Non-Degree Course: Pathogen Multiomics and Bioformatics

The growing access and availability of data generated by Next Generation Sequencing platforms has enabled new insights on the pathogenicity, pathophysiology and dissemination of diseases of infectious aetiology. As an entry-level bioinformatics course applied to the study of pathogens, the main objective is to cover a broad spectrum of analytical stages ranging from the introduction to NGS data and quality control to genome-wide association studies applied to different pathogens. Using a practical or hands-on approach, it is intended that the participants apprehend the concepts and fundaments of the analytical procedures that are necessary to translate the large data volumes generated by NGS platforms, while systematically consolidating the theoretical basis of this knowledge.

João Perdigão, Faculty of Pharmacy of the University of Lisbon

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.

Academic Qualifications: Bachelor or Master Degree in Pharmaceutical Sciences, Medicine, Biology as well as other Life and Health Sciences.

Date: 16-19 June, 2020

Local: Room A.3.1., Faculty of Pharmacy of University of Lisbon

Course schedule: 9h00 – 17h00

Total number of hours: 28 hours

• Theoretical hours: 5 hours;
• Practical hours: 23 hours.

Programme:

• Introduction to NGS data and Quality Control;
• Reference Assembly (mapping): mapping, data visualization, variant calling and functional annotation;
• De novo genome Assembly: concepts and optimization, contig ordering and scaffolding annotation;
• Introduction to Phylogenetics and Phylodynamics;
• Pathogen profiling toolbox: from NGS to phenotype;
• Transcriptomics and RNA-Seq;
• Introduction to Microbiome Analysis and Metagenomics;
• Genome-Wide Association Studies (GWAS).

The course comprehends a solid theoretical component that underpins the learning and development of the different analytical stages through practical sessions which comprise most of the course. The course will therefore include theoretical sessions and a strong practical computer-based approach to the analysis of genomic, transcriptomic or metagenomic data and, how to correlate this with the assessment of phenotypic traits (e.g. drug resistance, virulence) or 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 as to address different questions, of either fundamental or applied nature.

One computer will be available per participant and all analytical stages will be carried out using open-source software. 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 the available tools to carry out different analytical stages in order 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).

Registration Fee: 350€

Payment must be made by bank transfer to the IBAN: PT50 0035 0824 0001 1648 2303 3 and the respective proof of payment sent to the email posgraduados@ff.ulisboa.pt

Registration is only valid after receipt of proof of payment by Academic Services.

Note: FARM-ID – Faculty of Pharmacy Research and Development Association is the managing entity of this course. The respective expense can be classified as a general expense in the IRS (Personal Income Tax).

Registrations for the Non-Degree Course: Pathogen Multiomics and Bioinformaticas are made via Online Form until June 9, 2020.

Number of vacancies: minimum: 6 and maximum: 16

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

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