SYMBIONT

2022

10.1137/20M1364503 E. Feliu, C. Lax, S. Walcher, C. Wiuf
Quasi-Steady-State and Singular Perturbation Reduction for Reaction Networks with Noninteracting Species
SIAM J. Appl. Dyn. Syst., 21(2):782–816, 2022
2201.08980 C. Lüders, T. Sturm, O. Radulescu
ODEbase: A Repository of ODE Systems for Systems Biology
arxiv:2201.08980, 2022

2021

10.1007/s11786-020-00477-x F. Boulier, F. Lemaire, M. Moreno-Maza, A. Poteaux
A Short Contribution to the Theory of Regular Chains
Math. Comput. Sci., 15(2):177–188, 2021
10.3934/math.2021398 J. Eilertsen, M.R. Roussel, S. Schnell, S. Walcher
On the Quasi-steady-state Approximation in an Open Michaelis–Menten Reaction Mechanism
AIMS Mathematics, 6(7): 6781–6814, 2021
10.1007/s11786-020-00476-y M. England, W. Koepf, T. Sadykov, W. Seiler, T. Sturm
Foreword, with a Dedication to Andreas Weber
Math. Comput. Sci., 15(2):173–175, 2021
10.1098/rsif.2021.0146 T. Fuhrmann-Lieker, N. Kubetschek, J. Ziebarth, R. Klassen, W. Seiler
Is the Diatom Sex Clock a Clock?
J. R. Soc. Interface, 18(179):20210146, 2021
10.1007/s11786-020-00479-9 D. Grigoriev, A. Iosif, H. Rahkooy, T. Sturm, A. Weber
Efficiently and Effectively Recognizing Toricity of Steady State Varieties
Math. Comput. Sci., 15(2):199–232, 2021
10.1007/s11786-021-00515-2 N. Kruff, C. Lüders, O. Radulescu, T. Sturm, S. Walcher
Algorithmic Reduction of Biological Networks With Multiple Time Scales
Math. Comput. Sci., 15(3):499–534, 2021
10.1016/j.aam.2021.102266 M. Lange-Hegermann, D. Robertz, W. Seiler, M. Seiß
Singularities of Algebraic Differential Equations
Adv. Appl. Math., 131:102266, 2021
10.1007/978-3-030-85165-1_13 F. Lemaire, A. Poteaux
Decoupling Multivariate Fractions
CASC 2021, LNCS 12865, pp.209–231, 2021
10.1007/978-3-030-85165-1_18 H. Rahkooy, T. Sturm
Parametric Toricity of Steady State Varieties of Reaction Networks
CASC 2021, LNCS 12865, pp.314–333, 2021
10.1007/978-3-030-85165-1_19 H. Rahkooy, T. Sturm
Testing Binomiality of Chemical Reaction Networks Using Comprehensive Groebner Systems
CASC 2021, LNCS 12865, pp.334–352, 2021
10.1142/S0218127421500449 W. Seiler, M. Seiß
No Chaos in Dixon’s System
International Journal of Bifurcation and Chaos, 31(3):2150044, 2021
10.1016/j.jde.2021.02.010 W. Seiler, M. Seiß
Singular Initial Value Problems for Scalar Quasi-linear Ordinary Differential Equations
J. Differ. Equations, 281:258–288, 2021
10.1007/s11786-020-00485-x W. Seiler, M. Seiß, T. Sturm
A Logic Based Approach to Finding Real Singularities of Implicit Ordinary Differential Equations
Math. Comput. Sci., 15(2):333–352, 2021

