Irene Otero-Muras

Please visit my new site:

https://noisynbio.org/

I have moved to a new position as leader of the

Computational Synthetic Biology Group

Spanish National Research Council

Institute for Integrative Systems Biology (I2SYSBIO)

Valencia

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I formerly worked at the BioProcess Engineering Group (IIM-CSIC) developing tools for Biosystems Identification, Design and Control for Synthetic and Systems Biology applications

My research interests include:

> Systematic inference of design principles of biological networks (through optimization).

> Automated design of genetic circuits for Synthetic Biology.

> Effective detection of complex behaviour in biochemical networks exploiting their inherent structural properties. I am particularly interested in the emergence of bistability and oscillations in gene regulation and cell signaling.

> The effect of molecular noise in gene regulation, and how to incorporate molecular noise in the design of biocircuits.

e-mail: irene.otero.muras@csic.es twitter: @Otero_Muras

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

Background:

After graduating in Chemical Engineering at Santiago de Compostela University I joined the Bioprocess Engineering Group at IIM-CSIC, where I developed my PhD thesis Modeling, dynamic analysis and control of biological networks defended on May 2010.

In 2010 I joined the Computational Systems Biology Group (Department of Biosystems Science and Engineering) at ETH-Zurich for a 3 year postdoc where i worked in the EU FP7 project IFNAction: A system view on the differential activities of human type I interferons.

Since 2013 I work at the BioProcess Engineering Group (IIM-CSIC), in the projects MULTISCALES: Multi-scale inference, monitoring, optimization and control: from cells to bioreactors, and SYNBIOFACTORY: Synthetic biology for bioproduction enhancement: Design, optimization, monitoring and control.

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

Teaching:

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