Fabian Fröhlich

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Jan HasenauerUniversität BonnVerified email at uni-bonn.de
Fabian J TheisHelmholtz Munich, Technical University of MunichVerified email at helmholtz-muenchen.de
Daniel WeindlHelmholtz MunichVerified email at helmholtz-muenchen.de
Paul StaporInstitute of Computational Biology, Helmholtz Center, MunichVerified email at helmholtz-muenchen.de
Carolin LoosData Scientist at Roche Diagnostics GmbHVerified email at roche.com
Leonard SchmiesterUniversity of Oslo, Faculty of MedicineVerified email at medisin.uio.no
Julio R. Banga ( ORCID 0000-0002-42...Research Professor, MBG-CSIC, Pontevedra (Spain)Verified email at csic.es
Peter K. SorgerHarvard Medical SchoolVerified email at hms.harvard.edu
Alejandro F. VillaverdeUniversidade de VigoVerified email at uvigo.gal
Yannik SchälteUniversity of Bonn and Helmholtz Center MunichVerified email at uni-bonn.de
Atefeh KazeroonianProject Leader, Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, TechnischeVerified email at tum.de
Jeremy L MuhlichDirector of Software Engineering, Harvard Medical School Laboratory of Systems PharmacologyVerified email at hms.harvard.edu
Matthias HeinigInstitute of Computational Biology, Helmholtz Zentrum MünchenVerified email at helmholtz-muenchen.de
Dilan PathiranaUniversity of BonnVerified email at uni-bonn.de
Luca GerosaGenentech, Inc.Verified email at gene.com
Thomas Ligonindependent scientistVerified email at thomassligon.info
Joachim RaedlerProfessor für Physik, LMU MünchenVerified email at lmu.de
Denis SchapiroGroup Leader at the Heidelberg University HospitalVerified email at bioquant.uni-heidelberg.de
Gregory J. BakerAmerican Cancer Society (ACS) Postdoctoral Fellow, Harvard Medical SchoolVerified email at hms.harvard.edu
Lian YiFlorida State UniveristyVerified email at my.fsu.edu

Fabian Fröhlich

Francis Crick Institute

Verified email at crick.ac.uk - Homepage

Computational Biology


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Scalable parameter estimation for genome-scale biochemical reaction networks F Fröhlich, B Kaltenbacher, FJ Theis, J Hasenauer PLoS computational biology 13 (1), e1005331, 2017	137	2017
Benchmarking optimization methods for parameter estimation in large kinetic models AF Villaverde, F Fröhlich, D Weindl, J Hasenauer, JR Banga Bioinformatics 35 (5), 830-838, 2019	123	2019
Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model F Fröhlich, T Kessler, D Weindl, A Shadrin, L Schmiester, H Hache, ... Cell Systems, 2018	116	2018
PESTO: Parameter EStimation TOolbox P Stapor, D Weindl, B Ballnus, S Hug, C Loos, A Fiedler, S Krause, ... Bioinformatics, 2017	97	2017
GenSSI 2.0: Multi-experiment structural identifiability analysis of SBML models TS Ligon, F Fröhlich, OT Chi, JR Banga, E Balsa-Canto, J Hasenauer Bioinformatics, 2017	83	2017
Inference for stochastic chemical kinetics using moment equations and system size expansion F Fröhlich, P Thomas, A Kazeroonian, FJ Theis, R Grima, J Hasenauer PLoS computational biology 12 (7), e1005030, 2016	77	2016
Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells L Gerosa, C Chidley, F Fröhlich, G Sanchez, SK Lim, J Muhlich, JY Chen, ... Cell Systems, 2020	60*	2020
Uncertainty Analysis for Non-identifiable Dynamical Systems: Profile Likelihoods, Bootstrapping and More F Fröhlich, FJ Theis, J Hasenauer Computational Methods in Systems Biology 8859, 61-72, 2014	57	2014
PEtab—Interoperable specification of parameter estimation problems in systems biology L Schmiester, Y Schälte, FT Bergmann, T Camba, E Dudkin, J Egert, ... PLOS Computational Biology 17 (1), e1008646, 2021	50	2021
CERENA: ChEmical REaction Network Analyzer—a toolbox for the simulation and analysis of stochastic chemical kinetics A Kazeroonian, F Fröhlich, A Raue, FJ Theis, J Hasenauer PloS one 11 (1), e0146732, 2016	46	2016
Parameter estimation for dynamical systems with discrete events and logical operations F Fröhlich, FJ Theis, JO Rädler, J Hasenauer Bioinformatics 33 (7), 1049-1056, 2017	42	2017
Efficient parameterization of large-scale dynamic models based on relative measurements L Schmiester, Y Schälte, F Fröhlich, J Hasenauer, D Weindl Bioinformatics 36 (2), 594-602, 2020	37	2020
AMICI: High-performance sensitivity analysis for large ordinary differential equation models F Fröhlich, D Weindl, Y Schälte, D Pathirana, Ł Paszkowski, GT Lines, ... Bioinformatics 37 (20), 3676-3677, 2021	34	2021
A Hierarchical, Data-Driven Approach to Modeling Single-Cell Populations Predicts Latent Causes of Cell-To-Cell Variability C Loos, K Moeller, F Fröhlich, T Hucho, J Hasenauer Cell systems 6 (5), 593-603. e13, 2018	32	2018
Scalable inference of ordinary differential equation models of biochemical processes F Fröhlich, C Loos, J Hasenauer Gene Regulatory Networks: Methods and Protocols, 385-422, 2019	31	2019
Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis P Stapor, F Fröhlich, J Hasenauer Bioinformatics 34 (13), i151-i159, 2018	31*	2018
Sparse control of force field dynamics M Bongini, M Fornasier, F Frcöhlich, L Haghverdi 2014 7th International Conference on NETwork Games, COntrol and OPtimization …, 2014	31*	2014
A protocol for dynamic model calibration AF Villaverde, D Pathirana, F Fröhlich, J Hasenauer, JR Banga Briefings in Bioinformatics 23 (1), bbab387, 2022	27	2022
Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection F Fröhlich, A Reiser, L Fink, D Woschée, T Ligon, FJ Theis, JO Rädler, ... NPJ systems biology and applications 4 (1), 42, 2018	24	2018
Fides: Reliable trust-region optimization for parameter estimation of ordinary differential equation models F Fröhlich, PK Sorger PLOS Computational Biology 18 (7), e1010322, 2022	9	2022

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