NEW BUILDING IN THE
CENTER OF BERLIN
PHD PROGRAM,
PARTNERS & ACTIVITIES
SYSTEMS BIOLOGY
AT THE MDC
The Berlin Institute for Medical Systems Biology
at the Max Delbrück Center for Molecular Medicine Berlin-Buch
For further information contact Grietje Krabbe: [email protected]
MODEL ORGANISMS
Every
second
Friday systems
biology students
present their
work in
progress.
Christin
Zasada
(Kempa lab)
From pSIRM to
MARS - quantifying
stem cell and cancer
metabolism
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.
Campus Charité
Straßenniveau
34.16m ü NHN
Hannoversche Straße
+34.15m
Bundesministerium für Bildung und Forschung
IV
Haus 12
III
Hauptbahnhof
versenkbare
Poller
+34.20m
+34.15m
+34.05m
II
+33.95m
Mosaikpflaster
Sicherheitszaun
Bodendecker
+34.15m
Mastleuchten
Asphalt
Zufahrt Feuerwehr
+34.05m
I
Plattenbelag,
befahrbar
Mosaikpflaster
Rasen
+34.05m
+34.48m
Aufstellfläche
Feuerwehr
Haus 25 und
BIMSB
OK Traufe=+28.20m
+34.48m
Vegetationsinseln mit
Sitzelementen
OK Dach=+24.30m
Automatisches
Schiebetor
+34.25m
2 Stellplätze
Luftansaugbauwerk,
versetzt
+34.25m
Müllstandort, versetzt
9 Fahrradbügel, versetzt
+34.40m
OK Dach=+28.20m
Mosaikpflaster
Stickstofftank
BIMSB
Haupteingang
+34.48m
+34.48m
OK Absturzsicherung=+14.20m
OK Attika=+13.10m
IV
50 Fahrradstellplätze
Gasflaschen lager
Müllentsorgung
OK Terrasse=+12.98m
Einfriedungsmauer
Plattenbelag
6 Stufen 17/35
+34.50m
+34.40m
+34.25m
+11.98m
Anbindung
Haus 25
III
+34.49m
2 Behinderten stellplätze
Bundeskanzleramt
Lea
daempfling
(Zinzen lab)
Stefanie
Seelk
(Tursun lab)
A central role
of the histone
chaperone Lin-53
(Rbbp4/7) in muscle
homeostasis and
aging regulation
Proteins & Proteomics
Date
Djordje
Vasiljevic
28 October 2015
04 November 2015
(Selbach lab)
For further information contact Jennifer Stewart: [email protected]
Every Wednesday, from 09:30 to 10:30 AM
MDC.C Conference Center, MDC Berlin-Buch
Cell-type specific
Robert-Rössle-Str. 10, 13125 Berlin
protein-protein
interactions in C.
elegans
A global analysis
of early nervous
system specification by
key neural transcription
factors in Drosophila
melanogaster
All are most welcome to attend
For further information contact Jennifer Stewart: [email protected]
11 November 2015
Speaker
Jeroen Krijgsveldt, EMBL
Oliver Daumke, MDC
09 December 2015
Ulrich Stelzl, MPI Molecular Genetics
Protein-protein interaction networks
Jesper Olsen, CPR Copenhagen
Quantitative Phosphoproteomics to delineate cell
signaling pathways
06 January 2016
Phillip Selenko, FMP
Michiel Vermeulen, University Nijmegen Quantitative interaction proteomics for epigenetics
Erich Wanker, MDC
Neuroproteomics
03 February 2016
Anne-Claude Gavin, EMBL
Protein Metabolite Interactions
10 February 2016
Gunnar Dittmar, MDC
Targeted Proteomics / Proteomics of the Ubiquitine
Proteasome System
RNA binding proteins as modulators of coding and
noncoding RNA pathways
Ribosomal decoding fidelity and tautomerism of nucleic
acid bases
Julien Betune Heidelberg University
03-06-15 Dendrit 2-3
Cynthia Sharma University of
Würzburg
10-06-15 Dendrit 2-3
17-06-15 Axon 2
Florian Heyd FUB
Markus Landthaler MDC/BIMSB
macromolecular machines: the ribosome as an example
Messenger RNA quality control in health and disease
Regulatory RNAs
mRNA/endomembrane co-trafficking from yeast to
mammals
24-06-15 Dendrit 2-3
Witek Filipowicz FMI Basel
08-07-15 Dendrit 2-3
Ralf-Peter Jansen University of
Tübingen
(Zinzen lab)
Spatiotemporal
analysis of
chromatin states
in the developing
Drosophila nervous
system
Dynamical
modelling of DNA
damage-dependent
NF-kappaB activation
15-07-15 Dendrit 2-3
BIMSB researchers apply quantitative experimental and theoretical approaches to model systems suitable for highthroughput 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.
