BIMSB

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.

 

 

Latest BIMSB News

May 2018 Ana Pombo elected EMBO Member

April 2018 Stephan Preibisch receives Human Frontier Science Program (HFSP) Grant

March 2018 CORBEL launches 2nd Open Call for Research Projects

March 2018 Launch of LifeTime

February 2018 Süddeutsche Zeitung about Nikolaus Rajewsky and LifeTime

Events

Berlin Summer Meeting 2018

BIMSB Guest Speakers

BIMSB Seminar Series

Brochure

Faculty

BIMSB Groups

 

BIMSB Associated Groups

 

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.

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 FET Flagship Initiative

Predicting the onset and trajectory of a disease is the central vision of LifeTime a European Initiative applying to become a new FET Flagship. 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 Marie Vidal (Marie.Vidal@ mdc-berlin.de) or Christian Popp (Christian.Popp@ 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

New Building in the Centre of Berlin

BIMSB scientists are currently embedded and integrated in the MDC’s research infrastructure at the Campus in Berlin-Buch. In 2018, they will move to the centre of Berlin, Hannoversche Straße 28where the new BIMSB building is constructed on the central historical Campus of the Humboldt University. The inauguration of the new research site for BIMSB will make it 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 will perfectly be integrated into the given setting at the Humboldt Campus Nord. It will house up to 25 research groups, approximately half experimental and half computational, and provide 5400 qm of laboratory and office space. The building will host high-tech-labs, state-of-art technology platforms, flexible workspaces and communication areas, that will 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 façade has now been mounted and the cement works are finished. The central staircase is in place, serving as an eyecatcher and ascending through the oval cutouts of the impressive Atrium. Currently, the interior of the building and the external areas are being completed. The building and the rooftop terrace already offer great views over Berlin and the neighboring research landscape. If construction continues to run on plan, the building will be ready for BIMSB research groups to move in by fall 2018.

BIMSB group leaders visit the construction site of their future research building in January 2018.

 

Events

Berlin Summer Meeting

25.-27.10.2018

Dear Friends and Colleagues,

In October 2018, we will celebrate the beginning of a new era for us. By then, it will have been 10 years since the “Berlin Institute for Medical Systems Biology” (BIMSB) was founded. BIMSB is a new unit of the MDC for Molecular Medicine. It has its own scientific mission and institutionalized governmental funding. Having started with one group, BIMSB now accommodates ~250 scientists and staff. Seventeen group leaders have joined BIMSB to date, the vast majority of them hired from abroad. More group leaders (from Assistant Professor to Full Professor) will be hired within the next years. We have been incubating on the Campus in Berlin-Buch, and, we think, achieved to build a highly collaborative and successful new life science center in which the best scientists from different disciplines are coming together to unlock secrets of how genes are regulated in health and in disease.

With Staab Architekten, one of Germany’s leading architecture firms, we are building a beautiful new building, nearing completion, in the center of Berlin, right on the Life Science Campus of the Humboldt University, and in immediate vicinity of the Charité, the largest medical University in Europe. The new building has been designed with our ambition in mind to break boundaries between different scientific disciplines and levels of gene regulation. It will also serve to engage the public, the life sciences in Berlin, politics and the arts in open dialogues.

We are devoting the 11th annual Berlin Summer Meeting to celebrate the opening of our new home. We decided to invite scientists who we think have been essential for our science. We are honored to be hosting an outstanding selection of the very best scientists - including two Nobel laureates.

We warmly invite you to join us for the Grand BIMSB Opening Symposium and look forward to your participation.

Sincerely yours,

Nikolaus Rajewsky

Nikolaus Rajewsky, on behalf of all BIMSB group leaders

Our 11th Berlin Summer Meeting is scheduled as Grand BIMSB Opening Symposium from October 25 to 27, 2018. Save the date.

Further Information

Systems Biology Lectures

Summer Semester 2018

Scientific colleagues come together in Summer Semester 2018 to present lectures on the topic of Systems Biology & Cancer. All are welcome to attend.

