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Phone 49 (0) 30 9406 3034
Email [email protected]
Address Robert-Rössle-Str. 10, 13125 Berlin, Germany
Internet www.mdc-berlin.de/en/bimsb
SYSTEMS BIOLOGY AT THE MDC The Berlin Institute for Medical Systems Biology at the Max Delbrück Center for Molecular Medicine Berlin-Buch
PHD PROGRAM, PARTNERS & ACTIVITIES
BIMSB is fostering and maintaining institutional collaborations with national and international research institutes, universities, and other organizations to facilitate joint research projects, staff exchange, access to innovative technologies, and development of joint training activities.
As a core activity, BIMSB has launched an international PhD exchange program between the MDC and New York University (NYU) to educate the next generation of systems biologists. Ten BIMSB PhD students are able to spend up to two years working and studying at the Center for Genomics and Systems Biology at New York University. Both institutes have a strong reputation in systems biology and students can take advantage of state-of-the-art technology platforms and a training program of specialist courses and personal development opportunities. More international exchange is foreseen to develop with the MRC CSC (Medical Research Council, Clinical Science Center) in London.
Communication, conferences and training events such as the annual Berlin Summer Meeting contribute to a worldwide scientific exchange and network. BIMSB organizes lectures together with Berlin’s universities and Summer Schools for interdisciplinary systems biology education of young researchers.
Medical systems biology research requires a critical mass of disciplines, technologies, experts and collaborations in close proximity, and with easy access to a wide range of collaborators. The construction of a new building for BIMSB will make it the MDC’s first institutional expansion into the center of Berlin, supporting even closer interactions with major academic and medical institutions in the city and region. The new building offers open research space for 25 research teams, and state-of-the-art technologies, as well as communication & conference space.
BIMSB research groups will relocate to the central historical Campus Nord of the HUB in 2018. Construction has started in March 2015.
NEW BUILDING IN THE CENTER OF BERLIN
MODEL ORGANISMS
CONTACT BIMSBNikolaus Rajewsky, Head of the Berlin Institute for Medical Systems Biology at the MDC
Jutta Steinkötter, BIMSB ManagementNadine Ewald, Administrative AssistantGrietje Krabbe, Graduate Program
BIMSB researchers apply quantitative experimental and theoretical approaches to model systems suitable for high-throughput analyses on multiple levels. Model organisms such as Drosophila, nematodes and flatworms, zebrafish and cell culture are employed as they are particularly amenable to systems wide investigations. Strategies to translate BIMSB research to more disease relevant model organisms are undertaken in collaboration with MDC teams working on disease mechanisms and other MDC technology platforms.
Picture courtesy of Thomas W
illnow Lab
Campus Charité
Friedrichstraße
Hauptbahnhof
Bundeskanzleramt
Bauherr: MDC Max-Delbrück-Centrum für Molekulare MedizinGestaltungsplan, Entwurf G E LA03, Stand 28.05.2014, ohne Maßstab
Levin Monsigny Landschaftsarchitekten GmbHBrunnenstraße 181, 10119 Berlin, Telefon: +49 30 44 05 31 84
E-Mail: [email protected]
Berlin Institute for Medical Systems Biology
BIMSBHaupteingang
Plattenbelag, befahrbar
Vegetationsinseln mit Sitzelementen
Bundesministerium für Bildung und Forschung
Haus 12III
HU Forschungssporthalle
HU Haus 25
Aufstell�äche FeuerwehrHaus 25 und BIMSB
Zufahrt Feuerwehr
Mastleuchten
2 Stellplätze
Gas�aschen -lager
AnlieferungRettungsweg
50 Fahrradstellplätze
±0.00=34.50m üNN
OK Traufe=+28.20m
OK Dach=+24.30m
OK Absturzsicherung=+14.20m
OK Attika=+13.10m
OK Terrasse=+12.98m
+11.98m
OK Dach=+28.20m
Hannoversche StraßeStraßenniveau 34.16m ü NHN
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versenkbare Poller
Bodendecker
Mosaikp�aster
Asphalt
Mosaikp�aster
Rasen
Sticksto�tank
Müllentsorgung
Anbindung Haus 25
2 Behinderten -stellplätze Schotterrasen
Blockstufe Rasen
Plattenbelag
Sich
erhe
itsza
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Auto
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Schi
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Luftansaugbauwerk,versetzt
9 Fahrradbügel, versetzt
Müllstandort, versetzt
Mosaikp�aster
+11.98m
+34.25m +34.48m
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6 Stufen 17/35
+34.25m
Einf
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Student Seminar in Systems Biology
Friday 05 SeptemBer at 12 noon dendrit 2-3
For further information contact Jennifer Stewart: [email protected]
Christin Zasada
(Kempa lab)
From pSIRM to MARS - quantifying
stem cell and cancer metabolism
Lea daempfling
(Zinzen lab)
A global analysis of early nervous
system specification by key neural transcription
factors in Drosophila melanogaster
All are most welcome to attend
Every second
Friday systems biology students
present their work in
progress.
