© Christin Stottmeier, MDC
Medical Systems Biology
The Berlin Institute for Medical Systems Biology (BIMSB)
BIMSB News
Recent News
October 2018
11th Berlin Summer Meeting
We celebrated the 11th Berlin Summer Meeting - Grand BIMSB Opening Symposium with the three days filled with exciting science, covering topics that reflect our research at the Berlin Institute for Medical Systems Biology. Here are some snapshots!
Full article: Breaking down borders
May 2018
Ana Pombo elected EMBO Member.
Time to celebrate in the Pombo Lab! EMBO just elected 62 outstanding life scientists to its membership, joining a group of more than 1800 of the best researchers in Europe and around the world. The members are actively involved in the execution of the organization’s initiatives by serving on EMBO Council, Committees and Editorial Boards, by evaluating applications for EMBO funding, by mentoring young scientists and by providing suggestions and feedback on activities.
April 2018
Stephan Preibisch receives Human Frontier Science Program (HFSP) Grant.
The Human Frontier Science Program (HFSP) has provided 900,000 US dollars in funding for a project that uses machine learning, high-throughput methods, and automated image recognition to shed light on the function of enhancer sequences. The project is being led by Professor Nicolas Gompel of Ludwig-Maximilians-Universität München (LMU) and involves the collaboration of Dr. Stephan Preibisch from the Berlin Institute of Medical Systems Biology (BIMSB) at the Max Delbrück Center for Molecular Medicine (MDC), and Prof. Remo Rohs from the University of Southern California (USC) in Los Angeles.
The researchers are working to decipher the code for the basic functions of enhancer DNA regions so that they can eventually “program” their own artificial enhancers. The researchers are focusing on the so-called spot enhancer, which acts on the yellow gene and influences pigmentation patterns on the wings of fruit flies. As part of the project, BIMSB researcher Stephan Preibisch will place thousands of wings of genetically modified Drosophila flies under the microscope and produce automated scans, which he will then analyze and classify with the help of machine learning. These flies come from the laboratory of evolutionary biologist Nicolas Gompel, who breeds the insects while systematically changing the DNA sequence of the spot enhancer. The generated data will then be fed into Remo Rohs’ mathematical model, which uses bioinformatic methods to reveal how DNA and proteins interact – taking into account the three-dimensional structure of DNA – to influence gene activity. Together, the team is developing artificial intelligence that can connect differences in wing pigmentation to the underlying systematic changes made to the DNA and thus make predictions about the properties of synthetic genetic enhancers.
March 2018
2018 MDC "BOOST" idea competition goes to Christin Sünkel and Nikolaos Karaiskos
Christin Sünkel and Nikolaos Karaiskos are this year's winners of "BOOST" - the MDC idea competition for innovative ideas for commercialization. The award provides the duo with coaching and funding for developing a new single-cell RNA sequencing technique to facilitate tumor biology research.
The aim of BOOST is to encourage development of innovative ideas and early-stage projects that still require a proof of the idea or verification of their feasibility. The competition focuses primarily on the idea’s originality and its competitive advantage. Participation gives you early and vital feedback, access to coaching and financial support for the validation of your idea.Winners receive coaching and funding up to 40.000 € for their project.
March 2018
CORBEL launches 2nd Open Call for Research Projects
BIMSB is excited to be participating in the CORBEL 2nd Open Call for research projects. CORBEL is looking for innovative research projects at the interface between different biomedical and life science fields requiring service provision from multiple research infrastructures.
Are you working on a complex research project in need of multiple, different technologies? Would you benefit from access to state-of-the-art research infrastructures and services that are not available in your current research environment? Would integrated access to multiple research infrastructures take your research project to the next level?
If the answer is YES, participation in the CORBEL Open Call can help to boost your results!
For the second time, the CORBEL partners launched an Open Call and thereby offer to all academic and industrial scientists in Europe the chance to accelerate their research project. Through defined pipelines, called Access Tracks, high-end technologies and services offered by more than 20 CORBEL partner institutes from 10 participating research infrastructures, including the Bioinformatics platform of the BIMSB, will be made accessible to interested scientists.
