Molecular Systems Biology Seminar

The MSB seminars are organised by the systems biology groups Blüthgen, Herzel, Steuer, Relogio and Westermark at the Institute of Theoretical Biology, Charité-Universitaetsmedizin and Humboldt-Universität Berlin.

Location: ITB Seminar Room, Invalidenstraße 43, 10115 Berlin
Time: Friday 14:00

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Upcoming Seminars

Past Seminars

Friday, 12.08.2016, 14:00h
Michael Boettcher: Inferring genetic interactions through an orthogonal CRISPR screening approach
University of California San Francisco

Friday, 13.05.2016, 14:00h
Simon Cook: Tumour cell resistance to MEK inhibitors - causes and some unexpected consequences
Babraham Institute UK

Friday, 22.04.2016, 13:00h
Miguel Godinho Ferreira - The role of telomeres in cancer and ageing
Howard Hughes Medical Institute [host: Angela]

Friday, 18.03.2016, 14:00h
Toru Takumi: Molecular link between rhythm and mood via phosphorylation
RIKEN Brain Science Institute (BSI)

Friday, 18.12.2015, 14:00h
Davide Chiarugi: Signals of ribosome drop-off in ribisome profilingdata
MPI Golm

Friday, 04.12.2015, 14:00h
Achim Tresch: Bioinformatical and Biochemical methods for the analysis of periodic RNA transcription
Max-Planck-Institute Cologne and University of Cologne

Friday, 13.11.2015, 14:00h
Matthias König: Metabolic Modelling in Liver
Charite Berlin

Friday, 06.11.2015, 14:00h
Simone Reber: How the ideas of soft matter physics help us understand cellular organization.
HU Berlin - IRI for the Life Sciences

Friday, 30.10.2015, 14:00h
Jim Count: OFF is the new ON: why DUSP5 might both accelerate and suppress oncogenic signalling
University of Bath

Friday, 16.10.2015, 14:00h
Benedikt Beckmann: Development of novel methods to study RNA-protein interactions during infection
IRI for the Life Sciences HU Berlin

Friday, 02.10.2015, 14:00h
Leonie Ringrose: Analog enhancer meets digital polycomb response element
HU Berlin - IRI for the life sciences

Tuesday, 22.09.2015, 15:00h
Andrea Y. Weiße - Mechanistic links between cellular trade-offs gene expression and growth
University of Edinburgh United Kingdom [host: Ralf]

Friday, 03.07.2015, 14:00h
Ronny Straube: Analyzing Regulatory Biological Networks: From Network Motifs to Network Modules
MPI Magdeburg

Friday, 29.05.2015, 14:00h
Jochen Prehn: Systems modelling of cell death signalling in cancer:Towards novel predictive stratification tools.
Royal College of Surgeons in Ireland

Friday, 22.05.2015, 14:00h
Jan-Hendrik Hofmeyr: Fragile yet Persistent: Self-Fabrication asthe Key to Life
Universiteit van Stellenbosch / WiKo

Monday, 11.05.2015, 15:00h
Erik Arner - Dynamic enhancer usage in transitioning mammalian cells
RIKEN Yokohama Japan

Friday, 08.05.2015, 14:00h
Johannes Jäger: Life's attractors: the evolutionary and developmental dynamics of the gap gene network
CRG Barcelona / WiKo Berlin

Wednesday, 06.05.2015, 10:30h
Workshop "Evolution and Optimality in Cellular Systems"
Thomas Pfeiffer / Song Feng / Stefan Müller / Leif Blaese / Orkun Soyer / Ulrich Tillich / Tobias Grosskopf / Meike Wortel

Friday, 10.04.2015, 14:00h
Mini-Symposium: Metabolic Network Analysis

Friday, 06.03.2015, 14:00h
Pål Westermark - Applying Laplace-transforms in Modeling - Part 2

Friday, 13.02.2015, 14:00h
Pål Westermark - Applying Laplace-transforms in Modeling - An Introduction

Friday, 21.11.2014, 14:00h
Claudia Acquisti
Westfälische Wilhelms-Universität Münster [host: Hanspeter]

