BIMSB building

Medical Systems Biology

The Berlin Institute for Medical Systems Biology (BIMSB)

About

Systems Biology integrates high-throughput technologies, mathematics, bioinformatics, molecular biology, biochemistry and engineering to derive predictive, quantitative models for biological systems, which may be molecules, cells, organisms or entire species. In combination with biomedical research, Systems Biology has the potential to steer medicine into the next century of personalized medicine.

The Berlin Institute for Medical Systems Biology (BIMSB) was initiated and developed by Nikolaus Rajewsky (BIMSB Scientific Director). BIMSB is an expansion of the MDC into Medical Systems Biology. BIMSB received, starting 2008, 19 Mio € kick-off funding through the competitive federal initiative “Spitzenforschung in den neuen Bundesländern” (BMBF & Senate Berlin). After a highly successful external peer-review, the BMBF decided to provide additional institutionalized funding for BIMSB (17.5 Mio € /year + 2.5 Mio € /year MDC “Eigenanteil”). The Humboldt University included BIMSB in their successful participation in the “Exzellenzinitiative” and provided the real estate on the new life science Campus in Berlin Mitte. This neighborhood is important for the BIMSB scientific mission and promotes collaborations between the HU and the MDC. The BMBF provides additional money for the new building (33.5 Mio €). 

So far, BIMSB researchers newly acquired additional 38 Mio € in competitive third-party funds by the BMBF, DFG , EC, HFSP, NIH, industry, BIH and DZHK.
Total external funding to date: 57 Mio € (competitively acquired) + 86 Mio € (institutionalized funding by the BMBF). 

 

The LifeTime Initiative

BIMSB and the Institut Curie (Paris) co-coordinate LifeTime, a pan-European initiative involving 50+ research institutes in 18 countries. Its goal is to track the molecular make-up of human cells in time and space at single cell resolution in order to be able to predict onset and course of diseases.

Faculty

BIMSB Groups

 

BIMSB Associated Groups

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Scientific Technology Platforms

State-of-the-art in-house technology platforms are instrumental to carry out the data intensive research characterizing systems biology. BIMSB Scientific Technology Platforms provide core services, plan projects in close collaboration with both MDC groups and local/international partners, and also conduct research and method development projects, pushing forward novel scientific and in particular medical applications towards personalized medicine.

The BIMSB Scientific Technology Platforms currently offer:

The Scientific Technology Platforms allow the application of sophisticated, novel and specialized methodologies such as PAR-CLIP (photoactivatable- ribonucleoside- enhanced- crosslinking and immunoprecipitation),  eFACS (fluorescence-activated cell sorting of embryos), SILAC and pulsed SILAC (stable isotope labeling by amino acids in culture cells), different sequencing protocols, metabolic profiling and advanced imaging. Capacities and technologies are constantly extending according to the general expansion of the BIMSB.

Cooperations

Collaborations and International Networks 

Local Partners

 

Charité

Humboldt-Universität zu Berlin (HU)

Freie Universität Berlin (FU)

DFG research center for applied Mathematics (MATHEON)

German Center for Rheumatology Research (DRFZ)

Max Planck Institute for Molecular Genetics (MPI-MG)

Integrative Research Institute for Life Sciences (IRI-LS)

BIMSB is part of IRI-LS, which supports numerous collaborations between MDC, HU and Charité and educational activities in the field of systems biology.

Berlin Institute of Health (BIH)

With the Berlin Institute of Health (BIH), the MDC and the Charité - Universitätsmedizin Berlin have joined forces to build a research space for  translational research and overarching systems medicine approaches to bridge the gap between basic research and clinical application. BIMSB is a strong collaboration partner for BIH groups and projects.

HELMHOLTZ EINSTEIN INTERNATIONAL BERLIN RESEARCH SCHOOL IN DATA SCIENCE (HEIBRiDS)

HEIBRiDS is a joint school in Data Science between the Einstein Center Digital Future (ECDF) and the Helmholtz Association. Established in 2018, HEIBRiDS is an interdisciplinary program that trains young scientists in Data Science applications within a broad range of natural science domains, spanning from Earth & EnvironmentAstronomySpace & Planetary Research to GeosciencesMaterials & Energy and Molecular Medicine. HEIBRiDS brings together six Helmholtz Centers and four university partners from ECDF, with 25 fully-funded PhD projects at the intersection of Data ManagementMachine Learning and Deep Learning, Imaging, Mathematical Modelling and High-throughput Data Analytics. MDC is the Helmholtz coordinator and participates in the school with five PhD projects in collaboration with the Humboldt University of Berlin, the Technical University of Berlin and Charité university hospital. 

