Project funded positions
Position title: Research Assistant (PhD) (m/f)
Field: Environmental Biotechnology / Microbial Ecology / Bioinformatics / Computational Biology
The selected candidate will develop and implement advanced approaches to investigate polymer conversion by microbes and the bioremediation of contaminated environments within the Colloid biology (https://biocolloid.ijs.si/) research projects. The work will focus on two key projects:
(1) the conversion of plastic polymers by microbial consortia into useful, value-added substances, and
(2) the remediation of contaminated river sediments using microbial technologies and nature-based and bio-based solutions.
Their key responsibilities:
Organizing and supervising work in the laboratory or computational unit;
Planning, managing, and performing experimental work or bioinformatic and computational analyses within the scope of the projects mentioned above;
Establishing, optimizing, and characterising microbial consortia for efficient plastic polymer degradation and upcycling;
Developing and implementing biotechnological and nature-based solutions for the remediation of river sediments; Processing complex datasets (e.g., metagenomics, transcriptomics, metabolomics, or physical-chemical process modeling);
Participating in the preparation of research projects, reports, grant application documentation, and publishing scientific-research and research-development works;
Presentations at international meetings;
Training abroad;
Mentoring and providing professional supervision to students, PhD candidates, and technical staff.
Required education and qualifications:
PhD in bioinformatics, computational biology, biology, biotechnology, physics, or a related field of natural or technical sciences;
In-depth knowledge and several years of experience working in a laboratory or with bioinformatic data analysis;
Experience with microbial ecology, polymer conversion technologies, or bioremediation (desirable for experimentalists);
Experience with next-generation sequencing (NGS) data analysis, programming (Python, R), or bioinformatics tools (desirable for computational biologists and bioinformaticians).
Special Conditions:
Appointment to the title “Assistant with a PhD”;
Ability to conduct independent research;
Mentoring abilities.
Expected knowledge and competencies:
Precision, responsibility, and reliability in work;
Ability to think critically and solve problems;
Good command of English (written and spoken);
Ability to work in a team and collaborate in interdisciplinary environments.
We offer:
The selected candidate will be employed for a fixed term of 2 years, with the possibility of extension, and with a 3-month probationary period;
The starting salary grade for the position is grade 31;
Work in a research-oriented, interdisciplinary environment;
Opportunities to develop and implement advanced experimental or computational methods;
Participation in national and international research projects;
Opportunities for professional and scientific development.
The position is located at the Reactor Centre, Brinje 40, 1262 Dol pri Ljubljani, Slovenia.
Applications should be submitted by email to ales.lapanje@ijs.si no later than 13 July 2026. Applicants should include a short curriculum vitae (CV) with proof of meeting the requirements and a motivation letter.
Position title: Junior Researcher / PhD Student (m/f)
Field: Environmental Biotechnology / Microbial Ecology / Bioinformatics / Computational Biology
The selected PhD candidate will be integrated into the group’s research projects (https://biocolloid.ijs.si/) in environmental biotechnology, developing their skills under the mentorship of experienced researchers. The work will be tied to the fields of microbial conversion of plastic polymers into value-added substances, and the development of biological and nature-based solutions for the remediation of contaminated river sediments using microbial technologies. Depending on their profile (experimental or computational), the candidate will focus on laboratory work or computational/physical systems biology analysis.
Their key responsibilities will include:
Conducting research work towards the preparation of a PhD dissertation under the guidance of a mentor;
Participating in setting up experiments for microbial plastic degradation or sediment remediation (for experimentalists);
Performing bioinformatic analyses, statistical data processing, or physical modeling of biological processes (for bioinformaticians, computational biologists, and physicists);
Reviewing scientific literature and integrating findings into their own research work;
Participating in writing scientific papers, reports, and presenting results at national and international conferences;
Regular fulfillment of academic requirements within the PhD doctoral program;
Assisting with the day-to-day work in the laboratory or computational unit.
Required education and qualifications:
A university degree (Master's degree / 2nd Bologna cycle) in biology, bioinformatics, computational biology, physics, biotechnology, or other related fields of natural sciences;
An average grade point average across undergraduate and postgraduate studies meeting the national criteria for junior researchers/PhD students (preferably above 8.0/10);
Basic experience with laboratory work (for the experimental profile) or basic knowledge of programming (e.g., R, Python) and statistics (for the bioinformatic/computational/physics profile).
Special Conditions
Enrollment or eligibility for enrollment in a 3rd cycle PhD program for the academic year 2026/2027;
High motivation for scientific-research work and obtaining a PhD degree.
Expected knowledge and competencies:
Precision, curiosity, self-initiative, and responsibility;
Strong analytical thinking skills;
Good command of English (written and spoken);
Ability to work effectively within an interdisciplinary team.
We offer:
Employment for a fixed term (for the duration of the PhD program, typically up to 4 years) with a 3-month probationary period;
Funding for PhD tuition fees and a regular monthly salary;
Work on current, environmentally critical projects with high societal impact;
A top-tier research environment with access to modern computational and laboratory infrastructure;
Opportunities for international exchanges and networking within the global scientific community.
The position is located at the Reactor Centre, Brinje 40, 1262 Dol pri Ljubljani, Slovenia.
Applications should be submitted by email to ales.lapanje@ijs.si no later than 30 June 2026. Applicants should include a short curriculum vitae (CV), a motivation letter, and a transcript of records with their GPA.
Topic: Spatial succession of bacterial communities.
Background: Functional properties of bacterial communities enable them to be used in biotechnological, remediation or agricultural applications. Be it natural or synthetically prepared, the communities should be stable in order to be up-scaled and used in applications, to perform the function they were selected for, e.g. degradation of target compound/s or production or transformation of selected compound/s. Here, we hypothesize that quantitative parameters, not only ratio of strains and their activities, but more importantly, the parameters such as microgeograhic positioning of each of the members can importantly determine further succession of the community.
Aim: We need to understand the stability of bacterial communities, particularly synthetic, over a longer period of time. It is crucial to understand whether the community structure changes during biomass growth and after it is applied in situ. Even more importantly, since the communities can be spatially structured in the form of aggregates or biofilms, we need to examine how these structures develop over a longer time period and how stable they are.
Keywords: bacteria, cell aggregates, community succession
Topic: The physiology of physically entrapped bacterial cells
Background: Physical entrapment can change the physiology of a cell as it could theoretically prevent cell growth, division and exchange of nutrients. Preliminary experiments on bacterial encapsulation into rigid multi-layered nano-thick coatings have shown changes in cell morphology and metabolic activity, but it is not clear how the structure of the cell is changed or how the expression of genes is altered due to the physical pressure on the cell.
Aim: The study will focus on characterizing the morphological changes and changes in gene expression that arise due to the physical entrapment of bacterial cells. Physical entrapment of bacteria is also the natural state of bacteria in aggregates and biofilms present in the environments and this research will give important information of contribution of physical constraints solely on the physiological response in these conditions that microbes are faced with.
Key words: cell encapsulation, gene expression, layer-by-layer encapsulation, nano-capsule
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