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I'm Jake Warner

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About Me


I am a post-doctoral fellow at the institute for research on cancer and aging (IRCAN), part of the University of Nice, in the laboratory of Eric Röttinger. My main research interest is in deriving gene regulatory networks of developmental processes of marine invertebrates. Currently I am working to develop a gene regulatory network of regeneration in the sea anemone. Much more can be found on my Research Page.


Being born and raised in Rhode Island instilled in me a love of all things marine related and this has shaped my research interests ever since. In 2006 I received my Bachelor’s of Science in Biology at High Point University. I spent the following year pursuing my teaching interests working as an English teacher in Madrid, Spain. I returned to the US to pursue my PhD at Duke University in the genetics and genomics program. Under the guidance of my mentor, David McClay, I was awarded my doctorate in 2013. From there I moved to Nice, France to work as a post-doctoral fellow in the lab of Eric Röttinger.


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Current Projects

Comparitive transcriptomics in Nematostella

Regeneration, as it restores missing tissue, is thought to employ processes originally used during embryonic development. If so, how does injury trigger those processes? Furthermore, are the ensuing genetic interactions similar to those of embryonic development? This project explores the mechanistic basis of regeneration by comparing the gene regulatory networks (GRN) governing regeneration and development. To achieve this, we use the developmental model system Nematostella vectensis. This sea anemone can regrow half its body when bisected. Here we compare embryonic and regeneration RNAseq data sets to examine the global similarities and differences in transcription during these two processes. Using these data we are able to construct co-expression networks driving embryogenesis and regeneration and identify modules of genes that are conserved between these two processes. We have found that transcriptionally, regeneration is a modest process, using a small fraction of the genes deployed during embryogenesis. Among these genes however we are able to identify embryonic modules that are re-used during regeneration. Finally, we have begun to validate these modules by performing knockdowns and constructing sub-networks that could be used to predict the regenerative capacity of other organisms or tissues.

A Wnt directed network module to activate regeneration

Following injury, for example, the loss of a limb, mammals undergo a stereotypical process of wound healing after which growth stops and a scar forms (and the poor animal is left minus a limb). Other organisms including Axolotls, Zebrafish and Nematostella are able to transition from this stage of wound healing into a regenerative state. Achieving this wound healing to regeneration transition is a critical event if the goal is to regrow a missing body part, so how does this work? Nematostella is beginning to give us some clues. We know that wound healing occurs in Nematostella and that it does not rely on cell-proliferation. Regeneration in Nematostella however is a proliferation intense process. Key to activating this proliferation is Wnt signalling and I believe this to be the key to activating the regenerative program. I am currently using various tools including CRISPR to understand the spatial and temporal requirements of Wnt signalling and how it is responsible for coordinating the earliest events of the regenerative program. The aim of this project is to identify the gene regulatory subnetwork that activates regeneration.

Previous Projects

Hedgehog signalling and ciliary trafficking in the sea urchin embryo

A relatively small number of signalling pathways govern the early patterning processes of metazoan development. Since most animals use the same pathways, the architectural changes made over time to these few signaling pathways offers unique insights into the evolutionary process. In the case of Hh signaling, two very divergent mechanisms of pathway transduction have evolved. In vertebrates, effective signaling relies on the primary cilium, a specialized cell-surface organelle. In sharp contrast, protostomes, including flat worms and fruit flies, cilia are not necessary for Hh signal transduction, yet much of the transduction apparatus is the same for both animal groups. How divergent lineages could have adapted such a dramatically different way of activating the signaling pathway is an unanswered question. My research provides evidence that in the sea urchin, a basal deuterostome, cilia are required for embryonic Hh signal transduction. We found that inhibiting cilia assembly generates phenotypes nearly identical to those of Hh morphants, and we were able to visualize the Hh receptor, Smoothened, localize to cilia during active Hh signaling. This is the first evidence that Hh signaling requires cilia outside of the vertebrate lineage. Our findings support a model in which a complex signaling pathway may have evolved by co-option of components from a common single-celled ancestor and diverged mechanistically within protostome and deuterstome lineages.