For more information visit: https://www.heibrids.berlin/ or contact: Eirini.Kouskoumvekaki@mdc-berlin.de

National Networks

 

Single Cellomics Germany (SCOG)

Setting up a network for single-cell researchers in Germany and beyond is the goal of Single Cellomics Germany (SCOG). The initiative is jointly coordinated by Fabian Theis at the Institute of the Computational Biology HMGU in Munich, Nikolaus Rajewsky at the MDC/BIMSB and Jörn Walter at Saarland University and funded by the BMBF/DLR.

Single-cell research is revolutionising biology and medicine, combining omics technologies and microscopic analyses of single cells. Rapid technological advances now allow the profiling of genomes, transcriptomes, epigenomes and proteomes in individual cells at an unprecedented level of resolution. New computational methods are being developed and specifically tailored to harness the full potential of these single-cell omics data.

SCOG aims at bringing together national researchers with the mission to foster exchange of both computational and experimental methods and expertise and to strengthen single-cell research in Germany.

 

German Epigenome Programm (DEEP)

National Bioinformatics Infrastructure for RNA Biology (de.NBI)

European Initiatives

 

LifeTime Initiative

The project brings together scientists from over 50 research institutes in 18 countries and is co-coordinated by Nikolaus Rajewsky at the MDC and Geneviève Almouzni at the Institut Curie, Paris.

Following recent advances in single cell analysis, in particular in the fields of high-throughput sequencing and imaging, tracking the molecular make-up of human cells in time and space has become more than a distant dream. European experts in molecular and  computational biology as well as clinical research have joined forces in LifeTime, an open initiative continuously growing and gathering support.

 

circRTrain

circRTrain is a Marie Curie Innovative Training Network (ITN) funded by the European Union within the H2020 Programme. circRTrain seeks to understand the origin, function and application of circular RNAs, new large class of non-coding RNAs, by providing cross-disciplinary training in experimental and computational biology for a new generation of researchers. The circRTrain network consists of interdisciplinary experts from leading European institutes such as Aarhus University (Denmark), CRG (Spain), Justus-Liebig-University Giessen (Germany), MDC (Germany), La Sapienza (Italy), UMC Utrecht (Netherlands), and industrial partners Bioneer (Denmark), Eurice (Germany), Exosomics (Italy), Qiagen (Denmark), and qpa (Germany).

 

CORBEL - Coordinated Research Infrastructures Building Enduring Life-science Services

BIMSB  is a key partner in the cluster project CORBEL, funded by Horizon 2020 for four years (2015-2019). Within this consortium of thirteen biological and medical research infrastructures (BMS RIs) from the European Strategy Forum on Research Infrastructures (ESFRI), BIMSB represents the infrastructure for Systems Biology in Europe (ISBE). Together with Euro-BioImaging at the EMBL, BIMSB co-leads one of the biggest work packages of the project (WP4), focusing on bioscience use cases.

At the end of 2016, CORBEL organized a first Open Call for Research Projects. In this framework, academic and industrial scientists in Europe were offered access to more than 15 service providers from 8 research infrastructures, integrated services grouped into 4 access tracks and an application review based on scientific excellence and technical feasibility. 21 selected applicants have since benefitted from open access to cutting-edge technologies and services including support from the Bioinformatics platform of the BIMSB. Travel grants are enabling nearly 50 visits with transnational access.

Based on this successful first edition, a second Open Call offering even more services has been launched on 26 March 2018.

For more information on CORBEL or ISBE, please contact Sonja.Hansen@mdc-berlin.de.

Institutional Collaborations

 

BIMSB is fostering and maintaining collaborations with national and international research institutes, universities, and other organizations to facilitate joint research projects, staff exchange, access to cutting-edge technologies, and development of joint training activities.

 

MRC CSC London

Sapienza Universitá di Roma

 

PhD-Student exchange program with New York University

The MDC-NYU PhD Exchange program was launched in 2009 to train the next generation of systems biologists in experimental as well as computational approaches to understand the complex processes of life. Graduate students are jointly supervised by faculty from BIMSB and CGSB (Center for Genomics and Systems Biology) of the New York University Biology department. Short-term and long-term research visits within the program allow the students to take advantage of complimentary scientific and training expertise.

