PRR Project

Summary

??????? Job DescriptionFor this position, the employee/candidate is expected to:Design, plan and lead studies on the genomic epidemiology of bacterial pathogens such as Mycobacterium tuberculosis and Klebsiella pneumoniae including the analysis of dissemination and emergence using state-of-the-art typing methods and whole-genome sequencing;Participate and/or lead research networks or initiatives, of both national and international scope, envisioning the characterization of international and national dissemination patterns of relevant pathogens;Undertake complex bioinformatic analysis of whole-genome sequencing data as well as phylogenetic reconstruction and time-scaled phylogenetic reconstruction;Develop, implement and validate bioinformatic pipelines along with novel bioinformatic tools that can facilitate the analysis and integration of NGS data, including large-scale genomics, for relevant bacterial species.;Characterize bacterial resistance mechanisms, detailing its molecular determinants, mechanisms of mobilization, if applicable, and genetic context. The candidate should be able to implement different phenotypic testing methods, as well as genotypic methods aimed at the elucidation of resistance mechanisms, clinical significance and emergence.Design, and planning of research projects within the scientific area, particularly, in molecular microbiology, genomic epidemiology and antimicrobial resistance;Coordinate and participate in the development and strengthening of laboratory infrastructure and capacity development on bioinformatics and generation of NGS data;Assist the research community at the host institution with the design and planning of antibacterial drug discovery activities;Collaborate and supervise teaching and training programmes at the institution, namely by collaborating in the teaching programme of curricular Units such as Bacteriology, Food Microbiology and Bioinformatics. It is also expected that the recipient of this position will develop and direct a PhD Advanced Course on Bioinformatics to improve NGS data handling capacity at the institution. Scientific profileThe candidate should demonstrate a good track record in the field of epidemiology and molecular drug resistance with particular emphasis in the molecular epidemiology of tuberculosis, genome-wide data analysis and good understanding of the molecular basis of resistance in Mycobacterium tuberculosis and correlation with clinical significance. Experience with additional bacterial pathogens is also preferred. Furthermore, the candidate must demonstrate capacity to lead a research team and conduct research activities with a high level of independence. The candidate must be able to design, plan and perform complex assays involving bacterial pathogens and extensive expertise in the characterization of drug susceptibility to different antibiotics. Knowledge of GNU/Linux systems and proficiency in shell scripting and R/Python programming is required along with skills in deploying open-source software, command-line interfacing for bioinformatic analysis of NGS data pipeline development. The candidate should have a strong background in pharmaceutical microbiology and molecular biology and be proficient in the implementation of molecular biology assays and manipulation of bacterial pathogens including demonstrated working experience under BSL-2 and BSL-3 facilities. In addition, the candidate should have teaching experience at the undergraduate and postgraduate level, with particular emphasis at teaching curricular units from Integrated Master’s in Pharmaceutical Sciences. ???????RationaleThe requested position is aligned with the disciplinary area of Pharmaceutical Microbiology and Infectious Diseases, a core area in the field of Pharmaceutical Sciences that encompasses aspects such as the action mechanisms of antimicrobial drugs, resistance mechanisms, pharmacology, epidemiology and mechanisms of pathophysiology associated with infectious agents. This is also a pivotal area at iMed.ULisboa and transversal to its three main hubs (Scientific, Technological and Translational) with innovative multipronged approaches aiming at the prevention, early detection and intervention against public health threats such as tuberculosis. Moreover, by converging the multidisciplinary research encompassed in this scientific profile to applied research, it is not only possible to gain insights on the fundamental biology of important pathogens but also to inform public health decision and disease clinical management. The position and scientific profile requested increases the interface of iMed.ULisboa and its host institution with multiple players in the healthcare sector, thus strengthening this research area at iMed.ULisboa, increasing its visibility and outreach, while simultaneously enhancing current teaching methodologies, ensuring these remain up to date.