Does regeneration re-use developmental gene regulatory networks?
PhD in experimental and computational biology
Deadline for applications: 19 April 2024
Expected starting date: 1 October 2024
Expected starting date: 1 October 2024
A 3-year PhD fellowship is available at the Institut de Génomique Fonctionnelle de Lyon, in France, to discover and compare the gene regulatory networks that underpin leg development and regeneration in a model crustacean. The fellowship is funded by the ANR grant RePlay.
Research topic
This fully funded PhD project aims to compare the gene regulatory networks (GRNs) that drive leg development and regeneration in the crustacean model Parhyale hawaiensis. Our team has already established transgenic, live imaging and genomics approaches to study leg regeneration in Parhyale (see Paris et al, 2022). We have previously shown that although regeneration produces faithful replicas of the original legs (Almazan et al. 2022), the transcriptional and cellular dynamics associated with leg development and regeneration are different (Sinigaglia et al. 2022). These results suggest that identical structures could be generated by distinct mechanisms during development and regeneration. The recruited PhD student will take a single-cell omics approach to explore this question, by comparing the GRNs that underpin leg development and regeneration.
The project will involve both experimental and computational work, including generating scRNAseq and scATACseq data from developing and regenerating legs, computational processing of these data to reconstruct and compare GRNs, and transgenesis to validate key GRN nodes in vivo.
Work environment
The recruited student will join the Development, Regeneration and Evolution team of the Institut de Génomique Fonctionnelle de Lyon (IGFL), located at the campus of the École Normale Supérieure de Lyon in the south of Lyon, France. The IGFL provides a stimulating environment focusing on the interfaces of animal development, physiology and evolution. The research team is international and the working language is English.
The recruited student will be enrolled as a PhD student in the École Normale Supérieure de Lyon, and will be co-supervised by Mathilde Paris and Michalis Averof. S/he will receive training in single-cell genomics (scRNAseq and scATACseq), bioinformatics including handling/analysis of single-cell datasets and modeling of GRNs, as well as transgenesis and live imaging.
The project involves a collaboration with Arnau Sebé Pedrós at the Centre for Genomic Regulation (CRG) in Barcelona. The project is funded by the ANR grant Replay.
The recruited student will be enrolled as a PhD student in the École Normale Supérieure de Lyon, and will be co-supervised by Mathilde Paris and Michalis Averof. S/he will receive training in single-cell genomics (scRNAseq and scATACseq), bioinformatics including handling/analysis of single-cell datasets and modeling of GRNs, as well as transgenesis and live imaging.
The project involves a collaboration with Arnau Sebé Pedrós at the Centre for Genomic Regulation (CRG) in Barcelona. The project is funded by the ANR grant Replay.
Qualifications
Applicants should have a Masters degree in science, preferably in Biology or Bioinformatics. Practical experience in bioinformatics, genomics, molecular genetics or developmental biology will be an advantage. Candidates from all nationalities are invited to apply, provided they are able to communicate fluently in English (speaking French is not required).