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

Risultati finali

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

Pubblicazioni

PEtab—Interoperable specification of parameter estimation problems in systems biology

Autori: 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.
Pubblicato in: PLOS COMPUTATIONAL BIOLOGY, 2021, ISSN 1553-734X
Editore: Public Library of Science
DOI: 10.1371/journal.pcbi.1008646

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

Autori: Leonard Schmiester, Daniel Weindl, Jan Hasenauer
Pubblicato in: Bioinformatics, 2021, ISSN 1460-2059
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btab512

Benchmarking of numerical integration methods for ODE models of biological systems

Autori: Philipp Städter; Yannik Schälte; Leonard Schmiester; Jan Hasenauer; Jan Hasenauer; Paul Stapor
Pubblicato in: Nature, Numero 13, 2021, ISSN 0028-0836
Editore: Nature Publishing Group
DOI: 10.1038/s41598-021-82196-2

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

Autori: Lesley A. Ogilvie, Aleksandra Kovachev, Christoph Wierling, Bodo M. H. Lange, Hans Lehrach
Pubblicato in: Frontiers in Oncology, Numero 7, 2017, ISSN 2234-943X
Editore: Frontiers Media S. A.
DOI: 10.3389/fonc.2017.00219

PREMER: a Tool to Infer Biological Networks

Autori: Alejandro F. Villaverde, Kolja Becker, Julio R. Banga
Pubblicato in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017, Pagina/e 1-1, ISSN 1545-5963
Editore: IEEE Computer Society
DOI: 10.1109/TCBB.2017.2758786

PESTO: Parameter EStimation TOolbox

Autori: Paul Stapor, Daniel Weindl, Benjamin Ballnus, Sabine Hug, Carolin Loos, Anna Fiedler, Sabrina Krause, Sabrina Hroß, Fabian Fröhlich, Jan Hasenauer
Pubblicato in: Bioinformatics, Numero 34/4, 2017, Pagina/e 705-707, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btx676

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

Autori: Alejandro F Villaverde, Julio R Banga
Pubblicato in: Processes, Numero 5/4, 2017, Pagina/e 29, ISSN 2227-9717
Editore: MDPI
DOI: 10.3390/pr5020029

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

Autori: Attila Gábor, Alejandro F. Villaverde, Julio R. Banga
Pubblicato in: BMC Systems Biology, Numero 11/1, 2017, ISSN 1752-0509
Editore: BioMed Central
DOI: 10.1186/s12918-017-0428-y

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

Autori: Benjamin Ballnus, Steffen Schaper, Fabian J Theis, Jan Hasenauer
Pubblicato in: Bioinformatics, Numero 34/13, 2018, Pagina/e i494-i501, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/bty229

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

Autori: Yannik Schälte, Paul Stapor, Jan Hasenauer
Pubblicato in: IFAC-PapersOnLine, Numero 51/19, 2018, Pagina/e 98-101, ISSN 2405-8963
Editore: Science Direct
DOI: 10.1016/j.ifacol.2018.09.025

Sufficiently Exciting Inputs for Structurally Identifiable Systems Biology Models

Autori: Alejandro F. Villaverde, Neil D. Evans, Michael J. Chappell, Julio R. Banga
Pubblicato in: IFAC-PapersOnLine, Numero 51/19, 2018, Pagina/e 16-19, ISSN 2405-8963
Editore: Science Direct
DOI: 10.1016/j.ifacol.2018.09.015

Observability and Structural Identifiability of Nonlinear Biological Systems

Autori: Alejandro F. Villaverde
Pubblicato in: Complexity, Numero 2019, 2019, Pagina/e 1-12, ISSN 1076-2787
Editore: John Wiley & Sons Inc.
DOI: 10.1155/2019/8497093

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

Autori: Paul Stapor, Fabian Fröhlich, Jan Hasenauer
Pubblicato in: Bioinformatics, Numero 34/13, 2018, Pagina/e i151-i159, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/bty230

Hierarchical optimization for the efficient parametrization of ODE models

Autori: Hasenauer, Jan; Loos, Carolin; Krause, Sabrina
Pubblicato in: Bioinformatics Journal, Numero 2, 2018, Pagina/e 4266-4273, ISSN 1460-2059
Editore: Oxford University
DOI: 10.1101/247924

Input-Dependent Structural Identifiability of Nonlinear Systems

Autori: Alejandro F. Villaverde, Neil D. Evans, Michael J. Chappell, Julio R. Banga
Pubblicato in: IEEE Control Systems Letters, Numero 3/2, 2019, Pagina/e 272-277, ISSN 2475-1456
Editore: IEEE
DOI: 10.1109/lcsys.2018.2868608

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

Autori: 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
Pubblicato in: Cell Systems, Numero 7/6, 2018, Pagina/e 567-579.e6, ISSN 2405-4712
Editore: Cell Press
DOI: 10.1016/j.cels.2018.10.013

Benchmarking optimization methods for parameter estimation in large kinetic models