 

SignGene

with Technion - Israel Institute of Technology (TEC) and The Hebrew University of Jerusalem (HUJI):

The German-Israeli Research School "Frontiers in Cell Signaling and Gene Regulation" is part of the Helmholtz International Research School Initiative and brings together leading experts from MDC (Berlin, Germany), Technion (Haifa, Israel) and Hebrew University (Jerusalem, Israel). Students in the field of cell signaling, gene regulation, and quantitative biology are jointly supervised by investigators from Germany and Israel and spend up to 6 months in the partner laboratory abroad.

 

IBCH PAS

Poznan-Berlin collaborations in RNA biochemistry have a long-standing history tied to the late Prof. Dr. Volker Erdmann (FU Berlin , member of the Polish Academy of Sciences). The Institute of Bioorganic Chemistry (IBCH) of the Polish Academy of Sciences (PAS) has various interactions with BIMSB.  Young researchers from Poznan have joined the BIMSB with great success (e.g. Monika Piwecka et al., Science 2017). Nikolaus Rajewsky has collaborated with Jan Barciszewski (e.g. as editor for the Springer book series RNA Technologies). A joint retreat was organized on October 12, 2016 in Berlin. PIs of both institutions are enthusiastic about the initiative of joint research endeavors and the development of a long-term sustainable partnership.

PhD Exchange

The MDC-NYU PhD Exchange program was launched in 2009 to train the next generation of systems biologists. Ten BIMSB PhD students are able to to spend up to two years working and studying at the Center for Genomics and Systems Biology at New York University. Students can also take advantage of our state of the art technology platforms and a training programme of specialist courses and personal development opportunities.

Location

BIMSB Moved to the Centre of Berlin

Berlin Institute for Medical Systems Biology (BIMSB)
Hannoversche Str. 28,
10115 Berlin
Telephone: +49 30 9406-1300

In spring 2019, BIMSB scientists moved from MDC’s research infrastructure at the Campus in Berlin-Buch to the centre of Berlin (Hannoversche Straße 28). The building is entirely new and located on the central historical Campus of the Humboldt University. This new research site represents the first institutional and infrastructural expansion of the MDC into the centre of Berlin, supporting even closer interactions with major academic and medical institutions in the city and region.

The design for the new BIMSB building has been selected through an architectural competition and is perfectly integrated into the given setting at the Humboldt Campus Nord. It provides space for up to 25 research groups, approximately half experimental and half computational offering 5400 sqm of laboratory and office space. The building hosts high-tech-labs, state-of-art technology platforms, flexible workspaces and communication areas, that further promote innovative and interdisciplinary research.

After the site had been handed over to the MDC in November 2014, construction started in February 2015. Following clearance of the site, ground testing and construction of the passage to and from Hannoversche Straße, deep ground work and excavation took place in spring 2015.

The pouring of the concrete marked the completion of the second phase of construction. This was celebrated at the official dedication of the building on December 15, 2016, with the architects and representatives of the MDC, partner institutes, and the City of Berlin attending. 

The building was inaugurated by German Chancellor Angela Merkel in February 26, 2019. 

Directions

With public transport

  • Bus: 142 (Torstr./Oranienburger Tor)
  • Underground train: U6 (Oranienburger Tor)
  • S-Bahn city train: S1, S2, S25 (Nordbahnhof or Oranienburger Str.)
  • Tram: M12, M5 (Torstr./Oranienburger Tor)
  • By rail: via Hauptbahnhof

By car

  • parking at the street, rarely available (2€/h)
  • underground garage is nearby (2€/h)
    Hannoversche Straße 5b, 10115 Berlin

Events

BIMSB Lunchtime Concerts in coorporation with Barenboim-Said Academy - 12th Nov 2021

Breaking boundaries is part of our mission – between research and clinics, between science and society.

This is why we are introducing a new format, aiming to break boundaries between the worlds of science and music: starting on November 12th 2021, we invite you to join the inaugural installment of lunch-time concerts and enjoy world-class music performed by students of the renowned Barenboim-Said Akademie followed by the latest research presented by BIMSB students in the Student Seminar in Medical Systems Biology. 

