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Exploring the evolution of vertebrate development using single-cell genomics


Single Cell Genomics and Evolution

About the Project

We are seeking a highly motivated candidate to join our teams to work on an interdisciplinary project (experimental and computational) involving single-cell genomics and chromatin profiling in different chordate species. The research program for this position focuses on elucidating the origin and evolution of the regulatory programs controlling vertebrate morphogenesis and cell differentiation. To this end, you will apply and analyse advanced functional genomics to characterize cell types and regulatory genome features in vertebrate and non-vertebrate chordate species. Specifically, this involves: (i) scRNAseq to define cell type-specific gene expression across multiple developmental stages, and (ii) bulk ChIP-seq and ATAC-seq to map chromatin states and regulatory element usage. The candidate will spearhead the analysis, integration, and interpretation of these comparative omics datasets.

Our groups study genome regulation from an evolutionary systems perspective. In particular, we are interested in deciphering the evolution of animal cell type developmental programs and the regulatory mechanisms underlying these programs. To this end, we apply advanced single-cell genomics and chromatin experimental methods to molecularly dissect cell types and epigenomic landscapes in phylogenetically diverse organisms. We also develop computational tools to integrate these diverse data sources into models of cell type gene regulatory networks and we use phylogenetic methods to comparatively analyze these models. Our recent work has provided the first whole-organism cell type atlases in different species and mapped key regulatory features underlying both development and cell diversity in non-model invertebrate organisms and the origin of vertebrates (see "Relevant Publications" below). By analysing the development of chordate species at single-cell resolution, we now aim at dissecting the evolution of vertebrate cellular ontogenies and their underlying gene regulatory networks.

For further information you can directly email the PIs of the groups:

The successful applicant will enrol in the very active CRG International PhD program, which includes science and practical courses, a wide range of complementary skills training, access to many courses, mentoring via a thesis committee, and active participation in the organization of seminars, symposia and retreats.

Applications are accepted exclusively online. Please, click the "Institute Website" button to access our online application system.

The deadline for the receipt of complete applications is October 15, 2020. Proposals must be written in English.

CRG offers and promotes a diverse and inclusive environment and welcomes applicants regardless of age, disability, gender, nationality, race, religion or sexual orientation.

All personal data requested by CRG from applicants will be treated in accordance with the principles of the Data Protection Act (15/13 December 1999).

Funding Notes

The selected PhD student will receive an annual work contract with a competitive salary and additional funding.

Target start date: September 2020 to January 2021.

References

Sebé-Pedrós, A., Chomsky, E., Pang, K., Lara-Astiaso, D., Gaiti, F., Mukamel, Z., Amit, I., Hejnol, A., Degnan, B.M., and Tanay, A. (2018). Early metazoan cell type diversity and the evolution of multicellular gene regulation. Nat. Ecol. Evol. 2, 1176–1188.
Sebé-Pedrós, A., Saudememont, B., Chomsky, E., Mailhe, M.P., Pleisser, F., …, N., Steinmetz, P., Spitz, F., Tanay, A., Marlow, H. (2018). Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq. Cell, 173, 1520-1534.
Sebé-Pedrós, A., Degnan, B. M., Ruiz-Trillo, I. (2017) The origin of Metazoa: a unicellular perspective. Nat. Rev. Genet. 18, 498–512.
Sebé-Pedrós, A., Ballaré, C., Parra-Acero, H., Chiva, C., Tena, J.J., Sabidó, E., Gómez-Skarmeta, J.L., Di Croce, L., and Ruiz-Trillo, I. (2016). The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity. Cell 165, 1224–1237.

Full publications: https://www.ncbi.nlm.nih.gov/pubmed/?term=arnau+sebe-pedros

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