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 WeindlUniversity of BonnVerified email at uni-bonn.de
Paul StaporInstitute of Computational Biology, Helmholtz Center, MunichVerified email at stapor.de
Peter K. SorgerHarvard Medical SchoolVerified email at hms.harvard.edu
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
Dilan PathiranaUniversity of BonnVerified email at uni-bonn.de
Carolin LoosData Scientist at Roche Diagnostics GmbHVerified email at roche.com
Yannik SchaelteUniversity of Bonn and Helmholtz Center MunichVerified email at uni-bonn.de
Luca GerosaGenentech, Inc.Verified email at gene.com
Jeremy L MuhlichDirector of Software Engineering, Harvard Medical School Laboratory of Systems PharmacologyVerified email at hms.harvard.edu
Alejandro F. VillaverdeUniversidade de VigoVerified email at uvigo.gal
Jia-Yun ChenHarvard Medical School; Stanford University; National Taiwan UniversityVerified email at hms.harvard.edu
Matthias HeinigInstitute of Computational Biology, Helmholtz Zentrum MünchenVerified email at helmholtz-muenchen.de
Hans Rudolf LehrachMax Planck Institut für Molekulare GenetikVerified email at molgen.mpg.de
Thomas Ligonindependent scientistVerified email at thomassligon.info
Atefeh KazeroonianProject Leader, Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, TechnischeVerified email at tum.de
Denis SchapiroGroup Leader at the Heidelberg University HospitalVerified email at bioquant.uni-heidelberg.de
Gregory J. BakerAssistant Professor, OHSU Knight Cancer InstituteVerified email at ohsu.edu

Fabian Fröhlich

Francis Crick Institute

Verified email at crick.ac.uk - Homepage

Computational Biology


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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	186	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	174	2018
Scalable parameter estimation for genome-scale biochemical reaction networks F Fröhlich, B Kaltenbacher, FJ Theis, J Hasenauer PLoS computational biology 13 (1), e1005331, 2017	174	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	137	2017
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	125	2020
PESTO: Parameter EStimation TOolbox P Stapor, D Weindl, B Ballnus, S Hug, C Loos, A Fiedler, S Krause, ... Bioinformatics, 2017	121	2017
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	105	2021
A protocol for dynamic model calibration AF Villaverde, D Pathirana, F Fröhlich, J Hasenauer, JR Banga Briefings in Bioinformatics 23 (1), bbab387, 2022	93	2022
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	90	2021
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	90	2016
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	74	2014
pyPESTO: a modular and scalable tool for parameter estimation for dynamic models Y Schälte, F Fröhlich, PJ Jost, J Vanhoefer, D Pathirana, P Stapor, ... Bioinformatics 39 (11), btad711, 2023	55	2023
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	55	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	54	2017
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	52	2018
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	51	2020
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	48*	2018
Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance F Fröhlich, L Gerosa, J Muhlich, PK Sorger Molecular Systems Biology 19 (2), e10988, 2023	44	2023
Fides: Reliable trust-region optimization for parameter estimation of ordinary differential equation models F Fröhlich, PK Sorger PLOS Computational Biology 18 (7), e1010322, 2022	43	2022
Scalable inference of ordinary differential equation models of biochemical processes F Fröhlich, C Loos, J Hasenauer Gene regulatory networks: methods and protocols, 385-422, 2018	42	2018

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