Method for Microinjection of Patiria minata Zygotes. J Vis Exp. 2014 Sep 1;(91).

Cheatle Jarvela AM, Brubaker L, Vedenko A, Gupta A, Armitage BA, Bulyk ML, Hinman VF. Modular Evolution of DNA-Binding Preference of a Tbrain Transcription Factor Provides a Mechanism for Modifying Gene Regulatory Networks. Mol Biol Evol. 2014 Jul 12

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

McCauley BS, Akyar E, Filliger LZ, Hinman VF. Expression of Wnt and Frizzled genes in the embryos of the sea star Patiria miniata. (in press).

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

Le HS, Schulz M, McCauley BM, Hinman VF, Bar-Joseph Z. Probabilistic error correction for RNA sequencing. Nucleic Acids Research, 2013 April 4.

McCauley BS, Wright EP, Exner C, Kitazawa C, Hinman VF. 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.

Kadri S, Hinman VF, Benos PV. RNA deep sequencing reveals differential microRNA expression during development of sea urchin and sea star. PLoS One. 2011;6(12):e29217. doi: 10.1371/journal.pone.0029217. Epub 2011 Dec 28.

Yankura KA, Martik ML, Jennings CK, Hinman VF. Uncoupling of complex regulatory patterning during evolution of larval development in echinoderms. BMC Biol. 8:143, 2010 Nov 30. See commentary:BMC Biology 2011, 9:6;F1000 review.

McCauley BS, Weideman EP, Hinman VF. A conserved gene regulatory network subcircuit drives different developmental fates in the vegetal pole of highly divergent echinoderm embryos. Dev Biol. 340(2):200-8, 2010 Apr 15. Epub 2009 Nov 23.

Kadri S, Hinman V, Benos PV. HHMMiR: Efficient de novo prediction of microRNAs using hierarchical hidden Markov models. BMC Bioinformatics;10 Suppl 1:S35, 2009 Jan 30.

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

Hinman VF and Davidson EH. Evolutionary plasticity of developmental gene regulatory network architecture. Proceedings National Academy of Sciences (USA); 104(49):19404-9, 2007.

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