Student Seminar in Systems Biology
FRIDAY 06 FEBRUARY AT 12 NOON DENDRIT 2-3
For further information contact Jennifer Stewart: [email protected]
Stefanie Seelk
(Tursun lab)
A central role of the histone
chaperone Lin-53 (Rbbp4/7) in muscle
homeostasis and aging regulation
Djordje Vasiljevic (Selbach lab)
Cell-type specific protein-protein
interactions in C. elegans
All are most welcome to attend
Every second
Friday systems biology students
present their work in
progress.For further information contact Jennifer Stewart: [email protected]
Every Wednesday, from 09:30 to 10:30 AMMDC.C Conference Center, MDC Berlin-BuchRobert-Rössle-Str. 10, 13125 Berlin
Systems Biology LecturesRNA BiologyDate & Venue Speaker Topics
22-04-15 Axon 2 Christian Spahn CharitéMultiparticle cryo-electron microscopy ofmacromolecular machines: the ribosome as an example
29-04-15 Dendrit 2-3 Gunter Meister University of Regensburg
RNA binding proteins as modulators of coding and noncoding RNA pathways
06-05-15 Axon 2 Eric Westhof IBMC/CNRS Strasbourg Ribosomal decoding fidelity and tautomerism of nucleic acid bases
13-05-15 Dendrit 2-3 Niels Gehring University of Cologne Messenger RNA quality control in health and disease
20-05-15 Axon 2 Nikolaus Rajewsky MDC/BIMSB Regulatory RNAs
27-05-15 Dendrit 2-3 Julien Betune Heidelberg UniversitymRNA/endomembrane co-trafficking from yeast tomammals
03-06-15 Dendrit 2-3 Cynthia Sharma University of Würzburg
Regulatory RNAs in the pathogenicEpsilonproteobacteria, Helicobacter pylori andCampylobacter jejun
10-06-15 Dendrit 2-3 Florian Heyd FUBAlternative splicing in four dimensions: how, where,when and why?
17-06-15 Axon 2 Markus Landthaler MDC/BIMSBRegulation of gene expression by RNA-bindingproteins
24-06-15 Dendrit 2-3 Witek Filipowicz FMI BaselmiRNA repression in mammalian cells: structuralinsights into the mechanism and a role of miRNAs indevelopment and function of mouse retina
08-07-15 Dendrit 2-3 Ralf-Peter Jansen University of Tübingen Cooperation of membrane and mRNA transport
15-07-15 Dendrit 2-3 Wei Chen MDC/BIMSBTranscriptome characterization: past,present and future
For further information contact Grietje Krabbe: [email protected]
Date Speaker Topics
28 October 2015 Matthias Selbach, MDC Shotgun proteomics: an introduction
04 November 2015 Jeroen Krijgsveldt, EMBLProteome meets genome: dynamics of chromatin composition in embryonic stem cells
11 November 2015 Oliver Daumke, MDC Structure-function studies in dynamin superfamily proteins
18 November 2015 Knut Reinert, FU Berlin Bioinformatic Analysis of Proteomic Data using OpenMS and KNIME
25 November 2015 Mathias Dreger, Caprotech Capture Compound Mass Spectrometry: A Chemoproteo-mic approach to profile small molecule-protein interactions
09 December 2015 Ulrich Stelzl, MPI Molecular Genetics Protein-protein interaction networks
10 February 2016 Gunnar Dittmar, MDC Targeted Proteomics / Proteomics of the Ubiquitine Proteasome System
06 January 2016 Jesper Olsen, CPR CopenhagenQuantitative Phosphoproteomics to delineate cell signaling pathways
13 January 2016
20 January 2016 Michiel Vermeulen, University Nijmegen Quantitative interaction proteomics for epigenetics
27 January 2016 Erich Wanker, MDC Neuroproteomics
Systems Biology Lectures Proteins & Proteomics
Every Wednesday, From 09:30 to 10:30 AM MDC.C Conference Center, Dendrite 2/3Robert-Rössle-Str. 10, 13125 Berlin
02 December 2015
Phillip Selenko, FMP NMR
03 February 2016 Anne-Claude Gavin, EMBL Protein Metabolite Interactions
Drug action in the context of the proteomeMarcus Bantscheff, Cellzome
