Early Stage Researcher (22 months)

Job description

SilicoLife is seeking a highly motivated person with a committed personality who wants to develop his or her research as Early Stage Researcher (ESR) in an industrial environment and with a strong interest in design of biological systems using modelling/computational approaches for an expected period of 22 months.


This ESR position is part of the EU Marie Curie Action PaCMEN - Predictive & Accelerated Metabolic Engineering Network initiated in October 2016. PAcMEN is an European programme, which offers excellent training in biotech research and innovation for 16 talented young scientists. ESRs will carry out cutting-edge research in metabolic engineering, modeling, and molecular, systems, and synthetic biology. In collaboration with industrial partners, they will create novel solutions for sustainable production of fuels and chemicals. The ESRs will be prepared through research, business, and entrepreneurship training to launch their careers in industry or academia. www.pacmen-itn.eu


For this project/position there is 22 months of funding available (the contract must end before September 30 2020 - end of the ITN activities). The selected candidate will be enrolled in a PhD program, the new ESR will be hired for the remaining 22 months of funding still available, and the company will support the university fees for the complete period of the new ESR PhD studies if the candidate wishes to proceed with it. 

For the months of his/her PhD studies not funded by this ITN the selected candidate should seek national funding and/or other available funding opportunities for his/her living allowance. 

Responsibilities and tasks

Successful candidate will develop novel systems biology tools and data-driven algorithms for speeding rational metabolic engineering of yeast, and apply these to design yeast cell factories for production of bulk and fine chemicals in biorefineries. The candidate expected to employ systems biology approaches to metabolic engineering, tapping into the latest -omic technologies and metabolic modelling.

The candidate will publish their research results in international peer-reviewed journals and present at international conferences and seminars. Patenting activities can also be expected.

ESR project

The ESR  will work on the project “Development of advanced simulation/optimization methods and cellular objective functions” with the following objectives:

Development of advanced simulation/optimization methods for in silico metabolic engineering strategies to obtain desired microorganisms with industrial potential for producing bio-based chemicals. The predictive limitations usually associated with the current approaches based on genome-scale stoichiometric models will be tackled either by integrating ‘omics data and/or defining suitable cellular objective functions. Also, the creation of new metaheuristics for the optimization tasks to address genetic alterations for the over/under expression of enzymes or gene deletion leading to the maximization of the target compound will be performed. It is expected that new algorithms with improved predictions of cell behaviour will be developed and applied for metabolic engineering strategies predictions.


The ESR will be hired for 22 months (this contract must end before September 30 2020) and will be enrolled in a PhD program (at a Portuguese University). Salary will be excellent according to EU regulations (Marie Curie ITN Early Stage Researcher conditions). 

The ESR will be involved in a Marie-Curie network with excellent opportunities for scientific and personal development, including funding for short stays at top-class research groups and regular training events and meetings across Europe. The selected candidate will be employed by the company and will be part of an interdisciplinary team of experts in computer science, artificial intelligence, bioinformatics, systems biology and bioprocess engineering. Other benefits also include participation in internal talks, company retreats among other perks.

The select candidate will be exposed to highly innovative projects combining world-class science with disruptive business models to create sustainable and economically viable solutions addressing global challenges.

Application procedure

Please submit your online application no later than 20 November 2018.


About SilicoLife

SilicoLife develops state-of-the-art optimization algorithms and uses proprietary computational and modelling tools to accelerate the design of optimized microbial strains and novel pathways for the cost-effective production of specific target compounds such as chemicals, food ingredients or biopolymers. Leading chemical, materials and synthetic biology companies have chosen Silicolife as development partner to maintain their market edge in increasingly competitive markets. SilicoLife is considered a highly innovative company, including as one of the 40 Hottest Small Companies in the Advanced Bioeconomy by BiofuelsDigest and Startup of the week by Wired UK



Candidates must have MSc degree (or equivalent degree that enables access to PhD) in computer science, biology, engineering, bioinformatics, systems biology, applied mathematics, physics or a related discipline with a strong background in mathematical modeling/scientific computing and/or biology/cell metabolism.

Further qualifications:

  • Candidates must be in the first four years of their research career
  • Candidates may not have resided in Portugal for more than 12 months in the last 3 years (in this case you may apply for PhD positions with other partners of the network, see www.pacmen-itn.eu)
  • Excellent early achievement track record (publications, awards, conference presentations, etc.)
  • Strong work ethics and motivation to succeed within a competitive research field
  • Team spirit and excellent collaboration skills
  • Previous experience in the design of cell factories will be appreciated.