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Closed for Applications


Early Stage Researcher (ESR2)  

PhD fellowship in dynamics of cellular interactions

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 modelling, ecological dymamic modeling, systems biology

Application Deadline

31.05.2021, 23:59 ; prolonged till 15.06 2021 23:59 - Europe/Brussels

Envisaged Job Starting Date

01.10.2021 or earlier if agreed with the main supervisor


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 aim of the project is to understand microbial interactions through time during cheese ripening and how these interactions lead to certain cheese proporties. With that aim we intend to integrate experimental data (growth, external metabolites, environmental factors, etc.) into dynamic ecological models. The plan is to iteratively increase the level of detail of the developed models.  In a first stage, we will consider “classical” ecological models, to describe the interactions among microorganisms and environmental components. Subsequently, we will increase the level of detail to include metabolite-mediated relationships (competivite mechanisms, cross-feeding, etc). Ultimately models will be used to formulate and solve dynamic optimizaction problems to compute those environmental conditions that would   maximize cheese quality.

Expected Results

Concepts and open-source software tools for the multi-scale modelling of cellular consortia (model identification, model selection and cross-validation); Demonstration: modelling microbial consortia involved in cheese ripening; Validated model available in a public repository.

Planned Secondments

In total, 7 months will be spent at Vrije Universiteit Amsterdam in Netherlands.

Enrolment in Doctoral degree

Vrije Universiteit Amsterdam (VUA) (


Required Education Level

Master’s degree in systems biology, biological engineering, computational biology, biotechnology, physics with a strong numerical/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

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

  • Good numerical/computational skills 

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

  • 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

(Bio)Process Engineering Group at IIM-CSIC (Vigo, Spain) performs research in the area of Bioprocess Engineering, namely regarding the mathematical modelling and computer-aided simulation, optimization and control of: unit operations and processes in the bio-industries (e.g. food and biotechnology) and bio-systems (systems biology, synthetic biology).
The lead supervisor is Eva Balsa-Canto, researcher at the (Bio)Process Engineering Group at the (IIM-CSIC) in Vigo, Spain. She has supervised 6 PhD, 14 Masters and various post-docs. 4 PhD are hired at academic institutions, 1 PhD at industry, 1 PhD started a company. Co-supervisors are Prof. Bas Teusink (VUA) – the head of the Systems Biology Lab, which he runs together with prof. Dr. F. Bruggeman at Vrije Universiteit Amsterdam. The focus is on understanding regulatory principles of microbial physiology and ecology. Irene Otero-Muras - currently researcher at BioProcess Engineering Group (IIM-CSIC) developing tools for Biosystems Identification, Design and Control for Synthetic and Systems Biology applications. 

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 Group

The Bioprocess Engineering group performs research in the area of Bioprocess Engineering, namely regarding the mathematical modelling and computer-aided simulation, optimization and control of unit operations and processes in the bio-industries (e.g. food and biotechnology)  and bio-systems (systems biology and synthetic biology).

Some of our current research topics include:

  • Identification and parameter estimation in systems biology

  • Optimal control and design in biological pathways

  • Network inference in biological systems

  • Global optimization of bio-processes (e.g. bioreactors) and bio-systems

  • Dynamic optimization and nonlinear optimal control of bio-processes

  • Integrated process design and control

  • Robust control of nonlinear, distributed systems (convection-diffusion-reaction)

  • Web-based simulation and optimization tools for the bio-industries


For more details:

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