2020

10.1007/978-3-030-81698-8_7 F. Boulier, J. Cano, S. Falkensteiner, R. Sendra
Puiseux Series and Algebraic Solutions of First Order Autonomous AODEs — A MAPLE Package
MC 2020, CCIS 1414, pp.89–103, 2020
10.1016/j.jsc.2019.07.008
1902.04882
R. Bradford, J.H. Davenport, M. England, H. Errami, V. Gerdt, D. Grigoriev, C. Hoyt, M. Kosta, O. Radulescu, T. Sturm, A. Weber
Identifying the Parametric Occurrence of Multiple Steady States for Some Biological Networks
J. Symb. Comput., 98:84–119, 2020
10.1007/s11786-019-00423-6 E. Braun, W. Seiler, M. Seiß
On the Numerical Analysis and Visualisation of Implicit Ordinary Differential Equations
Math. Comput. Sci., 14(2):281–293, 2020
10.1007/978-3-030-60327-4_4 E. Degrand, F. Fages, S. Soliman
Graphical Conditions for Rate Independence in Chemical Reaction Networks
CMSB 2020, LNBI 12314, pp.61–78, 2020
10.1145/3373207.3404040 S. Falkensteiner, C. Garay-Lopez, M. Haiech, M. Noordman. Z. Toghani, F. Boulier
The Fundamental Theorem of Tropical Partial Differential Algebraic Geometry
ISSAC 2020, pp.178–185, ACM Press, 2020
10.1007/s00332-020-09610-3 E. Feliu, N. Kruff, S. Walcher
Tikhonov–Fenichel Reduction for Parameterized Critical Manifolds with Applications to Chemical Reaction Networks
J. Nonlinear Sci., 30(4):1355–1380, 2020
10.1007/978-3-030-60327-4_7 M. Hemery, F. Fages, S. Soliman
On the Complexity of Quadratization for Polynomial Differential Equations
CMSB 2020, LNBI 12314, pp.120–140, 2020
10.3934/dcdsb.2019170 C. Lax, S. Walcher
Singular Perturbations and Scaling
Discrete Cont. Dyn.-B, 25(1): 1-29, 2020
10.1007/978-3-030-60026-6_29
2002.12693
H. Rahkooy, O. Radulescu, T. Sturm
A Linear Algebra Approach for Detecting Binomiality of Steady State Ideals of Reversible Chemical Reaction Networks
CASC 2020, LNCS 12291, pp.492–509, 2020
10.1007/978-3-030-60026-6_30
2002.03586
H. Rahkooy, T. Sturm
First-Order Tests for Toricity
CASC 2020, LNCS 12291, pp.510–527, 2020
10.1109/SYNASC51798.2020.00027 H. Rahkooy, C. Vargas-Montero
A Graph Theoretical Approach for Testing Binomiality of Reversible Chemical Reaction Networks
SYNASC 2020, pp.101–108, IEEE, 2020
10.1007/978-3-030-60026-6_2 W. Seiler, M. Seiß
Algebraic and Geometric Analysis of Singularities of Implicit Differential Equations (Invited Talk)
CASC 2020, LNCS 12291, pp.14–41, 2020

2019

Open Access » F. Boulier
A Differential Algebra Introduction For Tropical Differential Geometry
Introductory course to a workshop on Tropical Differential Geometry, Queen Mary College, London, UK, 2019
Open Access » F. Boulier, M. Haiech
The Ritt–Raudenbush Theorem and Tropical Differential Geometry
Preprint, 2019
10.3934/mbe.2019255 N. Kruff, S. Walcher
Coordinate-independent Singular Perturbation Reduction for Systems with Three Time Scales
Math. Biosci. Eng., 16(5): 5062–5091, 2019

2018

10.1016/j.jtbi.2018.09.024 A. Baudier, F. Fages, S. Soliman
Graphical Requirements for Multistationarity in Reaction Networks and their Verification in BioModels
J. Theor. Biol., 459:79–89, 2018
10.1007/978-3-319-99639-4_6 F. Boulier, H. Castel, N. Corson, V. Lanza, F. Lemaire, A. Poteaux, A. Quadrat, N. Verdière
Symbolic-Numeric Methods for Nonlinear Integro-Differential Modeling
CASC 2018, LNCS 11077, pp.82–98, 2018
10.1145/3313880.3313885
Free Access »
F. Boulier, F. Fages, O. Radulescu, S. Samal, A. Schuppert, W. Seiler, T. Sturm, S. Walcher, A. Weber
The SYMBIONT Project: Symbolic Methods for Biological Networks
ACM Communications in Computer Algebra, 52(3):67–70, 2018
10.7490/f1000research.1115995.1 F. Boulier, F. Fages, O. Radulescu, S. Samal, A. Schuppert, W. Seiler, T. Sturm, S. Walcher, A. Weber
The SYMBIONT Project: Symbolic Methods for Biological Networks
Poster, F1000Research, 7:1341, 2018
10.1007/978-3-319-99639-4_17 H. Hong, T. Sturm
Positive Solutions of Systems of Signed Parametric Polynomial Inequalities
CASC 2018, LNCS 11077, pp.238–253, 2018

