85297 - Bioinformatics

Learning outcomes

By the end of the course, the student acquires computer science skills and tools used to solve bioinformatics problems. In particular, the student is able to understand algorithms behind most used bioinformatics software; to use existing tools to solve common bioinformatics problems; to design solutions to new problems using computer science techniques; to choose the best computer science tools needed to solve a specific problem.

Course contents

The course is organised into 8 credits (CFU) of lectures and 4 CFU of practicals

 

Lectures (8 CFU):

• Computational aspects of biology: the sequence/structure to function relationships of nucleic acids and proteins
• Algorithms for analysis and comparison of nucleic acids and proteins
• Distance and similarity measures of biological sequences
• Algorithms for the alignment of pairs of sequences, for the alignment of multiple sequences, for searching for similarities in sequence databases, for searching for sequence patterns
• Algorithms for phylogenetic inference
• The advent of next generation sequencing: platforms and data types
• Algorithms and pipelines for the analysis of high-throughput nucleic acids sequencing data
• Genome assembly, annotation and genotyping
• Transcriptome analysis: from gene expression to transcript reconstruction

Practicals (4 CFU)

The practicals will focus on applying the theoretical part to problem solving. Exercises and short projects will be focused on getting familiarity with genomic data types and their analysis. The principal analysis pipelines for analysis of RNA-Seq, ChIP-Seq and variant calling will be introduced.

Readings/Bibliography

Selected reviews, scientific articles and book chapters will be provided.

Teaching methods

Frontal lectures and practicals

Assessment methods

The final assessment verifies the candidate's skill on the topics discussed during the course, including the laboratory activities.

During the course, students are required to implement some fundamental bioinformatics algorithms. At the end of the lectures, students are evaluated by means of a written exam and an optional oral exam.

At the end of the practicals, students are evaluated through a written exam.

The final grade is computed as the sum of the lectures and practicals evaluations, weighted by the respective number of CFU

Teaching tools

PC, internet, videoprojector, board. Bioinformatic laboratory at the Battiferro Education Center.

Office hours

See the website of Fabrizio Ferrè

See the website of Federico Manuel Giorgi