Wei Chen MDC/BIMSB
MARK ROBINSON
University of Zurich,
Zurich, Switzerland
NICHOLAS D. SOCCI
Memorial Sloan Kettering Cancer Center,
New York, USA
18-24 OCT 2015 I Berlin
Germany I Berlin Institute
for Medical Systems Biology,
Max Delbrück Center
Application Deadline
30 July 2015
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
http://compgen2015.mdc-berlin.de
TOPIC 2015: Localization of cellular processes
at the MDC Berlin-Buch
Steven Altschuler, University of California, San Francisco, USA
Gary Bassell, Emory University School of Medicine, Atlanta, USA
Epsilonproteobacteria, Helicobacter pylori and
Campylobacter jejun
Xavier Darzacq, University of California, Berkeley, USA
Anne Ephrussi, EMBL Heidelberg, Germany,
Luca Giorgetti, Friedrich Miescher Institute, Basel, Switzerland
Christine Mayr, Memorial Sloan-Kettering Cancer Center, New York, USA
Dierk Niessing, Helmholtz Center Muenchen, Germany
Alternative splicing in four dimensions: how, where,
when and why?
Regulation of gene expression by RNA-binding
proteins
Mats Nilsson, Stockholm University, Sweden
Ana Pombo, BIMSB at the MDC, Berlin, Germany
insights into the mechanism and a role of miRNAs in
present and future
NIKOLAUS RAJEWSKY
Max Delbrück Center,
Berlin Institute for Medical Systems Biology
Kerstin Bystricky, CNRS Toulouse, France
Lionel Christiaen, New York University, New York, USA
development and function of mouse retina
Cooperation of membrane and mRNA transport
MEET
RICHARD BONNEAU
New York University,
New York, USA
UWE OHLER
Max Delbrück Center,
Berlin Institute for Medical Systems Biology
(Wolf lab)
Regulatory RNAs in the pathogenic
Transcriptome characterization: past,
LECTURERS / INSTRUCTORS
ALTUNA AKALIN
Max Delbrück Center,
Berlin Institute for Medical Systems Biology
Fabian
Konrath
miRNA repression in mammalian cells: structural
All are most welcome to attend
For further information contact Jennifer Stewart: [email protected]
8 Berlin Summer Meeting
Alexander
Glahs
Multiparticle cryo-electron microscopy of
Eric Westhof IBMC/CNRS Strasbourg
27-05-15 Dendrit 2-3
Every
second
Friday systems
biology students
present their
work in
progress.
Topics
Christian Spahn Charité
Gunter Meister University of
Regensburg
Niels Gehring University of Cologne
NMR
20 January 2016
27 January 2016
22-04-15 Axon 2
Nikolaus Rajewsky MDC/BIMSB
Student Seminar in
Systems Biology
Capture Compound Mass Spectrometry: A Chemoproteomic approach to profile small molecule-protein interactions
29-04-15 Dendrit 2-3
13-05-15 Dendrit 2-3
FRIDAY 10 APRIL 12 NOON DENDRIT 2-3
Structure-function studies in dynamin superfamily proteins
Bioinformatic Analysis of Proteomic Data using
OpenMS and KNIME
Drug action in the context of the proteome
06-05-15 Axon 2
20-05-15 Axon 2
Topics
Shotgun proteomics: an introduction
Proteome meets genome: dynamics of chromatin
composition in embryonic stem cells
Knut Reinert, FU Berlin
Marcus Bantscheff, Cellzome
13 January 2016
Date & Venue
Matthias Selbach, MDC
Mathias Dreger, Caprotech
02 December 2015
Systems Biology
Lectures
RNA Biology
Speaker
18 November 2015
25 November 2015
All are most welcome to attend
Antonella Riccio, University College London, UK
Joel Richter, University of Massachusetts Medical School, Worcester, USA
Silvia Santos, Imperial College London, UK
Stephen J. Small, New York University, New York, USA
June 4 -6 201 5 ,
Berlin, G erm any
Alexander Loewer, Nikolaus Rajewsky, Stephen Small, Robert Zinzen
Location: Umweltforum, Pufendorfstr. 11, 10249 Berlin
Contact:
Max Delbrück Center for Molecular Medicine
Berlin, 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) 150
Late registration (after April 15, 2015) 250
Students 80
For further information contact Jennifer Stewart: [email protected]
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.