Selected Earlier Publications 2013–2018

10.1007/s12346-017-0235-2 C. Lax, K. Seliger, S. Walcher
A Coordinate-independent Version of Hoppensteadt's Convergence Theorem
Qual. Theory Dyn. Syst., 17(1):7–28, 2018
10.1007/s10910-018-0891-8 M. Frank, C. Lax, S. Walcher, O. Wittich
Quasi-steady State Reduction for the Michaelis–Menten Reaction–diffusion System
J. Math. Chem., 56(6):1759–1781, 2018
10.1145/3087604.3087622
1704.08997
R. Bradford, J. Davenport, M. England, H. Errami, V. Gerdt, D. Grigoriev, C. Hoyt, M. Kosta, O. Radulescu, T. Sturm, A. Weber
A Case Study on the Parametric Occurrence of Multiple Steady States
ISSAC 2017, pp.45–52, ACM Press, 2017
10.1007/978-3-319-66320-3_8 M. England, H. Errami, D. Grigoriev, O. Radulescu, T. Sturm, A. Weber
Symbolic Versus Numerical Computation and Visualization of Parameter Regions for Multistationarity of Biological Networks
CASC 2017, LNCS 10490, pp.93–108, 2017
10.1016/j.physd.2016.12.002 A. Goeke, S. Walcher, E. Zerz
Classical Quasi-Steady State Reduction – A Mathematical Characterization
Physica D, 345:11–26, 2017
10.1016/j.jsc.2016.01.002 F. Boulier, F. Lemaire, J. Lallemand, G. Regensburger, M. Rosenkranz
Additive Normal Forms and Integration of Differential Fractions
J. Symb. Comput., 77:16–38, 2016
10.1016/j.biosystems.2016.07.004 S. Samal, A. Naldi, D. Grigoriev, A. Weber, N. Théret, O. Radulescu
Geometric Analysis of Pathways Dynamics: Application to Versatility of TGF-β Receptors
Biosystems, 149:3–14, 2016
10.1016/j.biosystems.2016.07.003 P. Traynard, C. Feillet, S. Soliman, F. Delaunay, F. Fages
Model-based Investigation of the Circadian Clock and Cell Cycle Coupling in Mouse Embryonic Fibroblasts: Prediction of RevErb-α Up-regulation During Mitosis
Biosystems, 149:59–69, 2016
10.1007/978-3-319-24021-3_8 F. Boulier, F. Lemaire
Finding First Integrals Using Normal Forms Modulo Differential Regular Chains
CASC 2015, LNCS 9301, pp.101–118, 2015
10.1016/j.jcp.2015.02.050 H. Errami, M. Eiswirth, D. Grigoriev, W. Seiler, T. Sturm, A. Weber
Detection of Hopf Bifurcations in Chemical Reaction Networks Using Convex Coordinates
J. Comput. Phys., 291:279–302, 2015
10.1016/j.jde.2015.02.038 A. Goeke, S. Walcher, E. Zerz
Determining "Small Parameters" for Quasi-Steady State
J. Differ. Equations, 259(3):1149–1180, 2015
10.1007/978-3-319-24021-3_10 A. Goeke, S. Walcher, E. Zerz
Quasi-Steady State – Intuition, Perturbation Theory and Algorithmic Algebra
CASC 2015, LNCS 9301, pp.135–215, 2015
10.1007/s11538-015-0118-0 S. Samal, D. Grigoriev, H. Fröhlich, A. Weber, O. Radulescu
A Geometric Method for Model Reduction of Biochemical Networks with Polynomial Rate Functions
Bull. Math. Biol., 77(12):2180–2211, 2015
10.1007/978-3-319-24021-3_31 S. Samal, D. Grigoriev, H. Fröhlich, O. Radulescu
Analysis of Reaction Network Systems Using Tropical Geometry
CASC 2015, LNCS 9301, pp.424–439, 2015
10.1007/s10910-014-0402-5 A. Goeke, S. Walcher
A Constructive Approach to Quasi-Steady State Reductions
J. Math. Chem., 52(10):2596–2626, 2014
10.1007/978-3-319-12982-2_1 F. Lemaire, A. Temperville
On Defining and Computing "Good" Conservation Laws
CMSB 2014, LNCS 8859, pp.1–19, 2014
10.1186/s13015-014-0024-2 S. Soliman, F. Fages, O. Radulescu
A Constraint Solving Approach to Model Reduction by Tropical Equilibration
Algorithms for Molecular Biology, 9:24, 2014
10.4230/DagRep.2.11.66 F. Boulier, A. Shiu, T. Sturm, A. Weber
Symbolic Methods for Chemical Reaction Networks
Dagstuhl Reports 2(11):66–86, 2013