Student Seminar in Systems Biology at the MDC

 

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

The seminars take place at 12:00 at the Max Delbrück Communications Center and all are welcome to attend.

Upcoming Seminars

Dec 14 - Haiyue Liu (AG Rajewsky) and Camilla Ciolli Mattioli (AG Chekulaeva)

2018

Nov 30 - Marco Uhrig (AG Rajewsky) and Marwan Zouinkhi (AG Preibisch)

Nov 16 - Tamas Sztanka-Toth (AG Rajewsky), Seung Joon Kim (AG Rajewsky) and Friedrich Preußer (AG Preibisch)

Nov 2 - Asija Diag (AG Rajewsky) and Jonathan Alles (AG Rajewsky)

Oct 5 - Martin Burkert (AG Ohler) and Ulrike Zinnall (AG Landthaler)

Sept 7 - Birte Arlt (AG Kempa), Gulinuer Yimingjiang (AG Chekulaeva) and Oscar Arturo Migueles Lozano (AG Wolf)

July 27 - Marina Petkovic (AG Schwarz), Nida ul Fatima (AG Tursun) and Selman Bulut (AG Tursun)

July 6 - Gesa Loof (AG Pombo) and Ella Bahry (AG Preibisch)

June 15 - Bo Hu (AG Junker), Carlos Vieira (AG Selbach) and Mareike Simon (AG Wolf)

June 1 - Jonathan Ronen (AG Akalin)

May 18 - Philipp Wahle (AG Zinzen) and Petar Glazar (AG N Rajewsky)

Apr 20 - Julia Löffler (AG Kempa), Lorena Sofia Lopez Zepeda (AG Ohler) and Alexander Gosdschan ( AG Akalin/Tursun) 

Apr 6 -Katarzyna Wreczycka (AG Akalin) and Roberto Arsie (AG Landthaler)

Mar 23 - Karoline Holler (AG Junker) and Boris Bogdanow (AG Selbach)

Mar 9 - Selman Bulut (AG Tursun), Stella de Biase (AG Schwarz) and Jonas Peters (AG Landthaler)

Feb 28 - Nicolai Kastelic (AG Landthaler) and Giulia Caglio (AG Pombo)

Feb 9 - Alexander Glahs (AG Zinzen) and Marcel Schilling (AG N Rajewsky)

Jan 26 - Henriette Miko (AG Ohler), Gülkiz Baytek (AG Tursun & AG Mertins) and Orsalia Hazapis (AG Landthaler)

2017

Dec 15 - Christin Stottmeister (AG N Rajewsky) and Joao Fernandes (AG Selbach)

Nov 03 - Nadine Royla (AG Kempa) and Stefan Stefanov (AG Meyer)

Oct 20 - Julia Löffler (AG Kempa) and Ruben Abreu (AG Landthaler)

Oct 06 - Inga Patarcic (AG Akalin) and Nina Mitic (AG Junker)

Sep 22 - Haiyue Liu (AG N Rajewsky) and Ana Miguel Fernandes (AG Pombo)

Sep 08 - Kamila Kutz (AG Selbach) and Yuliang Qu (AG Tursun)

July 28 - Klim Kolyvanov (AG Preibisch) and Cledi Cerda Jara (AG N Rajewsky)

July 14 - Christin Stottmeister (AG N Rajewsky) and Ulrike Zinnall (AG Landthaler)

June 14 (Wed) - Vera Zywitza (AG N Rajewsky) and Christian Martin Burkert (AG Ohler)

June 02 - Asija Diag (AG N Rajewsky) and Rieke Kempfer (AG Pombo)

May 19 - Ana Luisa Guimaraes (AG Zinzen) and Veronica Benito Delgado (AG DiVirgilio)

May 05 - Laura Breimann (AG Preibisch) and Petar Glazar (AG N Rajewsky)

Apr 21 - Bo Hu (AG Junker) and Camilla Ciolli Mattioli (AG Chekulaeva)

