Generation of the CanPath prototype - a platform for predictive cancer pathway modeling | CanPathPro | Project | Results | H2020 | CORDIS

Resultado final

Set-up of a webpage platform for the interface between user/client and pipeline

Setup of a webpage platform for the interface between userclient and pipeline

Publicaciones

PEtab—Interoperable specification of parameter estimation problems in systems biology

Autores: Schmiester, Leonard; Schälte, Yannik; Bergmann, Frank T.; Camba, Tacio; Dudkin, Erika; Egert, Janine; Frölich, Fabian; Fuhrmann, Lara; Hauber, Adrian L.; Kemmer, Svenja; Lakrisenko, Polina; Loos, Carolin; Merkt, Simon; Müller, Wolfgang; Pathirana, Dilan; Raimúndez, Elba; Refisch, Lukas; Rosenblatt, Marcus; Stapor, Paul L.; Städter, Philipp; Wang, Dantong; Wieland, Franz-Georg; Banga, Julio R.
Publicado en: PLOS COMPUTATIONAL BIOLOGY, 2021, ISSN 1553-734X
Editor: Public Library of Science
DOI: 10.1371/journal.pcbi.1008646

Efficient gradient-based parameter estimation for dynamic models using qualitative data

Autores: Leonard Schmiester, Daniel Weindl, Jan Hasenauer
Publicado en: Bioinformatics, 2021, ISSN 1460-2059
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btab512

Benchmarking of numerical integration methods for ODE models of biological systems

Autores: Philipp Städter; Yannik Schälte; Leonard Schmiester; Jan Hasenauer; Jan Hasenauer; Paul Stapor
Publicado en: Nature, Edición 13, 2021, ISSN 0028-0836
Editor: Nature Publishing Group
DOI: 10.1038/s41598-021-82196-2

Models of Models: A Translational Route for Cancer Treatment and Drug Development

Autores: Lesley A. Ogilvie, Aleksandra Kovachev, Christoph Wierling, Bodo M. H. Lange, Hans Lehrach
Publicado en: Frontiers in Oncology, Edición 7, 2017, ISSN 2234-943X
Editor: Frontiers Media S. A.
DOI: 10.3389/fonc.2017.00219

PREMER: a Tool to Infer Biological Networks

Autores: Alejandro F. Villaverde, Kolja Becker, Julio R. Banga
Publicado en: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017, Página(s) 1-1, ISSN 1545-5963
Editor: IEEE Computer Society
DOI: 10.1109/TCBB.2017.2758786

PESTO: Parameter EStimation TOolbox

Autores: Paul Stapor, Daniel Weindl, Benjamin Ballnus, Sabine Hug, Carolin Loos, Anna Fiedler, Sabrina Krause, Sabrina Hroß, Fabian Fröhlich, Jan Hasenauer
Publicado en: Bioinformatics, Edición 34/4, 2017, Página(s) 705-707, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btx676

Structural Properties of Dynamic Systems Biology Models: Identifiability, Reachability, and Initial Conditions

Autores: Alejandro F Villaverde, Julio R Banga
Publicado en: Processes, Edición 5/4, 2017, Página(s) 29, ISSN 2227-9717
Editor: MDPI
DOI: 10.3390/pr5020029

Parameter identifiability analysis and visualization in large-scale kinetic models of biosystems

Autores: Attila Gábor, Alejandro F. Villaverde, Julio R. Banga
Publicado en: BMC Systems Biology, Edición 11/1, 2017, ISSN 1752-0509
Editor: BioMed Central
DOI: 10.1186/s12918-017-0428-y

Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering

Autores: Benjamin Ballnus, Steffen Schaper, Fabian J Theis, Jan Hasenauer
Publicado en: Bioinformatics, Edición 34/13, 2018, Página(s) i494-i501, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/bty229

Evaluation of Derivative-Free Optimizers for Parameter Estimation in Systems Biology

Autores: Yannik Schälte, Paul Stapor, Jan Hasenauer
Publicado en: IFAC-PapersOnLine, Edición 51/19, 2018, Página(s) 98-101, ISSN 2405-8963
Editor: Science Direct
DOI: 10.1016/j.ifacol.2018.09.025

Sufficiently Exciting Inputs for Structurally Identifiable Systems Biology Models

