Observers for chemical reaction networks. - Madalena Chaves; Eduardo D. Sontag (ECC, 2001)

State-estimators for Chemical Reaction Networks of Feinberg-Horn-Jackson Zero Deficiency Type. - Madalena Chaves; Eduardo D. Sontag (Eur. J. Control, 2002)

Vehicle networks: achieving regular formation. - Sonja Glavaski; Madalena Chaves; Robert Day; Parthasarathi Nag; Anca Williams; Wei Zhang (ACC, 2003)

Gains and optimal design in signaling pathways. - Madalena Chaves; Eduardo D. Sontag; Robert J. Dinerstein (CDC, 2004)

Input-to-State Stability of Rate-Controlled Biochemical Networks. - Madalena Chaves (SIAM J. Control. Optim., 2005)

Stability of Rate-Controlled Zero-Deficiency Networks. - Madalena Chaves (CDC, 2006)

Structure and timescale analysis in genetic regulatory networks. - Madalena Chaves; Eduardo D. Sontag; Réka Albert (CDC, 2006)

Exact computation of amplification for a class of nonlinear systems arising from cellular signaling pathways. - Eduardo D. Sontag; Madalena Chaves (Autom., 2006)

Bistable Biological Systems: A Characterization Through Local Compact Input-to-State Stability. - Madalena Chaves; Thomas Eissing; Frank Allgöwer (IEEE Trans. Autom. Control., 2008)

Methods for qualitative analysis of genetic networks. - Madalena Chaves (ECC, 2009)

Operational interactions in genetic networks: Application to an apoptosis signalling pathway. - Laurent Tournier; Madalena Chaves (ECC, 2009)

Live and let die - A systems biology view on cell death. - Thomas Eissing; Madalena Chaves; Frank Allgöwer (Comput. Chem. Eng., 2009)

Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks. - Adel Dayarian; Madalena Chaves; Eduardo D. Sontag; Anirvan M. Sengupta (PLoS Comput. Biol., 2009)

Predicting the asymptotic dynamics of large biological networks by interconnections of Boolean modules. - Madalena Chaves; Laurent Tournier (CDC/ECC, 2011)

An observer for a piecewise affine genetic network model with Boolean observations. - Xiao-Dong Li; Jean-Luc Gouzé; Madalena Chaves (CDC/ECC, 2011)

Exact control of genetic networks in a qualitative framework: The bistable switch example. - Madalena Chaves; Jean-Luc Gouzé (Autom., 2011)

A Simple Model to Control Growth Rate of Synthetic E. coli during the Exponential Phase: Model Analysis and Parameter Estimation. - Alfonso Carta; Madalena Chaves; Jean-Luc Gouzé (CMSB, 2012)

Predictive analysis of dynamical systems: combining discrete and continuous formalisms. - Madalena Chaves (2013)

A linear reformulation of Boolean optimization problems and structure identification of gene regulation networks. - Christian Breindl; Madalena Chaves; Frank Allgöwer (CDC, 2013)

A Class of Switched Piecewise Quadratic Systems for Coupling Gene Expression with Growth Rate in Bacteria. - Alfonso Carta; Madalena Chaves; Jean-Luc Gouzé (NOLCOS, 2013)

Interconnection of asynchronous Boolean networks, asymptotic and transient dynamics. - Laurent Tournier; Madalena Chaves (Autom., 2013)

Continuous-switch piecewise quadratic models of biological networks: Application to bacterial growth. - Alfonso Carta; Madalena Chaves; Jean-Luc Gouzé (Autom., 2015)

Attractor computation using interconnected Boolean networks: Testing growth rate models in E. Coli. - Madalena Chaves; Alfonso Carta (Theor. Comput. Sci., 2015)

Periodic Oscillations for Nonmonotonic Smooth Negative Feedback Circuits. - Camille Poignard; Madalena Chaves; Jean-Luc Gouzé (SIAM J. Appl. Dyn. Syst., 2016)

A Stability Result for Periodic Solutions of Nonmonotonic Smooth Negative Feedback Systems. - Camille Poignard; Madalena Chaves; Jean-Luc Gouzé (SIAM J. Appl. Dyn. Syst., 2018)

Coupling and synchronization of piecewise linear genetic regulatory systems. - Madalena Chaves; Luca Scardovi; Eleni Firippi (CDC, 2019)

rPrism - A Software for Reactive Weighted State Transition Models. - Daniel Figueiredo 001; Eugénio Rocha; Manuel António Martins; Madalena Chaves (HSB, 2019)

Dynamics of complex feedback architectures in metabolic pathways. - Madalena Chaves; Diego A. Oyarzún (Autom., 2019)

Qualitative Analysis of Mammalian Circadian Oscillations: Cycle Dynamics and Robustness. - Ousmane Diop; Madalena Chaves; Laurent Tournier (CMSB, 2020)

Core Models of Receptor Reactions to Evaluate Basic Pathway Designs Enabling Heterogeneous Commitments to Apoptosis. - Marielle Péré; Madalena Chaves; Jérémie Roux (CMSB, 2020)

A model of apoptosis receptor reactions to study cell fate decision. - Luis C. Gomes-Pereira; Madalena Chaves; Jérémie Roux (MED, 2020)

Cell cycle period control through modulation of clock inputs. - Sofia Almeida; Madalena Chaves; Franck Delaunay (J. Bioinform. Comput. Biol., 2020)

Boolean dynamics revisited through feedback interconnections. - Madalena Chaves; Daniel Figueiredo 001; Manuel A. Martins 001 (Nat. Comput., 2020)

Special issue "International Symposium on Molecular Logic and Computational Synthetic Biology: MLCSB18". - Tomas Veloz; Madalena Chaves; Manuel António Martins (Soft Comput., 2021)

Qualitative Control Strategies for Synchronization of Bistable Gene Regulatory Networks. - Nicolas Augier; Madalena Chaves; Jean-Luc Gouzé (IEEE Trans. Autom. Control., 2023)

Benchmark for quantitative characterization of circadian clock cycles. - Odile Burckard; Michèle Teboul; Franck Delaunay; Madalena Chaves (Biosyst., 2025)