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Humboldt-Universität zu Berlin - IRI Life Sciences

Research portraits of the IRI Core Groups

 

Nils Bluethgen.jpg

Markus Landthaler.jpg

Leonie Ringrose.jpg

Prof. Dr. Nils Blüthgen

Computational Modelling
in Medicine

Prof. Dr. Markus Landthaler

RNA Biology

Prof. Dr. Leonie Ringrose

Quantitative Biology of 
the Eukaryotic Cell

 

Benedikt Beckmann.jpg

David Garfield.jpg

Simone Reber.jpg

Dr. Benedikt Beckmann

Molecular Infection Biology

Dr. David Garfield

Evolutionary Biology

Dr. Simone Reber

Quantitative Biology

 


 

Computational Modelling in Medicine

Blüthgen and his group use methods from mathematical modeling, bioinformatics and quantitative cell biology to investigate how structure and dynamics of networks relate to their biological function. Specifically, the main research aim of the group is to understand how oncogenic signaling pathways and their downstream gene regulatory networks mediate their oncogenic potential, how drugs can effectively modulate these networks and how resistance against targeted kinase inhibitors arises. Other research interests include dynamics of differentiation processes, how promoters integrate different signals, and how transcriptional and post-transcriptional regulation cooperate to generate specificity and reliability in gene expression.  
 


Nils Bluethgen.jpgProf. Dr. Nils Blüthgen mailicon

Charité - Universitätsmedizin Berlin
Institute for Pathology
IRI Life Sciences
Computational Modeling in Medicine                                    

Phone: +49 (0)30 2093-8924

Website

 


 

RNA Biology

The main interest of the Landthaler lab is the understanding of post-transcriptional regulatory networks that control gene expression. Post-transcriptional regulation is highly versatile and adaptable in exploiting cellular time and space. microRNAs and RNA-binding proteins play a key role in the regulation of spatial and temporal changes in protein synthesis through control of mRNA transport, storage and translation. Deregulation and failed coordination of these mechanisms contribute to pathophysiologicial development and conditions. 

 


Markus Landthaler.jpgProf. Dr. Markus Landthaler mailicon

Berlin Institute for Medical Systems Biology (BIMSB) at the Max-Delbrück-Center for Molecular Medicine (MDC) &
Humboldt-Universität zu Berlin

Department for Biology
RNA biology and posttransciptional regulation                                   

Phone: +49 (0)30 9406-3026

Website

 


 

Quantitative Biology of the Eukaryotic Cell

The main research focus of Leonie Ringrose and her group is on epigenetic regulation by the Polycomb and Trithorax group proteins. The highly conserved Polycomb (PcG) and Trithorax (TrxG) groups of proteins work in concert with enhancers to ensure genome-wide transcriptional fidelity. The PcG and TrxG work agonistically on several hundred developmentally important target genes, to maintain repressed (PcG) or active (TrxG) transcription states. Misexpression or loss of these essential regulatory proteins can lead to developmental defects and cancer.
Intriguingly this epigenetic regulatory system has bistable properties. "On" or  "off" states are inherently stable whereas intermediate states are less stable. However, despite its digital nature, the PcG/ TrxG system can effect a rich repertoire of outputs including thresholding, stabilisation, and epigenetic memory of transcriptional states. The quantitative readout of the system depends on parameters such as enhancer input, genomic context and developmental signaling. Furthermore the system can be fine-tuned by non-coding RNAs. Understanding the relationship between these input parameters and the transcriptional output of the system requires quantitative experimental analysis in combination with a robust theoretical framework.
We use a combination of quantitative live imaging, mathematical modelling, computational approaches and molecular and developmental biology to understand the interaction of the Polycomb and Trithorax proteins with their chromatin targets in vivo.

Video: Epigenetics - Myths, Mysteries and Molecules

 


Leonie Ringrose.jpgProf. Dr. Leonie Ringrose mailicon

Humboldt-Universität zu Berlin
IRI Life Sciences
Department for Biology
Quantitative Biology of the Eukaryotic Cell                                   

Phone: +49 (0)30 2093-49772

Website

 


 

Molecular Infection Biology

The independent junior group of Benedikt Beckmann group works in the field of molecular infection biology to understand the interaction of pathogenic bacteria and their host cells. The research focus is on RNA-protein interactions during infection; in particular, the group wants to identify and characterize bacterial non-coding RNAs and RNA-binding proteins that modify post-transcriptional regulation of gene expression of the host cell and thus contribute to the pathogenicity of the pathogen. Applying state-of-the-art systems biology approaches such as mRNA interactome capture, Beckman´s group will analyze how infection with e.g. Salmonella Typhimurium impacts (m)RNP composition in macrophages of human and mouse hosts as well as search for bacterial RNA-binding proteins (RBPs) forming cross-species RNA-protein interactions.

 


Benedikt Beckmann.jpgDr. Benedikt Beckmann mailicon

Humboldt-Universität zu Berlin
IRI Life Sciences
Department for Biology
Molecular Infection Biology                                   

Phone: +49 (0)30 2093-47910

Website

 


 

Evolutionary Biology

A fundamental tenet of Darwinian evolution is that differences between species arise first as variation within species. The work of the independent junior group of David Garfield hems closely to this principle by using population genetics and comparisons between closely related species to understand the mechanisms by which natural selection shapes embryonic development and, ultimately, gives rise to the diversity of animal forms we see all around us. The primary focus is on the evolutionary forces that shape gene expression profiles during development with particular interests in understanding the impacts of new mutations on phenotypes and how interactions between genes in development influences the visibility of mutations to natural selection. To address these questions, the Garfield lab make use of a variety of genomics tools (e.g ChIP-Seq, ATAC-Seq) and collaborate closely with other Berlin-based groups to bring cutting-edge tools normally associated with biomedical research to bear on problems in Evolutionary Biology. As part of their research mission, they also help to develop tools from Evolutionary Biology, in particular population genetics, to help biomedical researchers better understand and identify mutations associated with human disease.

 


David Garfield.jpgDr. David Garfield mailicon

Humboldt-Universität zu Berlin
IRI Life Sciences
Department for Biology
Evolutionary Biology                                   

Phone: +49 (0)30 2093-92382

Website

 


 

Quantitative Biology

The goal of the independent junior group headed by Simone Reber is to elucidate the biochemical and biophysical principles that underlie the self-organization and scaling of subcellular organelles. In particular, they are interested in how the mitotic spindle controls its defined length and shape. One reason why this question is so hard to answer is that the size of the spindle is generally not simply set by a “ruler” but is an emergent property of molecular collectives. “Emergence” describes the way complex properties and patterns of a system arise by numerous elements, which interact by relatively simple rules. Examples include the generation of an infinite variety of six-sided snowflakes from frozen water in snow. Similarly, “flocking”, the coordinated motion of animals observed in bird flocks, fish schools, or insect swarms, is considered an emergent behaviour. In physics emergent behaviours are commonly studied to describe complex systems. Physics thus provides a framework for relating the microscopic properties of individual molecules to the macroscopic properties of materials. This exactly is the key challenge in modern cell biology, bridging the gap between individual molecules and their collective behaviour. Therefore, the Reber lab combines cell biological experiments, single molecule studies, and mathematical modelling to dissect the principles that underlay cellular scaling.

 


Simone Reber.jpgDr. Simone Reber mailicon

Humboldt-Universität zu Berlin
IRI Life Sciences
Department for Biology
Quantitative Biology                                   

Phone: +49 (0)30 2093-47911

Website