Publications and other merits

Articles update

J Tellechea-Luzardo, H Martin Lazaro, C Fernandez Perez, D Henriques, I Otero-Muras, P Carbonell (2025) Context-Aware Biosensor Design Through Biology-Guided Machine Learning and Dynamical Modeling ACS Synthetic Biology https://doi.org/10.1021/acssynbio.4c00894

H Faquir, M Pájaro, I Otero-Muras (2024) A computational framework for optimal and Model Predictive Control of stochastic gene regulatory networks

arXiv:2409.11036 https://doi.org/10.48550/arXiv.2409.11036

MA Vághy, I Otero-Muras, G Szederkenyi (2024)

Analysis and control of gene regulation network models using kinetic semi-discretization, European Control Conference (ECC 2024), 1264-1269 https://doi.org/10.23919/ECC64448.2024.10591020

MA Vághy, I Otero-Muras, M Pájaro, G Szederkényi (2024)

A kinetic finite volume discretization of the multidimensional PIDE model for gene regulatory networks, Bulletin of Mathematical Biology 86 (2), 22, https://doi.org/10.1007/s11538-023-01251-3

C Sequeiros, M Pájaro, C Vázquez, JR Banga, I Otero-Muras (2023) IDESS: a toolbox for identification and automated design of stochastic gene circuits

Bioinformatics 39 (11), btad682 https://doi.org/10.1093/bioinformatics/btad682

C Sequeiros, C Vázquez, JR Banga, I Otero-Muras

(2023) Automated design of synthetic gene circuits in the presence of molecular noise, ACS Synthetic Biology 12 (10), 2865-2876 https://doi.org/10.1021/acssynbio.3c00033

I Otero-Muras, R Perez-Carrasco, JR Banga, CP Barnes (2023)

Automated design of gene circuits with optimal mushroom-bifurcation behavior, Iscience 26 (6) https://doi.org/10.1016/j.isci.2023.106836

C Sequeiros, I Otero-Muras, C Vázquez, JR Banga (2022)

Global optimization approach for parameter estimation in stochastic dynamic models of biosystems, IEEE/ACM transactions on computational biology and bioinformatics, 20(3):1971-1982 https://doi.org/10.1109/TCBB.2022.3225675

M Pájaro, NM Fajar, AA Alonso, I Otero-Muras

(2022) 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, Chaos, Solitons & Fractals 164, 112671 https://doi.org/10.1016/j.chaos.2022.112671

Novoa B, Ríos-Castro R, Otero-Muras I, Gouveia S, Cabo A, Saco A, Rey-Campos M, Pájaro M, Fajar N, Aranguren R, Romero A, Panebianco A, Valdés L, Payo P, Alonso AA, Figueras A, Cameselle C. (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, Science of the Total Environment 833, 155140, https://doi.org/10.1016/j.scitotenv.2022.155140

J Tellechea-Luzardo, I Otero-Muras, A Goñi-Moreno, P Carbonell

(2022) Fast biofoundries: coping with the challenges of biomanufacturing

Trends in biotechnology 40 (7), 831-842 https://doi.org/10.1016/j.tibtech.2021.12.006

S Jiang, I Otero-Muras, JR Banga, Y Wang, M Kaiser, N Krasnogor (2022) OptDesign: identifying optimum design strategies in strain engineering for biochemical production, ACS Synthetic Biology 11 (4), 1531-1541 https://doi.org/10.1021/acssynbio.1c00610

BC Reyes, I Otero-Muras, VA Petyuk

(2022) A numerical approach for detecting switch-like bistability in mass action chemical reaction networks with conservation laws

BMC bioinformatics 23 (1), 1 https://doi.org/10.1186/s12859-021-04477-x

C Fernández Pérez, H Faquir, M Pájaro, I Otero-Muras (2022) Feedback control of stochastic gene switches using PIDE models, IFAC-PapersOnline 55 (18): 62-67,

https://doi.org/10.1016/j.ifacol.2022.08.031

C Sequeiros, C Vázquez, JR Banga, I Otero-Muras (2022) Automated design of synthetic biocircuits in the stochastic regime, IFAC-PapersOnLine 55 (20), 630-634, https://doi.org/10.1016/j.ifacol.2022.09.166

M Pájaro, I Otero-Muras, AA Alonso (2022), First passage times as a measure of hysteresis in stochastic gene regulatory circuits, IFAC-PapersOnLine 55 (18), 50-55 https://doi.org/10.1016/j.ifacol.2022.08.029

BC Reyes, I Otero-Muras, VA Petyuk (2022) A general technique for the detection of switch-like bistability in chemical reaction networks governed by mass action kinetics with conservation laws, BMC Bioinformatics 23, 1 https://doi.org/10.1186/s12859-021-04477-x

I Otero-Muras, E Balsa-Canto (2021) Antonio A. Alonso. In memoriam. Contributions to modelling and control of food and bioprocesses, Food and Bioproducts Processing 126, 90-94 https://doi.org/10.1016/j.fbp.2020.12.007

I Otero-Muras, JR Banga (2021) Automated Biocircuit Design with SYNBADm

In: Menolascina, F. (eds) Synthetic Gene Circuits . Methods in Molecular Biology, vol 2229. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1032-9_4

I Otero-Muras, P Carbonell (2021) Automated engineering of synthetic metabolic pathways for efficient biomanufacturing, Metabolic Engineering 63, 61-80 https://doi.org/10.1016/j.ymben.2020.11.012