Student Seminar in Systems Biology
FRIDAY 10 APRIL 12 NOON DENDRIT 2-3
For further information contact Jennifer Stewart: [email protected]
Alexander Glahs
(Zinzen lab)
Spatiotemporal analysis of
chromatin states in the developing
Drosophila nervous system
Fabian Konrath
(Wolf lab)
Dynamical modelling of DNA
damage-dependent NF-kappaB activation
All are most welcome to attend
Every second
Friday systems biology students
present their work in
progress.
COMPUTATIONAL GENOMICS
http://compgen2015.mdc-berlin.de
LECTURERS / INSTRUCTORSALTUNA AKALIN
Max Delbrück Center, Berlin Institute for Medical Systems Biology
RICHARD BONNEAUNew York University,
New York, USA
UWE OHLERMax Delbrück Center,
Berlin Institute for Medical Systems Biology
NIKOLAUS RAJEWSKY Max Delbrück Center,
Berlin Institute for Medical Systems Biology
MARK ROBINSONUniversity of Zurich, Zurich, Switzerland
NICHOLAS D. SOCCIMemorial Sloan Kettering Cancer Center,
New York, USA
COURSE MODULES· Introduction to R & Bioconductor· Statistics and Exploratory Data analysis· Introduction to Next-gen sequencing· RNA-seq analysis· ChIP-seq analysis· Data integration and visualization
18-24 OCT 2015 I Berlin Germany I Berlin Institute for Medical Systems Biology, Max Delbrück CenterApplication Deadline 30 July 2015
A HANDS-ON COURSE ON DATA ANALYSIS
TOPIC 2015: Loca l i za t ion of ce l lu lar processes
8 Berlin Summer Meeting
June 4-6 2015, Ber l in , GermanyAlexander Loewer, Nikolaus Rajewsky, Stephen Small, Robert Zinzen
Location: Umweltforum, Pufendorfstr. 11, 10249 BerlinContact: Max Delbrück Center for Molecular MedicineBerlin, Germany, phone (+) 49 30 9406 2999 / 3720
LIMITED SPACE AVAILABLE !
Abstract submission deadline: March 30, 2015
Fees (in Euro)Early registration (until April 15, 2015) 150Late registration (after April 15, 2015) 250Students 80
Ana Pombo, BIMSB at the MDC, Berlin, Germany
at the MDC Berlin-Buch
MEET
Gary Bassell, Emory University School of Medicine, Atlanta, USA
Kerstin Bystricky, CNRS Toulouse, FranceLionel Christiaen, New York University, New York, USA
Xavier Darzacq, University of California, Berkeley, USAAnne Ephrussi, EMBL Heidelberg, Germany,Luca Giorgetti, Friedrich Miescher Institute, Basel, SwitzerlandChristine Mayr, Memorial Sloan-Kettering Cancer Center, New York, USADierk Niessing, Helmholtz Center Muenchen, Germany
Mats Nilsson, Stockholm University, Sweden
Antonella Riccio, University College London, UK
Silvia Santos, Imperial College London, UKStephen J. Small, New York University, New York, USA
Steven Altschuler, University of California, San Francisco, USA
Joel Richter, University of Massachusetts Medical School, Worcester, USA
Picture courtesy for background image: Google Maps
SCIENTIFIC MISSIONThe overall scientific BIMSB mission is to integrate different levels of gene regulation to better understand how phenotypes in health and disease are linked to genotypes. These levels of gene regulation include chromatin and epigenetic changes and (post)transcriptional as well as (post)translational regulation. BIMSB researchers apply quantitative experimental and theoretical approaches to model systems suitable for multi-level high-throughput analyses as well as targeted approaches. Drosophila, nematodes, zebrafish, and mammalian systems are instrumental to the BIMSB mission. Major research projects address basic cell biology, development, regeneration, stem cell biology, metabolism, genetic variability linked to cancer as well as cardiovascular and neurological diseases.
