Projects of 2021

Statistical methods for 3D spatial reconstruction of omic profiles

Omics data have opened new frontiers in the molecular description and understanding of how cells work. Nowadays, it is possible to probe gene activity, DNA accessibility and other molecular phenotypes with a single-cell resolution. However, spatial information...Read more

Keywords: spatial omics, mouse tissues, compotational models, developmentof statistical methods, Bayesian models

Supervisor: Dr. Antonio Scialdone
Group: Physics and data-based modelling of cellular decision making
Institute: Institute of Epigenetics and Stem Cells, Helmholtz Center Munich

Collaborating supervisor: Dr. Catalina Vallejos
Group: Biomedical Data Science
Institute: Institute of genetics and cancer MRC Human Genetics Unit, University of Edinburgh

Using epigenetics to discover mechanisms behind drug tolerance in a fungal pathogen

Fungal infections are often caused by yeast species called Candida. Around 99% of isolates of the most common, Candida albicans, are susceptible to the standard therapy fluconazole, but some infections still do not heal. Read more

Keywords: Candida albicans, Epigenetic drug resistance, quantitative time-lapse microscopy, mathematical modeling, transporter proteins

Supervisor: Dr. Carsten Marr
Group: Quantitative Single Cell Dynamics
Institute: Institute for Computational Biology , Helmholtz Center Munich

Collaborating supervisor: Dr. Peter Swain
Group: Swain Lab
Institute: Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh

3D genome organization during the first cell fate decision in mouse embryos

The project aims to address the dynamics and functional role of 3D genome interactions of regulatory regions, in cell fate decision in the early mouse embryo. In mammals, the first cell decision gives rise to the segregation of the pluripotent compartment – the inner cell mass – and the trophectoderm and occurs prior to embryo implantation. Read more

Keywords: 3D Genome interactions, mouse, establishment and maintenance of pluripontency, 3D imaging, single cell dissection, 3D-FISH, ATACseq RNAseq

Supervisor: Prof. Dr. Maria Elena Torres-Padilla
Group: Epigenetics and cell-fate in early mammalian development
Institute: Institute of Epigenetics and Stem Cells, Helmholtz Center Munich


Collaborating supervisor: Prof. Ian Chambers
Group: Embryonic stem cell biology
Institute: Institute for regeneration and reparair Centre for Regenerative Medicine, University of Edinburgh

Developing targeted epigenetic strategies for Ribosomopathies

Ribosomopathies are a group of congenital human diseases, which are caused by attenuated generation or activity of ribosomes. Patients’ cells possess reduced overall protein translation rates, ultimately resulting in complex pathologies. Read more

Keywords: CRISPR, epigenome editing (TAPIR), ribosomopathy, patient primary cells, iPSC

Supervisor: Dr. Stefan Stricker
Group: Epigenetic Engineering
institute: Institute of Stem Cell Research, Helmholtz Center Munich

collaborating supervisor: Prof. Dr. David Tollervey
Group: Tollervey lab
institute: Wellcome Trust Centre for Cell Biology, University of Edinburgh

RNA modifying enzymes in development and disease

Recent breakthroughs have transformed our understanding of the epitranscriptome and allow us now to interrogate modifications of RNA at an unprecedented scale. The aim of the project is i) to identify novel methyltransferases, ii) to determine their function and iii) of the respective modifications by applying a combination of in vitro and in vivo assays... Read more

Keywords: epitranscriptomics, novel methyltransferases, Crispr/Cas9/Cas13, RNA modifying pathways , therapy targets

Main supervisor: Prof. Dr. Robert Schneider
Group: Chromatin Dynamics and Epigenetics
institute: Institute of Functional Epigenetics, Helmholtz Center Munich

collaborating Supervisor: Prof. Donal O’Carroll 
Group: RNA function in germ and stem cell biology
institute: Center for regeneration and repair Centre for Regenerative Medicine, University of Edinburgh

Redox-regulation of epigenetic mechanisms in response to future climate conditions

Global temperatures and harmful atmospheric gases will continue to rise in the decades to come and adversely affect plant physiology, e.g. photosythesis. The photosythesis can be termed as the most important physiological process as it enables the conversion of light energy of the sun to chemical energy in the form of carbohydrates, the basis for life on earth. To cope with the stresful environmental conditions and to maintain effective photosynthesis... Read more

keywords: Climate change, environmental stress, A. thaliana, redox-signaling, redox regulated chromatin modifier, photosynthesis

Main supervisor: Dr. Christian Lindermayr
Group: Redox-Signaling and Chromatin Modulation
institute: Institute of Lung Health and Immunity

Collaborating partners at the Helmholtz Zentrum München
Prof. Dr. Jörg-Peter Schnitzler
Group: Research Unit Environmental Simulation
Institute: Institute of Biochemical Plant Pathology

Dr. Manuel Spannagl & Prof. Klaus Mayer
Group: Research Unit Plant Genome and Systems Biology

Collaborating partners at the University of Edinburgh
Prof. Steven Spoel
Group: Gene Expression in Response to Changing Environments
Institute: Insitute of Molecular Plant Science

Prof. Gary Loake
Group: Redox Signaling in Plant Immune Response
Institute: Insitute of Molecular Plant Science

Single-molecule analysis of replication origin chromatin

DNA replication is a fundamental process initiated at specialized regions named origins of replication. In yeast Saccharomyces cerevisiae origins, short (~200bp) autonomous replicating sequence (ARS) are present containing a conserved 11-bp AT-rich sequence named ARS consensus sequence (ACS), which serves as the binding site of the origin recognition complex (ORC). Read more

Keywords: DNA replication, origen of replication, yeast, electron microscopy, DNA methylation footprinting

Main supervisor: Dr. Stephan Hamperl
Group: Chromosome dynamics and genome stability
Institute: Institute of Epigenetics and Stem Cells, Helmholtz Center Munich

Collaborating supervisor: Prof. Nick Gilbert
Group: Chromatin Structure and Genome Integrity
Institute: Institute of Genetics and Cancer, MRC Human Genetics Unit, , University of Edinburgh


Paternal programming of offspring immune development

The project aims at understanding the role of paternal factors at conception on the ontogeny of the offspring immune system. Adult immune-cell compartments like mast cells and macrophages are highly heterogeneous, partly because fetal-derived and bone marrow-derived immune cells co-exist in adult tissues. Read more

Keywords: glucocorticoid signaling, immune development, single-cell (epi)genomic analyses, paternal factors, ontogeny and function of offspring immune system

Main Supervisor: Dr. Raffaele Teperino
Group: Environmental Epigenetics
Insitute: Institute of Experimental Genetics, Helmholtz Center Munich

Collaborating supervisor: Dr. Rebecca Gentek
Group: Gentek Lab: Immune Ontogeny
Institute: Edinburgh Medical School: Clinical Sciences, Centre for Inflamation Research, University of Edinburgh