相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。PEtab-Interoperable specification of parameter estimation problems in systems biology
Leonard Schmiester et al.
PLOS COMPUTATIONAL BIOLOGY (2021)
Efficient gradient-based parameter estimation for dynamic models using qualitative data
Leonard Schmiester et al.
BIOINFORMATICS (2021)
Bayesian inference using qualitative observations of underlying continuous variables
Eshan D. Mitra et al.
BIOINFORMATICS (2020)
SciPy 1.0: fundamental algorithms for scientific computing in Python
Pauli Virtanen et al.
NATURE METHODS (2020)
Calibration of ionic and cellular cardiac electrophysiology models
Dominic G. Whittaker et al.
WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE (2020)
Parameterization of mechanistic models from qualitative data using an efficient optimal scaling approach
Leonard Schmiester et al.
JOURNAL OF MATHEMATICAL BIOLOGY (2020)
Identifiability analysis for stochastic differential equation models in systems biology
Alexander P. Browning et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2020)
Benchmarking optimization methods for parameter estimation in large kinetic models
Alejandro F. Villaverde et al.
BIOINFORMATICS (2019)
Full observability and estimation of unknown inputs, states and parameters of nonlinear biological models
Alejandro F. Villaverde et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2019)
Closed-Loop Model-Based Design of Experiments for Kinetic Model Discrimination and Parameter Estimation: Benzoic Acid Esterification on a Heterogeneous Catalyst
Conor Waldron et al.
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH (2019)
Benchmark problems for dynamic modeling of intracellular processes
Helge Hass et al.
BIOINFORMATICS (2019)
SIAN: software for structural identifiability analysis of ODE models
Hoon Hong et al.
BIOINFORMATICS (2019)
Observability and Structural Identifiability of Nonlinear Biological Systems
Alejandro F. Villaverde
COMPLEXITY (2019)
Sequential Model-Based A-Optimal Design of Experiments When the Fisher Information Matrix Is Noninvertible
Ali Shahmohammadi et al.
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH (2019)
Nonlinear System Identification A USER-ORIENTED ROAD MAP
Johan Schoukens et al.
IEEE CONTROL SYSTEMS MAGAZINE (2019)
The Reactome Pathway Knowledgebase
Antonio Fabregat et al.
NUCLEIC ACIDS RESEARCH (2018)
Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering
Benjamin Ballnus et al.
BIOINFORMATICS (2018)
Hierarchical optimization for the efficient parametrization of ODE models
Carolin Loos et al.
BIOINFORMATICS (2018)
Control Theory for Synthetic Biology RECENT ADVANCES IN SYSTEM CHARACTERIZATION, CONTROL DESIGN, AND CONTROLLER IMPLEMENTATION FOR SYNTHETIC BIOLOGY
Victoria Hsiao et al.
IEEE CONTROL SYSTEMS MAGAZINE (2018)
Perfect Adaptation and Optimal Equilibrium Productivity in a Simple Microbial Biofuel Metabolic Pathway Using Dynamic Integral Control
Corentin Briat et al.
ACS SYNTHETIC BIOLOGY (2018)
Computational Re-design of Synthetic Genetic Oscillators for Independent Amplitude and Frequency Modulation
Marios Tomazou et al.
CELL SYSTEMS (2018)
Using both qualitative and quantitative data in parameter identification for systems biology models
Eshan D. Mitra et al.
NATURE COMMUNICATIONS (2018)
Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model
Fabian Froehlich et al.
CELL SYSTEMS (2018)
Design Constraints for Biological Systems That Achieve Adaptation and Disturbance Rejection
Harrison Steel et al.
IEEE TRANSACTIONS ON CONTROL OF NETWORK SYSTEMS (2018)
PESTO: Parameter EStimation TOolbox
Paul Stapor et al.
BIOINFORMATICS (2018)
GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models
Thomas S. Ligon et al.
BIOINFORMATICS (2018)
Data-driven reverse engineering of signaling pathways using ensembles of dynamic models
David Henriques et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks
Fabian Froehlich et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
Assessing the accuracy of predictive models for numerical data: Not r nor r2, why not? Then what?
