Ateneo - UPO

The course will provide an introduction to examples of concepts and instruments at the foundation of bioinformatics and genomics, in the framework of human health and pharmacogenomics in particular.

Scientific papers and slides, provided during the lessons, will represent the main teaching materials.
Further suggested books:
Arthur Lesk, “Introduction to Bioinformatics”, Oxford University Press
Arthur Lesk, “Introduction to Genomics”, Oxford University Press
Deonier et al., “Computational Genome Analysis – An introduction”, ed Springer
Andreas D. Baxevanis, Gary D. Bader, David S. Wishart, “Bioinformatics – fourth edition”, ed. John Wiley & Sons

Provide a basic view of the most commonly used bioinformatics and systems biology tools for the study of human health, with a focus in pharmacogenomics. Provide basic skills for reading and interpreting articles including bioinformatics content.

Basic knowledge in molecular biology and genetics.

PowerPoint presentations of classes and articles provided by the lecturer.

Students with physical disabilities, Learning Disabilities or Special Education Needs can request specific services and tools via the Staff Sviluppo e Coordinamento Carriere e Servizi alle Studentesse e agli Studenti, consulting the University webpage: https://www.uniupo.it/en/services/services- students-physical-or-learning-disabilities. Students with disabilities, learning disabilities or special education needs, once they have contacted the University Staff, can refer to the tutor in charge of the course to define the examination modalities, concerning academic aspects.

In-itinere written reports for a series of assignments (computer homeworks) and a final written exam. The final written exam will consist of a series of multiple-choice and open questions concerning all the topics covered during the course, including selected research articles.

Review of the fundamental concepts of the structure, organization, and function of the human genome. The Ensembl database: architecture, features, and applications. Structure of a human gene in Ensembl, including retrieval of sequence information, protein structure, and functional and clinical annotations. The UCSC Genome Browser: architecture, features, and applications. Structure of a human gene in UCSC, including retrieval of functional and gene expression information. Introduction to next-generation sequencing (NGS). Illumina sequencing technology. Introduction to RNA-seq methodology. Design of an RNA-seq experiment and its associated bioinformatics data analysis workflow. Introduction to Systems Biology and the theory of artificial neural networks. Examples of deep neural network applications for the analysis of biological data (deep learning). Introduction to pharmacogenomics. Examples of protein–protein interaction databases and drug–protein interaction databases. Discussion of selected research articles from PubMed addressing topics related to those covered during the course.

It is expected an increased knowledge-based and personalized judgement capability on basic applied bioinformatics, in particular concerning the human genome and its biomedical applications, including pharmacogenomics. Being able to understand independently and critically the content of research articles concerning bioinformatics and systems biology topics and results.