Apr 07 - Ella Bahry (AG Preibisch) and Marco Uhrig (AG Obermayer and AG N Rajewsky)

Mar 24 - Gesa Loof (AG Pombo) and Selman Bulut (AG Tursun)

Feb 24 - Student Symposium in Systems Biology - Program

Mar 10 - Jonathan Ronen (AG Akalin) and Nida ul Fatima (AG Tursun)

Feb 10 - Jonathan Froehlich (AG N Rajewsky) and Giulia Caglio (AG Pombo)

Jan 27 - Karoline Holler (AG Junker) and Sophia Bauch (AG Ohler)

Jan 13 - Katarzyna Wreczycka (AG Akalin), Katrina Meyer (AG Selbach) and Ekatarina Eroshok (AG Ohler)

 

Symposia, Workshops, Summer Schools etc.

 

Upcoming Events

2019

May 12 - 14 - Cell Symposia Regulatory RNAs

2018

June 28 - 29 - IRI Lifesciences Symposium

Past Events

2018

May 23-25 - Computational Genomics Course

2017

Nov 14 - Model Systems, Organoids and the Human Cell Atlas 

Sep 25-29 - Summer School - Poster
Computational Genomics and RNA Biology

Jul 05 & 10 - Summer Special - Poster
Michael Elowitz, California Institute of Technology, Pasadena, USA

Mar 07 - Presentation and Workshop - Program
BIMSB/BIH Genomics Platform

Feb 24 - Symposium - Program
Student Symposium in Systems Biology

2016

Nov 14-18 - Workshop
Biological Image - Reconstruction and Analysis

Nov 08 - Berlin Translational Dialogue
RNA-Medicine: From RNA Discoveries to Future Therapies

Oct 12 - Retreat - Program
Bilateral Retreat of the Institute of Bioorganic Chemistry, Polish Academy of Sciences and the Berlin Institute for Medical Systems Biology at the MDC Berlin-Buch

Sep 26 - Symposium - Program
Independent Junior Group Leader in Systems Biology

Sep 12-23 - Workshop - Poster
Computational Genomics - Approaches to precision medicine

Jun 27-28 - Lectures - Poster
Nikolaus Rajewsky - 5 Lectures in 2 days on RNA

Jun 01-03 - Conference - Program
European Worm Meeting 2016

Apr 29 - Symposium - Program
1st Student Symposium in Systems Biology

Feb 24-25 - Symposium - Program
Scientific Platform Leader in Microscopy

 

BIMSB Seminar Series

 

The aim of the BIMSB Seminar Series is to share and discuss the latest results and developments in Systems Biology. It features both scientists from BIMSB as well as guests from around the world. Each year, around four world-leading scientists are invited to give special Distinguished Speaker lectures.

The seminar takes place on Tuesdays, 2 pm at the MDC.C Axon 2. We cordially invite everybody interested to join this event. No registration is required.

Distinguished Speakers

14.02.2017 | Alexander van Oudenaarden | Hubrecht Institute, Utrecht

06.12.2016 | Wolf Reik | Babraham Institute, Cambridge

01.09.2016 | Oliver Hobert | Columbia University New York

26.05.2015 | Anders Krogh | University of Copenhagen

05.05.2015 | Eric Westhof | IBMC/CNRS Strasbourg 

21.04.2015 | Matthias Hentze | EMBL Heidelberg

01.07.2014 | Hans R. Schoeler | MPI Muenster

04.06.2014 | Xiaoliang Sunney Xie | Harvard University, Cambridge

17.09.2013 | Patrick Cramer | Gene Center Munich | LMU

20.06.2013 | Michael Levine | University of California, Berkeley

Read more about the Distinguished Speaker visits.

BIMSB Guest Speakers

 

This event brings together Berlin based 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!

Past Seminars

Aug 28 - Tineke Lenstra, the Netherlands Cancer Institute

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

Upcoming Seminars

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

 

 

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