Autori: Alejandro F Villaverde, Fabian Fröhlich, Daniel Weindl, Jan Hasenauer, Julio R Banga
Pubblicato in: Bioinformatics, Numero 35/5, 2018, Pagina/e 830-838, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/bty736

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

Autori: Thomas S Ligon, Fabian Fröhlich, Oana T Chiş, Julio R Banga, Eva Balsa-Canto, Jan Hasenauer
Pubblicato in: Bioinformatics, Numero 34/8, 2017, Pagina/e 1421-1423, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btx735

Structural Identifiability of Dynamic Systems Biology Models

Autori: Alejandro F. Villaverde, Antonio Barreiro, Antonis Papachristodoulou
Pubblicato in: PLOS Computational Biology, Numero 12/10, 2016, Pagina/e e1005153, ISSN 1553-7358
Editore: Plos
DOI: 10.1371/journal.pcbi.1005153

On the relationship between sloppiness and identifiability

Autori: Oana-Teodora Chis, Alejandro F. Villaverde, Julio R. Banga, Eva Balsa-Canto
Pubblicato in: Mathematical Biosciences, Numero 282, 2016, Pagina/e 147-161, ISSN 0025-5564
Editore: Elsevier BV
DOI: 10.1016/j.mbs.2016.10.009

Structural Identifiability Analysis via Extended Observability and Decomposition

Autori: Alejandro F. Villaverde, Antonio Barreiro, Antonis Papachristodoulou
Pubblicato in: IFAC-PapersOnLine, Numero 49/26, 2016, Pagina/e 171-177, ISSN 2405-8963
Editore: Elsevier
DOI: 10.1016/j.ifacol.2016.12.121

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

Autori: Alejandro F. Villaverde, Nikolaos Tsiantis, Julio R. Banga
Pubblicato in: Journal of The Royal Society Interface, Numero 16/156, 2019, Pagina/e 20190043, ISSN 1742-5689
Editore: The Royal Society
DOI: 10.1098/rsif.2019.0043

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

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

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

Autori: Leonard Schmiester, Yannik Schälte, Fabian Fröhlich, Jan Hasenauer, Daniel Weindl
Pubblicato in: Bioinformatics, 2019, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btz581

A Comparison of Methods for Quantifying Prediction Uncertainty in Systems Biology

Autori: Alejandro F. Villaverde, Elba Raimúndez, Jan Hasenauer, Julio R. Banga
Pubblicato in: IFAC-PapersOnLine, Numero 52/26, 2019, Pagina/e 45-51, ISSN 2405-8963
Editore: ScienceDirect
DOI: 10.1016/j.ifacol.2019.12.234

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

Autori: Eva-Maria Kapfer, Paul Stapor, Jan Hasenauer
Pubblicato in: IFAC-PapersOnLine, Numero 52/26, 2019, Pagina/e 58-64, ISSN 2405-8963
Editore: ScienceDirect
DOI: 10.1016/j.ifacol.2019.12.236

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

Autori: Glenn Terje Lines, Łukasz Paszkowski, Leonard Schmiester, Daniel Weindl, Paul Stapor, Jan Hasenauer
Pubblicato in: IFAC-PapersOnLine, Numero 52/26, 2019, Pagina/e 32-37, ISSN 2405-8963
Editore: ScienceDirect
DOI: 10.1016/j.ifacol.2019.12.232

A protocol for dynamic model calibration

Autori: Alejandro F Villaverde; Dilan Pathirana; Fabian Fröhlich; Jan Hasenauer; Julio R Banga
Pubblicato in: Briefings in Bioinformatics, Numero 1, 2021, ISSN 1477-4054
Editore: Oxford University Press
DOI: 10.1093/bib/bbab387

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

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

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

Autori: Marc Beishon
Pubblicato in: Cancer World, 2017
Editore: European School of Oncology

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

Autori: Bodo Lange
Pubblicato in: EY Spot on Innovation! Deutsche Biotechnologie Report, 2017
Editore: Ernst & Young

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

Autori: Justin Feigelman, Daniel Weindl, Carsten Marr, Jan Hasenauer
Pubblicato in: Springer Verlag, Numero Proceedings of the 16th International Conference on Computational Methods in Systems Biology, 2018, Pagina/e 300-306
Editore: Springer Verlag
DOI: 10.5281/zenodo.1287771

PREMER: Parallel Reverse Engineering of Biological Networks with Information Theory

Autori: Alejandro F. Villaverde, Kolja Becker, Julio R. Banga
Pubblicato in: Lecture Notes in Computer Science, 2016, Pagina/e 323-329
Editore: 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

Autori: Alejandro Vilaverde, Julio R. Banga
Pubblicato in: Libro de actas, 2019, Pagina/e 631-638, ISBN 9788-497497169
Editore: Universidade da Coruña. Servizo de Publicacións
DOI: 10.17979/spudc.9788497497169.631

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

Risultati finali

Pubblicazioni

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