Postdoctoral Researcher - microbiology: Portugal

The Instituto de Medicina Molecular João Lobo Antunes (iMM) opens a call for a Postdoctoral research fellowship with the funding support from Projeto de Investigação Científica e Desenvolvimento Tecnológico (IC&DT) Programa de Actividades Conjuntas – projeto n.º 016417 (PD2) “Oneida (Plataforma ómica para prevenção e controlo de infecções e de resistência aos antimicrobianos)” – Sistema de Apoio à Investigação Científica e Tecnológica, financiado pelos Fundos Europeus Estruturais e de Investimento (FEEI) – Comissão Diretiva do Programa Operacional Regional de Lisboa e pelo Orçamento de Estado – Fundação para a Ciência e a Tecnologia, I.P.


  • in Microbiology, Biology, Health Sciences, Computer Science or related fields with emphasis in Bioinformatics data analysis
  • Knowledge of data analysis of High Throughput Sequencing data, namely de novo assembly and read mapping methods
  • Proficiency in Python and Javascript
  • Experience in HTS clusters execution, namely, using workflow managers
  • Preference for previous experience in microbial bioinformatics data analysis
  • Autonomy, critical mind, sensibility and motivation to work in interdisciplinary teams
  • A strong analytical profile, accustomed to work by goals and to fulfill deadlines
  • Excellent domain of English

Work Plan and Goals

  • The candidate will be integrated in a team for the development and use of high throughput sequencing (HTS) data analysis pipelines for bacterial identification, antibiotic resistance and virulence factor detection and phylogenetic analysis incorporating other metadata
  • Participation in the development of new data analysis and visualization methods
  • Data analysis of HTS for surveillance and outbreak characterization purposes in hospital settings
  • Creation of user-friendly data analysis reports for the use in hospital settings by non-experts
  • Phylogenetic and evolutionary analysis of HTS data for population structure analysis of major human pathogens

Duration of Fellowship: 6 (SIX) months on an exclusive basis, eventually renewable, not exceeding the eligible period of the project.

Law and Regulation: Estatuto do Bolseiro de Investigação (Lei n.º 40/2004, de 18 de Agosto, republished in attachment to Decreto-Lei n.º 202/2012, de 27 de Agosto), Regulation of Fellowships of Fundação para a Ciência e a Tecnologia, Career By-Law and Assessment Regulation of iMM.

The iMM undertakes to ensure compliance with the principles of non-discrimination and equality and to that extent, provides that no candidate can be privileged, benefited, harmed or deprived of any right or exempted from any duty due in particular ancestry, age, gender, sexual orientation, marital status, family status, economic status, education, social origin or condition, genetic heritage, reduced working capacity, disability, chronic disease, nationality, ethnic origin or race, place of origin, language, religion, political or ideological convictions and trade union membership.

Monthly Remuneration: 1.495€ according to the values defined directly by FCT Regulation Fellowship in force ( The amount will be paid through bank transfer, at the end of the month.

Selection process

Necessary Documents for Applications: – Motivation Letter; – Recommendation Letter (Optional); – Detailed CV; – PhD certificate.

The non-compliance with these requirements determines the immediate rejection of the application.

Evaluation:  Applications will be evaluated by a jury composed by Professors Mário Ramirez, João Carriço and Catarina Silva e Costa (all PhD’s).

Selection Method: First stage: Curricular evaluation and Research Experience (70%); Second stage: interview (30%).  The jury will select for an interview the maximum of 5 candidates with a highest score from the first stage and with at least 35 points.

Deadlines and Submission of Applications: The call will be open for 10 working days, starting on 10th August and ending on 7thSeptember 2018.

Applications should be sent to iMM Human Resources through the email, indicating the reference of fellowship (mandatory). The non-compliance with these requirements determines the immediate rejection of the application.

Further details
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