Teaching code

4S00183

Teacher

Nicola Vitulo

Coordinator

Nicola Vitulo

Credits

6

Language

Italian

Scientific Disciplinary Sector (SSD)

BIO/11 - MOLECULAR BIOLOGY

Period

Semester 1  dal Oct 1, 2024 al Jan 31, 2025.

Courses Single

Authorized with reserve

Lessons timetable Moodle Seminars 0

Learning objectives

Over the last decade the technological improvements of sequencing technologies (Next Generation Sequencing, NGS) had an enormous impact on the understanding of the genomes complexity and had provided interesting opportunities for the development of bioinformatics tools and programs for data analysis and management. The course aims to provide a general overview of the different computational methods applied in the field of NGS and omics science. These new technologies, which made possible to move from a reductionist to a holistic approach, have made it necessary to develop new strong interdisciplinary methods for data interpretation and integration. The course will provide students with basic knowledge on bioinformatics tools for the interpretation and integration of different omics data applied to the study of genomes, of gene expression and of metagenomic data for community analysis and microbial characterization. The course will also include a part performed in a computer lab where the computational programs necessary for the manipulation and interpretation of biological data will be illustrated.

Prerequisites and basic notions

No specific prerequisites are required. Basic knowledge of bioinformatics (e.g. sequence alignment) may be helpful but is not essential to better understand the program.

Program

Introduction to next-generation sequencing data (NGS)
a. Bias and technology sequencing errors illuminate
b. FastQ format
c. Sequences quality check
d. Sequences pre-processing
2. NGS data alignment on a reference genome
a. Alignment of genomic and rna-seq sequences
b. SAM / BAM format
3. Analysis of transcriptomic data and RNA-seq
a. Transcripts reconstruction (genome-guided / denovo)
b. Gene quantification
c. Data normalization
d. Identification of differentially expressed genes
4. Genomes analysis
a. Genome assembly
b. Resequencing and identification of variants
c. Structural variants
d. VCF and gVCF file format
5. Computational methods for the analysis of metagenomic data
a. Metabarcoding
b. Whole Metagenome Sequencing
c. Taxonomic assignment
d. Metrics for the analysis of microbial complexity (alpha and beta diversity)

Bibliography

Didactic methods

The teaching methods adopted in the course are:
- Frontal lessons
- Reading and presentation of scientific articles

Learning assessment procedures

The exam consists of a written test of the level of knowledge acquired on the topics covered in the course. The test consists of 6 open questions. The student must demonstrate that he/she has understood the functioning and application of the main bioinformatics programs and approaches explained in class. Students who decide to carry out the activity related to the presentation of a scientific article can have a bonus of up to 2 points to be added to the exam result

Evaluation criteria

The level of understanding of the topics and the command of language will be evaluated.

Criteria for the composition of the final grade

Each question will be assigned a score of 10, the final grade will be scaled to 31. Grades higher than 30.5 will be awarded honors. The activity of presenting scientific articles is not mandatory, students who intend to present a scientific article may have a bonus of up to two points to add to the exam grade

Exam language

Italiano