Irene Otero-Muras
Computational Synthetic Biology · I2SYSBIO
Associated Unit I2SYSBIO - CRM · I2SYSBIO
Biography
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Chemical engineer by training, I did my PhD in applied mathematics at the BioProcess Engineering Group (CSIC) under the supervision of Antonio A. Alonso and Julio R. Banga. Since the beginning of my scientific career I was interested in understanding the complex dynamic behavior of biomolecular networks and its connection with relevant biological functions. During my postdoc at ETH (D-BSSE) with J Stelling, I became familiar with the open questions and challenges in systems and synthetic biology. Back at CSIC I started my work on the automated design of biocircuits for synthetic biology and on efficient methods for stochastic modeling and simulation of gene regulatory networks, helping to provide insight on cellular decisions under stochastic noise. One of my fundamental research aims is to understand the role of molecular noise in relevant cellular functions and exploit this knowledge for the advanced design, analysis and control of biosystems. |
Profile
| Institution | I2SYSBIO |
| Position | Científica Titular |
| Home page | https://noisynbio.org |
| Contact email | irene.otero.muras@csic.es |
| ORCID | 0000-0003-2895-997X |
BCB Hub
| BCB Committee | Not a member |
| BCB Tools | SYNBADm |
| BCB Services |
Research
Research topics
Gene regulatory networksSystems BiologySynthetic biology
Research lines
None
Projects, networks, transfer & teaching
Funded projects 1
Publications 46 entries
- Engineering phenotypic heterogeneity for functional organization in microbial populations Preprint · 15 Sep 2026
- BiosInt: Biosensor-based smart design of pathway dynamic regulation for industrial biomanufacturing Preprint · 17 Nov 2025
- A Computational Framework for Optimal and Model Predictive Control of Stochastic Gene Regulatory Networks Article · Nov 2025
- Context-Aware Biosensor Design Through Biology-Guided Machine Learning and Dynamical Modeling Software · 3 Jun 2025
- IDESS: a toolbox for identification and automated design of stochastic gene circuits Article · 1 Nov 2023
View all (41 more)
- Automated Design of Synthetic Gene Circuits in the Presence of Molecular Noise Article · 9 Oct 2023
- Global Optimization Approach for Parameter Estimation in Stochastic Dynamic Models of Biosystems Article · 1 May 2023
- Stochastic SIR model predicts the evolution of COVID-19 epidemics from public health and wastewater data in small and medium-sized municipalities: A one year study Article · Nov 2022
- Wastewater and marine bioindicators surveillance to anticipate COVID-19 prevalence and to explore SARS-CoV-2 diversity by next generation sequencing: One-year study Article · Aug 2022
- Fast biofoundries: coping with the challenges of biomanufacturing Article · Jul 2022
- Automated design of gene circuits with optimal mushroom-bifurcation behaviour Preprint · 10 May 2022
- OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production Article · 7 Apr 2022
- Automated design of synthetic biocircuits in the stochastic regime Article · 2022
- Automated engineering of synthetic metabolic pathways for efficient biomanufacturing Article · Jan 2021
- Automated Biocircuit Design with SYNBADm Book / chapter · 2021
- Synthetic Gene Circuit Analysis and Optimization Book / chapter · 13 Nov 2020
- A general technique for the detection of switch-like bistability in chemical reaction networks governed by mass action kinetics with conservation laws Preprint · 8 Nov 2020
- Solving the Competitive Binding Equilibria between Many Ligands: Application to High-Throughput Screening and Affinity Optimization Article · 19 Aug 2020
- Transient hysteresis and inherent stochasticity in gene regulatory networks Article · 8 Oct 2019
- Distilling Robust Design Principles of Biocircuits Using Mixed Integer Dynamic Optimization Article · 13 Feb 2019
- Multiobjective optimization of gene circuits for metabolic engineering Article · 2019
- Routes to Multiple Equilibria for Mass‐Action Kinetic Systems Article · Jan 2018
- Optimization-based prediction of fold bifurcations in nonlinear ODE models Article · 2018
- Mixed Integer Multiobjective Optimization Approaches for Systems and Synthetic Biology Article · 2018
- Automated Design Framework for Synthetic Biology Exploiting Pareto Optimality Article · 12 Apr 2017
- Chemical Reaction Network Theory elucidates sources of multistability in interferon signaling Article · 3 Apr 2017
- Design Principles of Biological Oscillators through Optimization: Forward and Reverse Analysis Article · 15 Dec 2016
- SYNBADm: A tool for optimization-based automated design of synthetic gene circuits Software · 8 Jul 2016
- Exploring Design Principles of Gene Regulatory Networks via Pareto Optimality Article · 2016
- Multicriteria global optimization for biocircuit design Article · 24 Sep 2014
- Optimization based design of synthetic oscillators from standard biological parts Book / chapter · 2014
- Erratum: Characterizing multistationarity regimes in biochemical reaction networks (PLoS ONE (2013) 8:1 DOI: 10.1371/annotation/b5283cc5-5a93-4c96-abc4- c5112266fabe) Article · 15 Jan 2013
- Characterizing multistationarity regimes in biochemical reaction networks Article · 3 Jul 2012
- Advances in Chemical Reaction Network Theory for the Identification of Kinetic Models Article · Jul 2012
- Inducing sustained oscillations in mass action kinetic networks of a certain class Article · 2012
- Contributing to fisheries sustainability by making the best possible use of their resources: the BEFAIR initiative Article · Nov 2010
- Generic parameterization for a pharmacokinetic model to predict Cd concentrations in several tissues of different fish species Article · Apr 2010
- Dynamic multi-compartmental modelling of metal bioaccumulation in fish: Identifiability implications Article · Mar 2010
- Parametric condition for multistationarity in biochemical reaction networks Article · 2010
- Exploring Multiplicity Conditions in Enzymatic Reaction Networks Article · May 2009
- Dynamic analysis and control of biochemical reaction networks Article · Dec 2008
- Local dissipative Hamiltonian description of reversible reaction networks Article · Jul 2008
- A systematic approach to plant-wide control based on thermodynamics Article · May 2007
- Network theory in control engineering: Applications in dynamic analysis and process control,La teoría de redes en ingeniería de control: Aplicación al análisis dinámico y al control de procesos Article · Jan 2007
- Improved optimization methods for the multiobjective design of bioprocesses Article · 2 Sep 2006
- A thermodynamic based plant-wide control design procedure of the tennessee eastman process Book / chapter · 2006