A systematic approach to plant-wide control based on thermodynamics. - Luis T. Antelo; Irene Otero-Muras; Julio R. Banga; Antonio A. Alonso (Comput. Chem. Eng., 2007)

Dynamic analysis and control of biochemical reaction networks. - Irene Otero-Muras; Gábor Szederkényi; Katalin M. Hangos; Antonio A. Alonso (Math. Comput. Simul., 2008)

Local dissipative Hamiltonian description of reversible reaction networks. - Irene Otero-Muras; Gábor Szederkényi; Antonio A. Alonso; Katalin M. Hangos (Syst. Control. Lett., 2008)

Dynamic multi-compartmental modelling of metal bioaccumulation in fish: Identifiability implications. - Irene Otero-Muras; Amaya Franco-Uría; Antonio A. Alonso; Eva Balsa-Canto (Environ. Model. Softw., 2010)

Optimization Based Design of Synthetic Oscillators from Standard Biological Parts. - Irene Otero-Muras; Julio R. Banga (CMSB, 2014)

Multicriteria global optimization for biocircuit design. - Irene Otero-Muras; Julio R. Banga (BMC Syst. Biol., 2014)

A method for inverse bifurcation of biochemical switches: inferring parameters from dose response curves. - Irene Otero-Muras; Pencho Yordanov; Jörg Stelling (BMC Syst. Biol., 2014)

SYNBADm: a tool for optimization-based automated design of synthetic gene circuits. - Irene Otero-Muras; David Henriques; Julio R. Banga (Bioinform., 2016)

Chemical Reaction Network Theory elucidates sources of multistability in interferon signaling. - Irene Otero-Muras; Pencho Yordanov; Jörg Stelling (PLoS Comput. Biol., 2017)

SELANSI: a toolbox for simulation of stochastic gene regulatory networks. - Manuel Pájaro; Irene Otero-Muras; Carlos Vázquez 002; Antonio A. Alonso (Bioinform., 2018)

Routes to Multiple Equilibria for Mass-Action Kinetic Systems. - Antonio A. Alonso; Irene Otero-Muras; Manuel Pájaro (Complex., 2018)

CRNT4SBML: a Python package for the detection of bistability in biochemical reaction networks. - Brandon Reyes; Irene Otero-Muras; Michael T. Shuen; Alexandre M. Tartakovsky; Vladislav A. Petyuk (Bioinform., 2020)

BioSwitch: a tool for the detection of bistability and multi-steady state behaviour in signalling and gene regulatory networks. - Pencho Yordanov; Jörg Stelling; Irene Otero-Muras (Bioinform., 2020)

Chemical Master Equation model to predict the COVID-19 epidemic spread. - Manuel Pájaro; Antonio A. Alonso; Irene Otero-Muras (XoveTIC, 2022)

A numerical approach for detecting switch-like bistability in mass action chemical reaction networks with conservation laws. - Brandon Reyes; Irene Otero-Muras; Vladislav A. Petyuk (BMC Bioinform., 2022)

Global Optimization Approach for Parameter Estimation in Stochastic Dynamic Models of Biosystems. - Carlos Sequeiros; Irene Otero-Muras; Carlos Vázquez 002; Julio R. Banga (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

IDESS: a toolbox for identification and automated design of stochastic gene circuits. - Carlos Sequeiros; Manuel Pájaro; Carlos Vázquez 002; Julio R. Banga; Irene Otero-Muras (Bioinform., 2023)

Analysis and Control of Gene Regulation Network Models Using Kinetic Semi-Discretization. - Mihály A. Vághy; Irene Otero-Muras; Gábor Szederkényi (ECC, 2024)