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Job: Two Postdoc Positions in Evolutionary Single-Cell Genomics (experimental and computational)
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gravatar for Wolfgang Huber
16 months ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:

Joint interdisciplinary postdoctoral positions in the research groups of:

  • Detlev Arendt, European Molecular Biology Laboratory (EMBL)
  • Wolfgang Huber, European Molecular Biology Laboratory (EMBL)
  • Henrik Kaessmann, Center for Molecular Biology (ZMBH), Heidelberg University

Cell types are the fundamental units of multicellular life. They make up distinct tissues and organs in vertebrates and invertebrates. However, the cellular origins and diversification events underlying the emergence of new animal tissues during evolution remain poorly understood. The recent revolution in single-cell genomics technologies now allows for detailed investigations of the evolutionary and cellular origins of tissues and organ systems as well as the underlying gene regulatory networks. We are particularly interested in the origin and evolution of the vertebrate/bilaterian nervous system.

 

The host labs:

The three labs combine complementary expertise in cell type and nervous tissue evolution (Arendt group), statistical computing (Huber group), and vertebrate evolutionary (functional) genomics (Kaessmann group). This setting provides a unique framework for carrying out groundbreaking interdisciplinary postdoctoral projects in evolutionary single-cell biology.

 

Projects:

We call for proposals of specific biological projects, to be developed by you with feedback from the three mentors, within the overall frame outlined above. We envisage that one of the projects will focus on the development and application of single-cell sequencing protocols for profiling transcriptomes and epigenomes across tissues and developmental stages from multiple, carefully selected species. This project will also include follow-up experiments (e.g., FISH to assess the distribution and abundance of cell types using markers predicted from whole transcriptome analyses). The other project will focus on the development of statistical and bioinformatics approaches for detailed analyses and understanding of single-cell sequencing data in the evolutionary context. Particular challenges include spatio-temporal registration and modelling of cells and the identification of functional homologies and divergences of cells and their gene regulatory programs. We expect both projects to take a highly collaborative approach between each other and with the other members of the host labs. We also expect candidates to acquire interdisciplinary skills in the course of the project (i.e., a wet lab postdoc will learn and perform bioinformatics approaches; a bioinformatics postdoc will perform targeted experiments).

 

The candidates:

The ideal experimentally oriented candidate has experience and strong experimental skills in molecular and cell biology. Expertise in developmental biology, the biology of specific organs (e.g., the brain), and/or genome-scale work is a plus. For computational candidates, we expect outstanding quantitative and analytical skills. We are looking for candidates with PhD level education in molecular biology, bioinformatics, statistics, mathematics or a related field, who aim to make an impact on our understanding of fundamental aspects of cellular evolutionary biology. Experience in the analysis of high-throughput sequencing data and/or the development and optimization of statistical approaches is desired. Experience in the analysis of single-cell genomic or transcriptomic data is a plus.

Both candidates should ideally be driven by a passion for evolutionary biology, and both positions require the ability to independently take responsibility for their projects, as well as strong teamwork and communication skills, problem-solving abilities, reliability, attention to detail and effective time management.

The selected candidates will be encouraged to apply for independent funding, including the EMBL Interdisciplinary Postdocs (EIPOD) fellowship program (http://www.embl.de/training/postdocs/08-eipod).

 

Research environment and location:

The language of our institutes (EMBL and ZMBH) is English and host scientists from around the world. The institutes are located in Heidelberg, a picturesque cosmopolitan city that offers a very stimulating, diverse and collaborative research environment also thanks to nearby cutting-edge institutions, such as the German Cancer Research Center (DKFZ) and the Center for Organismal Studies (COS).

For more information, please refer to our websites at www.embl.de/research/units/dev_biology/arendt/ and www.huber.embl.de and http://www.zmbh.uni-heidelberg.de/Kaessmann/

Please submit a CV, statement of research interest, references, a list of publications or other research output to Detlev Arendt (arendt@embl.de), Wolfgang Huber (whuber@embl.de), and Henrik Kaessmann (h.kaessmann@zmbh.uni-heidelberg.de).

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Selected recent publications from our labs:

Ignatiadis N, Klaus B, Zaugg JB, Huber W. (2016) Data-driven hypothesis weighting increases detection power in genome-scale multiple testing. Nat. Meth. 13: 577-580.

Brennecke P, Reyes A, Pinto S, Rattay K, Nguyen M, Küchler R, Huber W, Kyewski B, Steinmetz LM. (2015) Single-cell transcriptome analysis reveals coordinated ectopic gene-expression patterns in medullary thymic epithelial cells. Nat. Immunol. 16: 933-41.

Huber W, Carey VJ, Gentleman R, Morgan M, et al. Orchestrating high-throughput genomic analysis with Bioconductor  Nat. Meth., 12:115-121, 2015.

Lauri A, Brunet T, Handberg-Thorsager M, Fischer AH, Simakov O, Steinmetz PR,  Tomer R, Keller PJ, Arendt D. (2014) Development of the annelid axochord: insights into  notochord evolution. Science 345: 1365-8.

Necsulea, A., Soumillon, M., Warnefors, M., Liechti, A., Daish, T., Zeller, U., Baker, J.C., Grutzner, F., and Kaessmann, H. (2014) The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature 505: 635-640.

Necsulea A and Kaessmann H (2014) Evolutionary dynamics of coding and noncoding transcriptomes. Nat. Rev. Genet. 5: 734-48.

Achim K, Pettit J-B, Saraiva LR, Gavriouchkina D, Larsson T, Arendt D*, Marioni, JC* (2015) Single-cell expression profiling and spatial mapping into tissue of origin. Nat. Biotechnol. 33(5):503-9

Brawand D, Soumillon M, Necsulea A, Julien P, Csardi G, Harrigan P, Weier M, Liechti A, Aximu-Petri A, Kircher M, Albert FW, Zeller U, Khaitovich P, Grutzner F, Bergmann S, Nielsen R, Paabo S, and Kaessmann H (2011) The evolution of gene expression levels in mammalian organs. Nature 478: 343-348.

Tomer R, Denes AS, Tessmar-Raible K, Arendt D (2010) Profiling by image registration reveals common origin of annelid mushroom bodies and vertebrate pallium. Cell 142: 800-9.


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