FriSBi schedule

The Friday Systems Biology (FriSBi) seminar series is a forum for those interested in quantitative ways of understanding biological phenomena. We have local and invited speakers present interdisciplinary topics that we hope excites biologists, physicists, and computer scientists alike.

Welcome to join us in Mondi 3 at 15.00 on Fridays! (If not otherwise indicated below)

Fall 2018

14 September Liquid plug formation in human airways
Francesco Romano, University of Michigan

21 September CRISPR, herd immunity and transduction – the unexpected ways of how bacteria have sex
Pavel Payne, Bollback group

19 October Biophysically realistic genotype-phenotype maps for genetic regulatory networks
Rok Grah, Guet and Tkacik groups.

23 October 3D vertex models of organoids
Primoz Ziherl, Jožef Stefan Institute

9 November The influence of shear stress on endothelial cell proliferation and the optimization of biofluidic transport networks.
Michael Riedl, Hof group

16 November TBA
Dmitrii, Kondrashov group

23 November Individual and group-level decisions in ants.
Barbara Casillas Perez, Cramer Group

27 November (Tuesday 10am) TBA
Rosalind Allen, University of Edinburgh

7 December Architecture of gene expression and gene regulation
Michal Hiedik, Barton and Tkacik groups

14 December TBA
Urban Bezeljak, Loose Group

11 January Why does actomyosin contract?
Martin Lenz, LPTMS of CNRS and Université Paris-Sud

18 January TBA
Bernat Corominas-Murtra, Hannezo Group

25 January Quantitative principles of re-entering cell-cycle from quiescence
Hyun Youk, Delft University of Technology

1 February Dynamics of marRAB system in E. coli
Kirti Jain, Guet Group

8 February TBA
Calin Guet

22 February Interactions and emergence in the lung microbiome of persons with cystic fibrosis
Stefanie Widder, Medical University of Vienna and Center for Molecular Medicine of the Austrian Academy of Sciences

Spring 2018:

1 March (Thursday 15.00, Lab Building East Ground Floor)
Physical insights on cell membrane function from complex mimetics.
Georg Pabst, University of Graz

9 March Can we have specificity without stable complexes?
Rok Grah, Guet and Tkacik Groups

15 March (Thursday 13.00, Mondi 1)
Mathematical Model of Growth of Budding Yeast.
Peter Barancok, Comenius University in Bratislava

23 March Crosstalk results in improved estimates of ligand concentrations.
Roshan Prizak, Barton and Tkacik Groups

6 AprilInterferon codes in innate immunity / Hidden memory in cell-cycle times.
Nils Becker, University of Heidelberg

13 AprilCan noise speed up evolutionary search for fit sequences?
Gasper Tkacik

20 April    Revisiting diauxic growth: lessons from single-cell approaches.
Thomas Jolou, University of Basel

27 April    Mechano-chemical descriptions of active gels.
Edouard Hannezo

4 May   Experimental droplet techniques for investigating codon survival probability. 
Mike Hennessey, Hof Group

18 May    Phage vs. Bacteria: The art of war among the unseen majority.
Namiko Mitarai, University of Copenhagen

25 MaySource and target driven patterning in the developing spinal cord.
Marcin Zagorzski, Kicheva Group

8 June What makes a bacterial promoter? Observations from walks through random sequence space.
Magdalena Steinrueck, Guet Group

 

Schedule fall 2017:

  • Sept 22: Bor (Tkacik group) – The translation stage-specific effects on antibiotic susceptibility
  • Sept 29: Anna A (Tkacik and Guet Group) – Uneven partitioning, a structured population, and the question of whether it can bee seen?
  • Oct 5: (Thursday) Remy (Guet Group) – Shaping bacterial population behavior through computer-interfaced control of individual cells
  • Oct 13: Paulo (Loose Group) – Modulation of Z-ring Assembly by Bacterial Crosslinkers
  • Oct 19: (Thursday) Claudia (Guet Group) – Crosstalk between temperate phages
  • Nov 3: Kathrin (Guet Group)- Phase variation as a mechanism to establish recurrent (urinary tract) infections?
  • Nov 10: Sarah (Tkacik group) – Information estimation for dynamic, single-cell signals
  • Nov 17: Urban (Loose Group)-Rebuilding Rab5 activation in vitro
  • Nov 24: Maria (Friml and Seikhaus Group)-Plant root growth inhibition by auxin: the role of auxin transport
  • Dec 1: Srdjan (Barton and Guet Group)-predicting the expression of a promotor sequence using 1) convolutional neural networks and 2) biophysical models.

