85306 - Proteomes, Interactomes and Biological Networks

Learning outcomes

By the end of the course, the student has the basic knowledge of the experimental techniques for analyzing at large proteins expressed in a biological systems and their interactions. The student is familiar with the publicly available databases collecting proteomics and interactomics data and knows how to represent and analyze the structural complexity of interactions with the Network theory.

Course contents

Theoretical Session (4 CFU):

1. Principles of protein structure properties
2. Lab-techniques for proteomics
3. Reference databases for proteins
4. Protein complexes and interactions
5. Types of macromolecular interactions
6. Lab-techniques for interactomics
7. Reference databases for interactors
8. Functional enrichment
9. Information retrieval in web-available databases
10. Graph theory
11. Properties of biological networks

Practical Part (2 CFU):

1. Files and formats for handling proteins and networks
2. Analysis and visualization of protein structure and protein-protein complexes
3. Analysis and visualization of biological networks
4. Tools for proteomics and interactomics

Readings/Bibliography

Slides, selected articles and reviews will be made available in online

Teaching methods

Lectures, laboratory activities, and script implementation.

Report: development of a personal paper which encourages the student to experiment what they have learned with curiosity and creativity, encouraging the development of transversal skills such as team-building and problem-solving.

The course participates in the University's teaching experimentation project for Integrative Digital Teaching.

Assessment methods

For the final oral exam, the student is expected to answer questions relating to the topics addressed in both modules (practical and theoretical). 

At the end of the practical lectures and before attending the final oral exam, the student has to provide the written report on the practical project.

In order to enhance and recognize the student's participatory commitment, there will be moments of intermediate self-assessment in the form of questionnaires (also using digital resources), while the positive outcome of the report will be considered in the final evaluation of the exam.

Teaching tools

Online, Public Data Bases, PubMed, and materials (pdf of the lectures and selected articles) on Virtuale/MS teams.

During practical sections, students are encouraged to use their personal laptop and install directly some spread and free tools for proteomics/interactomics (ChimeraX, Cytoscape, LigPlus) and to refresh and reinforce their notion of programming (Bash, R, Python).

 

Before starting the practical part, students should follow Modules 1 and 2 of the online Security Course for Informatic Laboratory: https://elearning-sicurezza.unibo.it/

Office hours

See the website of Giulia Babbi