Tracing the evolution of metazoan cell type and genome regulation using single-cell and functional genomics approaches

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    Centre de Regulacio Genomica
    Biological sciencesBiology
    First Stage Researcher (R1)
    23/06/2019 23:00 - Europe/Brussels
    Spain › Barcelona

1 PhD position open to work in the Single Cell Genomics and Evolution Lab at CRG, Barcelona.

Our group studies genome regulation from an evolutionary systems perspective. In particular, we are interested in deciphering the evolutionary dynamics of animal cell type programs and in reconstructing the emergence of genome regulatory mechanisms linked to cell type differentiation (from transcription factor binding through chromatin states to the physical architecture of the genome). To this end, we apply advanced single-cell genomics and chromatin experimental methods to molecularly dissect cellular phenotypes 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 analyse these models. Our recent work has provided the first whole-organism cell type atlases in different species and mapped key regulatory genome features underlying these cellular programs (see Sebé-Pedrós 2018 Cell, Sebé-Pedrós 2018 NEE, Sebé-Pedrós 2016 Cell). By sampling additional species and chromatin features at single-cell resolution, we now aim at tracing the evolution of cell types by modelling their underlying gene regulatory networks. 

Applications are accepted exclusively online. The deadline for the receipt of complete applications (including reference letters) is June 23, 2019. Proposals must be written in English. 


The Single-cell genomics and evolution lab has currently 4 members (2 postdocs + 2 PhD students) with multidisciplinary backgrounds, including developmental biology, evolution, computational biology, and genomics. The group is part of the CRG Systems biology program, which is a unique centre of excellence in Europe for quantitative biology. The CRG and the other institutes of the PRBB including EMBL Barcelona provide an ideal ecosystem for this program, being very strong in both genomics and mechanistic molecular biology. The institute receives substantial core funding, has excellent core facilities, and a beautiful location on the seafront in Barcelona. 

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. 

Eligibility criteria

Applicants must have obtained a University Degree and a Masters Degree in a field of life sciences, engineering and/or physics within the European Higher Education System (minimum 300 ECTS) or equivalent by September 2019, and should have substantial research experience.

Applications are accepted exclusively online through our online application system

The deadline for the receipt of complete applications (including reference letters) is the 23rd of June, 2019. 

Additional comments

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. 

Offer Requirements

    ENGLISH: Excellent


We are seeking a highly motivated candidate to join our team to work on an interdisciplinary project (experimental and computational) involving single-cell genomics and chromatin profiling in different systems. The research program for this position focuses on elucidating the origin and early evolution of animal genome regulation and cell type diversity (neurons, muscles, secretory cells, etc). To this end, you will apply advanced functional genomics to characterize cell types and regulatory genome features in diverse non-bilaterian metazoan species (Porifera, Ctenophora, Placozoa and Cnidaria). Specifically, this involves: (i) scRNAseq to define cell type-specific gene expression, (ii) fluorescent in situ hybridization (FISH) to validate scRNAseq-predicted cell type markers, and (iii) bulk ChIP-seq and HiC to map chromatin states and the physical compartmentalization of the genome. You will also participate in the analysis, integration, and interpretation of these omics datasets. 

This is a strongly collaborative project and, as such, it will involve visits to laboratories in different countries, particularly to sample different organisms. Our laboratory has advanced single-cell infrastructure and you will be trained and regularly use a droplet-based single-cell platform (Indrops), as well as our liquid-handling robot. Previous experience in basic molecular biology procedures is an advantage. Creativity and intellectual independence are desirable, as is the ability to work collaboratively.

Work location(s)
1 position(s) available at
Centre de Regulacio Genomica (CRG), Barcelona
Dr. Aiguader, 88

EURAXESS offer ID: 408692


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