Friday, 31.10.2014, 14:00h
Kajetan Bentele - Phenotypic stress persistence in yeast: Molecularmechanism and functional consequences
Weizmann Institute of Science

Friday, 17.10.2014, 14:00h
Zhike Zi - Quantitative analysis of TGF-beta signaling dynamics
MPI Molecular Genetics

Friday, 26.09.2014, 14:00h
Diego A. Oyarzún - Optimality feedback and noise in genetic regulation of metabolism
Imperial College London UK [host: Ralf]

Thursday, 21.08.2014, 14:00h
Nikolaus Schultz (MSKCC): Cacer Genomics /

Friday, 27.06.2014, 14:00h
Mattias Rydenfelt: The Transcription Factor Titration Effect Dictates Level of Gene Expression
California Institute of Technology [host: Nils]

Friday, 23.05.2014, 14:00h
Ryan Kellogg - NFkB signal processing under dynamic input
ETH Zürich [host: Hanspeter]

Friday, 09.05.2014, 14:00h
Alexander Skupin - Multiscale approaches to brain energy metabolismfrom the perspective of Parkinson's disease
University of Luxembourg [host: Manuela]

Friday, 04.04.2014, 14:00h
William Schwartz - In Search of Circadian Synchrony
University of Massachusetts Medical School [host: Hanspeter]

Friday, 24.01.2014, 14:00h
Jun Yan - De novo purine synthesis mediates circadian control of cell cycle in zebrafish
[host: Hanspeter] CAS-MPG Partner Institute for Computational Biology Shanghai

Friday, 10.01.2014, 14:00h
Celine Feillet - Models of clock and cell cycle coupling
Institute of Biology Valrose Nice [host: Hanspeter]

Friday, 13.12.2013, 14:00h
Ann Ehrenhofer-Murray - Molecular views of the yeast epigenome
HU Berlin [host: Hanspeter]

Friday, 29.11.2013, 14:00h
Uli Stelzl - Coordination of post-translational modifications in human protein interaction networks
MPI Molecular Genetics Berlin

Friday, 22.11.2013, 14:00h
Wolfram Liebermeister - Cost-benefit analysis of metabolic models with periodic perturbations
Charite Berlin

Friday, 15.11.2013, 14:00h
Oliver Ebenhöh - Exploring the diurnal regulation of starch metabolism in plants with mathematical models
University of Aberdeen and GFZ German Centre for Geosciences Potsdam

Friday, 08.11.2013, 14:00h
Mini-Symposium: Metabolic Network Analysis

Friday, 26.07.2013, 14:00h
Elad Noor - Connecting Pathway Thermodynamics to Enzyme Investment
Weizmann Institute of Science [host: Ralf]

Friday, 05.07.2013, 14:00h
Stefan Schuster - Cells in the Prisoner’s Dilemma: Warburg effect survival of the weakest and colours of muscle tissue
Friedrich-Schiller-University Jena [host: Ralf]

Friday, 17.05.2013, 14:00h
Himadri Pakrasi - A day and a night in the life of a photosyntheticbacterium
Washington University in St. Louis [host: Ralf]

Friday, 26.04.2013, 14:00h
Jörn Schmiedel - MicroRNAs decrease intrinsic noise and improve stoichiometric co-expression
ITB HU Berlin

Thursday, 21.03.2013, 14:00h
Anna-Carina Jungkamp: In vivo and transcriptome-wide identificationof RNA binding protein target sites
MDC Berlin

Friday, 08.03.2013, 14:00h
Andrea Ciliberto - Mechanisms of adaptation to continous cell cyclearrest

Friday, 01.03.2013, 14:45h
Susanna Röblitz (Konrad-Zuse-Zentrum Berlin)
Systems biology andbeyond: From data to mathematical models

Friday, 01.03.2013, 14:00h
Jan Hasenauer (TU Munich)
Model-based assessment of proliferationdynamics: Application toimmune and cancer cells

Friday, 01.02.2013, 13:30h
Mini Symposium Models of Gene Regulation

Friday, 25.01.2013, 14:00h
Uwe Ohler
MDC and Duke University [host: Hanspeter]

