FriSBi schedule

The 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 2019

  • Oct 18: Yiteng Dang (TU Delft) – Collective dynamics in systems of communicating secrete-and-sense cells
  • Oct 25: Oleksandr Ostrenko (Hannezo and Heisenberg Groups) – Mathematical Modeling of Transport Processes in the Liver: Bile Flow and Vesicular Trafficking
  • Nov 8: Christoph Flamm (University of Vienna) – TBC
  • Nov 22: Mehmet Can Ucar (Hannezo Group) – Collective behaviour of molecular motors
  • Nov 29: Diana Fusco (University of Cambridge) – The role of spatial constraints in evolution: insights from microbes and phage
  • Dec 6: Nick Jones (Imperial College, London) – Stochastic Survival of the Densest and Invasion Waves of Disadvantaged Mutations In Muscle Ageing
  • Dec 13: Michal Komorowski (IPPT PAN, Warsaw) – TBC
  • Jan 17: Jens Elgeti (Forschungszentrum Jülich) – TBC

Spring 2019

  • March 1:  Georgia Squyres (Harvard University) – The role and regulation of FtsZ dynamics in bacterial cytokinesis
  • March 18: Chase Broedersz (LMU Munich) – Dynamics of Confined Cell Migration
  • March 22: Bor Kavcic (Tkacik Group) – Perturbations of protein synthesis — from antibiotics to genetics and physiology
  • March 25: Bart Smeets (KU Leuven) – Tissue structure and dynamics from active cell mechanical properties Theory and computational models
  • April 5: Suyash Naik (IST Austria) – Tissue mechanics of a somersault
  • April 12: Trevor  Graham (Barts Cancer Institute QMUL) – Measuring evolutionary dynamics of human cancers from genomic data
  • April 15: Mike Springer (Harvard Medical School) – How and why cells decouple the decisions of whether and how strongly to express a gene
  • April 18: Rudolf Hanel (MedUni Vienna) – Caught in the act: Elements of an Emerging Theory of Complex Adaptive Processes and their Applications
  • April 26: Aditya Gilra (Tkacik Group) – Biologically-plausible learning in neural networks for movement control and cognitive tasks
  • May 3: David Wolpert (Santa Fe Institute) – Fundamental limits on the thermodynamics of circuits
  • May 10: Kathrin Tomasek (Guet Group) – How E. coli trick our immune system during UTIs
  • May 17: Thomas Sokolowski (Tkacik Group) – Deriving the Drosophila gap gene system ab-initio from an optimization principle
  • May 24: Shayan Shamipour (Heisenberg Group) – Phase Segregation in Zebrafish Oocytes
  • June 7: Mantas Gabrielaitis (Tkacik Group) – Efficient coding at the first synapse in the auditory pathway
  • June 14: Wiktor Mlynarski (Tkacik Group) – Adaptability and efficiency in neural coding
  • July 19: Stefan Münster (MPI Dresden) – An integrin-mediated adhesion between embryonic tissue and vitelline membrane affects gastrulation of insects
  • July 25: Dagmar Iber (ETH Zurich) – From Networks to Function: Computational Models of Organogenesis
  • August 6: Nir Gov (Weizmann Institute) – The physics of cooperative transport in groups of ants

Fall 2018

  • September 14: Francesco Romano (University of Michigan) – Liquid plug formation in human airways
  • September 21: Pavel Payne (Bollback group) – CRISPR, herd immunity and transduction – the unexpected ways of how bacteria have sex
  • October 19: Rok Grah (Guet and Tkacik groups) – Biophysically realistic genotype-phenotype maps for genetic regulatory networks
  • October 23: Primoz Ziherl (Jožef Stefan Institute) – 3D vertex models of organoids
  • November 9: Michael Riedl (Hof group) – The influence of shear stress on endothelial cell proliferation and the optimization of biofluidic transport networks
  • November 16: Dmitry (Kondrashov group) – How to find epistasis in fitness landscapes?
  • November 23: Barbara Casillas Perez (Cramer Group) – Individual and group-level decisions in ants
  • November 27: Rosalind Allen (University of Edinburgh) – Modelling how cell wall targeting antibiotics work
  • December 7: Michal Hiedik (Barton and Tkacik groups) – Architecture of gene expression and gene regulation
  • December 14: Urban Bezeljak (Loose Group) – Cooperativity in Rab regulatory networks
  • January 11: Martin Lenz (LPTMS of CNRS and Université Paris-Sud) – Why does actomyosin contract?
  • January  18: Bernat Corominas-Murtra (Hannezo Group) – Global Rex1 expression patterns and the loss of pluripotency: The simplest dynamical hypothesis
  • January 25: Hyun Youk (Delft University of Technology) – Quantitative principles of re-entering cell-cycle from quiescence
  • February 1: Kirti Jain (Guet Group) – Dynamics of marRAB system in E. coli
  • February 22: Stefanie Widder (Medical University of Vienna and Center for Molecular Medicine of the Austrian Academy of Sciences) – Interactions and emergence in the lung microbiome of persons with cystic fibrosis

Spring 2018

    • March 1: Georg Pabst (University of Graz) – Physical insights on cell membrane function from complex mimetics
    • March 9: Rok Grah (Guet and Tkacik Groups) – Can we have specificity without stable complexes?
    • March 15: Peter Barancok (Comenius University in Bratislava) – Mathematical Model of Growth of Budding Yeast
    • March 23: Roshan Prizak (Barton and Tkacik Groups) – Crosstalk results in improved estimates of ligand concentrations
    • April 6: Nils Becker (University of Heidelberg) – Interferon codes in innate immunity / Hidden memory in cell-cycle times
    • April 13: Gasper Tkacik – Can noise speed up evolutionary search for fit sequences?
    • April 20: Thomas Jolou (University of Basel) – Revisiting diauxic growth: lessons from single-cell approaches
    • April 27: Edouard Hannezo – Mechano-chemical descriptions of active gels
    • May 4: Mike Hennessey (Hof Group) – Experimental droplet techniques for investigating codon survival probability
    • May 18: Namiko Mitarai (University of Copenhagen) – Phage vs. Bacteria: The art of war among the unseen majority
    • May 25: Marcin Zagorzski (Kicheva Group) – Source and target driven patterning in the developing spinal cord
    • June 8: Magdalena Steinrueck (Guet Group) – What makes a bacterial promoter? Observations from walks through random sequence space
    • June 18: Steffen Rulands (MPI Dresden) – Understanding cell fate regulation: from molecules to tissues

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: 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: 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.

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

Fall 2016

  • September 16: Qi Qin (Bollenbach group) – Dissecting the molecular basis of interactions between trimethoprim and two macrolide drugs
  • September 22: 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 : Pavel (Barton/Bollback group) – The dynamics of CRISPR-based herd immunity in phage-bacterial communities
  • October 13: 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

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)

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

Spring 2015

Fall 2014

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

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)

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)