 

Berlin Summer Meeting: "Innovative RNA: from Basic Discoveries to Future Medicine"  - 18th June 2021

18 June 2021

We are excited to announce the 14th Berlin Summer Meeting 'Innovative RNA: from Basic Discoveries to Future Medicine', which this year – since we had to rethink it in light of the pandemic – is going to take place as a virtual event.

https://berlin-summer-meeting.org

LifeTime Conference 2.0 - 16th & 17th June 2021

16th & 17th June 2021

We are delighted to announce the LifeTime Conference 2.0 on June 16-17, 2021. This second meeting about cell-based interceptive medicine brings together an exciting selection of international speakers, including selected short talks from abstracts. Moreover, this year’s meeting will be conjoined with the annual Berlin Summer Meeting on June 18th, also organized by the Berlin Institute for Medical Systems Biology (BIMSB) at the Max Delbrück Center (MDC)

 

 

Symposium: Fly Cell Atlas 3

29 - 30 April 2021: Hybrid event held in Berlin and virtually

Drosophila melanogaster has been an incredible model organism for basic research for well over 100 years. Hallmarks include its genetic tractability and the sheer variety and flexibility of the molecular, genetic and genomic tools available to probe organismal biology.

For general information about the FlyCellAtlas, please visit the MDC FlyCellAtlas webpage or www.flycellatlas.org.

For further information about the program and registration please send an email to webseminar@mdc-berlin.de.

Please register via this link

Systems Biology Lectures 

Scientific colleagues come together to present lectures on the topic of Systems Biology. BIMSB welcomes these Lectures as an opportunity to also invite scientists from other research institutions to join. 

 

Student Seminar in Medical Systems Biology at the MDC

Every second Friday, our students present their work and invite fellow students and scientific faculty to join the discussion. 

The seminars take place on Fridays at 12:00 Berlin Time. BIMSB welcomes this Seminar as an opportunity to also invite scientists from other research institutions to join.

Upcoming Seminars:

 

 

28 May

  • Leo Epstein, Harrington lab: "Detection and tracking to analyze endothelial migration and protein colocalization"
  • Julia Markowski, Schwarz lab: "Towards haplotype-specific chromatin contact maps from GAM"
  • Lisa Emmenegger, Rajewsky lab: ​​​​​"MicroRNAs function in viral infections: an optogenetic-based DICER perturbation"

7 May

  • Miriam Faxel (Zinzen lab):"Reconstruction of regulatory networks driving patterned expression in the Drosophila embryo based on spatially resolved single-cell sequencing data"
  • Simone Del Giudice (Landthaler lab): "Cellular interactions and transcriptional dynamics in cancer and invertebrate development"
  • Fearghal Donaghy (Haghverdi lab): "Fine-tuning RNA Velocity"

30 Apr 2021

  • Mirjam van Bentum (Selbach lab): "Profiling cellular signalling by targeted phoshoproteomics”
  • Iris Marchal (Tursun lab): "Characterization of the histone chaperone FACT as a safeguard of cellular identity in C. elegans"

 

16 Apr 2021

  • Konstantinos Papadakis (Zinzen lab): "Conservation of neurogenic regulatory nodes from fly to mouse"
  • Robert Kerridge (Selbach lab): "Proteomic Analysis of Altered Translation in Autism Spectrum Disorder"
  • Safak Bayram (Kempa lab): "Tracing glutaminase-inhibitor resistance at atomic resolution"

 

19 Mar 2021 (Virtual Meeting)
  • Mariam Hammoud (Ohler lab): "Transcriptional regulatory dynamics during zebrafish embryonic development"
  • Stefan Stefanov (Meyer lab): "The advantages of full circRNA sequence knowledge in determining functional associations"
  • Artem Baranovskii (Chekulaeva lab): "mRNA stability as a determinant of mRNA's subcellular localization in neurons"

 

5 Mar 2021 (Virtual Meeting)

  • Erik Becher (Chekulaeva lab, BIMSB): "Modeling amyotrophic lateral sclerosis: generating functional motoneurons from patient-derived stem cells"
  • Jonas Brandenburg (Landthaler lab, BIMSB): "Dynamics of gene regulatory element usage across early sea urchin development"
  • Dominika Vojtasova (Pombo lab, BIMSB): "Effects of Shank3 and sleep deprivation on genome architecture in the mouse hippocampus"

19 Feb 2021 (Virtual Meeting)

  • Teresa Melder (Selbach lab, MDC): Development of a Cellulose-based High-throughput Screen Targeting the Interaction Landscape of Pharmaceutical Compounds Applying Shotgun Proteomics
  • Remo Monti (Ohler lab, BIMSB): Identifying key metabolic regulators from large exome sequencing data using functionally informed kernel-based association tests