Friday, 18.01.2013, 14:00h
Christian Bodenstein - Seasonal adaptation of circadian clocks - How network structure shapes SCN activity
Friedrich-Schiller-University Jena [host: Hanspeter]

Friday, 11.01.2013, 14:00h
Peter Dittrich Assessing Semantic Biological Information with Molecular Codes
Uni Jena

Friday, 14.12.2012, 14:00h
Georgi Muskhelishvili: Systemic organisational and structural-functional integration of the bacterial gene regulation
Jacobs University Bremen

Friday, 07.12.2012, 14:00h
Inna Lavrik - Dynamics of apoptosis signaling networks
Uni Magdeburg

Wednesday, 21.11.2012, 16:00h
Emmanuel Barilott: Modeling cancer signalling networks
Institute Curie Paris

Friday, 09.11.2012, 14:00h
Mini-Symposium oscillatory time series

Friday, 02.11.2012, 14:00h
Alexander Hoffmann: A Dynamical Code to specify Immune Responses

Friday, 12.10.2012, 14:00h
Ed Trifonov - Origin and evolution of genes and genomes. Life neverstopped emerging.
Genome Diversity Center Institute of Evolution University o

Friday, 21.09.2012, 14:00h
Daniel Hoffman: Retroviral Evolution in Patients and Populations
Universität Duisburg-Essen [host: Nils]

Friday, 20.07.2012, 14:00h
Andre Estevez-Torres: Molecular choreography within microfluidic reactors
CNRS Laboratory for photonics and nanostructures

Friday, 13.07.2012, 14:00h
Luca Giorgetti -Noncooperative Interactions between Transcription Factors and Clustered DNA Binding Sites Enable Graded Transcriptional Responses to Environmental Inputs
Institute Curie Paris

Friday, 06.07.2012, 11:30h
Gerhart Wagner: Bacterial sRNAs interplay of sRNAs and transcription factors
Uppsala Universitet

Friday, 06.07.2012, 10:00h
Peter Stadler: mRNA-like ncRNAs: mosaics of conservation and innovation
Uni Leipzig

Tuesday, 26.06.2012, 16:00h
Jana Stöckel: Novel insights into the metabolism of the cyanobacterium Cyanothece using omics level analyses
Washington University St. Louis MO

Friday, 22.06.2012, 14:00h
Matteo Barberis - Timing in Systems Biology: the Cell Cycle
HU Berlin

Friday, 08.06.2012, 14:00h
Martyn Amos - DNA computing
Manchester Metropolitan University

Friday, 04.05.2012, 14:00h
Herve Isambert: On the expansion of “dangerous” gene repertoires bywhole genome duplications in early vertebrates
Institut Curie Paris

Friday, 27.04.2012, 14:00h
Marc Lefranc – Robustness and flexibility of Ostreococcus tauri circadian clock
Université des Sciences et Technologies de Lille

Friday, 13.04.2012, 14:00h
Rainer Machne: Chromosomal domain organization und non-coding transcript associations of the yeast growth program

Friday, 30.03.2012, 14:00h
Christoph Schmal - Modeling a circadian clock's slave oscillator in Arabidopsis thaliana
Bielefeld University [host Hanspeter]

Friday, 23.03.2012, 14:00h
Nir Keren - Transition metals in photosynthetic organisms: What canlaboratory experiments teach us about what really happens in the environment?
The Hebrew University Jerusalem

Friday, 09.03.2012, 14:15h
Tal Dagan: Trends and barriers to lateral gene transfer in prokaryotes (Heinrich-Heine-Universität Düsseldorf)

Friday, 24.02.2012, 14:00h
Ilka Diester - Optogenetic versus electrical stimulation in the motor cortex
Ernst Strüngmann Institute (Frankfurt/Main)

Friday, 17.02.2012, 14:00h
Tim Beissbarth: Modelling drug resistance in breast cancer throughnetwork reconstruction based on longitudinal protein array data

Friday, 03.02.2012, 14:00h
Julia Rausenberger: Same photoreceptor - different action: dynamicnetwork tunes phytochrome A's response profile.
Hochschule für Life Sciences Nordwestschweiz - Uni Freiburg [Ho

