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On a model of online analog computation in the cell with absolute functional robustness: Algebraic characterization, function compiler and error control

Theoretical computer science, 2024-04, Vol.991, p.114432, Article 114432

2024

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Recent Advances in Constraints: Joint ERCIM/CoLogNET International Workshop on Constraint Solving and Constraint Logic Programming, CSCLP 2003, Budapest, Hungary, June 30 - July 2, 2003, Selected Papers

1, 2004

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Long-term model predictive control of gene expression at the population and single-cell levels

Proceedings of the National Academy of Sciences - PNAS, 2012-08, Vol.109 (35), p.14271-14276

2012

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Inferring reaction systems from ordinary differential equations

Theoretical computer science, 2015-09, Vol.599, p.64-78

2015

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Graphical requirements for multistationarity in reaction networks and their verification in BioModels

Journal of theoretical biology, 2018-12, Vol.459, p.79-89

2018

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A Constraint-Based Mathematical Modeling Library in Prolog with Answer Constraint Semantics

Functional and Logic Programming, p.135-150

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BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge

Bioinformatics, 2006-07, Vol.22 (14), p.1805-1807

2006

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Computer‐aided biochemical programming of synthetic microreactors as diagnostic devices

Molecular systems biology, 2018-04, Vol.14 (4), p.e7845-n/a

2018

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Mathematical modeling of the microtubule detyrosination/tyrosination cycle for cell-based drug screening design

PLoS computational biology, 2022-06, Vol.18 (6), p.e1010236-e1010236

2022

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Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation

Bioinformatics (Oxford, England), 2016-09, Vol.32 (17), p.i772-i780

2016

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A skin microbiome model with AMP interactions and analysis of quasi-stability vs stability in population dynamics

Theoretical computer science, 2024-02, Vol.983, p.114294, Article 114294

2024

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Model learning to identify systemic regulators of the peripheral circadian clock

Bioinformatics, 2021-07, Vol.37 (Supplement_1), p.i401-i409

2021

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Abstract interpretation and types for systems biology

Theoretical computer science, 2008-08, Vol.403 (1), p.52-70

2008

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Computational modelling predicts impaired barrier function and higher sensitivity to skin inflammation following pH elevation

Experimental dermatology, 2023-02, Vol.32 (2), p.177-185

2023

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A graphical method for reducing and relating models in systems biology

Bioinformatics, 2010-09, Vol.26 (18), p.i575-i581

2010

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A general computational method for robustness analysis with applications to synthetic gene networks

Bioinformatics, 2009-06, Vol.25 (12), p.i169-i178

2009

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Computer‐aided biochemical programming of synthetic microreactors as diagnostic devices

Molecular systems biology, 2018-06, Vol.14 (6), p.e8441-n/a

2018

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On Estimating Derivatives of Input Signals in Biochemistry

Computational Methods in Systems Biology, 2023, Vol.14137, p.78-96

2023

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Simulations of pH-effects on kallikrein activity predict compromised skin barrier and predisposition to irritations and dryness characteristic of atopic dermatitis (poster abstract)

Journal of investigative dermatology, 2021-10, Vol.141 (10)

2021

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On Robustness Computation and Optimization in BIOCHAM-4

Computational Methods in Systems Biology, p.292-299

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Principles and Practice of Semantic Web Reasoning: Third International Workshop, PPSWR 2005, Dagstuhl Castle, Germany, September 11-16, 2005, Proceedings

2005., 2005

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Algebraic Biochemistry: A Framework for Analog Online Computation in Cells

Computational Methods in Systems Biology, p.3-20

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Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measures

Theoretical computer science, 2011-06, Vol.412 (26), p.2827-2839

2011

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Model-based investigation of the circadian clock and cell cycle coupling in mouse embryonic fibroblasts: Prediction of RevErb-α up-regulation during mitosis

BioSystems, 2016-11, Vol.149, p.59-69

2016

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On enumerating minimal siphons in Petri nets using CLP and SAT solvers: theoretical and practical complexity

Constraints : an international journal, 2016-04, Vol.21 (2), p.251-276

2016

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On a model of online analog computation in the cell with absolute functional robustness: Algebraic characterization, function compiler and error control

Recent Advances in Constraints: Joint ERCIM/CoLogNET International Workshop on Constraint Solving and Constraint Logic Programming, CSCLP 2003, Budapest, Hungary, June 30 - July 2, 2003, Selected Papers

Long-term model predictive control of gene expression at the population and single-cell levels

Inferring reaction systems from ordinary differential equations

Graphical requirements for multistationarity in reaction networks and their verification in BioModels

A Constraint-Based Mathematical Modeling Library in Prolog with Answer Constraint Semantics

BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge

Computer‐aided biochemical programming of synthetic microreactors as diagnostic devices

Mathematical modeling of the microtubule detyrosination/tyrosination cycle for cell-based drug screening design

Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation

A skin microbiome model with AMP interactions and analysis of quasi-stability vs stability in population dynamics

Model learning to identify systemic regulators of the peripheral circadian clock

Abstract interpretation and types for systems biology

Computational modelling predicts impaired barrier function and higher sensitivity to skin inflammation following pH elevation

A graphical method for reducing and relating models in systems biology

A general computational method for robustness analysis with applications to synthetic gene networks

Computer‐aided biochemical programming of synthetic microreactors as diagnostic devices

On Estimating Derivatives of Input Signals in Biochemistry

Simulations of pH-effects on kallikrein activity predict compromised skin barrier and predisposition to irritations and dryness characteristic of atopic dermatitis (poster abstract)

On Robustness Computation and Optimization in BIOCHAM-4

Principles and Practice of Semantic Web Reasoning: Third International Workshop, PPSWR 2005, Dagstuhl Castle, Germany, September 11-16, 2005, Proceedings

Algebraic Biochemistry: A Framework for Analog Online Computation in Cells

Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measures

Model-based investigation of the circadian clock and cell cycle coupling in mouse embryonic fibroblasts: Prediction of RevErb-α up-regulation during mitosis

On enumerating minimal siphons in Petri nets using CLP and SAT solvers: theoretical and practical complexity

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