Jin Li
PLOS ONE (2017)
Computational design of biological circuits: putting parts into context
Eleni Karamasioti et al.
MOLECULAR SYSTEMS DESIGN & ENGINEERING (2017)
Identifiability of affine linear parameter-varying models
Ziad Alkhoury et al.
AUTOMATICA (2017)
Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy
David R. Penas et al.
BMC BIOINFORMATICS (2017)
Fast integration-based prediction bands for ordinary differential equation models
Helge Hass et al.
BIOINFORMATICS (2016)
Further results on identifiability of discrete-time nonlinear systems
Sven Nomm et al.
AUTOMATICA (2016)
L1 regularization facilitates detection of cell type-specific parameters in dynamical systems
Bernhard Steiert et al.
BIOINFORMATICS (2016)
Analysis of CFSE time-series data using division-, age- and label-structured population models
Sabrina Hross et al.
BIOINFORMATICS (2016)
Metabolic engineering with multi-objective optimization of kinetic models
Alejandro F. Villaverde et al.
JOURNAL OF BIOTECHNOLOGY (2016)
Enzymatic study on AtCCD4 and AtCCD7 and their potential to form acyclic regulatory metabolites
Mark Bruno et al.
JOURNAL OF EXPERIMENTAL BOTANY (2016)
A Six-Stage Workflow for Robust Application of Systems Pharmacology
K. Gadkar et al.
CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY (2016)
New Concepts for Evaluating the Performance of Computational Methods
Clemens Kreutz
IFAC PAPERSONLINE (2016)
A fast algorithm to assess local structural identifiability
Johannes D. Stigter et al.
AUTOMATICA (2015)
Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems
A. Raue et al.
BIOINFORMATICS (2015)
A consensus approach for estimating the predictive accuracy of dynamic models in biology
Alejandro F. Villaverde et al.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE (2015)
Nonlinear ill-posed problem analysis in model-based parameter estimation and experimental design
Diana C. Lopez C et al.
COMPUTERS & CHEMICAL ENGINEERING (2015)
Higher-order Lie symmetries in identifiability and predictability analysis of dynamic models
Benjamin Merkt et al.
PHYSICAL REVIEW E (2015)
A Novel Protocol for Model Calibration in Biological Wastewater Treatment
Ao Zhu et al.
SCIENTIFIC REPORTS (2015)
On the observability and identifiability of nonlinear structural and mechanical systems
Manolis N. Chatzis et al.
STRUCTURAL CONTROL & HEALTH MONITORING (2015)
Kernel methods in system identification, machine learning and function estimation: A survey
Gianluigi Pillonetto et al.
AUTOMATICA (2014)
Reverse engineering and identification in systems biology: strategies, perspectives and challenges
Alejandro F. Villaverde et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2014)
A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation
Juliane Liepe et al.
NATURE PROTOCOLS (2014)
Kinetic models in industrial biotechnology - Improving cell factory performance
Joachim Almquist et al.
METABOLIC ENGINEERING (2014)
On Finding and Using Identifiable Parameter Combinations in Nonlinear Dynamic Systems Biology Models and COMBOS: A Novel Web Implementation
Nicolette Meshkat et al.
PLOS ONE (2014)
Profile likelihood in systems biology
Clemens Kreutz et al.
FEBS JOURNAL (2013)
High-dimensional Bayesian parameter estimation: Case study for a model of JAK2/STAT5 signaling
S. Hug et al.
MATHEMATICAL BIOSCIENCES (2013)
Lessons Learned from Quantitative Dynamical Modeling in Systems Biology
Andreas Raue et al.
PLOS ONE (2013)
Convergence in parameters and predictions using computational experimental design
David R. Hagen et al.
INTERFACE FOCUS (2013)
Modeling metabolic systems: the need for dynamics
Hyun-Seob Song et al.
CURRENT OPINION IN CHEMICAL ENGINEERING (2013)
An integrated strategy for prediction uncertainty analysis
J. Vanlier et al.
BIOINFORMATICS (2012)
Likelihood based observability analysis and confidence intervals for predictions of dynamic models
Clemens Kreutz et al.