Schedule Spring 2017:

  • March 3: Claudia (Bollback and Guet group) – Does E. coli have a good or a bad memory?
  • March 10: Katka (Tkacik and Barton group) – Inference of probabilistic models of animal behavior
  • March 17: Marta (Bollenbach group) – Modulating the evolvability of antibiotic resistance
  • March 24: Anna (Guet group) – Comprehensive shuffling of relative gene order as a source of phenotypic diversity
  • March 31: Gasper (Tkacik group) – Information in a genetic network is optimally decoded to establish unique cell identities
  • April 7: Bor (Bollenbach and Tkacik group)  – Predicting bacterial growth in response to antibiotic combinations using growth laws 
  • April 21: Daniele (Tkacik group) – Statistical mechanics of metabolic networks
  • April 28: Urban (Loose group) – Rebuilding a signaling cascade from bottom up
  • May 5: Roshan (Tkacik group) – Evolution of new regulatory functions on biophysically realistic fitness landscapes
  • May 26: Natalia (Loose group) Reconstitution of bacterial cell wall synthesis
  • June 2: Thomas (Tkacik group) – Using eGFRD for particle-based stochastic simulation of simple synthetic promoter architectures
  • June 9: Bella and Rok(Guet group) – Gene amplification as a primitive means of gene regulation

Schedule Fall 2016:

  • September 16: Qi Qin (Bollenbach group) – Dissecting the molecular basis of interactions between trimethoprim and two macrolide drugs
  • September 22 (Thursday): Jakob (Henzinger/Tkacik group) – A stochastic modeling perspective of bacterial restriction modification systems
  • September 30: Nela (Guet group) – Activation of the MazF toxin promotes growth heterogeneity between single bacterial cells
  • October 6 (Thursday): Pavel (Barton/Bollback group) – The dynamics of CRISPR-based herd immunity in phage-bacterial communities
  • October 13 (Thursday): Matthias (Cremer group) – Viral diversity in ant communities
  • October 21: Maros (Guet group) – Temperate bacteriophages meet restriction-modification systems: The pioneers of Molecular Biology in an ecological context
  • October 28: Sarah (Tkacik group) – Estimating information jointly carried by multiple intracellular signals at a temporally-resolved, single-cell level 
  • November 11: Srdjan and Mato (Barton and Guet group) – Context Dependence in RNA Polymerase Binding
  • November 18: Andreas (Bollenbach group) – A growth-dependent negative feedback loop lowers the sensitivity to antibiotics
  • November 25: Magdalena (Guet group) – Genetic basis of chromosomal neighborhood effects on adaptive evolution of gene expression
  • December 2: Moritz (Guet group) – When being perfect is not good enough: Adaptation, Invariance, Internal Models and Differentiation
  • December 16: Fabienne (Bollback group) – The lac operon in the wild, part II: A natural genotype-phenotype map

Schedule Spring 2016:

  • March 4: Tobias (Guet group) – Asymmetry in bacteria: concepts, mechanisms and consequences
  • March 11: Fabienne (Bollback group) – Tales from the wild: uncovering the structure of a natural genotype-phenotype map
  • March 18: Tamar and Roshan (Barton and Tkacik group) – An evolutionary-biophysical model of subfunctionalization in gene regulation
  • April 1: Isabella (Guet group) – Amplifications as a crude means of gene regulation?
  • April 8: Anna K. (Kicheva group)
  • April 15: Jakob (Henzinger/Tkacik group)
  • April 22: Marcin (Bollenbach group)
  • May 13: Martin (Bollenbach group)
  • May 31 (Tuesday!): Veronika (Bollenbach group)
  • Jun 10: Hande (Bollback group)

Schedule Fall 2015:

  • October 16: Marta, Sebastian, Tiago (Bollenbach and Barton group) – Stress-induced mutagenesis: The more diverse the challenges, the better for the mutator.
  • October 23: Anna A. (Guet group) – Reiteration no. 1 of a model of asymmetric division at cell division
  • October 30: Gasper (Tkacik group) – Beyond the French Flag
  • November 06: Karin (Bollenbach group) – Cause and physiological relevance of acid stress induction by Trimethoprim in bacteria
  • November 13: Tomek (Tkacik group) – Constructing a predictive spatial-stochastic model of early embryogenesis
  • November 20: Moges KibretAntibiotics in the wild
  • November 27: Stefan Klumpp (U Göttingen), QSB seminar
  • December 04: Katka (Tkacik group) – How quantitative traits follow entropy maximization principle
  • December 10 (Thursday!): Karsten Kruse (U Saarland), QSB seminar
  • December 18: Lenka (Uhler group) – Inferring causality in gene expression
  • January 15: Georg (Tkacik group) – Biophysical constraints and the evolution of gene expression
  • January 29: Murat (Barton group) – Biophysical and evolutionary characteristics of RNA polymerase binding in E. coli
  • February 05: Sarah (Tkacik group) – Estimation of mutual information from pulsatile dynamics in yeast

Schedule Spring 2015:

Schedule Fall 2014:

  • September 11: Murat (Barton group)
  • September 26: Gasper (Tkacik group)
  • October 24: Mateusz (Heisenberg group)

Schedule Spring 2014:

  • February 06: Georg (Tkacik group)
  • February 21: Tamar (Barton group)
  • February 28: Martin (Graduate school)
  • March 21: Guillaume (Bollenbach group)
  • March 28: Maros (Guet group)
  • April 04: Pavel (Bollback group)
  • April 25: Karin (Bollenbach group)
  • June 27: Isa (Bollback group)
  • July 04: Marjon (Bollenbach group)

Schedule Fall 2013:

  • October 04: Georg (Tkacik group)
  • October 11: Hande (Bollback group)
  • November 21: Anna A. (Tkacik group)
  • November 22: Anna S. (Guet group)
  • November 29: Murat (Barton group)