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Humboldt-Universität zu Berlin - IRI Life Sciences

Current Projects
  • HantaHunt: Structure and function analyses of the Hantavirus envelope glycoproteins and their role in virus assembly, virus entry and immune recognition as novel targets for antiviral treatment
  • IRTG 2290: Crossing Boundaries: Molecular Interaction in Malaria
  • How to Shape Living Structures — Factors Controlling Spindle Geometry
  • IRTG 2403: Dissecting and Reengineering the Regulatory Genome
  • ITN PEP-Net: Predicitive Epignetics
  • Modelling Enzymes 100 years after Michaelis-Menten
  • ERC Starting Grant: Constraint, adaptation, and heterogeneity: genomic and single-cell approaches to understanding the evolution of developmental gene regulatory networks
  • RTG 2424: Computational Methods in Oncolocy - Towards Personalized Medicine in Cancer Research


Current Projects

HU-PU Profile Partnership: How to Shape Living Structures — Factors Controlling Spindle Geometry

Funding: HU Berlin / Princeton

Period: 2017 - 2019

Project partner: Simone Reber (IRI Life Sciences), Sabine Petry (PU)


simone princtonThe goal of this research project is to understand the way in which cells engineer larger scale structures, in particular the mitotic spindle. In particular, we wish to understand (1) how the biochemical heterogeneity of tubulin effects spindle organization, how the correct (2) number and (3) length of microtubules is regulated to build a spindle of the correct size. An important objective of our proposal continues to be graduate and postgraduate training including lab exchanges. Taken together, the proposed work will provide important insights into the physical principles that underlie the organization of the mitotic spindle as a molecular machine, which is likely to have important implications for its function in cell proliferation and molecular origins of diseases.


IRTG 2290 - Crossing Boundaries: Molecular Interaction in Malaria

Homepage: www.allianceberlincanberra.org

Funding: DFG

Period: 2017 - 2022

Project partner: Kai Matuschewski (HU, spokesperson), Edda Klipp (HU), Christian Schmitz-Linneweber (HU), Simone Reber (IRI Life Sciences), Benedikt Beckmann (IRI Life Sciences), Nishith Gupta (HU), Alyssa Ingmundsson (HU), Leif-Erik Sander (Charité), Frank Mockenhaupt (Charité), Frank Seeber (RKI) and 8 PIs at the Australian National University (ANU)


LogoThe Berlin-Canberra alliance addresses fundamental issues in malaria through an International Research Training Program (IRTG 2290). Molecular insights into Plasmodium infections can generate novel evidence-based strategies to develop curative and prophylactic drugs and immunization strategies that elicit lasting protection against the disease.



HantaHunt: Structure and function analyses of the Hantavirus envelope glycoproteins and their role in virus assembly, virus entry and immune recognition as novel targets for antiviral treatment

Funding: BMBF

Period: 2016 - 2019

Project partner: Andreas Herrmann (HU, Coordinator), Detlev Krüger (Charité), Yechiel Shai (The Weizmann Institute of Science), Felix Rey (Institut Pasteur/ Structural Virology Unit) 


HantaHuntHantaviruses (HV), which belong to the Bunyaviridae family of RNA viruses, are emerging pathogens that cause life-threatening human zoonoses with case fatalities reaching 50% and is ranked among the top five reportable virus infections by the Robert Koch Institute in Berlin. In spite of its medical importance, our knowledge of HV biology is extremely fragmentary. This project focuses on HV envelope glycoproteins Gn and Gc, which form a heterodimer exposed at the virus surface, carrying the main viral antigenic determinants. Both are responsible for entry into host cells by recognizing a receptor at the plasma membrane and by catalyzing membrane fusion in the endosomes after receptor-mediated endocytosis. The heterodimer also plays a crucial role in the morphogenesis of newly formed HV via interaction of the cytosolic domains with the viral genomic RNA and by driving virion assembly and budding. This project is tackled by a consortium of four complementary groups, combining experts in molecular virology, cell and structural biology, biochemistry and biophysics to provide an in-depth analysis of the glycoproteins and their crucial interactions with other cellular and viral factors including the segmented HV RNA genome. In this context a multiude of state-of-the-art methods and techniques will be established and utilized. Our results will thereby characterize important potential interactions to be targeted for therapeutic intervention, e.g. the receptor site and the fusogenic conformational change of the Gn/Gc complex.


IRTG 2403: Dissecting and Reengineering the Regulatory Genome

Homepage: www.regulatory-genome.org

Funding: DFG

Period: 2019 - 2023

Project partner: Uwe Ohler (HU/MDC, spokesperson), David Garfield (IRI Life Sciences), Kerstin Kaufmann (HU), Ana Pombo (HU/MDC), Nikolaus Rajewsky (MDC), Robert Zinzen (MDC), Martin Vingron (MPIMG), Edda Schulz (MPIMG), Andreas Mayer (MPIMG), Stefan Mundlos (Charité), Martin Kircher (BIH) and 11 PIs at Duke University.