+11.98m
Anlieferung
Rettungsweg
HU Forschungssporthalle
Every
second
Friday systems
biology students
present their
work in
progress.
Friday 05 SeptemBer at 12 noon dendrit 2-3
A HANDS-ON
COURSE ON
DATA ANALYSIS
Systems Biology
Lectures
Student Seminar
in Systems Biology
Student Seminar in
Systems Biology
COMPUTATIONAL
GENOMICS
Every Wednesday, From 09:30 to 10:30 AM
MDC.C Conference Center, Dendrite 2/3
Robert-Rössle-Str. 10, 13125 Berlin
FRIDAY 06 FEBRUARY AT 12 NOON DENDRIT 2-3
Schotterrasen
Blockstufe
+34.95m
Rasen
II
+34.90m
HU Haus 25
+34.48m
+34.25m
±0.00=34.50m üNN
+34.90m
Berlin Institute for Medical Systems Biology
Bauherr: MDC Max-Delbrück-Centrum für Molekulare Medizin
Gestaltungsplan, Entwurf G E LA03, Stand 28.05.2014, ohne Maßstab
BIMSB research groups will relocate to the central historical Campus Nord of the
HUB in 2018. Construction has started in March 2015.
Levin Monsigny Landschaftsarchitekten GmbH
Brunnenstraße 181, 10119 Berlin, Telefon: +49 30 44 05 31 84
E-Mail: [email protected]
Friedrichstraße
CONTACT BIMSB
Nikolaus Rajewsky, Head of the Berlin Institute for
Medical Systems Biology at the MDC
Phone
Jutta Steinkötter, BIMSB Management
Address Robert-Rössle-Str. 10, 13125 Berlin, Germany
Nadine Ewald, Administrative Assistant
Grietje Krabbe, Graduate Program
49 (0) 30 9406 3034
[email protected]
Internetwww.mdc-berlin.de/en/bimsb
Picture courtesy of Thomas Willnow Lab
Picture courtesy for background image: Google Maps
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.
FOUNDING&FUNDING
GROUP LEADERS
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 intrainstitutional collaborations, resulting in a number of shared publications, BIMSB group leaders expand their interactions
INNOVATIONS &
TECHNOLOGIES
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.
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.
SCIENTIFIC MISSION
The 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.
Uwe Ohler
Computational
Regulatory
Genomics
Nikolaus Rajewsky
Systems Biology of
Gene Regulatory
Elements
Markus Landthaler
RNA Biology and
Posttranscriptional
Regulation
Stefan Kempa
Integrative
Proteomics and
Metabolomics
Platform
Jan-Phillipp Junker
Quantitative Biology
of Developmental
Pattern Formation
Wei Chen
Functional Genomics
& Scientific Genomics
Platform
Marina Chekulaeva
Non-coding RNAs
and Mechanisms of
Cytoplasmic Gene
Regulation
Altuna Akalin
Scientific
Bioinformatics
Platform
Stephan Preibisch
Microscopy, Image
Analysis and Modeling
of Developing
Organisms
Ana Pombo
Epigenetic
Regulation and
Chromatin
Architecture
Baris Tursun
Gene Regulation
and Cell Fate
Decision in
C. elegans
Irmtraud Meyer
RNA Structure
Modelling
Robert Zinzen
Systems Biology
of Neural Tissue
Differentiation
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 technology 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.