Advanced Training Course and Postgraduate Course: PATHOGEN MULTIOMICS AND BIOINFORMATICS

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.

Coordination:

João Ruben Lucas Mota Perdigão, Investigador Junior do Departamento de Farmácia, Farmacologia e Tecnologias da Saúde, Faculdade de Farmácia da Universidade de Lisboa. 

PhD students at the FFUL.

The Course will also be open to other participants, namely professionals in the fields of pharmaceutical sciences, medicine, nursing, biology and other related areas, master’s and doctoral students, or doctoral researchers working in related areas.

This course will run from June 03, 2023 to june 07, 2023. It has a total of 35 h of training

Total of ECTS: 6 ECTS.

The training hours are distributed as follows:

• Theoretical Hours: 7
• Practical hours: 28
• Laboratory Hours: 0
• Tutorial Hours: 0

The course will take place over 5 days, from 09:30h to 18:00h, in hybrid format with the possibility of participating in person at the FFUL or, exclusively online in synchronous sessions.

PROGRAM

(click to acess)

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Teaching Methodology: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.

Evaluation Methodology: For evaluation purposes as a non-degree course and with a pass/fail grade, a report will be required on the relevance of the methodologies presented to the research work to be developed by the participant or to his/her professional practice.

As an advanced training course for doctoral students, they will be required, alternatively, to present a written research project or implementation of the methodologies studied (in groups) in order to obtain credit for the course with a quantitative evaluation (0-20). Both the report and the research project must be submitted within three weeks of the completion of the course and thus comprise work carried out autonomously.

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);

Applications and Enrollment: by june 01, 2023

Course Start and Completion Date: june 03 to june 07, 2023

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Access Qualifications:

Bachelor’s or Master’s degree in Pharmaceutical Sciences, Medicine, Biology and other related fields.

Selection and seriation criteria:

Order of entry of applications.

• Minimum number of students to function: 6
• Maximum number of trainees to run: 35

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Enrolment fee:

• 175€ for student enrolment,
• 450€ for professional and corporate enrolment
• 220€ for post-doc researchers

Note: FFUL doctoral students who wish to take the course as part of their 1st year curricular component are exempt from paying the registration fee.

School Insurance: 2.03€

By application of paragraph e) of point 2 of Article 42 of the University of Lisbon’s Statutes, and taking into account the terms for the attribution of PRR funding under the “Impulso Adultos” program, the Organic Unit responsible for the coordination of each course may award academic performance prizes.

Access to the FenixEdu Platform:

• If you have never been a student at FFULisboa you must pre-register on the FenixEdu Platform.
• If you are a former student of FFULisboa and have already had an account campus@ulisboa or @edu.ulisboa.pt you should access the FenixEdu Platform and authenticate yourself with your account data. If you have lost access to your account, you can recover your password in the ULisboa users area.
• If you are a former student of FFULisboa and have never had an account campus@ulisboa or @edu.ulisboa.pt you must send an email to posgraduados@ff.ulisboa.pt indicating your full name and ID document number.

Access the FenixEdu Platform.

• On the tab “Candidate”, choose the type of application: “Non Degree Courses – 2022/2023”, select the course “Advanced Training Course – Advanced Course in Pathogen Multiomics and Bioinformatics”.
• Fill out the online form and attach all documents in digital format.
• Select the “Submit” option.

For information regarding the organization of the course, please contact the Academic Services: doutoramentos@ff.ulisboa.pt

For scientific information regarding the teaching of the course, please contact the Course Coordination.