I Otero-Muras, JR Banga (2021) Synthetic gene circuit analysis and optimization

Methods Mol Biol; 2189:89-103. https://doi. 10.1007/978-1-0716-0822-7_8

V Blay, I Otero-Muras, DA Annis (2020) Solving the competitive binding equilibria between many ligands: application to high-throughput screening and affinity optimization, Analytical Chemistry 92 (18), 12630-12638 https://doi.org/10.1021/acs.analchem.0c02715

Participation in Recent/Upcoming Conferences:

Invited honorable speaker at the “Quantitative Modelling of Cell Metabolism Conference”, Novo Nordisk Foundation, to be held in Copenhagen, Spring 2021 https://www.eventbrite.com/e/quantitative-modelling-of-cell-metabolism-conference-workshop-registration-91595238825
Keynote speaker at Gordon Conference “Biological Modeling, Directed Evolution and Complexity from Design to Application” (Waterville Valley, NH, USA) July 14-19, 2019 https://www.grc.org/synthetic-biology-conference/2019/
Plenary lecturer at the Advanced Lecture Course on Computational Systems Biology CompSysBio 2019 (March 31-April 6 Aussois, France) https://project.inria.fr/compsysbio2019/.
Plenary speaker at the Bio-Inspired Analysis of Dynamical Systems International Workshop 2019 (January 10-12 Esztergom, Hungary) https://efop362.itk.ppke.hu/conferences

Scientific Committees:

Program Commitee IWBDA 2020 International Workshop on Bio-Design Automation
Scientific Commitee CompSysBio 2021 Advanced Lecture Course on Computational Systems Biology
Member of the Technical Committee on BioProcesses and Biosystems of the International Federation of Automatic Control (IFAC).
National Organizing Committee of the 8th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE 2019). http://fosbe2019.ai2.upv.es/

Recent Publications:

Reyes B, Otero-Muras I, Shuen MT, Tartakovsky AB, Petyuk VA, 2020 CRNT4SBML: a Python package for the detection of bistability in biochemical reaction networks Bioinformatics, https://doi.org/10.1093/bioinformatics/btaa241
Yordanov P, Stelling J, Otero-Muras I 2019. BioSwitch: a tool for the detection of bistability and multi-steady state behaviour in signaling and gene regulatory networks, Bioinformatics https://doi.org/10.1093/bioinformatics/btz746
Pájaro M*, Otero-Muras I*, Vázquez C, Alonso AA 2019. Transient hysteresis and inherent stochasticity in gene regulatory networks, Nature Communications 10:4581.
Otero-Muras I, Banga JR, 2019. Distilling robust design principles of biocircuits using Mixed Integer Dynamic Optimization, 2019 Processes (Special Issue Computational Systems Biology, in press).
Pájaro M, Otero-Muras I, Vázquez C, Alonso AA, 2018. Inherent stochasticity precludes hysteresis in gene regulatory networks. Arxiv https://arxiv.org/abs/1810.10409
Alonso AA, Otero-Muras I, Pájaro M, 2018. Routes to Multiple equilibria in Mass-Action kinetic systems. Complexity ID 3912627. https://doi.org/10.1155/2018/3912627
Pájaro M, Otero-Muras I, Vázquez C, Alonso AA, 2018. SELANSI: a toolbox for Simulation of Stochastic Gene Regulatory Networks, Bioinformatics https://doi.org/10.1093/bioinformatics/btx645
Otero-Muras I, Yordanov P, Stelling J, 2017. Chemical Reaction Theory elucidates sources of multistationarity in Interferon signaling. PLoS Computational Biology 13(4):e1005454 http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005454
Otero-Muras I, Banga JR, 2017. Automated Design Framework for Synthetic Biology exploiting Pareto Optimality. ACS Synthetic Biology DOI: 10.1021/acssynbio.6b00306 http://pubs.acs.org/doi/abs/10.1021/acssynbio.6b00306
Pájaro M, Alonso AA, Otero-Muras I, Vázquez C, 2017. Stochastic modeling and numerical simulation of gene regulatory networks with protein bursting. Journal of Theoretical Biology 421:51-70. http://www.sciencedirect.com/science/article/pii/S0022519317301352
Otero-Muras I, Banga JR, 2016. Design Principles of Biological Oscillators through Optimization: Forward and Reverse Analysis. PLoS ONE 11(12): e0166867 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0166867
Otero-Muras I, Henriques D, Banga JR, 2016. SYNBADm: a tool for optimization-based automated design of synthetic gene circuits. Bioinformatics 32(21): 3360-3362 https://www.ncbi.nlm.nih.gov/pubmed/27402908

You can find all my publications here: https://www.researchgate.net/profile/Irene_Otero-Muras

Teaching:

CSIC-UIMP Master on Integrative Synthetic Biology MISB (starting september 2021)

University of Vigo (2015)
M.Sc. in Biological Sciences> Systems Biology module (joint course).
ETH-Zürich (2010-2013)
Lecturer

Structural Analysis of Biochemical Reaction Networks , Spring 2012
Bioinformatics in Depth (joint course), Spring 2012
Bioinformatics in Depth (joint course), Spring 2011

Assistant

Synthetic Biology (J. Stelling and S. Panke), Spring 2011
Synthetic Biology (J. Stelling and S. Panke), Spring 2010

Editorial work:

from 2019 – Editorial Board Member of BMC Bioinformatics
from 2017- Editorial Board Member of BMC Systems Biology
from 2018- Editorial Board Member of Complexity