Early Stage Researcher in Bioinformatics

University of Thessaly is offering a position in bioinformatics with expected commencement June 2023 or as soon as possible thereafter. The position is offered in the frame of the project RATION, an HORIZON Europe project (Risk Assessment Innovation of Low Risk Pesticides). It is a 4-year project which has stared at 1.11.2022.

Brief Project Description

Low risk pesticides (LRP) including (i) plant extracts (ii) semiochemicals like pheromones and allelochemicals, (iii) microbial pesticides, are gaining ground in the global market, as substitutes of synthetic pesticides. In addition, new microbial solutions (phages, protists, microbial consortia) and ds-RNA pesticides are emerging, low-risk solutions expect to reach the market in coming years. Despite ongoing regulatory efforts by the European Commission, we are still lacking a concrete risk assessment (RA) scheme relevant to LRPs, a point which blocks LRPs reaching the EU market. RATION timely comes to address these regulatory constraints and aims to develop a novel RA scheme, supported by the necessary guidance on methods and tools, tailored to the specific characteristics of established and emerging LRP solutions. This main goal will be achieved through a series of interrelated WPs aiming (i) to map the current status of LRPs in Europe and identify main regulatory constraints (WP1). In this quest it will be supported by a stakeholders forum composed of all relevant actors (industry, regulators, academics, famers, general public); (ii) to develop and validate, through a proof-of-concept exercise, innovative RA (and associated tools) for microbials (WP2), plant extracts, semiochemicals, pheromones (WP3) and, ds-RNA (WP4); and from there (iii) build a harmonized RA for all LRP and determine its socioeconomic impact (WP5), (iv) to effectively communicate and disseminate the new RA knowledge and its associated tools developed by RATION to relevant actors ensuring sustainability beyond project duration (WP6). RATION will benchmark EU regulatory science, uplift blockers holding back LRP uptake by the EU market and motivate research innovation in plant protection. To achieve these goals 22 partners from academia, industry and regulatory bodies, representing 10 member states and 2 non-EU member states, will join forces in a multi-sectoral and multidisciplinary effort.

Principal Investigator: Prof. Dimitrios Karpouzas, dkarpouzas@uth.gr, +30-2410565294

Collaborators: Dr Sotirios Vasileiadis sovasileiadis@uth.gr, +30-2410565223; Prof. Kalliope Papadopoulou kalpapad@uth.gr,

Job description

The position is available for 36 months. The main working tasks of the successful candidate will be:

• To be able to use appropriate bioinformatic tools for assembly and functional annotation of whole genome sequence of bacteria, fungi and other microorganisms destined to be used as biopesticides
• To help in the development of analytical pipelines for the detection of antibiotic resistance genes in whole genome sequence data from microorganisms and identify their localization and transposition potential using appropriate tools and databases
• To help in the development of analytical pipelines for the identification of biosynthetic pathways for secondary metabolites in whole genome sequence data from microorganisms using appropriate tools and databases
• To analyse the data using appropriate bioinformatic and ecological statistical tools
• To be able to collaborate with other researchers, understand biological scientific questions and provide analytical solutions to complex datasets
• To work closely with the PI, Postdocs and other researchers working on RATION
• To be able to right reports and scientific documents