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Closed for Applications


Early Stage Researcher (ESR3)  

PhD fellowship in feed-back control of individual cells in microorganism populations.

Project Title

“E-MUSE Complex microbial ecosystems multiscale modelling: mechanistic and data driven approaches integration” MSCA-ITN-2020 European Training Network

Hosting Organization

Agencia Estatal Consejo Superior Deinvestigaciones Cientificas (CSIC), established in Calle Serrano 117, Madrid 28006, Spain  

Researcher Profiles


Research Field

(bio)process modeling, (bio)process control, stochastic dynamic systems, gene regulation in bacteria

Application Deadline

31.05.2021, 23:59 ; prolonged till 23.06.2021, 23:59 - Europe/Brussels

Envisaged Job Starting Date



3 years

Contract Type

full-time employment (based on COVID-19 evolution and restrictions, possibility to start remotely, once situation allows the presence is required)


2.963,34/month or €3.361,68/month (with family aid if applicable)

(included €600 gross mobility allowance/month)

Taxation and Social (including Pension) Contribution deductions based on National and company regulations apply.


The objective of the project is 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. The central questions to be addressed are, on the one hand, the appropriate system representation for control, which also includes uncertainty compensation for robust tracking and regulation; On the other hand, the technology and inference methods for heterogeneity quantification and monitoring. The proposed control paradigm will be demonstrated on cheese ecosystems, controlling environmental variables towards specific final product characteristics.

Expected Results

We expect to deliver i) a proper model of the bacterial system that incorporates the underlying probability distributions associated to protein expression and their dynamics, ii) identification of the appropriate input-to-state and state-to-outputs maps needed for control iii) on-line information of the current level of heterogeneity, taking advantage of on-line flow cytometry (FC) to get sampled distributions of the target species. iv) a reliable feed-back controller, capable of enabling robust regulation in the face of uncertainty and disturbances. 

Planned Secondments

In total, 2 months will be spent at French National Research Institute for Agriculture Food and Environment (INRAE) in France (cheese ripening) and 4 months at KU Leuven in Belgium.

Enrolment in Doctoral degree

Applied Mathematics Doctoral Program at the Universidade de Vigo - Spain (UVigo)


Required Education Level

Master’s degree in engineering, physics, systems biology, applied mathematics or biology with a strong theoretical/computational component no later than September 2021. You should NOT have any kind of PhD degree. Previous research experience (which must be no longer than 4 years) although appreciated, is not mandatory. 

Skills / Qualifications

  • Good mathematical/computational background. Dynamic Nonlinear systems skills (Appreciated). 

  • Ability to (learn to) communicate with different disciplines (experimental, computational, theoretical) 

  • Educational background and previous research experience relevant for the chosen position

  • Networking and good communications skills (writing and presentation skills)

  • Willingness to travel abroad for the purpose of research, training and dissemination

Specific Requirements

For the eligibility please check: Eligibility Criteria

Required Languages

English: B2, good oral and written communication skills in English are compulsory

Supervisors Team

The lead supervisor is Irene Otero-Muras. Currently at the (Bio)Process Engineering Group at the (IIM-CSIC), she is moving soon to Valencia where she’s starting a new biosystems engineering group at I2SysBio (where the ESR project will be developed). The group research will focus on  the design, analysis and control of biosystems, with particular interest in biomolecular networks (which are nonlinear, stochastic, complex systems) with relevance in cell regulation and metabolic processes. In this context, we aim to advance fundamental understanding and to address innovative applications for systems and synthetic biology. 
See websites for more information (trajectory at IIM-CSIC) (new site)
The co-supervisors are Eva Balsa-Canto - researcher at the (Bio)Process Engineering Group at the (IIM-CSIC) in Vigo, Spain and prof. J. Van Impe – the Division Head and founder of BioTeC (Chemical and Biochemical Process Technology and Control) research group at KU Leuven.

The Host Institution 

The Spanish National Research Council (CSIC-Agencia Estatal Consejo Superior de Investigaciones Científicas) is an autonomous, multi-disciplinary public research body affiliated to the Spanish Ministry of Science and Innovation. The CSIC has its own legal structure and is represented throughout the Spanish territory with a total of 105 centres/institutes. CSIC is the first Spanish organization by number of projects and economic return in the Framework Program of the European Union.

The host institute I²SysBio

The I²SysBio  is a joint research institute involving Universitat de València (UV) and CSIC.  I²SysBio  Scientific Programs focus on research into structure, function, dynamics, evolution, and manipulation of complex biological systems. The mission of I²SysBio includes the following areas of action:
•    Create a multi- and inter-disciplinary work environment where scientists from different backgrounds work together dynamically and continuously to solve common problems.
•    Develop high-quality research and achieve excellence in the field of integrative systems biology.
•    Produce high value-added knowledge with potential transfer to industry.
•    Train researchers in a multidisciplinary field with broad future projection.
The I²SysBio seeks to provide solutions to problems that may arise in the pharmaceutical, biotechnological, biomedical and agribusiness sectors that are open to a systems approach (e.g., through metabolic engineering and synthetic biology).

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