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

Project Information

CanPathPro

Grant agreement ID: 686282

DOI

10.3030/686282

Project closed

EC signature date 25 February 2016

Start date 1 March 2016

End date 30 November 2021

Funded under

• INDUSTRIAL LEADERSHIP - Leadership in enabling and industrial technologies – Biotechnology

Total cost

€ 10 713 058,48

EU contribution

€ 9 862 545,98

Coordinated by

ALACRIS THERANOSTICS GMBH
Germany

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Documents, reports (2)

Dissemination Plan
Management Guide

Demonstrators, pilots, prototypes (1)

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

Publications

Peer reviewed articles (29)

PEtab—Interoperable specification of parameter estimation problems in systems biology

Author(s): 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.
Published in: PLOS COMPUTATIONAL BIOLOGY, 2021, ISSN 1553-734X
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1008646

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

Author(s): Leonard Schmiester, Daniel Weindl, Jan Hasenauer
Published in: Bioinformatics, 2021, ISSN 1460-2059
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab512

Benchmarking of numerical integration methods for ODE models of biological systems

Author(s): Philipp Städter; Yannik Schälte; Leonard Schmiester; Jan Hasenauer; Jan Hasenauer; Paul Stapor
Published in: Nature, Issue 13, 2021, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-82196-2

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

Author(s): Lesley A. Ogilvie, Aleksandra Kovachev, Christoph Wierling, Bodo M. H. Lange, Hans Lehrach
Published in: Frontiers in Oncology, Issue 7, 2017, ISSN 2234-943X
Publisher: Frontiers Media S. A.
DOI: 10.3389/fonc.2017.00219

PREMER: a Tool to Infer Biological Networks

Author(s): Alejandro F. Villaverde, Kolja Becker, Julio R. Banga
Published in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017, Page(s) 1-1, ISSN 1545-5963
Publisher: IEEE Computer Society
DOI: 10.1109/TCBB.2017.2758786

PESTO: Parameter EStimation TOolbox

Author(s): Paul Stapor, Daniel Weindl, Benjamin Ballnus, Sabine Hug, Carolin Loos, Anna Fiedler, Sabrina Krause, Sabrina Hroß, Fabian Fröhlich, Jan Hasenauer
Published in: Bioinformatics, Issue 34/4, 2017, Page(s) 705-707, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btx676

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

Author(s): Alejandro F Villaverde, Julio R Banga
Published in: Processes, Issue 5/4, 2017, Page(s) 29, ISSN 2227-9717
Publisher: MDPI
DOI: 10.3390/pr5020029

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

Author(s): Attila Gábor, Alejandro F. Villaverde, Julio R. Banga
Published in: BMC Systems Biology, Issue 11/1, 2017, ISSN 1752-0509
Publisher: BioMed Central
DOI: 10.1186/s12918-017-0428-y

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

Author(s): Benjamin Ballnus, Steffen Schaper, Fabian J Theis, Jan Hasenauer
Published in: Bioinformatics, Issue 34/13, 2018, Page(s) i494-i501, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/bty229

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

Author(s): Yannik Schälte, Paul Stapor, Jan Hasenauer
Published in: IFAC-PapersOnLine, Issue 51/19, 2018, Page(s) 98-101, ISSN 2405-8963
Publisher: Science Direct
DOI: 10.1016/j.ifacol.2018.09.025

Sufficiently Exciting Inputs for Structurally Identifiable Systems Biology Models

Author(s): Alejandro F. Villaverde, Neil D. Evans, Michael J. Chappell, Julio R. Banga
Published in: IFAC-PapersOnLine, Issue 51/19, 2018, Page(s) 16-19, ISSN 2405-8963
Publisher: Science Direct
DOI: 10.1016/j.ifacol.2018.09.015

Observability and Structural Identifiability of Nonlinear Biological Systems

Author(s): Alejandro F. Villaverde
Published in: Complexity, Issue 2019, 2019, Page(s) 1-12, ISSN 1076-2787
Publisher: John Wiley & Sons Inc.
DOI: 10.1155/2019/8497093

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

Author(s): Paul Stapor, Fabian Fröhlich, Jan Hasenauer
Published in: Bioinformatics, Issue 34/13, 2018, Page(s) i151-i159, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/bty230

Hierarchical optimization for the efficient parametrization of ODE models

Author(s): Hasenauer, Jan; Loos, Carolin; Krause, Sabrina
Published in: Bioinformatics Journal, Issue 2, 2018, Page(s) 4266-4273, ISSN 1460-2059
Publisher: Oxford University
DOI: 10.1101/247924

Input-Dependent Structural Identifiability of Nonlinear Systems

Author(s): Alejandro F. Villaverde, Neil D. Evans, Michael J. Chappell, Julio R. Banga
Published in: IEEE Control Systems Letters, Issue 3/2, 2019, Page(s) 272-277, ISSN 2475-1456
Publisher: IEEE
DOI: 10.1109/lcsys.2018.2868608

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

Author(s): 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
Published in: Cell Systems, Issue 7/6, 2018, Page(s) 567-579.e6, ISSN 2405-4712
Publisher: Cell Press
DOI: 10.1016/j.cels.2018.10.013

Benchmarking optimization methods for parameter estimation in large kinetic models