Successful applicants will have the unique opportunity to access multiple research infrastructures with just one application. Available services are grouped into five different Access Tracks:
(1) Genotype-to-phenotype analysis, (2) Predictive systems pharmacology for safer drugs and chemical products, (3) Structure-function analysis of large protein complexes, (4) Marine metazoan developmental models (5) Complex multimodal biomarker profiling
Importantly, the grouping of services into Access Tracks is flexible, and also alternative combinations can be requested! Costs for travel to partner sites will be reimbursed by CORBEL and access to service providers will be granted without access fee (extra costs for consumables may apply). Projects will be supported at every stage, with CORBEL project managers helping scientists to navigate between different service providers and exploit the full potential of the offers available.
Proposal submission for the 2nd CORBEL Open Call for research projects is now open. For more information, please visit the project website (http://www.corbel-project.eu/open-call.html).
February 2018
LifeTime, a visionary proposal for an EU Flagship
Nikolaus Rajewsky (BIMSB) and Geneviève Almouzni (Institut Curie, Paris) jointly coordinate LifeTime, a proposal for a EU flagship with the aim to follow and ultimately predict the course of diseases with the help of single cell technologies.
For more information see:
www.mdc-berlin.de/news/press/lifetime-visionary-proposal-eu-flagship
November 2017
Christoph Lippert heads new Statistical Genomics lab
After spending five exciting years on America’s West Coast, Christoph Lippert has returned to Germany to lead the Statistical Genomics lab, a junior research group of the BIMSB in November 2017.
Lippert’s main research interest is genome-wide association studies of populations. He is looking for answers to questions like “Which genes make us different from each other?” and “What affect do these genetic differences have on our organism, on physical characteristics such as our height, or on our individual risk factors for diseases?”
An exact understanding of such differences will provide the basis for developing more and more individualized diagnostic techniques and therapies. But this requires the collection and analysis of huge amounts of data and the calculation of probabilities. Bioinformaticians build the complex software and algorithms needed for such tasks.
Lippert studied bioinformatics at the University of Tübingen, where he earned his PhD with work on mixed models for genome-wide association studies. Other stops in his scientific career include Microsoft Research and Human Longevity, Inc. (HLI) in California. HLI is a start-up founded by J. Craig Venter that aims to prevent disease through a comprehensive analysis of all health data.
At the MDC, Lippert’s lab is focusing on developing techniques that link genomic data to various measurements from wearable sensors as well from imaging methods and high-throughput DNA sequencing.
November 2017
A red thread in motor neuron disorders - Under a new grant from the EU, Marina Chekuleava will lead a multinational consortium to find common mechanisms in diverse motor neuron diseases
Most of the things we enjoy – from things as simple as reading a text to the highly skilled motions of athletes – depend on motor neurons that connect the brain to skeletal muscles throughout the body. A at some point in our lives, about one in every 300 of us will experience a degeneration of these nerves, with consequences including progressive paralysis and severe disabilities. BIMSB group leader Marina Chekulaeva says that many forms of motor neuron disorders, or MNDs, stem from a common set of cellular defects. The EU has just awarded her a major grant to coordinate an international effort that will shed more light on these shared mechanisms.
“The pathogenic processes that lead to MNDs often arise from abnormalities in the way cells splice RNA molecules to create different proteins from the same gene, or transport them to their cellular destinations,” Chekulaeva says. “Other problems include stress on structures called the endoplasmic reticulum, which processes a huge number of proteins, and dysfunctions in energy-producing organelles called mitochondria.”
Clarifying how these problems produce MNDs by disrupting networks of cellular processes will require diverse expertise. Drawing it together is a central goal of the EU’s Joint Program on Neurodegenerative Disease, the largest global research initiative devoted to these conditions. The grant will provide ~915.000 Euro for a period of 3 years to link Chekulaeva’s lab to important international partners. She will coordinate the project, combining her group’s work on RNA biology with computational expertise from the Weizmann Institute of Science in Israel, studies of neurodegenerative diseases using fly and mouse models at Radboud University in the Netherlands, and clinical research at the ALS Clinical Research Center in Italy.