As an educator I strive to meet the following goals: a) That students develop critical thinking skills as this is the core of the science process; b) that students, especially those not destined for a career in science, gain enthusiasm for biology; c) to prepare students with technical knowledge and ability so that they are competitive scientifically in their future careers. To achieve these ends my teaching philosophy relies heavily on two principles: 1) Students attain the learning outcomes via problem based active learning, a method which is strongly supported in the literature and education community; 2) Student achievement is maximized by using frequent formative assessment to evaluate both student progress and the effectiveness of the course in achieving the student outcomes.


-- Master's Student Mentor (M2): Advised and mentored a Master's student through a sixth month long project and thesis. University of Nice, France.

2012 - 2013

-- Section Lecturer and Teaching Assistant: Bio 329D, Animal Physiology. Duke University, Durham, NC.


-- Section Lecturer and Teaching Assistant: Bio 220, Developmental Cell Biology. Duke University, Durham, NC.

2008 - 2012

-- Undergraduate Mentor: Guided two undergraduate students through long term independent study projects in our lab. Duke University, Durham, NC.

2011 - 2012

-- Preparing Future Faculty Fellow: Guest Lectured at Guilford College under the guidance of a faculty mentor.


-- Laboratory Lecturer and Teaching Assistant: Bio 101, Molecular Biology. Duke University, Durham, NC.

2008 - 2011

-- Volunteer Lecturer: North Carolina DNA day sends scientists to teach genetics at high schools and junior highs in rural and urban areas.


-- Teaching Assistant: Gene Regulatory Networks Course. Marine Biological Laboratory, Woods Hole, MA.


-- Guest Lecturer: Lecture and laboratory section for the Developmental Biology Course. High Point University, High Point, NC.

2006 - 2007

-- English Teacher: 500+ contact hours teaching english for several private institutes as well as the Instituto de Estudios Fiscales. Madrid, Spain


Web apps:



A web tool for exploring gene expression during regeneration and embryogenesis


The virtual embryo

A 3D model and gene expression database of the Nematostella embryo


Formula 1 stats

An app for visualising and exploring Formula 1 race results

Other stuff I contribute to:



An educational outreach initiative.



A blog of bioinformatics tutorials



All of my code!


Warner JF, Guerlais V, Amiel AR, Honston H, Nedoncelle K, Rottinger ER (2018) NvERTx: A gene expression database to compare Embryogenesis and Regeneration in the sea anemone Nematostella vectensis. Preprint: BioRxiv; doi: doi.org/10.1101/242370. BioRxiv.

Warner JF, Miranda EL, McClay DR (2016) Contribution of hedgehog signaling to the establishment of left-right asymmetry in the sea urchin. Developmental Biology 411(2):314-24. PubMed.

Amiel AR, Johnston HT, Nedoncelle K, Warner JF, Ferreira S, Röttinger E (2015) Characterization of Morphological and Cellular Events Underlying Oral Regeneration in the Sea Anemone, Nematostella vectensis. International Journal of Molecular Sciences 16(12):28449-71. PubMed.

Warner JF, McClay DR (2014) Left-right asymmetry in the sea urchin. Genesis 52(6):481-487. Genesis.

Warner JF, McCarthy AM, Morris RL, McClay DR (2014) Hedgehog signaling requires motile cilia in the sea urchin. Molecular Biology and Evolution 31(1):18-22. PubMed.

Warner JF, McClay DR (2014) Perturbations to the hedgehog pathway in sea urchin embryos. Methods in Molecular Biology 1128:211-21. PubMed.

Warner JF, Lyons DC, McClay DR (2012) Left-right asymmetry in the sea urchin embryo: BMP and the asymmetrical origins of the adult. Plos Biology 10(10):e1001404. PubMed.

Walton KD, Warner JF, Hertzler PH, McClay DR (2009) Hedgehog signaling patterns mesoderm in the sea urchin. Developmental Biology 331(1):26-37. PubMed.

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