Friday, 27.01.2012, 14:00h
Douglas B. Murray - Recent work on redox regulation in budding yeast
Keio University Japan [host: Ralf]

Friday, 13.01.2012, 14:00h
Hauke Busch + Melanie Boerries : Deciphering in vitro cell-cell communication between keratinocytes and fibroblasts using communication theoretic approaches
FRIAS Uni Freiburg [host: Nils]

Friday, 06.01.2012, 14:00h
Sarah Reece - Evolution of survival strategies: the circadian coordination of malaria infections
University of Edinburgh [host: Hanspeter]

Friday, 16.12.2011, 14:00h
Ines Thiele - A community-generated reconstruction of the human metabolic network
University of Iceland [host: Ralf]

Friday, 09.12.2011, 14:00h
Rolf Wagner: Non-coding RNAs in bacteria – versatile regulators forgrowth adaptation and viral defence
Professor HHU Düsseldorf

Monday, 28.11.2011, 15:00h
Deborah Marks - Protein Structure from High Throughput Sequencing
Harvard Medical School

Friday, 25.11.2011, 14:00h
Chris Sander - Perturbation Cell Biology and Cancer
Memorial Sloan Kettering Cancer Center

Friday, 18.11.2011, 14:00h
Tim Kolmsee - The role of small regulatory RNAs and the codon-usagein the regulation of the RpoS-subunit of RNA polymerase in E. coli

Friday, 11.11.2011, 14:00h
Ladislav Nedbal - On the dynamics of cyanobacterial bioenergetics
Brno [host: Ralf]

Friday, 04.11.2011, 14:00h
Alexander Loewer
MDC Berlin [host: Nils]

Friday, 21.10.2011, 14:00h
Steffen Waldherr - Dynamical robustness from biomolecular networksto interacting cell populations
Universität Stuttgart [host: Ralf]

Friday, 14.10.2011, 14:00h
Rainer Machne and Stefan Mueller - Modelling a Photobioreactor: anopen discussion
Universität Wien/ITB

Friday, 07.10.2011, 14:00h
Pål Westermark - Cellular Aging and the Circadian Clock

Friday, 30.09.2011, 14:00h
Rainer Machne - Metabolic feedback on chromatin structure may gatetranscription during respiratory oscillations
[host: Ralf]

Thursday, 28.07.2011, 14:00h
Alexander Shaw - Developing Models of the Mammalian Cell S Phase
Manchester Interdisciplinary Biocentre University of Manchest

Friday, 22.07.2011, 14:00h
Stefan Müller - Towards quantitative models of cellular growth dyna
Radon Institute for Computational and Applied Mathematics (RICA

Friday, 15.07.2011, 14:00h
Morten Ernebjerg: Macroscopic Structure in Microbial Communities
Harvard Medical School [host: Nils]

Friday, 15.07.2011, 13:00h
Jens Georg: A hidden layer of genetic information - Regulatory nonprotein-coding RNAs in Synechocystis PCC6803
ALU Freiburg AG Hess

Friday, 08.07.2011, 14:00h
Fernando de la Cruz: Conjugation
Universidad de Cantabria [host: nils+ilka]

Friday, 01.07.2011, 14:00h
Rupert Mutzel: Long-term continuous cultivation of a microbial prey
FU Berlin Institut für Biologie Mikrobiologie II

Friday, 17.06.2011, 14:00h
Caroline Friedel - High resolution profiling of RNA synthesis and decay
University Heidelberg [host: Nils]

Friday, 27.05.2011, 14:00h
Katja Tummler: Deterministic and Stochastic Approaches for ModelingBiological Systems
Vorstellung für Diplomarbeit

Friday, 20.05.2011, 14:00h
Sabrina Hoffmann - Minimal flux modes: A conceptually new flux balance approach for the prediction metabolic fluxes
Charité Berlin [host: Ralf]

Friday, 13.05.2011, 14:00h
Heinrich Huber - Collateral Benefit: Systems Models and Live Cell Imaging in Programmed Cell Death
Royal College of Surgeons in Ireland [host: Nils]

Friday, 06.05.2011, 14:00h
Paul Thaben - Bioinformatic analysis of a genomewide shRNA-Screen for regulators of the mamalian Clock
Charité [host: Pål]