Logo transparent neuIn an alliance between Berlin institutions and Duke University, the DFG-funded international training research group aims to teach the next generation of researchers in quantitative understanding of genome function and gene regulation in the context of biological systems. Combining experimental and computational approaches, the IRTG provides opportunities for doctoral students to work in three complementary areas: (1) high-throughput genomic and editing, (2) computational biology and machine learning, and (3) developmental systems biology. Doctoral researchers obtain a significant amount of their training at the partner institution, thereby benefitting from the synergy and the expertise at both sites. They are co-advised by computational and biological experts from both sides of the Atlantic throughout their training.


ITN Pep-Net: Predicitive Epignetics

Funding: EU Horizon 2020

Period: 2019 - 2024

Project partner: Leonie Ringrose (IRI Life Sciences, coordinator), Marc Rehmsmeier (HU), Ana Pombo (MDC), Edda Schulz (MPIMG) and 12 international academic partners and companies

PepNet image


Epigenetic mechanisms of gene regulation are profoundly implicated in human health and disease. However, we are still far from a complete mechanistic understanding of many epigenetic processes. Without an understanding of mechanisms we cannot fully understand function in healthy cells, in disease states, and the effects and side effects of therapeutic interventions. Research in epigenetics has typically been based on experiments and not on theory. Although this has delivered large amounts of information, information alone is not sufficient. Further progress urgently needs a paradigm shift in the way in which we study epigenetics, namely: epigenetics needs mathematics. Mathematical models are essential to capture and understand the complex, dynamic and stochastic nature of epigenetic regulation. Models are immensely powerful because they identify unifying concepts and enable predictions of system properties. One of the greatest challenges to uniting biology and mathematics is the barrier between disciplines, because education in each field has traditionally been mono-disciplinary. The PEP-NET ITN will overcome these barriers by uniting 16 outstanding European academic laboratories and companies who have pioneered the successful combination of theoretical and experimental epigenetics. PEP-NET will train a new cohort of European researchers to combine quantitative experiments with predictive theoretical models, and to apply this knowledge to basic and applied questions of epigenetic function.


HU-PU Profile Partnership: Modelling Enzymes 100 years after Michaelis-Menten

Funding: HU Berlin / Princeton

Period: 2018 - 2020

Project partner: Nils Blüthgen (IRI Life Sciences), Stanislav Shvartzman (PU)


ERKactivationNetworkMathematical models played a key role in the development of Biochemistry, starting from Michaelis and Menten, who established a mathematical language for describing the rates of single enzymatic reactions. Our project is designed to continue this great tradition, focusing on enzyme networks. We will combine biochemistry and systems biology to develop computational models of a network that is critically involved in cell-cell communication. The enzymatic reactions comprising this network are commonly deregulated in human diseases, making it an important drug target. The project will study this network at multiple levels of complexity, from single reactions to cells and tissues, building on the highly complementary expertise of our team members. 


evolSingleCellGRN - Constraint, adaptation, and heterogeneity: genomic and single-cell approaches to understanding the evolution of developmental gene regulatory networks

Funding: ERC Starting Grants

Period: 2019 - 2024

Project leader: David Garfield (IRI Life Sciences)


UrchinArt12Cell types in development arise from precise patterns of gene expression driven by differential usage of DNA regulatory elements. Mutations affecting these elements, or proteins binding them, are major contributors to disease and underlie the evolution of new morphologies. To better understand these elements and how they evolve, that: A) identify tissue-specific regulatory elements and expression profiles by interrogating individual cells, B) allow for a precise read-out of developmental responses to mutation and perturbation, including cell-fate re-specification, C) lead to the development of a regulatory-information based concept of homology that will be used to understand developmental evolution.


RTG 2424: Computational Methods in Oncolocy - Towards Personalized Medicine in Cancer Research

Homepage: www.comp-cancer.de 

Funding: DFG

Period: 2019 - 2023

Project partner: Nils Blüthgen (IRI Life Sciences, spokesperson), Hans-Peter Herzel (Charité), Christine Sers (Charité), Frederick Klauschen (Charité), Clemens Schmitt (Charité), Claudia Baldus (Charité), Ulf Leser (HU), Leonie Ringrose (IRI Life Sciences), Roland Schwarz (MDC), Martin Vingron (MPIMG)


CompCancerLogoAs part of this research programme, a new generation of researchers will be developing computer-based tools for use in cancer research. Until a few years ago, the analysis of tumor samples was based on visible tissue characteristics. Today, state-of-the-art high-throughput technologies enable scientists to obtain the detailed molecular profile of a specific cancer. These technologies produce vast volumes of data. Collating and interpreting these complex data sets represents a major challenge — one which requires innovative, computer-based technologies and mathematical models. Under the auspices of the new Research Training Group, a large number of doctoral students will receive support from interdisciplinary teams made up of experts from computer science, data modelling, research and genetics. As part of their doctoral projects, they will be involved in the research and development of new computer-based technologies which are to address important questions from the field of cancer research.