Jan 22 2021 (Virtual Meeting)

  • Lorena Sofia Lopez Zepeda (Ohler lab, BIMSB): TBA
  • Trendelina Rrustemi (Selbach lab, BIMSB): TBA
  • Robert Bücking (Meyer lab, BIMSB): Prediction of RNA-RNA interactions in phage infected bacteria

Feb 5 2021 (Virtual Meeting)

  • Jonas Peters (Landthaler lab, BIMSB): How individual eIF4F proteins shape the translation profile
  • Irene Mota Gomez Argente (Lupianez lab, BIMSB):3D-Chromatin dynamics during mammalian sex determination

Jan 22 2021 (Virtual Meeting)

  • Lorena Sofia Lopez Zepeda (Ohler lab, BIMSB):Understanding gene regulation using CRISPR Screens
  • Trendelina Rrustemi (Selbach lab, BIMSB):Investigating mutated phosphorylation sites within intrinsically disordered regions using a peptide based interaction screen
  • Robert Bücking (Meyer lab, BIMSB):Prediction of RNA-RNA interactions in phage infected bacteria

Jan 8 2021(Virtual Meeting)

  • Maria Stella de Biase (Schwarz lab, BIMSB): Nasal gene expression provides insights into smoking injury response and disease status

 

    BIMSB Guest Speakers

    This event brings together researchers in the field of Medical Systems Biology.

    The periodic events are an occasion where invited speakers provide us with updates on recent developments from both Germany and abroad. All members of the campus are welcome to join!

    Seminars

    2021

    Oct 27: in-person Seminar: Dr Valerie Hilgers (MPI of Immunobiology and Epigenetics, Freiburg)

    Oct 25: in-person Seminar: Prof Massimiliano Pagani (University of Milan)

    Oct 5: Virtual Seminar: Dr André Rendeiro (Weill Cornell Medical College)

    June 15: Virtual Seminar: Sina Wittmann (MPI-CBG Dresden​​​​​​)

    Mar 9: Virtual meeting: Elvira Maas (Limes-Institut, Bonn)

    Mar 17Virtual meeting: Geraldine Seydoux (Johns Hopkins University School of Medicine, Baltimore)

     

    2019

    Nov 14
    Michael Sigal (Charité)

    Sept 2
    Joachim Schultze from the University of Bonn | LIMES Institute

    July 18
    Hinrich Boeger from the University of California, Santa Cruz

    June 11
    Remo Rohs from University of Southern California

    June 4
    Erik van Nimwegen, Biozentrum, University of Basel

    June 3
    Alexander Hoffmann from the University of California, Los Angeles   

    June 5
    Manuel Irimia from the the Centre for Genomic Regulation (CRG Barcelona)

    March 12
    Abderrahman Khila​​​​​​, Institute Genomics Functional De Lyon

    March 7
    Michael Kaminski, Institute for Medical Engineering and Science, Massachusetts Institute of Technology

    August 28
    Tineke Lenstra, the Netherlands Cancer Institute

    August 31
    Peter Kharchenko, the Department of Biomedical Informatics of the Harvard Medical School 

    April 1
    Jeremy E. Wilusz, Department of Biochemistry & Biophysics, University of Pennsylvania Perelman School of Medicine

    Distinguished Speakers

    Each year, around four world-leading scientists are invited to give special Distinguished Speaker lectures.

    26 November, 2019
    Gunter Meister (Full professor and Chair of Biochemistry, University of Regensburg)

    28 October, 2019
    Itai Yanai (Director, Institute for Computational Medicine; Professor, Biochemistry and Molecular Pharmacology; New York University, School of Medicine)

    Breaking Boundaries - Virchow 2.0

    Berlin has a long tradition as a medical metropolis and also the potential to become an international hub for the life sciences, comparable to Boston. On September 28, researchers from both cities discussed this issue with the Governing Mayor of Berlin, Michael Müller.

    Watch the event:

    1st "Condensates & Phase Transitions" Workshop,  (online event)

    27 November 2020

    Register HERE.

    Recruitment Symposiums “Single Cell goes Clinical" and "Advanced Imaging Applications for Systems Biology" &"Computational/Theoretical Approaches for Deciphering Human Disease Data"

    Feb 6, 2020, 9 am – 6:40 pm and Feb 24, 2020, 9 am – 6:15 pm