Author(s): Alejandro F Villaverde, Fabian Fröhlich, Daniel Weindl, Jan Hasenauer, Julio R Banga
Published in: Bioinformatics, Issue 35/5, 2018, Page(s) 830-838, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/bty736

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

Author(s): Thomas S Ligon, Fabian Fröhlich, Oana T Chiş, Julio R Banga, Eva Balsa-Canto, Jan Hasenauer
Published in: Bioinformatics, Issue 34/8, 2017, Page(s) 1421-1423, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btx735

Structural Identifiability of Dynamic Systems Biology Models

Author(s): Alejandro F. Villaverde, Antonio Barreiro, Antonis Papachristodoulou
Published in: PLOS Computational Biology, Issue 12/10, 2016, Page(s) e1005153, ISSN 1553-7358
Publisher: Plos
DOI: 10.1371/journal.pcbi.1005153

On the relationship between sloppiness and identifiability

Author(s): Oana-Teodora Chis, Alejandro F. Villaverde, Julio R. Banga, Eva Balsa-Canto
Published in: Mathematical Biosciences, Issue 282, 2016, Page(s) 147-161, ISSN 0025-5564
Publisher: Elsevier BV
DOI: 10.1016/j.mbs.2016.10.009

Structural Identifiability Analysis via Extended Observability and Decomposition

Author(s): Alejandro F. Villaverde, Antonio Barreiro, Antonis Papachristodoulou
Published in: IFAC-PapersOnLine, Issue 49/26, 2016, Page(s) 171-177, ISSN 2405-8963
Publisher: Elsevier
DOI: 10.1016/j.ifacol.2016.12.121

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

Author(s): Alejandro F. Villaverde, Nikolaos Tsiantis, Julio R. Banga
Published in: Journal of The Royal Society Interface, Issue 16/156, 2019, Page(s) 20190043, ISSN 1742-5689
Publisher: The Royal Society
DOI: 10.1098/rsif.2019.0043

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

Author(s): David Hoksza, Piotr Gawron, Marek Ostaszewski, Jan Hasenauer, Reinhard Schneider
Published in: Briefings in Bioinformatics, 2020, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbaa030

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

Author(s): Leonard Schmiester, Yannik Schälte, Fabian Fröhlich, Jan Hasenauer, Daniel Weindl
Published in: Bioinformatics, 2019, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz581

A Comparison of Methods for Quantifying Prediction Uncertainty in Systems Biology

Author(s): Alejandro F. Villaverde, Elba Raimúndez, Jan Hasenauer, Julio R. Banga
Published in: IFAC-PapersOnLine, Issue 52/26, 2019, Page(s) 45-51, ISSN 2405-8963
Publisher: ScienceDirect
DOI: 10.1016/j.ifacol.2019.12.234

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

Author(s): Eva-Maria Kapfer, Paul Stapor, Jan Hasenauer
Published in: IFAC-PapersOnLine, Issue 52/26, 2019, Page(s) 58-64, ISSN 2405-8963
Publisher: ScienceDirect
DOI: 10.1016/j.ifacol.2019.12.236

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

Author(s): Glenn Terje Lines, Łukasz Paszkowski, Leonard Schmiester, Daniel Weindl, Paul Stapor, Jan Hasenauer
Published in: IFAC-PapersOnLine, Issue 52/26, 2019, Page(s) 32-37, ISSN 2405-8963
Publisher: ScienceDirect
DOI: 10.1016/j.ifacol.2019.12.232

A protocol for dynamic model calibration

Author(s): Alejandro F Villaverde; Dilan Pathirana; Fabian Fröhlich; Jan Hasenauer; Julio R Banga
Published in: Briefings in Bioinformatics, Issue 1, 2021, ISSN 1477-4054
Publisher: Oxford University Press
DOI: 10.1093/bib/bbab387

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

Author(s): Fabian Fröhlich; Daniel Weindl; Yannik Schälte; Dilan Pathirana; Łukasz Paszkowski; Glenn Terje Lines; Paul Stapor; Jan Hasenauer
Published in: BIOINFORMATICS, 2021, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab227

Book chapters (2)

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

Author(s): Marc Beishon
Published in: Cancer World, 2017
Publisher: European School of Oncology

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

Author(s): Bodo Lange
Published in: EY Spot on Innovation! Deutsche Biotechnologie Report, 2017
Publisher: Ernst & Young

Conference proceedings (3)

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

Author(s): Justin Feigelman, Daniel Weindl, Carsten Marr, Jan Hasenauer
Published in: Springer Verlag, Issue Proceedings of the 16th International Conference on Computational Methods in Systems Biology, 2018, Page(s) 300-306
Publisher: Springer Verlag
DOI: 10.5281/zenodo.1287771

PREMER: Parallel Reverse Engineering of Biological Networks with Information Theory

Author(s): Alejandro F. Villaverde, Kolja Becker, Julio R. Banga
Published in: Lecture Notes in Computer Science, 2016, Page(s) 323-329
Publisher: 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

Author(s): Alejandro Vilaverde, Julio R. Banga
Published in: Libro de actas, 2019, Page(s) 631-638, ISBN 9788-497497169
Publisher: Universidade da Coruña. Servizo de Publicacións
DOI: 10.17979/spudc.9788497497169.631