Non-Degree Course: Pathogen Multiomics and Bioinformatics

This course consists of an entry-level bioinformatics course focused on the analytical stages of omics data applied to the study of pathogens. The course will include theoretical sessions and a strong practical computer-based approach to the analysis of genomic, transcriptomic or metagenomic data and how to translate it or correlate with phenotypic traits (e.g. drug resistance, virulence) or the assessment of public health and epidemiological risk for pathogen dissemination. This will enable participants to perform different analytical steps involving data obtained by Next Generation Sequencing methodologies in order to address different questions, of either fundamental or applied nature.

Teaching Methodology

The Pathogen Multiomics and Bioinformatics course is structured around seven distinct modules that span the entire spectrum from the introduction to NGS data and quality control to genome-wide association studies applied to different pathogens. The course comprehends a solid theoretical component that underpins the learning and execution of the different analytical stages, but it is, foremost, a practical hands-on course with the practical sessions comprising most of the course. It is intended that the participants apprehend the concepts and fundaments of the analytical procedures that are necessary to translate large data volumes generated by NGS platforms while systematically consolidating the theoretical basis of this knowledge.

The 2021 edition of this course will be taught in an e-learning mode. All course material and a Virtual Machine containing all necessary software and datasets will be made available to all participants. Assistance towards VM deployment in local computers will be provided in advance. Furthermore, online interactive group sessions will be promoted for the discussion of results and networking between participants.

Learning Topics and Skills to be Acquired by the Participants

The course program intends to provide the course participants with a broader and deeper understanding with diverse omics technologies, bioinformatic terminology and tools available to carry out different analytical stages as to capacitate the participants to independently undertake these tasks. In the end, the course participants should be able to:

1. Understand, interpret and assess the different types and formats of data generated by NGS platforms as well as to perform quality-control steps;
2. Map sequence data to a reference genome, identify variants on a genome-wide scale as well as performing its functional annotation;
3. Carry out de novo assembly steps, including comparative analysis and genomic annotation;
4. Integrate the previous analytical steps to genome-wide phylodynamic approaches aiming to study the evolution and dissemination of pathogens of public health importance;
5. Perform transcriptomic analysis, evaluation and identification of differentially expressed genes;
6. Characterize polymicrobial samples envisaging the assessment of its microbial composition and metagenome;
7. Understand, interpret and perform Genome-Wide Association Studies (GWAS);

Coordinator:

João Perdigão, Investigator, Faculty of Pharmacy of University of Lisbon (FFUL)

Professionals coming from different areas such as pharmaceutical sciences, medicine, biology or other related areas including master or PhD students and post-doctoral researchers aiming to develop work that involves NGS data.

Dates: 17th june to 2th july 2021

Study regime: e-learning

Total number of hours: 23

• theoretical hours: 5
• practical hours: 23

Hours: 5:00 pm to 8:30 pm (Lisbon, Portugal time)

> Programme of the Non-Degree Course Pathogen Multiomics and Bioinformatics

For registration for the Pathogen Multiomics and Bioinformatics Course you must fill out Online Form, until June 5, 2021. Registration will be validated by email and payment must be made by bank transfer after instructions by academic services.

Vacancies:

Minimum: 6
Maximum: 20

Registration fee: 225 eur

Information regarding the organization of the Course, you should contact the Academic Services: naoconferentesgrau@ff.ulisboa.pt.

Scientific information on the course’s teaching, you should contact the Course Coordinator, Professor João Perdigão: jperdigao@ff.ulisboa.pt.