Medical Systems Biology

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 & Environment, Astronomy, Space & Planetary Research to Geosciences, Materials & 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 Management, Machine 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

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)

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.

Human Cell Atlas

IHEC (International Human Epigenome Consortium)

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.

Where: BIMSB Large conference room 0.61, ground floor.

When: 24^th June 2022 music:science

1:00 – 2:00 pm: Student Seminar Medical Systems Biology

4:00 – 5:00 pm: Concert by Barenboim-Said Academy Students

5:00 – 7:00 pm: Drinks reception/Get-Together on our rooftop terrace

Second edition of our concert series after wonderful feedback after last year's premiere! Students of MDC and the Barenboim-Said-Academy will meet over music and science (and coffee, obviously). 

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. 

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

BSM-Poster.pdf (PDF, 1.17 MB)

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)

LifeTime 2021 (PDF, 322.37 KB)

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

Fly Cell Atlas Poster (PNG, 612.42 KB)

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"

• 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

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

2022

Dec 08: Talk: Petra Hajkova (Medical Research Council London Institute of Medical Sciences)

Oct 6: Talk: Yasuhiro Murakawa (Institute for the Advanced Study of Human Biology (ASHBi) and Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University)

May 25: Talk: Stefano (Piccolo University of Padua School of Medicine & IFOM (AIRC Institute of Molecular Oncology)

Jan 13: Virtual Talk: Stephan Preibisch (HHMIs Janelia Research Campus, Ashburn, Virginia)

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)

Aug 13: in-person Talk: Prof. Tom Tuschl (Rockefeller University, New York)

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

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

Mar 17: Virtual 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

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)

Deutsch: https://youtu.be/BPA_m23XQ8U

English: https://youtu.be/KbEw76BKDP8

Register HERE.