GROUP LEADERS
Nikolaus RajewskySystems Biology of Gene Regulatory Elements
Marina ChekulaevaNon-coding RNAs and Mechanisms of Cytoplasmic Gene Regulation
Ana PomboEpigenetic Regulation and Chromatin Architecture
Stephan PreibischMicroscopy, Image Analysis and Modeling of Developing Organisms
Stefan KempaIntegrative Proteomics and Metabolomics Platform
Robert ZinzenSystems Biology of Neural Tissue Differentiation
Markus LandthalerRNA Biology and Posttranscriptional Regulation
Baris TursunGene Regulation and Cell Fate Decision in C. elegans
Irmtraud MeyerRNA Structure Modelling
Uwe OhlerComputational Regulatory Genomics
Jan-Phillipp JunkerQuantitative Biology of Developmental Pattern Formation
Altuna AkalinScientific Bioinformatics Platform
Wei ChenFunctional Genomics & Scientific Genomics Platform
Medical systems biology research combines various disciplines, technologies and experts. BIMSB group leaders are international scientists, recognized leaders in their field and expert in innovative technologies. Additional to various intra-institutional collaborations, resulting in a number of shared publications, BIMSB group leaders expand their interactions to regional partners from the Charité, Humboldt University Berlin (HU), Free University Berlin (FU), Max Planck and Leibniz Institutes and international partners such as New York University and MRC CSC London.
BIMSB combines high-throughput technologies and innovative methodologies with scientific expertise in genome, transcriptome, proteome, metabolome and image analysis as well as bioinformatics in a unique research environment of the MDC and partners in Berlin.
BIMSB Technology Platforms currently comprise newest Illumina Sequencing technolo-gy along with a Single Molecule Real Time Platform (Pacific Biosciences), as well as single cell sequencing. Mass spectrometry is represented with ample capacities for quantitative proteome and metabolome analysis and automation. Data are processed, analyzed and integrated with state-of-the-art computer clusters and -dynamics. Capacities and areas of technologies are expected to expand with the recruitment of more groups.
The unique potential of BIMSB is not only the application of high-end technologies but also the combination of cutting-edge methodologies such as PAR-CLIP (photo-activatable-ribonucleoside-enhanced-crosslinking and immunoprecipitation), sorting of cells and even whole organisms, SILAC (stable isotope labeling by amino acids in culture cells), and Genome architecture mapping, with computational analysis and mathematical modelling. Data from the various biological and experimental systems are integrated into sophisticated BIMSB databases. In addition we recently established single molecule imaging and live imaging technologies using high-end light-sheet microscopy. With this BIMSB research helps developing new tools to deepen our insights in life – literally speaking.
INNOVATIONSTECHNOLOGIES
&
The Berlin Institute for Medical Systems Biology (BIMSB) is the Systems Biology program of the Max Delbrück Center for Molecular Medicine (MDC). Launched in 2008 with start-up grants from the BMBF and the Senate of Berlin (until 2013), BIMSB now receives MDC institutional funding. BIMSB’s successive international recruitments of Junior and Senior group leaders will reach a total of up to 25 research teams, including technology platforms. The teams competed successfully for third party funding from local, national and international science funding agencies.
BIMSB is focused on the elucidation of gene regulatory networks and their impact on molecular and cellular mechanisms. This area lies at the heart of today’s biological and biomedical research on health and disease. BIMSB integrates experimental and computational research approaches with the central themes of MDC research and other partner institutions in Berlin.
FOUNDING&FUNDING