Friday, 29.04.2011, 14:00h
Lutz Brusch - Regulation of membrane identity in the endocytic pathway
TU Dresden [host: Nils]

Friday, 15.04.2011, 14:00h
Mikael Huss - How predictable is transcription factor binding?
SciLifeLab Stockholm [host: Pål]

Friday, 08.04.2011, 14:00h
Jens Timmer - Data Analysis and Modeling of Dynamic Processes in the Life Sciences
Institute of physics University of Freiburg [host: Nils]

Friday, 01.04.2011, 14:00h
Karin Mitosch - Bistability in bacterial metabolism: the role of flux noise and how cells can stabilize their decisions
[host: Pål]

Friday, 25.03.2011, 14:00h
Jaap Kaandorp - Computational modelling and analysis of spatio-temporal gene regulation and cell movement in embryogenesis
University of Amsterdam [host: Nils]

Friday, 18.03.2011, 14:00h
Julio Saez-Rodriguez - Modular Analysis of Signaling Networks
EMBL-EBI [host: Nils]

Friday, 11.03.2011, 14:00h
Guillaume Cogne - Constraint-based modeling and in silico analysisof Chlamydomonas reinhardtii photoautotrophic metabolism
University of Nantes [host: Ralf]

Friday, 04.03.2011, 14:00h
Natalie Stanford - Developing a minimal data approach to large-scale kinetic model construction in Sacchromyces cerevisiae
University of Manchester [host: Ralf]

Friday, 25.02.2011, 14:00h
Magnus Rattray - Regulatory network inference using probabilistic gene regulation models
University of Sheffield [host: Nils]

Friday, 11.02.2011, 14:00h
Hands-on tutorial on flux-balance analysis (FBA) with FASIMU
material for preparation:

Friday, 04.02.2011, 14:00h
Jiří Jablonský - Current approaches in kinetic modeling: The lightvs dark photosynthetic reactions in cyanobacteria
University of Rostock [host: Ralf]

Wednesday, 02.02.2011, 14:00h
Kevin Foster - Social Evolution in Microbes
St John's College Oxford [host: Ralf]

Friday, 28.01.2011, 14:00h
Kevin Thurley - Intrinsically noisy Ca(2+) dynamics exhibit functional robustness - insights about cell-signalling from a new modelling technique combined with life-cell imaging
MDC Berlin [host: Nils]

Friday, 17.12.2010, 14:00h
Alexis Webb - Heterogeneous oscillators benefit systems - Lessonsfrom in vitro and in silico approaches
MPI of Molecular Cell Biology and Genetics Dresden [host: Hanspeter]

Friday, 10.12.2010, 14:00h
Stefan Klumpp - Growth-rate dependent effects on gene expression inbacteria
MPI für Kolloid- und Grenzflächenforschung Potsdam [host: Nils]

Friday, 03.12.2010, 14:00h
Olaf Weiss - stochastic risk modelling in financial/insurance regulation - Bundesanstalt für Finanzdienstleistungsaufsicht
[host: Nils]

Friday, 26.11.2010, 14:00h
Daniel Santa Cruz Damineli: Unraveling the structure of two-oscillator circadian systems using conflicting environmental cues
ITQB Lisboa group of Andreas Bohn

Friday, 19.11.2010, 14:00h
Christian Fleck - Pattern formation
Universität Freiburg [host: Nils]

Friday, 12.11.2010, 14:00h
Wassim Abou-Jaoudé - Oscillations and bistability in the p53-Mdm2 network
INRIA France [host: Hanspeter]

Friday, 05.11.2010, 14:00h
Matthias Selbach: Genome-wide parallel quantification of mRNA and protein levels and turnover in mammalian cells
MDC Berlin

Friday, 22.10.2010, 14:00h
Elke Dittmann: Temporal and spatial heterogeneity of cyanobacteria
Universität Potsdam

Friday, 15.10.2010, 13:00h
Annegret Wilde: The function of regulatory RNA and the RNA chaperone Hfq in cyanobacteria
JLU Gießen