BMC SYSTEMS BIOLOGY (2012)
SABIO-RK-database for biochemical reaction kinetics
Ulrike Wittig et al.
NUCLEIC ACIDS RESEARCH (2012)
Experimental Design for Parameter Estimation of Gene Regulatory Networks
Bernhard Steiert et al.
PLOS ONE (2012)
A practical protocol for calibration of nutrient removal wastewater treatment models
Giorgio Mannina et al.
JOURNAL OF HYDROINFORMATICS (2011)
Structural Identifiability of Systems Biology Models: A Critical Comparison of Methods
Oana-Teodora Chis et al.
PLOS ONE (2011)
An iterative identification procedure for dynamic modeling of biochemical networks
Eva Balsa-Canto et al.
BMC SYSTEMS BIOLOGY (2010)
Decoupling of Receptor and Downstream Signals in the Akt Pathway by Its Low-Pass Filter Characteristics
Kazuhiro A. Fujita et al.
SCIENCE SIGNALING (2010)
Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood
A. Raue et al.
BIOINFORMATICS (2009)
Systems biology: parameter estimation for biochemical models
Maksat Ashyraliyev et al.
FEBS JOURNAL (2009)
Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems
Tina Toni et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2009)
Optimal experimental design and some related control problems
Luc Pronzato
AUTOMATICA (2008)
Identifiability of discrete-time nonlinear systems: The local state isomorphism approach
Floriane Anstett et al.
AUTOMATICA (2008)
Model-based design of experiments for parameter precision: State of the art
Gaia Franceschini et al.
CHEMICAL ENGINEERING SCIENCE (2008)
Parameter estimation and optimal experimental design
Julio R. Banga et al.
ESSAYS IN BIOCHEMISTRY: SYSTEMS BIOLOGY, VOL 45 (2008)
Computational procedures for optimal experimental design in biological systems
E. Balsa-Canto et al.
IET SYSTEMS BIOLOGY (2008)
Bayesian ranking of biochemical system models
Vladislav Vyshemirsky et al.
BIOINFORMATICS (2008)
Data-based identifiability analysis of non-linear dynamical models
S. Hengl et al.
BIOINFORMATICS (2007)
Ensemble modeling for analysis of cell signaling dynamics
Lars Kuepfer et al.
NATURE BIOTECHNOLOGY (2007)
Optimal experimental design in an epidermal growth factor receptor signalling and down-regulation model
F. P. Casey et al.
IET SYSTEMS BIOLOGY (2007)
Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments
Natal A. W. van Riel
BRIEFINGS IN BIOINFORMATICS (2006)
Linking data to models: data regression
Khuloud Jaqaman et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2006)
Exploiting the bootstrap method for quantifying parameter confidence intervals in dynamical systems
M. Joshi et al.
METABOLIC ENGINEERING (2006)
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
Nicolas Le Novere et al.
NUCLEIC ACIDS RESEARCH (2006)
Model structure simplification of nonlinear systems via immersion
T Ohtsuka
IEEE TRANSACTIONS ON AUTOMATIC CONTROL (2005)
Identification for control: From the early achievements to the revival of experiment design
M Gevers
EUROPEAN JOURNAL OF CONTROL (2005)
Web-based kinetic modelling using JWS Online
BG Olivier et al.
BIOINFORMATICS (2004)
The statistical mechanics of complex signaling networks: nerve growth factor signaling
KS Brown et al.
PHYSICAL BIOLOGY (2004)
The systems biology markup language (SBML):: a medium for representation and exchange of biochemical network models
M Hucka et al.
BIOINFORMATICS (2003)
A probabilistic algorithm to test local algebraic observability in polynomial time
A Sedoglavic
JOURNAL OF SYMBOLIC COMPUTATION (2002)
KEGG: Kyoto Encyclopedia of Genes and Genomes
M Kanehisa et al.
NUCLEIC ACIDS RESEARCH (2000)
分享论文
