Clemens Kreutz

26 papers Misc 1Journal 25
YearRankTypeTitle / Venue / Authors
2024 J jnl
Dynamic modelling of signalling pathways when ordinary differential equations are not feasible.
Bioinform.
Timo Rachel, Eva Brombacher, Svenja Wöhrle, Olaf Groß, Clemens Kreutz
2024 J jnl
RTF: an R package for modelling time course data.
Bioinform.
Eva Brombacher, Clemens Kreutz
2023 J jnl
A statistical approach to latent dynamic modeling with differential equations.
CoRR
Maren Hackenberg, Astrid Pechmann, Clemens Kreutz, Janbernd Kirschner, Harald Binder
2023 J jnl
Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models.
PLoS Comput. Biol.
Christian Tönsing, Bernhard Steiert, Jens Timmer, Clemens Kreutz
2023 J jnl
Rcall: An R interface for MATLAB.
SoftwareX
Janine Egert, Clemens Kreutz
2021 J jnl
PEtab - Interoperable specification of parameter estimation problems in systems biology.
PLoS Comput. Biol.
Leonard Schmiester, Yannik Schälte, Frank T. Bergmann, Tacio Camba, Erika Dudkin, Janine Egert, Fabian Fröhlich, Lara Fuhrmann, Adrian L. Hauber, Svenja Kemmer, Polina A. Lakrisenko, Carolin Loos, Simon Merkt, Wolfgang Müller, Dilan Pathirana, Elba Raimúndez-Álvarez, Lukas Refisch, Marcus Rosenblatt, Paul Stapor, Philipp Städter, Dantong Wang, Franz-Georg Wieland, Julio R. Banga, Jens Timmer, Alejandro F. Villaverde, Sven Sahle, Clemens Kreutz, Jan Hasenauer, Daniel Weindl
2021 J jnl
Rcall: Calling R from Matlab.
CoRR
Janine Egert, Clemens Kreutz
2020 J jnl
A Blind and Independent Benchmark Study for Detecting Differentially Methylated Regions in Plants.
Bioinform.
Clemens Kreutz, Nilay S. Can, Ralf Schulze Bruening, Rabea Meyberg, Zsuzsanna Mérai, Noé Fernández-Pozo, Stefan A. Rensing
2020 J jnl
A blind and independent benchmark study for detecting differentially methylated regions in plants.
Bioinform.
Clemens Kreutz, Nilay S. Can, Ralf Schulze Bruening, Rabea Meyberg, Zsuzsanna Mérai, Noé Fernández-Pozo, Stefan A. Rensing
2020 J jnl
Using Differentiable Programming for Flexible Statistical Modeling.
CoRR
Maren Hackenberg, Marlon Grodd, Clemens Kreutz, Martina Fischer, Janina Esins, Linus Grabenhenrich, Christian Karagiannidis, Harald Binder
2019 J jnl
Benchmark problems for dynamic modeling of intracellular processes.
Bioinform.
Helge Hass, Carolin Loos, Elba Raimúndez-Álvarez, Jens Timmer, Jan Hasenauer, Clemens Kreutz
2019 J jnl
Guidelines for benchmarking of optimization approaches for fitting mathematical models.
CoRR
Clemens Kreutz
2018 J jnl
An easy and efficient approach for testing identifiability.
Bioinform.
Clemens Kreutz
2016 J jnl
Fast integration-based prediction bands for ordinary differential equation models.
Bioinform.
Helge Hass, Clemens Kreutz, Jens Timmer, Daniel Kaschek
2016 J jnl
Identification of Cell Type-Specific Differences in Erythropoietin Receptor Signaling in Primary Erythroid and Lung Cancer Cells.
PLoS Comput. Biol.
Ruth Merkle, Bernhard Steiert, Florian Salopiata, Sofia Depner, Andreas Raue, Nao Iwamoto, Max Schelker, Helge Hass, Marvin Wäsch, Martin E. Böhm, Oliver Mücke, Daniel B. Lipka, Christoph Plass, Wolf D. Lehmann, Clemens Kreutz, Jens Timmer, Marcel Schilling, Ursula Klingmüller
2015 J jnl
Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems.
Bioinform.
Andreas Raue, Bernhard Steiert, Max Schelker, Clemens Kreutz, Tim Maiwald, Helge Hass, Joep Vanlier, Christian Tönsing, Lorenz Adlung, Raphael Engesser, Wolfgang Mader, Tim Heinemann, Jan Hasenauer, Marcel Schilling, Thomas Höfer, Edda Klipp, Fabian J. Theis, Ursula Klingmüller, Birgit Schoeberl, Jens Timmer
2015 J jnl
Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models.
PLoS Comput. Biol.
Jonathan R. Karr, Alex H. Williams, Jeremy D. Zucker, Andreas Raue, Bernhard Steiert, Jens Timmer, Clemens Kreutz, Simon Wilkinson, Brandon A. Allgood, Brian M. Bot, Bruce R. Hoff, Michael R. Kellen, Markus W. Covert, Gustavo A. Stolovitzky, Pablo Meyer
2014 J jnl
Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.
BMC Syst. Biol.
Pablo Meyer, Thomas Cokelaer, Deepak Chandran, Kyung Hyuk Kim, Po-Ru Loh, George Tucker, Mark Lipson, Bonnie Berger, Clemens Kreutz, Andreas Raue, Bernhard Steiert, Jens Timmer, Erhan Bilal, Herbert M. Sauro, Gustavo Stolovitzky, Julio Saez-Rodriguez
2012 J jnl
Comprehensive estimation of input signals and dynamics in biochemical reaction networks.
Bioinform.
Max Schelker, Andreas Raue, Jens Timmer, Clemens Kreutz
2012 J jnl
Likelihood based observability analysis and confidence intervals for predictions of dynamic models.
BMC Syst. Biol.
Clemens Kreutz, Andreas Raue, Jens Timmer
2012 J jnl
TSSi - an R package for transcription start site identification from 5′ mRNA tag data.
Bioinform.
Clemens Kreutz, J. S. Gehring, Daniel Lang, Ralf Reski, Jens Timmer, Stefan A. Rensing
2009 J jnl
Estimation of Gene Induction Enables a Relevance-Based Ranking of Gene Sets.
J. Comput. Biol.
Kilian Bartholomé, Clemens Kreutz, Jens Timmer
2009 J jnl
Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood.
Bioinform.
Andreas Raue, Clemens Kreutz, Thomas Maiwald, Julie Bachmann, Marcel Schilling, Ursula Klingmüller, Jens Timmer
2007 J jnl
An error model for protein quantification.
Bioinform.
Clemens Kreutz, M. M. Bartolome Rodriguez, Thomas Maiwald, Maxmilian Seidl, H. E. Blum, L. Mohr, Jens Timmer
2007 J jnl
Data-based identifiability analysis of non-linear dynamical models.
Bioinform.
Stefan Hengl, Clemens Kreutz, Jens Timmer, Thomas Maiwald
2003 Misc conf
Controlling the Continuos Positive Airway Pressure-Device Using Partial Observable Markov Decision Processes.
HPSC
Clemens Kreutz, Josef Honerkamp