Functional genomics and bioinformatics

A.A. 2020/2021
Crediti massimi
Ore totali
BIO/11 BIO/18
Obiettivi formativi
Functional Genomics is the field of molecular genetics that is involved with assigning function and interactions to genes and their products and ranges from the detailed study of individual genes to large scale experimental approaches designed to capture genome wide effects and interactions. The aim of the course is to provide students a thorough overview of recent high-tech analytical approaches in molecular genetics, which have revolutionized genomics. In particular, Next Generation Sequencing has wide application to many functional genomics settings. Students of the Molecular Biotechnology and Bioinformatics Laurea Magistrale also follow an additional teaching unit of 4 CFU, where a range of these applications, are introduced, focusing on the nature of data generated, its strengths and limitations as well as computational and statistical approaches used to analyse genomic and transcriptomic datasets in various contexts. Practical sessions focusing on the use of the R programming language provide hands on experience of analysing genome-wide datasets, giving students the perspective required design, interpret and critically appraise large scale functional genomics studies and providing the foundation for the development of specific specialized expertise in bioinformatics.
The course is ideally linked to those dealing with bioinformatics and genetics.
Risultati apprendimento attesi
After following this course, the students will have a deep knowledge about the latest genome wide and single gene approaches to study gene functions in model organisms. Teaching is especially focused on helping students gain the expertise required to decide which approaches and technologies to use to investigate biological pathways and the function of genes involved in them.
Programma e organizzazione didattica

Edizione unica

Primo semestre
Functional Genomics part:
Lectures are provided via Ariel asynchronously by power point presentations with audio files. Regularly lessons (total 12 CFU) will take place via the Zoom platform to help and facilitate a better understanding of the lessons.

Evaluation will be through written exams (online) using the / SEB protocol and Zoom surveillance (see instruction manual on Ariel). The examination consists of 6 open questions of which the students will have to select 5 questions to answer.
The content and other considerations are all unchanged.

Bioinformatics part:
Lectures will be taught SYNCHRONOUSLY through the MS Teams platform. All lectures and additional recorded materials as well as selected papers will be made available to students through the Teams platform.

Evaluation will be through written exams (online) using the / SEB protocol (see provisions on unimi website)
A written exam (around 15 multiple choice questions and 3 or 4 open questions to which short answers must be provided. Multiple choice and open questions carry the same total weight (each contributes 50% of the EVALUATION of the bioinformatics teaching unit (4cfu)).
The content and other considerations are all unchanged.
The course is divided in three biological levels of gene function analysis: (i) the DNA level: this part focuses on the history of DNA sequencing from the start to the latest technologies and allows the choice of the right technology for different application. Furthermore, technologies to generate mutants in model organisms will be discussed. (ii) the RNA level: this part focuses on transcriptome analysis and how these analyses are used to understand gene functions. (iii). The protein level: identification and analysis of the proteome, analysis of protein complexes and trafficking to understand gene functions. Furthermore, the bioinformatics teaching unit will introduce characteristics of next-generation sequencing data: read lengths, error profiles, base quality scores, data formats, data quality control, the preparation of sequencing libraries, coverage biases and the impact of PCR, targeted resequencing, indexed libraries, variant discovery and structural variation between genomes as well as de novo genome assembly, the annotation of genes, transcripts and alternative splicing, quantitative transcriptomics the analysis of small non-coding RNAs and other innovative applications of NGS in functional genomics as well as providing 8 practical sessions (16 hours total).
Good knowledge of molecular biology and genetics
Metodi didattici
Frontal teaching with a high level of teacher interaction supported by projected teaching material that is available to students from a dedicated website. Extensive discussions to allow the development of critical faculties and encourage constructive individual involvement in the teaching/learning process. 8 practical sessions in an informatics lecture theatre are included in the bioinformatics teaching unit.
Materiale di riferimento
This course is not covered by a text book since the latest technologies will be discussed. Literature will be provided during the lessons and through the website ( The material is made available only to registered students of the Degree Course in Molecular Biotechnology and Bioinformatics and should not be distributed to others.
Modalità di verifica dell’apprendimento e criteri di valutazione
To pass the examination students will have to follow the lessons since self-study is difficult due to the absence of a textbook that covers the course. The exam for the functional genomics teaching unit consists of 6 open questions of which the student selects 5 to answer. The examination is in English.
While the bioinformatics teaching unit is evaluated through a written exam consisting of around 15 multiple choice questions and 3 or 4 open questions to which short answers must be provided. Multiple choice and open questions carry the same total weight (50%).
Final votes are a weighted mean of results obtained from each teaching unit (6/10+4/10).
Esercitazioni: 16 ore
Lectures: 72 ore
Siti didattici
Mercoledì 15:00-17:00
Secondo piano torre B
Giovedi 14.00 - 17.00
Via Celoria 26, Torre B, Piano 2
Please write me for an appointment by email
Via Celoria 26, Milano - Tower A, Fifth floor