Bioinformatics and biostatistics

A.Y. 2020/2021
9
Max ECTS
88
Overall hours
SSD
FIS/01 FIS/02 FIS/03 FIS/04 FIS/05 FIS/06 FIS/07 FIS/08 INF/01 MAT/01 MAT/02 MAT/03 MAT/04 MAT/05 MAT/06 MAT/07 MAT/08 MAT/09 SECS-S/01 SECS-S/02
Language
Italian
Learning objectives
Bioinformatics: the course aims at providing students with the basic theoretical and practical concepts of the most widely used bioinformatic analysis tools: sequencing, assembly and annotation of genomes; identification of alternative transcripts and splicing isoforms; functional annotation of genes and gene families; evolutionary analysis of genes and gene families; characterization and quantification of gene expression.

Biostatistics will introduce the basic concepts of probability theory and statistics, and their main applications in the analysis of biological data.
Expected learning outcomes
At the end of the course the students will be able to:
- be proficient in using the main bioinformatic resources, like genome browser and databases;
- perform simple sequence evolutionary analyses, and understand the results;
- understand and interpret the results obtained by methods for the quantification of gene expression;
- understand and apply to simple case studies the main techniques of probability theory and statistics, and to interpret correctly the results obtained by their application.
Course syllabus and organization

Single session

Responsible
Lesson period
First semester
Lessons will be on line on the Microsoft Teams platform, and students will be able to follow them both in real time according to the course timetable, or through the recordings that will be made available to them.
Course syllabus
Bioinformatics (6 CFU)
Introduction: definition and aims of Bioinformatics. Genome projects and next-generation sequencing. Gene and genome annotations. A bioinformatic view of the structure of protein-coding genes: exons, introns, promoters, and alternative splicing. The structure of mature eukaryotic mRNAs. Primary and specialized biological databases. Genome browsers. Definition of sequence similarity, homology, orthology, and paralogy. Global and local alignments. Scoring matrices for nucleotide and amino acid sequence alignments (PAM and BLOSUM). BLAST sequence similarity search: algorithm and usage. Multiple sequence alignments. Expression data: microarray and RNA-Seq. Functional gene annotation and gene ontology.

Biostatistics (3 CFU)
Data representation and variable types. Tables, scatterplots and histograms. Mean, median, mode, percentiles. Variance and standard deviation. Definition of probability and conditional probability. Distributions of random variables: normal distribution, hypergeometric distribution, binomial distribution, Poisson distribution. Sampling and sampling distributions. Statistical hypothesis testing: Student's t-test.
Prerequisites for admission
Knowledge of the fundamentals of genetics, molecular biology and biochemistry.
Teaching methods
Theoretical lectures will be alternated with practical exercises with the PC.
Teaching Resources
Slides and handouts will be shared with students.
Reference textbook (suggested):
M. Helmer Citterich, F. Ferrè, G. Pavesi, C. Romualdi, G. Pesole, Fondamenti di bioinformatica, Zanichelli editore 2018
Assessment methods and Criteria
Bioinformatics: students will perform bioinformatics analyses, describing methods employed and results obtained in a lab notebook. At the exam, students will discuss the notebook with the teacher, and the grade will depend on their understanding of the methods employed as well as the results obtained.
Biostatistics: written multiple choice test.
The final grade will be the weighted mean of the grades obtained in Bioinformatics and Biostatistics.
FIS/01 - EXPERIMENTAL PHYSICS - University credits: 0
FIS/02 - THEORETICAL PHYSICS, MATHEMATICAL MODELS AND METHODS - University credits: 0
FIS/03 - PHYSICS OF MATTER - University credits: 0
FIS/04 - NUCLEAR AND SUBNUCLEAR PHYSICS - University credits: 0
FIS/05 - ASTRONOMY AND ASTROPHYSICS - University credits: 0
FIS/06 - PHYSICS OF THE EARTH AND OF THE CIRCUMTERRESTRIAL MEDIUM - University credits: 0
FIS/07 - APPLIED PHYSICS - University credits: 0
FIS/08 - PHYSICS TEACHING AND HISTORY OF PHYSICS - University credits: 0
INF/01 - INFORMATICS - University credits: 0
MAT/01 - MATHEMATICAL LOGIC - University credits: 0
MAT/02 - ALGEBRA - University credits: 0
MAT/03 - GEOMETRY - University credits: 0
MAT/04 - MATHEMATICS EDUCATION AND HISTORY OF MATHEMATICS - University credits: 0
MAT/05 - MATHEMATICAL ANALYSIS - University credits: 0
MAT/06 - PROBABILITY AND STATISTICS - University credits: 0
MAT/07 - MATHEMATICAL PHYSICS - University credits: 0
MAT/08 - NUMERICAL ANALYSIS - University credits: 0
MAT/09 - OPERATIONS RESEARCH - University credits: 0
SECS-S/01 - STATISTICS - University credits: 0
SECS-S/02 - STATISTICS FOR EXPERIMENTAL AND TECHNOLOGICAL RESEARCH - University credits: 0
Single bench laboratory practical: 32 hours
Lessons: 56 hours
Professor: Pavesi Giulio
Educational website(s)
Professor(s)
Reception:
Tuesday or Friday, h. 15.00- 17.00
Via Celoria 26 (Department of Biosciences), 2nd Floor Tower B