People
Irene Otero-Muras
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.
Hamza Faquir
I’m currently a PhD fellow with the CSIC group COMPUTATIONAL SYNTHETIC BIOLOGY under the supervision of Dr. Irene Otero-Muras,as part of the MSCA-ITN-2020 project E-MUSE. I had my first master’s degree from the Faculty of sciences and technologies Marrakech, on Mathematical modeling and PDE analysis, Then I joined Lyon 1 university for a master’s degree in Mathematics for biology and medicine. I’m generally interested in the application of mathematical deterministic and probabilistic methods to explore biological networks, and to have better insights on biosystems that can lead to several applications in biomedical sciences and industrial biotechnology. My doctoral research will be focused on feedback control of individual cells in microorganism populations, more precisely, we will be working on developing a novel control paradigm to guide the modulation of the underlying stochastic gene circuits of bacterial systems that regulate metabolic activity and therefore phenotype heterogeneity through the available environmental stress variables. Through the collaboration with different research groups in the E-muse project, we will apply our results on processes of importance to the fermented food industry.
Christian Fernández
After graduating as a mathematician from the University of Santiago de Compostela (USC), I started a master’s degree in Industrial Mathematics (M2i) in 2020, specialising in mathematical modelling. After completing these studies, I had the opportunity to do an internship at the CSIC, specifically at the Institute of Integrative Systems Biology (I²SysBio), on the control of biomolecular networks for synthetic biology applications using PIDE model-based control, under the supervision of Dr. Irene Otero-Muras and Dr. Manuel Pájaro Diéguez. Thanks to the Gain Oportunius Grant, I started working for the CSIC, where I have been able to give continuity to the studies started during my internship. My research project consists of developing, by means of control theory methods, nonlinear analysis and PIDE models, analysis and control strategies for biomolecular networks and biocircuits in presence of high molecular noise, understanding the emergent propoperties in presence of noise, and controling cell populations in different scenarios of interest in systems and synthetic biology.
HASHMAT SINGH BAKSHI
After completing my Master’s degree in Biomedical Engineering at École Polytechnique, Institut Polytechnique de Paris, I joined the Computational Synthetic Biology Group at the Institute for Integrative Systems Biology as a PhD fellow as part of the MSCA-DN FAIROmics. This double doctorate programme is jointly conducted between Universitat Politècnica de València and Université Paris-Saclay under the direction of Dr Irene Otero-Muras and Prof Cristian Trelea. Prior this, my academic and research experiences spanned a broad range of disciplines; from thin-film surface modification to medical device design. My Master’s thesis involved the development of a simulation framework for transporting passive objects via phototaxis-driven active matter. During my Bachelor of Engineering studies at the University of Sydney, as a Dalyell Scholar, I did my Honours research in investigating quantum tunnelling and heavy-ion fusion. For my doctoral research, in the context of understanding and controlling metabolic shifts in bacteria, I am developing a system-agnostic toolbox for bistability detection to identify the key players in biochemical networks that govern cellular responses and behaviour. This links to my ultimate goal of developing strategies for robust control of stochastic gene regulatory networks driving these metabolic transitions.
Mara Pisani
After obtaining my Master’s degree in Biology from the University of Salerno, I joined the Synthetic and Systems Biology for Biomedicine Laboratory at the Istituto Italiano di Tecnologia (IIT), where I developed a strong interest in mammalian synthetic biology and genetic circuit design. I then pursued a PhD in Synthetic and Systems Biology with the Open University in partnership with IIT, under the supervision of Dr. Velia Siciliano. My doctoral research focused on understanding synthetic circuit–host cell interactions and developing strategies to optimize intracellular resource allocation and enhance gene expression performance. The results of this work were published in Nature Communications and presented at several international conferences, including the Mammalian Synthetic Biology Workshop and Next Generation Synthetic Biology.
During my PhD, I was awarded an EMBO Exchange Fellowship to conduct research at the Institute of Integrative Systems Biology (I²SysBio) in Valencia, Spain, under the supervision of Dr. Irene Otero-Muras. Following this collaboration, I joined I²SysBio as a postdoctoral researcher in Dr. Otero-Muras’s group, where I am currently working on the CellWise ERC project. The research focuses on developing mathematical and computational frameworks to understand and control cell population behaviors and synthetic circuits in noisy environments, and my aim is to bridge experimental synthetic biology and theoretical modeling to design more robust and predictable biological systems.
During my PhD, I was awarded an EMBO Exchange Fellowship to conduct research at the Institute of Integrative Systems Biology (I²SysBio) in Valencia, Spain, under the supervision of Dr. Irene Otero-Muras. Following this collaboration, I joined I²SysBio as a postdoctoral researcher in Dr. Otero-Muras’s group, where I am currently working on the CellWise ERC project. The research focuses on developing mathematical and computational frameworks to understand and control cell population behaviors and synthetic circuits in noisy environments, and my aim is to bridge experimental synthetic biology and theoretical modeling to design more robust and predictable biological systems.
Former Members
Ramón Catalán
I joined the I2SysBio as a physics undergraduate student at the University of Valencia as part of the “Alumn Colaborador” program promoted by this university, under the supervision of Dr. Irene Otero-Muras. My interests during this stay focused on the analysis of complex dynamical biosystems—a hallmark of systems biology—particularly in the context of biochemical reaction networks, including gene regulatory networks and signalling pathways. During this time at I2SysBio, my research project involved applying bifurcation theory to study novel phenomena observed in biological systems far from the thermodynamic limit (characterized by low copy numbers and highly stochastic behaviour), which cannot be explained by standard deterministic analysis.