Autores: Alejandro F. Villaverde, Neil D. Evans, Michael J. Chappell, Julio R. Banga
Publicado en: IFAC-PapersOnLine, Edición 51/19, 2018, Página(s) 16-19, ISSN 2405-8963
Editor: Science Direct
DOI: 10.1016/j.ifacol.2018.09.015

Observability and Structural Identifiability of Nonlinear Biological Systems

Autores: Alejandro F. Villaverde
Publicado en: Complexity, Edición 2019, 2019, Página(s) 1-12, ISSN 1076-2787
Editor: John Wiley & Sons Inc.
DOI: 10.1155/2019/8497093

Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis

Autores: Paul Stapor, Fabian Fröhlich, Jan Hasenauer
Publicado en: Bioinformatics, Edición 34/13, 2018, Página(s) i151-i159, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/bty230

Hierarchical optimization for the efficient parametrization of ODE models

Autores: Hasenauer, Jan; Loos, Carolin; Krause, Sabrina
Publicado en: Bioinformatics Journal, Edición 2, 2018, Página(s) 4266-4273, ISSN 1460-2059
Editor: Oxford University
DOI: 10.1101/247924

Input-Dependent Structural Identifiability of Nonlinear Systems

Autores: Alejandro F. Villaverde, Neil D. Evans, Michael J. Chappell, Julio R. Banga
Publicado en: IEEE Control Systems Letters, Edición 3/2, 2019, Página(s) 272-277, ISSN 2475-1456
Editor: IEEE
DOI: 10.1109/lcsys.2018.2868608

Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model

Autores: Fabian Fröhlich, Thomas Kessler, Daniel Weindl, Alexey Shadrin, Leonard Schmiester, Hendrik Hache, Artur Muradyan, Moritz Schütte, Ji-Hyun Lim, Matthias Heinig, Fabian J. Theis, Hans Lehrach, Christoph Wierling, Bodo Lange, Jan Hasenauer
Publicado en: Cell Systems, Edición 7/6, 2018, Página(s) 567-579.e6, ISSN 2405-4712
Editor: Cell Press
DOI: 10.1016/j.cels.2018.10.013

Benchmarking optimization methods for parameter estimation in large kinetic models

Autores: Alejandro F Villaverde, Fabian Fröhlich, Daniel Weindl, Jan Hasenauer, Julio R Banga
Publicado en: Bioinformatics, Edición 35/5, 2018, Página(s) 830-838, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/bty736

GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models

Autores: Thomas S Ligon, Fabian Fröhlich, Oana T Chiş, Julio R Banga, Eva Balsa-Canto, Jan Hasenauer
Publicado en: Bioinformatics, Edición 34/8, 2017, Página(s) 1421-1423, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btx735

Structural Identifiability of Dynamic Systems Biology Models

Autores: Alejandro F. Villaverde, Antonio Barreiro, Antonis Papachristodoulou
Publicado en: PLOS Computational Biology, Edición 12/10, 2016, Página(s) e1005153, ISSN 1553-7358
Editor: Plos
DOI: 10.1371/journal.pcbi.1005153

On the relationship between sloppiness and identifiability

Autores: Oana-Teodora Chis, Alejandro F. Villaverde, Julio R. Banga, Eva Balsa-Canto
Publicado en: Mathematical Biosciences, Edición 282, 2016, Página(s) 147-161, ISSN 0025-5564
Editor: Elsevier BV
DOI: 10.1016/j.mbs.2016.10.009

Structural Identifiability Analysis via Extended Observability and Decomposition

Autores: Alejandro F. Villaverde, Antonio Barreiro, Antonis Papachristodoulou
Publicado en: IFAC-PapersOnLine, Edición 49/26, 2016, Página(s) 171-177, ISSN 2405-8963
Editor: Elsevier
DOI: 10.1016/j.ifacol.2016.12.121

Full observability and estimation of unknown inputs, states and parameters of nonlinear biological models

Autores: Alejandro F. Villaverde, Nikolaos Tsiantis, Julio R. Banga
Publicado en: Journal of The Royal Society Interface, Edición 16/156, 2019, Página(s) 20190043, ISSN 1742-5689
Editor: The Royal Society
DOI: 10.1098/rsif.2019.0043

