Ateneo - UPO

The course will provide an introduction to examples, concepts and instruments at the foundation of Big Data Analysis for bioinformatics and genomics, in the framework of human health and cancer in particular. Students will gain an introduction to the theory and practice of genomic and protein sequence databases along with tools for retrieving and interpreting functional and annotation data for the human genome. Basic knowledge on new generation sequencing and related bioinformatics data analysis tools will be introduced, focusing on transcriptomes and cancer genomics. Basics of the Python programming language will be discussed. In the final part, an introduction to the concepts of complex systems, network theory and system biology will be considered also through the discussion of research articles.

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 in the framework of “Big Data” analysis for human health, with a focus for cancer genomics. Provide basic skills for reading and interpreting articles including bioinformatics content.

Basic knowledge in molecular biology and genetics.

Lectures in classroom and computer classroom.

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 oral exam are planned. In-itinere written reports for a series of assignments (computer homeworks) and a final written exam are planned. The final written exam will consist of a series of multiple choice questions, plus a series of open questions. The questions will cover all the topics covered during the course and the discussion of two focus papers. The aim of the exam is both to check the theoretical knowledge acquired by the students, and the practical knowledge of basic bioinformatics tools, together with the ability to analyze research articles in the field of omics technologies.

Review of basic concepts on the structure, organization and functioning of the human genome. The Ensembl database, description and operation. Structure of a human gene in Ensembl, sequence information retrieval, protein structure, functional and clinical annotations. The UCSC browser genome, description and operation. UCSC structure and annotation of a human gene, retrieval of functional and expression information. Introduction to NGS Sequencing. Illumina sequencing methodology. Introduction to RNA-seq methodology. Design of an RNA-seq experiment and related bioinformatics data analysis. Cancer genomics and the TCGA project. Introduction to systems biology and network theory. Examples of networks in biology and genomics. Basic elements of the Python programming language. The Google Colab environment. Examples of research articles available on Pubmed discussing topics related to arguments related to the course.

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