September 2017
BIMSB welcomes genome architect Darío Lupíañez
At the beginning of September, Darío G. Lupíañez joined BIMSB. He is now leading the new junior group “Epigenetics and Sex Development”.
Lupíañez received his PhD from the University of Granada (Spain), where he worked with Dr. Rafael Jimenez on sex determination and gonadal development in the Iberian mole (Talpa occidentalis). From 2012 to 2017, he worked as a postdoc in the lab of Prof. Stefan Mundlos at the Max Planck Institute for Molecular Genetics (Berlin), focusing on chromatin architecture and disease.
The long-term research goal of Lupíañez’s lab at the MDC is understanding gene regulation in the context of a three-dimensional genome. He aims to decipher how cellular fate is determined and maintained in vivo and how this information is encoded in the mammalian genome by using the bipotential gonad as a model. His lab combines various new methods and technologies to detect regulatory elements and to define and perturb regulatory landscapes in vivo to assess their functionality.
April 2017
Markus Landthaler promoted to Professor
With April 1st, systems biologist Markus Landthaler of the MDC has been appointed Professor for “RNA Systems Biology” at the Humboldt-Universität zu Berlin.
Markus Landthaler is a group leader at the Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC). He wants to understand how proteins bind to and modulate the function of the messenger RNA (mRNA) and influence the transmission of genetic information. His new chair “RNA Biology” at the Humboldt-Universität zu Berlin (HU) was appointed within the framework of the Integrative Research Institute of Life Sciences (IRI Life Sciences). IRI Life Sciences is a collaboration between the HU, the MDC and the Charité – Universitätsmedizin Berlin. The chair is intended to bridge the activities at IRI Life Sciences and the Berlin Institute for Medical Systems Biology (BIMSB) of the MDC.
“The Reviewers and the Scientific Council emphasized that the MDC, the Humboldt-Universität and Berlin can count themselves lucky to retain such a cooperative scientist and inspiring colleague like Markus Landthaler,” Thomas Sommer said in his laudation, who is chair of the appointments committee and Deputy Scientific Chair of the MDC.
April 2017
PUBLICATION: A three-dimensional map of the genome
Gene mapping technique promises to unlock the power of proximity to find genes implicated in diseases.
Cells face a daunting task. They have to neatly pack a several meter-long thread of genetic material into a nucleus that measures only five micrometers across. This origami creates spatial interactions between genes and their switches, which can affect human health and disease. Now, an international team of scientists has devised a powerful new technique that ‘maps’ this three-dimensional geography of the entire genome.
(Photo/Copyright: MDC)
SEMINAR SERIES: Alexander van Oudenaarden - Distinguished Speaker in the BIMSB Seminar Series
On February 14, 2017, we had the pleasure to host Alexander van Oudenaarden, director of the Hubrecht Institute in Utrecht, as a distinguished speaker in our seminar series. Alexander is a world-leader in systems biology of single cells. At the Berlin Institute of Medical Systems Biology he spoke about systematic approaches to identify novel cell types and about emerging methods for determining cell-cell interactions and lineage history by single cell sequencing.
In addition to meetings with individual group leaders and discussions with PhD students and postdocs over lunch and dinner, Alexander also gave the closing lecture of our lecture series on single cell technologies on February 15.
February 2017
Of bits, bytes, and bacteria: a week of systems biology at the MDC
Can the lives of microorganisms be described through mathematics? It is one of the questions that pupils participating in the MINT Excellence Academy in “Systems Biology” have asked scientists during their visit to the MDC from Feb 6 to 10 this year. Twenty pupils from across Germany have come to catch a glimpse of how researchers combine laboratory and computational science into models of biological processes.
February 2017
Algorithms help navigate through the data thicket of biological systems
If one looks beyond individual molecules, biology quickly becomes complex. All life processes seem to affect one another. The computer scientist Uwe Ohler and his team of researchers at the Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) are using algorithms and mathematical models to map a path through this tangle of dependencies.