Research Program B: Functional and Structural Genomics

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Below you will find DKFZ divisions and research groups of the Research Program Functional and Structural Genomics who are interested in recruiting Postdocs within the 2018 DKFZ Postdoctoral Fellowships Selection.

Please note that this is not an exhaustive list and new groups are continously added.

You may also contact the principal investigator of the DKFZ research group of your choice directly to discuss about current possibilities. More information about hiring labs can be found below and descriptions of DKFZ research programs via the general topic locator.

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Somatic Evolution and Early Detection – Dr. Angela Goncalves

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RESEARCH PROFILE and PROJECT TOPICS

Dr. Angela Goncalves  is looking for computational Postdoctoral Scientists to join her group. This is a great opportunity for a self-motivated, innovative and meticulous candidate with excellent communication skills to work in a dynamic laboratory undertaking cutting edge research.

The aim of the group is to understand how mutant clones arise and expand during the stages preceding the development of malignancy. We combine experimental approaches  such as deep DNA sequencing and single-cell RNA sequencing with bioinformatic analyses and statistical modelling to study these early stages, with a long-term view of improving early detection of cancer.  This role is an exciting opportunity to join a multidisciplinary team to study these problems.

We are looking for candidates for projects applying single sequencing to the problems of identifying the cell type of origin in cancer and the effects of somatic mutation on gene expression. Our group has a particular focus on gynaecological cancers of the lower reproductive tract, but we also consider other cancer entities. The post-holder will have access to unique, functional genomics data sets generated in the group and at DKFZ.

Candidates with a background in biology with an interest in quantitative analysis are encouraged to apply. We also welcome candidates with a background in physics, statistics or computer science with interest in computational biology. Programming skills and ability to work as part of a team are essential.

 

Please visit our website for further information on our research and recent publications.

LINK: https://www.dkfz.de/en/somatische-evolution-frueherkennung

RNA Biology and Cancer – Prof. Dr. Sven Diederichs

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RESEARCH PROFILE

The research in the Division of RNA Biology & Cancer focuses on the role of RNA - protein complexes especially in lung and liver cancer including lncRNAs, RNPs and mutations in the non-coding genome space. Our method spectrum spans molecular and cellular biology, biochemistry and bioinformatics including high throughput approaches in human cell model systems.

 

PROJECT TOPICS

A future postdoc project could investigate the function of RNA-dependent protein complexes in cell cycle progression and in epigenetic mechanisms. We have already identified RNA-dependent protein complexes in a proteome-wide approach by mass spectrometry (unpublished), which this project will build on. The project will aim to elucidate the molecular mechanisms of the RNA-dependent protein complex, identify the responsible RNA(s) and establish their functions at the cellular and molecular level in human cancer cells.
References: Goyal A et al. NAR 2017, Diederichs S et al. EMBO Mol Med 2016, Roth A et al. Nature 2015, Nachmani D et al. Nat Commun 2014, Gutschner T et al. Cancer Res 2013, Diederichs S et al. Cell 2007

 

Please visit our website for further information on our research and recent publications.

LINK: http://www.dkfz.de/en/molekulare-rna-biologie

Prof. Duncan Odom

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RESEARCH PROFILE

Dr Odom’s laboratory studies how genetic sequence information shapes the cell's DNA regulatory landscape and thus the trajectory of cancer genome evolution. To date, their use of interspecies comparisons of matched functional genomic data has resulted in fundamental discoveries, including the extensive and rapid turn-over of tissue-specific transcription factor binding (Schmidt et al Science 2010, Stefflova et al Cell 2013), insulator elements (Schmidt et al Cell 2012), polymerase occupancies (Kutter et al Nature Genetics 2011), and enhancer activities (Villar et al Cell 2015) during organismal evolution, as well as the mechanisms underlying this regulatory plasticity (Wilson et al Science 2008). To demonstrate that genetic sequences were the major determinant of transcription and transcriptional regulation, the Odom lab re-purposed a fascinating aneuploidy mouse model of Down syndrome (previously developed by collaborators) that carries an almost complete copy of human chromosome 21 (Ward et al Molecular Cell 2013). Profiling the functional behaviour of a human chromosome in a mouse nucleus provided an elegant and powerful demonstration that cis-acting sequences have a greater impact than trans influences on transcription factor binding, chromatin state, and gene expression. Recently, his laboratory has begun exploiting single-cell RNA-sequencing and large-scale whole genome sequencing in understanding molecular evolution. Specifically, the Odom lab have recently used single-cell transcriptional analysis to conclusively demonstrate that ageing results in substantial increases in cell-to-cell transcriptional variability (Martinez et al Science 2017), as well as undertaken a large-scale analysis of how genetic and epigenetic differences between alleles can fundamentally alter the location and intensity of mutagenesis during tumour evolution.

 

PROJECT TOPICS

The Odom lab will be re-opening at DKFZ in early 2019. Postdoctoral opportunities will be available to work particularly in the areas of single-cell functional genomics, and the influence of genetic sequence variation on cancer genome evolution. Successful candidates should be highly versant with a diversity of modern genomics methods, and able to perform basic computational biology to facilitate interaction with dedicated computational collaborators. 

 

LINK: not available yet

Chromatin Networks – Prof. Dr. Karsten Rippe

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RESEARCH PROFILE

We investigate how epigenetic signals like histone and DNA methylation are linked to chromatin remodeling and determine cell-type specific gene expression programs via distinct patterns of active or repressive chromatin states. These patterns are 'memorized' through cell division by interconnected networks of factors that set, remove or readout chromatin marks. Any errors that occur in this process can lead to aberrant gene regulation, DNA replication or DNA repair associated with cancer and other diseases. To understand how the underlying chromatin networks operate we integrate deep-sequencing and fluorescence microscopy methods with quantitative biophysical modeling.
In our current work we dissect the interplay of genetic and epigenetic heterogeneity in different leukemias to rationalize why cell subpopulations respond differently (or not at all) to drugs. By applying genome-wide sequencing methods (RNA and accessible chromatin) to single cells we identify differences between individual cells as well as changes of the cell type composition of the whole population upon drug treatment.

 

PROJECT TOPICS

For this work we are seeking a postdoctoral fellow to conduct the bioinformatic analyses of single cell sequencing data (including machine learning approaches) and to subsequently develop models that predict features of the cancer pathophenotype. We are looking for someone with good computational skills and experience in model development who wants to work in an interdisciplinary team. The fellow will have the possibility to further shape the theoretical single cell sequencing work of the division as we will continuously expand these activities.

 

LINK: https://www.dkfz.de/en/chromatin-networks/index.php , external Bioquant website

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