Friday, 23.07.2010, 14:00h
Katharina Nöh (FZ Juelich): Tools for Metabolome-based 13C Flux Analysis - Challenges and Future Perspectives
Title: tba

Friday, 16.07.2010, 14:00h
Berenike Maier: Conotrolling molecular motors in bacteria
Uni Muenster [host: Ilka]

Friday, 09.07.2010, 14:00h
Friedrich Simmel: Artificial molecular devices and reaction networks based on nucleic acids
TU Muenchen [host: Ilka & Nils]

Friday, 02.07.2010, 14:00h
Boris Kholodenko: Cell signalling dynamics in space and time
University College Dublin [host: Nils]

Friday, 25.06.2010, 14:00h
Jens Rupprecht (MPIMP Golm): From systems biology to fuel - the potential of systems biology to improve biofuel production

Friday, 11.06.2010, 14:00h
Katja Nowick: Evolutionary and functional characterization of transcription factors in primates
host: Hanspeter Herzel

Friday, 21.05.2010, 14:00h
Peter Swain
University of Edinburgh [host: Marcus]

Tuesday, 11.05.2010, 16:30h
Mans Ehrenberg: Theory of DNA sequence dependent variation of speedand accuracy of operon transcription
University of Upsala [host: Nils]

Friday, 07.05.2010, 14:00h
Debora Marks: A system-level approach to microRNA regulation
Harvard Medical School [host: Hanspeter]

Friday, 16.04.2010, 14:00h
Barbara Di Ventura
Uni Heidelberg [host: Markus]

Friday, 09.04.2010, 14:00h
Frank Bruggeman: Eukaryotic transcription: A molecular ratchet prone to burst
Centre for Mathematics and Computer Science Amsterdam [host:Nils]

Friday, 26.03.2010, 14:00h
Marc Friedlaender: Discovery and profiling of small RNAs using deepsequencing
MDC Berlin [host: Michael]

Friday, 19.03.2010, 14:00h
Helge Roider: CpG-depleted promoters harbor tissue-specific transcription factor binding signals
MPI for Molecular Genetics [host: Hanspeter]

Friday, 12.03.2010, 15:00h
Rebecca Rose: Structural characterization of macromolecular systemsusing native mass spectrometry
Netherlands Proteomics Centre Utrecht University

Friday, 12.03.2010, 14:00h
Steffen Klamt: Qualitative modeling of cellular signaling networks:Concepts algorithms and application
MPI Magdeburg [host: Nils]

Friday, 05.03.2010, 14:00h
Martin Falcke: Random and reliable: Stochasticity and robustness
MDC Berlin [Hanspeter]

Friday, 26.02.2010, 14:00h
Carsten Carlberg: Systems biology approaches to nuclear receptor signaling
Université du Luxembourg [Nils]

Friday, 19.02.2010, 14:00h
Alexander Skupin: Torwards signaling in Chlamydomonas - About the clock and the heat shock response
MPI for Molecular Plant Physiology Potsdam Golm

Friday, 12.02.2010, 14:00h
Tom Schneider: Molecular Information Theory
National Institutes of Health in Frederick MD [host: Hanspeter]

Friday, 05.02.2010, 14:00h
Christian Brettschneider: A sequestration feedback determines dynamics and temperature entrainment of the KaiABC circadian clock
Institute for Theoretical Biology Humboldt University Berlin

Friday, 29.01.2010, 14:00h
Szymon Kielbasa: LAST - an efficient algorithm for comparing large repeat-rich sequences
MPI Molecular Genetics Berlin [host: Ilka]

Friday, 22.01.2010, 14:00h
Anne Rediger: Characterization of hypothalamic G-protein coupled receptors which are involved in weight regulation
Charité Berlin

Friday, 15.01.2010, 14:00h
Hanspeter Herzel: Diffusion as a non-stationary stochastic process
Institute for Theoretical Biology Charité Berlin

Friday, 08.01.2010, 10:00h
Workshop Managing and curating Biological Pathways

Friday, 18.12.2009, 14:00h
Zoya Ignatova: Pausing the ribosomal traffic: an integrative view through molecular
Universitaet Potsdam [Nils]

Friday, 04.12.2009, 14:00h
José Faro
Universidade de Vigo