Staff

Source: HMGU

Fabian Fröhlich
PhD Student

Phone: +49 89 3187-4855
E-mail
Building/Room: 58a / 009

GoogleScholar  ResearchGate 

Short CV

I studied Mathematics in Biosciences at the Technische Universität München from 2008 until 2013. The topics of my studies were numerical mathematics, dynamical systems, physics and molecular biology. During my studies, I successfully participated in the international Genetically Engineered Machine competition multiple times (see below) which led me to pursue a career in computational biology. After my graduation in 2013 I received a fellowship from the Graduate School of Quantitative Biosciences Munich(QBM) and started working as a PhD Student at the Institute for Computational Biology. I am the student representatitive for the Class of 2013 in the QBM graduate school.

Research

I am interested in efficient methods for parameter estimation, uncertainty analysis and model selection for pathway-scale to genome-scale mechanistic dynamic models. These models typically include

  • moment approximations (System Size Expansion, Moment Equations) for stochastic biological processes
  • non-linear mixed effect models for heterogeneous cell populations
  • dynamic models with discrete events 
  • reaction rate equation models of (cancer related) signal transduction pathways

Software

I am a co-developer of the following software packages:

AMICI: a MATLAB-based toolbox for the generation of scalable simulation and sensitivity analysis routines for ODE and DAE models.

PESTO: a MATLAB-based toolbox for parameter estimation featuring local gradient based and global optimization schemes

MEMOIR: a MATLAB-based toolbox for Multi-Experiment Mixed Effect Modelling

 CERENA: a MATLAB-based toolbox for the simulation and analysis of chemical reaction networks using approximations of the Chemical Master Equation solution statistics.

Publications

  1. Loos, C; Moeller, K.; Fröhlich, F.; Hucho, T.; Hasenauer, J.; Mechanistic hierarchical population model identifies latent causes of cell-to-cell variability. submitted
  2. Fröhlich, F. ; Kaltenbacher, B. ; Theis, F.J. ; Hasenauer, J. Scalable parameter estimation for genome-scale biochemical reaction networks. PLoS Computational Biology13(1): e1005331 (2017)
  3. Fröhlich, F. ; Theis, F.J. ; Rädler, J.O. ; Hasenauer, J. 
    Parameter Estimation for Dynamical Systems with Discrete Events and Logical Operations. Bioinformatics btw764 (2016)
  4. Fröhlich, F. ; Thomas, P. ; Kazeroonian, A. ; Theis, F.J. ; Grima, R. ; Hasenauer, J. Inference for stochastic chemical kinetics using moment equations and system size expansion. PLoS Comput Biol 12(7):e1005030 (2016)
  5. Kazeroonian, A.; Fröhlich, F. ; Raue, A. ; Theis, F.J. ; Hasenauer, J. CERENA: ChEmical REaction Network Analyzer - A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics. PLoS ONE 11:e0146732 (2016)
  6. Fröhlich, F. ; Theis, F.J. ; Hasenauer, J. Uncertainty analysis for non-identifiable dynamical systems: Profile likelihoods, bootstrapping and more. Lecture Notes Comp. Sci. 8859, 61-72 (2014)
  7. Fröhlich, F. ; Hross, S. ; Theis, F.J. ; Hasenauer, J. Radial basis function approximations of Bayesian parameter posterior densities for uncertainty analysis. Lecture Notes Comp. Sci. 8859, 73-85 (2014)
  8. Morath, V. ; Truong, D.J.J. ; Albrecht, F. ; Polte, I. ; Ciccone, R.A. ; Funke, L.F. ; Reichart, L. ; Wolf, C.G. ; Brunner, A.D. ; Fischer, K. ; Schneider, P.C. ; Brüggenthies, J.B. ; Fröhlich, F. ; Wiedemann, G. ; Reski, R. ; Skerra, A. Design and characterization of a modular membrane protein anchor to functionalize the moss Physcomitrella patens with extracellular catalytic and/or binding activities. ACS Synth. Biol. 3, 990-994 (2014)
  9. Bongini, M. ; Fornasier, M. ; Fröhlich, F. ; Hagverdi, L. Sparse control of force field dynamics, International Conference on NETwork Games, COntrol and  OPtimization (2014)

Teaching

  • Parameter Estimation for Dynamic Biological Systems I, summer term 2015
  • Parameter Estimation for Dynamic Biological Systems II, winter term 2015/2016

iGEM

I successfully participated in the iGEM competition multiple times:

  • 2016 (Paris-Saclay, Mentor) iJAIME
  • 2014 (LMU, Supervisor) BaKillus 
    • Best Wiki (overgrad, worldwide)
  • 2013 (TUM, Supervisor) PhyscoFilter
    • 1st Runner Up (undergrad, worldwide)
    • Best Environmental Project (undergrad, worldwide)
    • Best Wiki (undergrad, europe)
    • Advanced to Worldwide Jamboree
  • 2012 (TUM, Student) TUM-Brew
    • Sweet Sixteen (worldwide)
    • Advanced to Worldwide Jamboree
  • 2011 (TUM, Student) E.XPRESS3D
    • Advanced to Worldwide Jamboree