Closing the gap between formats for storing layout information in systems biology

Autores: David Hoksza, Piotr Gawron, Marek Ostaszewski, Jan Hasenauer, Reinhard Schneider
Publicado en: Briefings in Bioinformatics, 2020, ISSN 1467-5463
Editor: Oxford University Press
DOI: 10.1093/bib/bbaa030

Efficient parameterization of large-scale dynamic models based on relative measurements

Autores: Leonard Schmiester, Yannik Schälte, Fabian Fröhlich, Jan Hasenauer, Daniel Weindl
Publicado en: Bioinformatics, 2019, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btz581

A Comparison of Methods for Quantifying Prediction Uncertainty in Systems Biology

Autores: Alejandro F. Villaverde, Elba Raimúndez, Jan Hasenauer, Julio R. Banga
Publicado en: IFAC-PapersOnLine, Edición 52/26, 2019, Página(s) 45-51, ISSN 2405-8963
Editor: ScienceDirect
DOI: 10.1016/j.ifacol.2019.12.234

Challenges in the calibration of large-scale ordinary differential equation models

Autores: Eva-Maria Kapfer, Paul Stapor, Jan Hasenauer
Publicado en: IFAC-PapersOnLine, Edición 52/26, 2019, Página(s) 58-64, ISSN 2405-8963
Editor: ScienceDirect
DOI: 10.1016/j.ifacol.2019.12.236

Efficient computation of steady states in large-scale ODE models of biochemical reaction networks

Autores: Glenn Terje Lines, Łukasz Paszkowski, Leonard Schmiester, Daniel Weindl, Paul Stapor, Jan Hasenauer
Publicado en: IFAC-PapersOnLine, Edición 52/26, 2019, Página(s) 32-37, ISSN 2405-8963
Editor: ScienceDirect
DOI: 10.1016/j.ifacol.2019.12.232

A protocol for dynamic model calibration

Autores: Alejandro F Villaverde; Dilan Pathirana; Fabian Fröhlich; Jan Hasenauer; Julio R Banga
Publicado en: Briefings in Bioinformatics, Edición 1, 2021, ISSN 1477-4054
Editor: Oxford University Press
DOI: 10.1093/bib/bbab387

AMICI: high-performance sensitivity analysis for large ordinary differential equation models

Autores: Fabian Fröhlich; Daniel Weindl; Yannik Schälte; Dilan Pathirana; Łukasz Paszkowski; Glenn Terje Lines; Paul Stapor; Jan Hasenauer
Publicado en: BIOINFORMATICS, 2021, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btab227

Virtual trials in virtual patients. Is this how we will accelerate progress in personalized treatments?

Autores: Marc Beishon
Publicado en: Cancer World, 2017
Editor: European School of Oncology

CanPathPro – eine innovative Plattform für die prädiktive Modellierung von Krebs-Signalprozessen

Autores: Bodo Lange
Publicado en: EY Spot on Innovation! Deutsche Biotechnologie Report, 2017
Editor: Ernst & Young

LNA++: Linear Noise Appr oximation with First and Second Order Sensitivities

Autores: Justin Feigelman, Daniel Weindl, Carsten Marr, Jan Hasenauer
Publicado en: Springer Verlag, Edición Proceedings of the 16th International Conference on Computational Methods in Systems Biology, 2018, Página(s) 300-306
Editor: Springer Verlag
DOI: 10.5281/zenodo.1287771

PREMER: Parallel Reverse Engineering of Biological Networks with Information Theory

Autores: Alejandro F. Villaverde, Kolja Becker, Julio R. Banga
Publicado en: Lecture Notes in Computer Science, 2016, Página(s) 323-329
Editor: Springer International Publishing
DOI: 10.1007/978-3-319-45177-0_21

Análisis de observabilidad e identificabilidad estructural de modelos no lineales: aplicación a la vía de señalización JAK/STAT

Autores: Alejandro Vilaverde, Julio R. Banga
Publicado en: Libro de actas, 2019, Página(s) 631-638, ISBN 9788-497497169
Editor: Universidade da Coruña. Servizo de Publicacións
DOI: 10.17979/spudc.9788497497169.631

Generation of the CanPath prototype - a platform for predictive cancer pathway modeling

Resultado final

Publicaciones

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